Loading and saving Demes graphsdemes.load(filename, *, format='yaml')[source]¶
Load a graph from a YAML or JSON file.
The keywords and structure of the input are defined by the
-Specification.
+Specification.
- Parameters:
-filename (Union[str, os.PathLike, FileLike]) – The path to the file to be loaded, or a file-like object
+
filename (Union[str, os.PathLike, FileLike]) – The path to the file to be loaded, or a file-like object
with a read() method.
format (str) – The format of the input file. Either “yaml” or “json”.
format (str) – The format of the input file. Either “yaml” or “json”.
- Returns:
@@ -212,9 +212,9 @@ Loading and saving Demes graphs
- Parameters:
-filename (Union[str, os.PathLike, FileLike]) – The path to the file to be loaded, or a file-like object
+
filename (Union[str, os.PathLike, FileLike]) – The path to the file to be loaded, or a file-like object
with a read() method.
format (str) – The format of the input file. Either “yaml” or “json”.
format (str) – The format of the input file. Either “yaml” or “json”.
- Returns:
@@ -222,7 +222,7 @@ Loading and saving Demes graphsReturn type:
--
+
-
Loading and saving Demes graphsdemes.loads(string, *, format='yaml')[source]¶
Load a graph from a YAML or JSON string.
The keywords and structure of the input are defined by the
-Specification.
+Specification.
- Parameters:
-
- Returns:
@@ -260,8 +260,8 @@ Loading and saving Demes graphs
- Parameters:
-
- Returns:
@@ -269,7 +269,7 @@ Loading and saving Demes graphsReturn type:
--
+
-
Loading and saving Demes graphs---.
The keywords and structure of each document are defined by the
-Specification.
+Specification.
- Parameters:
-filename (Union[str, os.PathLike, FileLike]) – The path to the file to be loaded, or a file-like object
+
filename (Union[str, os.PathLike, FileLike]) – The path to the file to be loaded, or a file-like object
with a read() method.
- Returns:
@@ -300,18 +300,18 @@ Loading and saving Demes graphsdemes.dump(graph, filename, *, format='yaml', simplified=True)[source]¶
Dump the specified graph to a file.
The keywords and structure of the output are defined by the
-Specification.
+Specification.
- Parameters:
graph (demes.Graph) – The graph to dump.
filename (Union[str, os.PathLike, FileLike]) – Path to the output file, or a file-like object with a
+
filename (Union[str, os.PathLike, FileLike]) – Path to the output file, or a file-like object with a
write() method.
format (str) – The format of the output file. Either “yaml” or “json”.
simplified (bool) – If True, the output file follows the Human Data Model,
+
format (str) – The format of the output file. Either “yaml” or “json”.
simplified (bool) – If True, the output file follows the Human Data Model,
which has many fields omitted and is thus more compact.
If False, the output file is fully-resolved and follows the
-Machine Data Model.
@@ -322,23 +322,23 @@ Loading and saving Demes graphsdemes.dumps(graph, *, format='yaml', simplified=True)[source]¶
Dump the specified graph to a YAML or JSON string.
The keywords and structure of the output are defined by the
-Specification.
+Specification.
- Parameters:
graph (demes.Graph) – The graph to dump.
format (str) – The format of the output file. Either “yaml” or “json”.
simplified (bool) – If True, returns a string following the Human Data Model,
+
format (str) – The format of the output file. Either “yaml” or “json”.
simplified (bool) – If True, returns a string following the Human Data Model,
which has many fields omitted and is thus more compact.
If False, returns a string that is fully-resolved following the
-Machine Data Model.
- Returns:
The YAML or JSON string.
- Return type:
--
+
-
@@ -351,12 +351,12 @@ Loading and saving Demes graphsParameters:
graphs – An iterable of graphs to dump.
filename (Union[str, os.PathLike, FileLike]) – Path to the output file, or a file-like object with a
+
filename (Union[str, os.PathLike, FileLike]) – Path to the output file, or a file-like object with a
write() method.
simplified (bool) – If True, the output file follows the Human Data Model,
+
simplified (bool) – If True, the output file follows the Human Data Model,
which has many fields omitted and is thus more compact.
If False, the output file is fully-resolved and follows the
-Machine Data Model.
Building Demes graphsThe Builder class provides a set of convenient methods for
incrementally constructing a demographic model.
The state of the demographic model is stored internally as a dictionary
-of objects following Demes’ Human Data Model.
+of objects following Demes’ Human Data Model.
The content of this dictionary is not resolved and is not verified.
The Builder object may be converted into a resolved and validated
Graph object using the resolve() method.
- Variables:
-data (dict) –
The data dictionary of the demographic model’s current state.
+
data (dict) –
The data dictionary of the demographic model’s current state.
The objects nested within this dictionary should follow
-Demes’ data model, as described in the Human Data Model schema.
+Demes’ data model, as described in the Human Data Model schema.
Note
Users may freely modify the data dictionary, such as temporarily
-adding or deleting fields, as long as the Human Data Model
+adding or deleting fields, as long as the Human Data Model
is not violated when the resolve() method is called.
@@ -395,16 +395,16 @@ Building Demes graphs
- Parameters:
-description (str) – A human readable description of the demography.
time_units (str) – The units of time used for the demography. This is
+
description (str) – A human readable description of the demography.
time_units (str) – The units of time used for the demography. This is
commonly years or generations, but can be any string.
generation_time (float) – The generation time of demes, in units given
+
generation_time (float) – The generation time of demes, in units given
by the time_units parameter.
doi (list[str]) – If the graph describes a published demography, the DOI(s)
+
doi (list[str]) – If the graph describes a published demography, the DOI(s)
should be be given here as a list.
defaults (dict) – A dictionary of default values, following the
-Human Data Model schema for defaults.
metadata (dict) – A dictionary of arbitrary additional data.
defaults (dict) – A dictionary of default values, following the
+Human Data Model schema for defaults.
metadata (dict) – A dictionary of arbitrary additional data.
@@ -419,16 +419,16 @@ Building Demes graphs
- Parameters:
-name (str) – A string identifier for the deme.
description (str) – A description of the deme.
ancestors (list[str]) – List of deme names for the deme’s ancestors.
proportions (list[float]) – The proportions of ancestry from each ancestor.
+
name (str) – A string identifier for the deme.
description (str) – A description of the deme.
ancestors (list[str]) – List of deme names for the deme’s ancestors.
proportions (list[float]) – The proportions of ancestry from each ancestor.
This list has the same length as ancestors, and must sum to 1.
start_time (float) – The deme’s start time.
epochs (list[dict]) – List of epoch dictionaries. Each dictionary
-follows the Human Data Model schema for an epoch object.
defaults (dict) – A dictionary of default deme values, following the
-Human Data Model schema for deme defaults.
start_time (float) – The deme’s start time.
epochs (list[dict]) – List of epoch dictionaries. Each dictionary
+follows the Human Data Model schema for an epoch object.
defaults (dict) – A dictionary of default deme values, following the
+Human Data Model schema for deme defaults.
@@ -452,15 +452,15 @@ Building Demes graphs
Parameters:
-demes (list[str]) – List of deme names. If specified, migration is symmetric
+
demes (list[str]) – List of deme names. If specified, migration is symmetric
between all pairs of demes in this list.
source (str) – The name of the source deme. If specified, migration is asymmetric
+
source (str) – The name of the source deme. If specified, migration is asymmetric
from this deme.
dest (str) – The name of the destination deme. If specified, migration is
+
dest (str) – The name of the destination deme. If specified, migration is
asymmetric into this deme.
rate (float) – The rate of migration per generation.
start_time (float) – The time at which the migration rate is enabled.
end_time (float) – The time at which the migration rate is disabled.
rate (float) – The rate of migration per generation.
start_time (float) – The time at which the migration rate is enabled.
end_time (float) – The time at which the migration rate is disabled.
Building Demes graphs
Parameters:
-sources (list(str)) – A list of names of the source deme(s).
dest (str) – The name of the destination deme.
proportion (list(float)) – At the instant after migration, this is the expected proportion(s)
+
sources (list(str)) – A list of names of the source deme(s).
dest (str) – The name of the destination deme.
proportion (list(float)) – At the instant after migration, this is the expected proportion(s)
of individuals in the destination deme made up
of individuals from the source deme(s).
time (float) – The time at which migrations occur.
time (float) – The time at which migrations occur.
Building Demes graphsParameters:
data (MutableMapping) – The data dictionary to initialise the Builder’s state.
The objects nested within this dictionary should follow
-Demes’ Human Data Model, but see the note for
+Demes’ Human Data Model, but see the note for
Builder.data.
Returns:
@@ -533,7 +533,7 @@ Working with Demes graphsclass demes.Graph(*, description='', time_units, generation_time=None, doi=_Nothing.NOTHING, metadata=_Nothing.NOTHING)[source]¶
The Graph class is a resolved and validated representation of a
demographic model.
-A Graph object matches Demes’ Machine Data Model, with a small number of
+
A Graph object matches Demes’ Machine Data Model, with a small number of
additional redundant attributes that make the Graph a more convenient
object to use when inspecting a model’s properties.
Graph objects are not intended to be constructed directly—demographic
@@ -547,21 +547,21 @@
Working with Demes graphs
Variables:
-description (str) – A human readable description of the demography.
time_units (str) – The units of time used for the demography. This is
+
description (str) – A human readable description of the demography.
time_units (str) – The units of time used for the demography. This is
commonly years or generations, but can be any string.
This field is intended to be useful for documenting a demography,
but the actual value provided here should not be relied upon.
generation_time (float) – The generation time of demes, in units given
+
generation_time (float) – The generation time of demes, in units given
by the time_units parameter. Concretely, dividing all times
by generation_time will convert the graph to have time
units in generations.
See also: in_generations().
doi (list[str]) – A list of publications that describe the demographic model.
metadata (dict) – A dictionary of arbitrary additional data.
migrations (list[AsymmetricMigration]) – The continuous asymmetric migrations for the demographic model.
pulses (list[Pulse]) – The instantaneous pulse migrations for the demographic model.
doi (list[str]) – A list of publications that describe the demographic model.
metadata (dict) – A dictionary of arbitrary additional data.
migrations (list[AsymmetricMigration]) – The continuous asymmetric migrations for the demographic model.
pulses (list[Pulse]) – The instantaneous pulse migrations for the demographic model.
Working with Demes graphs
Parameters:
-deme_name (str) – The name of the deme.
+deme_name (str) – The name of the deme.
Return type:
-
+
Returns:
True if the deme is in the graph, False otherwise.
@@ -598,7 +598,7 @@ Working with Demes graphs
Parameters:
-deme_name (str) – The name of the deme.
+deme_name (str) – The name of the deme.
Return type:
@@ -615,10 +615,10 @@ Working with Demes graphs
Returns:
-A data dictionary following the Machine Data Model.
+A data dictionary following the Machine Data Model.
Return type:
-
+
@@ -629,10 +629,10 @@ Working with Demes graphs
Returns:
-A data dictionary following the Human Data Model.
+A data dictionary following the Human Data Model.
Return type:
-
+
@@ -656,10 +656,10 @@ Working with Demes graphsParameters:
other (Graph) – The graph to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Working with Demes graphsMerge, and Admix objects.
Return type:
-
+
@@ -701,8 +701,8 @@ Working with Demes graphs
Parameters:
-data (dict) – A data dictionary following either the
-Human Data Model or the Machine Data Model.
+data (dict) – A data dictionary following either the
+Human Data Model or the Machine Data Model.
Returns:
A resolved and validated demographic model.
@@ -732,7 +732,7 @@ Working with Demes graphsisclose(other, *, rel_tol=1e-09, abs_tol=1e-12)[source]¶
Returns true if the graph and other implement essentially
the same demographic model. Numerical values are compared using the
-math.isclose() function, from which this method takes its name.
+math.isclose() function, from which this method takes its name.
Furthermore, the following implementation details are ignored during
the comparison:
@@ -747,17 +747,17 @@ Working with Demes graphsParameters:
other (Graph) – The graph to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Returns:
True if the two graphs implement the same model, False otherwise.
Return type:
-
+
@@ -807,7 +807,7 @@ Working with Demes graphsend_times are a list of end times for each matrix.
Return type:
-tuple[list[list[list[float]]], list[float]]
+
Working with Demes graphsA NetworkX compatible dict-of-lists graph of the demes’ predecessors.
Return type:
-
+
@@ -842,7 +842,7 @@ Working with Demes graphs
Parameters:
-names (dict) – A dictionary with deme names and new names.
+names (dict) – A dictionary with deme names and new names.
Returns:
A demographic model with renamed demes.
@@ -872,7 +872,7 @@ Working with Demes graphsA NetworkX compatible dict-of-lists graph of the demes’ successors.
Return type:
-
+
@@ -887,15 +887,15 @@ Working with Demes graphs
Variables:
-name (str) – A concise string that identifies the deme.
description (str) – A description of the deme.
start_time (float) – The time at which the deme begins to exist.
ancestors (list[str]) – List of deme names for the deme’s ancestors.
proportions (list[float]) – The proportions of ancestry from each ancestor,
+
name (str) – A concise string that identifies the deme.
description (str) – A description of the deme.
start_time (float) – The time at which the deme begins to exist.
ancestors (list[str]) – List of deme names for the deme’s ancestors.
proportions (list[float]) – The proportions of ancestry from each ancestor,
ordered to correspond with the same order as the ancestors
list.
If there are one or more ancestors, the proportions sum to 1.
epochs (list[Epoch]) – A list of epochs that span the time interval over which the
+
epochs (list[Epoch]) – A list of epochs that span the time interval over which the
deme exists. Epoch time intervals are non-overlapping,
completely cover the deme’s existence time interval,
and are listed in time-descending order (from the past
@@ -914,10 +914,10 @@
Working with Demes graphsParameters:
other (Deme) – The deme to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Working with Demes graphs
- Return type:
--
+
-
@@ -943,17 +943,17 @@ Working with Demes graphsParameters:
other (Deme) – The deme to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two demes are equivalent, False otherwise.
- Return type:
--
+
-
@@ -967,13 +967,13 @@ Working with Demes graphs
- Parameters:
-time (float) – The time at which the size should be calculated.
+time (float) – The time at which the size should be calculated.
- Returns:
The deme size.
- Return type:
--
+
-
@@ -984,7 +984,7 @@ Working with Demes graphs
- Return type:
--
+
-
@@ -1004,16 +1004,16 @@ Working with Demes graphs
- Variables:
-start_time (float) – The start time of the epoch.
+
start_time (float) – The start time of the epoch.
This value is greater than zero and may be infinity.
end_time (float) – The end time of the epoch.
+
end_time (float) – The end time of the epoch.
This value is greater than or equal to zero and finite.
start_size (float) – Population size at start_time.
end_size (float) – Population size at end_time.
+
start_size (float) – Population size at start_time.
end_size (float) – Population size at end_time.
If start_size != end_size, the population size changes
between the start and end times according to the
size_function.
size_function (str) –
The size change function. This is either
+
size_function (str) –
The size change function. This is either
constant, exponential or linear, though it is possible
that additional values will be added in the future.
@@ -1041,8 +1041,8 @@ Working with Demes graphsfloat) – The selfing rate for this epoch.
cloning_rate (float) – The cloning rate for this epoch.
selfing_rate (float) – The selfing rate for this epoch.
cloning_rate (float) – The cloning rate for this epoch.
Working with Demes graphsParameters:
other (Epoch) – The epoch to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Working with Demes graphsParameters:
other (Epoch) – The epoch to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two epochs are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1097,7 +1097,7 @@ Working with Demes graphs
- Return type:
--
+
-
@@ -1118,11 +1118,11 @@ Continuous demographic events
- Variables:
-source (str) – The source deme for asymmetric migration.
dest (str) – The destination deme for asymmetric migration.
start_time (float) – The time at which the migration rate is activated.
end_time (float) – The time at which the migration rate is deactivated.
rate (float) – The rate of migration per generation.
source (str) – The source deme for asymmetric migration.
dest (str) – The destination deme for asymmetric migration.
start_time (float) – The time at which the migration rate is activated.
end_time (float) – The time at which the migration rate is deactivated.
rate (float) – The rate of migration per generation.
Continuous demographic eventsParameters:
other (AsymmetricMigration) – The migration to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Continuous demographic eventsParameters:
other (AsymmetricMigration) – The migration to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two epochs are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1188,10 +1188,10 @@ Discrete demographic events
- Variables:
-dest (str) – The destination deme.
time (float) – The time of migration.
proportions (list(float)) – Immediately following migration, the proportion(s)
+
dest (str) – The destination deme.
time (float) – The time of migration.
proportions (list(float)) – Immediately following migration, the proportion(s)
of individuals in the destination deme made up of migrant individuals or
having parents from the source deme(s).
@@ -1208,10 +1208,10 @@ Discrete demographic eventsParameters:
other (Pulse) – The pulse to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Discrete demographic eventsParameters:
other (Pulse) – The pulse to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two pulses are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1254,9 +1254,9 @@ Discrete demographic events
- Variables:
-
@@ -1271,10 +1271,10 @@ Discrete demographic eventsParameters:
other (Split) – The split to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Discrete demographic eventsParameters:
other (Split) – The split to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two splits are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1316,9 +1316,9 @@ Discrete demographic events
- Variables:
-
@@ -1333,10 +1333,10 @@ Discrete demographic eventsParameters:
other (Branch) – The branch to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Discrete demographic eventsParameters:
other (Branch) – The branch to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two branches are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1377,11 +1377,11 @@ Discrete demographic events
- Variables:
-
@@ -1396,10 +1396,10 @@ Discrete demographic eventsParameters:
other (Merge) – The merge to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Discrete demographic eventsParameters:
other (Merge) – The merge to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two merges are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1440,11 +1440,11 @@ Discrete demographic events
- Variables:
-
@@ -1459,10 +1459,10 @@ Discrete demographic eventsParameters:
other (Admix) – The admixture to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Discrete demographic eventsParameters:
other (Admix) – The admixture to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two admixtures are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1530,14 +1530,14 @@ Conversion functions
- Parameters:
-command (str) – The ms command line.
N0 (float) – The reference population size (\(N_0\)) used to translate
+
command (str) – The ms command line.
N0 (float) – The reference population size (\(N_0\)) used to translate
from coalescent units. For a command that specifies a
\(\theta\) value with the -t theta option,
this can be calculated as \(N_0 = \theta / (4 \mu L)\),
where \(\mu\) is the per-generation mutation rate and
\(L\) is the length of the sequence being simulated.
deme_names (list[str]) – A list of names to use for the demes.
+
deme_names (list[str]) – A list of names to use for the demes.
If not specified, demes will be named deme1, deme2, etc.
Conversion functions
- Parameters:
-N0 (float) – The reference population size used to translate into coalescent units.
+
N0 (float) – The reference population size used to translate into coalescent units.
See from_ms() for details.
samples (list(int)) – A list of haploid sample numbers, one for each deme, in the same
+
samples (list(int)) – A list of haploid sample numbers, one for each deme, in the same
order as the order of demes in the graph.
The parameter is ignored for demographic models with only one deme.
The given sampling scheme will be used with the -I argument.
@@ -1576,7 +1576,7 @@
Conversion functionsThe ms command line.
- Return type:
--
+
-
diff --git a/main/introduction.html b/main/introduction.html
index b84f08d..20a45cd 100644
--- a/main/introduction.html
+++ b/main/introduction.html
@@ -175,8 +175,8 @@ Quick search
Introduction¶
The demes Python package provides an API for defining, parsing, and sharing
-Demes demographic models. Applications can use
-demes to parse human-readable Demes YAML files
+Demes demographic models. Applications can use
+demes to parse human-readable Demes YAML files
into fully-resolved demographic models. In addition, demes provides
convenient data structures to simplify manipulation of demographic models.
If you find an error in the documentation or a bug in the software,
@@ -192,7 +192,7 @@
MotivationDemes Specification aims to make defining demographic
+
The Demes Specification aims to make defining demographic
models more intuitive, less prone to error or ambiguity, and readily
interchangeable between simulation platforms.
Demographic models, which define populations (or demes), their properties,
@@ -203,7 +203,7 @@
Motivation¶
The following YAML file implements a two-epoch demographic
history for a single deme, where the deme doubles in size 100 generations ago.
-See the Demes tutorial for a detailed introduction to
+See the Demes tutorial for a detailed introduction to
writing Demes YAML files.
description: Single-population two-epoch demography.
time_units: generations
@@ -233,7 +233,7 @@ Example<Axes: ylabel='time ago (generations)'>
-
+
diff --git a/main/quickstart.html b/main/quickstart.html
index 9f74fc2..1161bba 100644
--- a/main/quickstart.html
+++ b/main/quickstart.html
@@ -231,7 +231,7 @@ Loading a Demes graph
-
+
This YAML file can be loaded into Python with the load() function,
to obtain a Graph instance (modify the filename as appropriate).
@@ -402,7 +402,7 @@ Plotting a Demes graph<Axes: ylabel='time ago (generations)'>
-
+
Load a graph from a YAML or JSON file. The keywords and structure of the input are defined by the -Specification.
+Specification.- Parameters:
-
-
filename (Union[str, os.PathLike, FileLike]) – The path to the file to be loaded, or a file-like object +
filename (Union[str, os.PathLike, FileLike]) – The path to the file to be loaded, or a file-like object with a
read()method.
-format (str) – The format of the input file. Either “yaml” or “json”.
+format (str) – The format of the input file. Either “yaml” or “json”.
- Returns: @@ -212,9 +212,9 @@
- Parameters:
-
-
filename (Union[str, os.PathLike, FileLike]) – The path to the file to be loaded, or a file-like object +
filename (Union[str, os.PathLike, FileLike]) – The path to the file to be loaded, or a file-like object with a
read()method.
-format (str) – The format of the input file. Either “yaml” or “json”.
+format (str) – The format of the input file. Either “yaml” or “json”.
- Returns: @@ -222,7 +222,7 @@
-
+
Loading and saving Demes graphs
Loading and saving Demes graphsReturn type:
-
Load a graph from a YAML or JSON string. The keywords and structure of the input are defined by the -Specification.
+Specification.- Parameters:
- Returns: @@ -260,8 +260,8 @@
- Parameters:
- Returns: @@ -269,7 +269,7 @@
-
+
Loading and saving Demes graphs
Loading and saving Demes graphsReturn type:
-
Loading and saving Demes graphs---.
The keywords and structure of each document are defined by the
-Specification.
+Specification.
- Parameters:
-filename (Union[str, os.PathLike, FileLike]) – The path to the file to be loaded, or a file-like object
+
filename (Union[str, os.PathLike, FileLike]) – The path to the file to be loaded, or a file-like object
with a read() method.
- Returns:
@@ -300,18 +300,18 @@ Loading and saving Demes graphsdemes.dump(graph, filename, *, format='yaml', simplified=True)[source]¶
Dump the specified graph to a file.
The keywords and structure of the output are defined by the
-Specification.
+Specification.
- Parameters:
graph (demes.Graph) – The graph to dump.
filename (Union[str, os.PathLike, FileLike]) – Path to the output file, or a file-like object with a
+
filename (Union[str, os.PathLike, FileLike]) – Path to the output file, or a file-like object with a
write() method.
format (str) – The format of the output file. Either “yaml” or “json”.
simplified (bool) – If True, the output file follows the Human Data Model,
+
format (str) – The format of the output file. Either “yaml” or “json”.
simplified (bool) – If True, the output file follows the Human Data Model,
which has many fields omitted and is thus more compact.
If False, the output file is fully-resolved and follows the
-Machine Data Model.
@@ -322,23 +322,23 @@ Loading and saving Demes graphsdemes.dumps(graph, *, format='yaml', simplified=True)[source]¶
Dump the specified graph to a YAML or JSON string.
The keywords and structure of the output are defined by the
-Specification.
+Specification.
- Parameters:
graph (demes.Graph) – The graph to dump.
format (str) – The format of the output file. Either “yaml” or “json”.
simplified (bool) – If True, returns a string following the Human Data Model,
+
format (str) – The format of the output file. Either “yaml” or “json”.
simplified (bool) – If True, returns a string following the Human Data Model,
which has many fields omitted and is thus more compact.
If False, returns a string that is fully-resolved following the
-Machine Data Model.
- Returns:
The YAML or JSON string.
- Return type:
--
+
-
@@ -351,12 +351,12 @@ Loading and saving Demes graphsParameters:
graphs – An iterable of graphs to dump.
filename (Union[str, os.PathLike, FileLike]) – Path to the output file, or a file-like object with a
+
filename (Union[str, os.PathLike, FileLike]) – Path to the output file, or a file-like object with a
write() method.
simplified (bool) – If True, the output file follows the Human Data Model,
+
simplified (bool) – If True, the output file follows the Human Data Model,
which has many fields omitted and is thus more compact.
If False, the output file is fully-resolved and follows the
-Machine Data Model.
Building Demes graphsThe Builder class provides a set of convenient methods for
incrementally constructing a demographic model.
The state of the demographic model is stored internally as a dictionary
-of objects following Demes’ Human Data Model.
+of objects following Demes’ Human Data Model.
The content of this dictionary is not resolved and is not verified.
The Builder object may be converted into a resolved and validated
Graph object using the resolve() method.
- Variables:
-data (dict) –
The data dictionary of the demographic model’s current state.
+
data (dict) –
The data dictionary of the demographic model’s current state.
The objects nested within this dictionary should follow
-Demes’ data model, as described in the Human Data Model schema.
+Demes’ data model, as described in the Human Data Model schema.
Note
Users may freely modify the data dictionary, such as temporarily
-adding or deleting fields, as long as the Human Data Model
+adding or deleting fields, as long as the Human Data Model
is not violated when the resolve() method is called.
@@ -395,16 +395,16 @@ Building Demes graphs
- Parameters:
-description (str) – A human readable description of the demography.
time_units (str) – The units of time used for the demography. This is
+
description (str) – A human readable description of the demography.
time_units (str) – The units of time used for the demography. This is
commonly years or generations, but can be any string.
generation_time (float) – The generation time of demes, in units given
+
generation_time (float) – The generation time of demes, in units given
by the time_units parameter.
doi (list[str]) – If the graph describes a published demography, the DOI(s)
+
doi (list[str]) – If the graph describes a published demography, the DOI(s)
should be be given here as a list.
defaults (dict) – A dictionary of default values, following the
-Human Data Model schema for defaults.
metadata (dict) – A dictionary of arbitrary additional data.
defaults (dict) – A dictionary of default values, following the
+Human Data Model schema for defaults.
metadata (dict) – A dictionary of arbitrary additional data.
@@ -419,16 +419,16 @@ Building Demes graphs
- Parameters:
-name (str) – A string identifier for the deme.
description (str) – A description of the deme.
ancestors (list[str]) – List of deme names for the deme’s ancestors.
proportions (list[float]) – The proportions of ancestry from each ancestor.
+
name (str) – A string identifier for the deme.
description (str) – A description of the deme.
ancestors (list[str]) – List of deme names for the deme’s ancestors.
proportions (list[float]) – The proportions of ancestry from each ancestor.
This list has the same length as ancestors, and must sum to 1.
start_time (float) – The deme’s start time.
epochs (list[dict]) – List of epoch dictionaries. Each dictionary
-follows the Human Data Model schema for an epoch object.
defaults (dict) – A dictionary of default deme values, following the
-Human Data Model schema for deme defaults.
start_time (float) – The deme’s start time.
epochs (list[dict]) – List of epoch dictionaries. Each dictionary
+follows the Human Data Model schema for an epoch object.
defaults (dict) – A dictionary of default deme values, following the
+Human Data Model schema for deme defaults.
@@ -452,15 +452,15 @@ Building Demes graphs
Parameters:
-demes (list[str]) – List of deme names. If specified, migration is symmetric
+
demes (list[str]) – List of deme names. If specified, migration is symmetric
between all pairs of demes in this list.
source (str) – The name of the source deme. If specified, migration is asymmetric
+
source (str) – The name of the source deme. If specified, migration is asymmetric
from this deme.
dest (str) – The name of the destination deme. If specified, migration is
+
dest (str) – The name of the destination deme. If specified, migration is
asymmetric into this deme.
rate (float) – The rate of migration per generation.
start_time (float) – The time at which the migration rate is enabled.
end_time (float) – The time at which the migration rate is disabled.
rate (float) – The rate of migration per generation.
start_time (float) – The time at which the migration rate is enabled.
end_time (float) – The time at which the migration rate is disabled.
Building Demes graphs
Parameters:
-sources (list(str)) – A list of names of the source deme(s).
dest (str) – The name of the destination deme.
proportion (list(float)) – At the instant after migration, this is the expected proportion(s)
+
sources (list(str)) – A list of names of the source deme(s).
dest (str) – The name of the destination deme.
proportion (list(float)) – At the instant after migration, this is the expected proportion(s)
of individuals in the destination deme made up
of individuals from the source deme(s).
time (float) – The time at which migrations occur.
time (float) – The time at which migrations occur.
Building Demes graphsParameters:
data (MutableMapping) – The data dictionary to initialise the Builder’s state.
The objects nested within this dictionary should follow
-Demes’ Human Data Model, but see the note for
+Demes’ Human Data Model, but see the note for
Builder.data.
Returns:
@@ -533,7 +533,7 @@ Working with Demes graphsclass demes.Graph(*, description='', time_units, generation_time=None, doi=_Nothing.NOTHING, metadata=_Nothing.NOTHING)[source]¶
The Graph class is a resolved and validated representation of a
demographic model.
-A Graph object matches Demes’ Machine Data Model, with a small number of
+
A Graph object matches Demes’ Machine Data Model, with a small number of
additional redundant attributes that make the Graph a more convenient
object to use when inspecting a model’s properties.
Graph objects are not intended to be constructed directly—demographic
@@ -547,21 +547,21 @@
Working with Demes graphs
Variables:
-description (str) – A human readable description of the demography.
time_units (str) – The units of time used for the demography. This is
+
description (str) – A human readable description of the demography.
time_units (str) – The units of time used for the demography. This is
commonly years or generations, but can be any string.
This field is intended to be useful for documenting a demography,
but the actual value provided here should not be relied upon.
generation_time (float) – The generation time of demes, in units given
+
generation_time (float) – The generation time of demes, in units given
by the time_units parameter. Concretely, dividing all times
by generation_time will convert the graph to have time
units in generations.
See also: in_generations().
doi (list[str]) – A list of publications that describe the demographic model.
metadata (dict) – A dictionary of arbitrary additional data.
migrations (list[AsymmetricMigration]) – The continuous asymmetric migrations for the demographic model.
pulses (list[Pulse]) – The instantaneous pulse migrations for the demographic model.
doi (list[str]) – A list of publications that describe the demographic model.
metadata (dict) – A dictionary of arbitrary additional data.
migrations (list[AsymmetricMigration]) – The continuous asymmetric migrations for the demographic model.
pulses (list[Pulse]) – The instantaneous pulse migrations for the demographic model.
Working with Demes graphs
Parameters:
-deme_name (str) – The name of the deme.
+deme_name (str) – The name of the deme.
Return type:
-
+
Returns:
True if the deme is in the graph, False otherwise.
@@ -598,7 +598,7 @@ Working with Demes graphs
Parameters:
-deme_name (str) – The name of the deme.
+deme_name (str) – The name of the deme.
Return type:
@@ -615,10 +615,10 @@ Working with Demes graphs
Returns:
-A data dictionary following the Machine Data Model.
+A data dictionary following the Machine Data Model.
Return type:
-
+
@@ -629,10 +629,10 @@ Working with Demes graphs
Returns:
-A data dictionary following the Human Data Model.
+A data dictionary following the Human Data Model.
Return type:
-
+
@@ -656,10 +656,10 @@ Working with Demes graphsParameters:
other (Graph) – The graph to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Working with Demes graphsMerge, and Admix objects.
Return type:
-
+
@@ -701,8 +701,8 @@ Working with Demes graphs
Parameters:
-data (dict) – A data dictionary following either the
-Human Data Model or the Machine Data Model.
+data (dict) – A data dictionary following either the
+Human Data Model or the Machine Data Model.
Returns:
A resolved and validated demographic model.
@@ -732,7 +732,7 @@ Working with Demes graphsisclose(other, *, rel_tol=1e-09, abs_tol=1e-12)[source]¶
Returns true if the graph and other implement essentially
the same demographic model. Numerical values are compared using the
-math.isclose() function, from which this method takes its name.
+math.isclose() function, from which this method takes its name.
Furthermore, the following implementation details are ignored during
the comparison:
@@ -747,17 +747,17 @@ Working with Demes graphsParameters:
other (Graph) – The graph to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Returns:
True if the two graphs implement the same model, False otherwise.
Return type:
-
+
@@ -807,7 +807,7 @@ Working with Demes graphsend_times are a list of end times for each matrix.
Return type:
-tuple[list[list[list[float]]], list[float]]
+
Working with Demes graphsA NetworkX compatible dict-of-lists graph of the demes’ predecessors.
Return type:
-
+
@@ -842,7 +842,7 @@ Working with Demes graphs
Parameters:
-names (dict) – A dictionary with deme names and new names.
+names (dict) – A dictionary with deme names and new names.
Returns:
A demographic model with renamed demes.
@@ -872,7 +872,7 @@ Working with Demes graphsA NetworkX compatible dict-of-lists graph of the demes’ successors.
Return type:
-
+
@@ -887,15 +887,15 @@ Working with Demes graphs
Variables:
-name (str) – A concise string that identifies the deme.
description (str) – A description of the deme.
start_time (float) – The time at which the deme begins to exist.
ancestors (list[str]) – List of deme names for the deme’s ancestors.
proportions (list[float]) – The proportions of ancestry from each ancestor,
+
name (str) – A concise string that identifies the deme.
description (str) – A description of the deme.
start_time (float) – The time at which the deme begins to exist.
ancestors (list[str]) – List of deme names for the deme’s ancestors.
proportions (list[float]) – The proportions of ancestry from each ancestor,
ordered to correspond with the same order as the ancestors
list.
If there are one or more ancestors, the proportions sum to 1.
epochs (list[Epoch]) – A list of epochs that span the time interval over which the
+
epochs (list[Epoch]) – A list of epochs that span the time interval over which the
deme exists. Epoch time intervals are non-overlapping,
completely cover the deme’s existence time interval,
and are listed in time-descending order (from the past
@@ -914,10 +914,10 @@
Working with Demes graphsParameters:
other (Deme) – The deme to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Working with Demes graphs
- Return type:
--
+
-
@@ -943,17 +943,17 @@ Working with Demes graphsParameters:
other (Deme) – The deme to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two demes are equivalent, False otherwise.
- Return type:
--
+
-
@@ -967,13 +967,13 @@ Working with Demes graphs
- Parameters:
-time (float) – The time at which the size should be calculated.
+time (float) – The time at which the size should be calculated.
- Returns:
The deme size.
- Return type:
--
+
-
@@ -984,7 +984,7 @@ Working with Demes graphs
- Return type:
--
+
-
@@ -1004,16 +1004,16 @@ Working with Demes graphs
- Variables:
-start_time (float) – The start time of the epoch.
+
start_time (float) – The start time of the epoch.
This value is greater than zero and may be infinity.
end_time (float) – The end time of the epoch.
+
end_time (float) – The end time of the epoch.
This value is greater than or equal to zero and finite.
start_size (float) – Population size at start_time.
end_size (float) – Population size at end_time.
+
start_size (float) – Population size at start_time.
end_size (float) – Population size at end_time.
If start_size != end_size, the population size changes
between the start and end times according to the
size_function.
size_function (str) –
The size change function. This is either
+
size_function (str) –
The size change function. This is either
constant, exponential or linear, though it is possible
that additional values will be added in the future.
@@ -1041,8 +1041,8 @@ Working with Demes graphsfloat) – The selfing rate for this epoch.
cloning_rate (float) – The cloning rate for this epoch.
selfing_rate (float) – The selfing rate for this epoch.
cloning_rate (float) – The cloning rate for this epoch.
Working with Demes graphsParameters:
other (Epoch) – The epoch to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Working with Demes graphsParameters:
other (Epoch) – The epoch to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two epochs are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1097,7 +1097,7 @@ Working with Demes graphs
- Return type:
--
+
-
@@ -1118,11 +1118,11 @@ Continuous demographic events
- Variables:
-source (str) – The source deme for asymmetric migration.
dest (str) – The destination deme for asymmetric migration.
start_time (float) – The time at which the migration rate is activated.
end_time (float) – The time at which the migration rate is deactivated.
rate (float) – The rate of migration per generation.
source (str) – The source deme for asymmetric migration.
dest (str) – The destination deme for asymmetric migration.
start_time (float) – The time at which the migration rate is activated.
end_time (float) – The time at which the migration rate is deactivated.
rate (float) – The rate of migration per generation.
Continuous demographic eventsParameters:
other (AsymmetricMigration) – The migration to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Continuous demographic eventsParameters:
other (AsymmetricMigration) – The migration to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two epochs are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1188,10 +1188,10 @@ Discrete demographic events
- Variables:
-dest (str) – The destination deme.
time (float) – The time of migration.
proportions (list(float)) – Immediately following migration, the proportion(s)
+
dest (str) – The destination deme.
time (float) – The time of migration.
proportions (list(float)) – Immediately following migration, the proportion(s)
of individuals in the destination deme made up of migrant individuals or
having parents from the source deme(s).
@@ -1208,10 +1208,10 @@ Discrete demographic eventsParameters:
other (Pulse) – The pulse to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Discrete demographic eventsParameters:
other (Pulse) – The pulse to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two pulses are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1254,9 +1254,9 @@ Discrete demographic events
- Variables:
-
@@ -1271,10 +1271,10 @@ Discrete demographic eventsParameters:
other (Split) – The split to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Discrete demographic eventsParameters:
other (Split) – The split to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two splits are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1316,9 +1316,9 @@ Discrete demographic events
- Variables:
-
@@ -1333,10 +1333,10 @@ Discrete demographic eventsParameters:
other (Branch) – The branch to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Discrete demographic eventsParameters:
other (Branch) – The branch to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two branches are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1377,11 +1377,11 @@ Discrete demographic events
- Variables:
-
@@ -1396,10 +1396,10 @@ Discrete demographic eventsParameters:
other (Merge) – The merge to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Discrete demographic eventsParameters:
other (Merge) – The merge to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two merges are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1440,11 +1440,11 @@ Discrete demographic events
- Variables:
-
@@ -1459,10 +1459,10 @@ Discrete demographic eventsParameters:
other (Admix) – The admixture to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Discrete demographic eventsParameters:
other (Admix) – The admixture to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two admixtures are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1530,14 +1530,14 @@ Conversion functions
- Parameters:
-command (str) – The ms command line.
N0 (float) – The reference population size (\(N_0\)) used to translate
+
command (str) – The ms command line.
N0 (float) – The reference population size (\(N_0\)) used to translate
from coalescent units. For a command that specifies a
\(\theta\) value with the -t theta option,
this can be calculated as \(N_0 = \theta / (4 \mu L)\),
where \(\mu\) is the per-generation mutation rate and
\(L\) is the length of the sequence being simulated.
deme_names (list[str]) – A list of names to use for the demes.
+
deme_names (list[str]) – A list of names to use for the demes.
If not specified, demes will be named deme1, deme2, etc.
Conversion functions
- Parameters:
-N0 (float) – The reference population size used to translate into coalescent units.
+
N0 (float) – The reference population size used to translate into coalescent units.
See from_ms() for details.
samples (list(int)) – A list of haploid sample numbers, one for each deme, in the same
+
samples (list(int)) – A list of haploid sample numbers, one for each deme, in the same
order as the order of demes in the graph.
The parameter is ignored for demographic models with only one deme.
The given sampling scheme will be used with the -I argument.
@@ -1576,7 +1576,7 @@
Conversion functionsThe ms command line.
- Return type:
--
+
-
diff --git a/main/introduction.html b/main/introduction.html
index b84f08d..20a45cd 100644
--- a/main/introduction.html
+++ b/main/introduction.html
@@ -175,8 +175,8 @@ Quick search
Introduction¶
The demes Python package provides an API for defining, parsing, and sharing
-Demes demographic models. Applications can use
-demes to parse human-readable Demes YAML files
+Demes demographic models. Applications can use
+demes to parse human-readable Demes YAML files
into fully-resolved demographic models. In addition, demes provides
convenient data structures to simplify manipulation of demographic models.
If you find an error in the documentation or a bug in the software,
@@ -192,7 +192,7 @@
MotivationDemes Specification aims to make defining demographic
+
The Demes Specification aims to make defining demographic
models more intuitive, less prone to error or ambiguity, and readily
interchangeable between simulation platforms.
Demographic models, which define populations (or demes), their properties,
@@ -203,7 +203,7 @@
Motivation¶
The following YAML file implements a two-epoch demographic
history for a single deme, where the deme doubles in size 100 generations ago.
-See the Demes tutorial for a detailed introduction to
+See the Demes tutorial for a detailed introduction to
writing Demes YAML files.
description: Single-population two-epoch demography.
time_units: generations
@@ -233,7 +233,7 @@ Example<Axes: ylabel='time ago (generations)'>
-
+
diff --git a/main/quickstart.html b/main/quickstart.html
index 9f74fc2..1161bba 100644
--- a/main/quickstart.html
+++ b/main/quickstart.html
@@ -231,7 +231,7 @@ Loading a Demes graph
-
+
This YAML file can be loaded into Python with the load() function,
to obtain a Graph instance (modify the filename as appropriate).
@@ -402,7 +402,7 @@ Plotting a Demes graph<Axes: ylabel='time ago (generations)'>
-
+
filename (Union[str, os.PathLike, FileLike]) – The path to the file to be loaded, or a file-like object +
filename (Union[str, os.PathLike, FileLike]) – The path to the file to be loaded, or a file-like object
with a read() method.
Loading and saving Demes graphsdemes.dump(graph, filename, *, format='yaml', simplified=True)[source]¶
Dump the specified graph to a file.
The keywords and structure of the output are defined by the
-Specification.
+Specification.
- Parameters:
graph (demes.Graph) – The graph to dump.
filename (Union[str, os.PathLike, FileLike]) – Path to the output file, or a file-like object with a
+
filename (Union[str, os.PathLike, FileLike]) – Path to the output file, or a file-like object with a
write() method.
format (str) – The format of the output file. Either “yaml” or “json”.
simplified (bool) – If True, the output file follows the Human Data Model,
+
format (str) – The format of the output file. Either “yaml” or “json”.
simplified (bool) – If True, the output file follows the Human Data Model,
which has many fields omitted and is thus more compact.
If False, the output file is fully-resolved and follows the
-Machine Data Model.
@@ -322,23 +322,23 @@ Loading and saving Demes graphsdemes.dumps(graph, *, format='yaml', simplified=True)[source]¶
Dump the specified graph to a YAML or JSON string.
The keywords and structure of the output are defined by the
-Specification.
+Specification.
- Parameters:
graph (demes.Graph) – The graph to dump.
format (str) – The format of the output file. Either “yaml” or “json”.
simplified (bool) – If True, returns a string following the Human Data Model,
+
format (str) – The format of the output file. Either “yaml” or “json”.
simplified (bool) – If True, returns a string following the Human Data Model,
which has many fields omitted and is thus more compact.
If False, returns a string that is fully-resolved following the
-Machine Data Model.
- Returns:
The YAML or JSON string.
- Return type:
--
+
-
Dump the specified graph to a file. The keywords and structure of the output are defined by the -Specification.
+Specification.- Parameters:
graph (demes.Graph) – The graph to dump.
-filename (Union[str, os.PathLike, FileLike]) – Path to the output file, or a file-like object with a +
filename (Union[str, os.PathLike, FileLike]) – Path to the output file, or a file-like object with a
write()method.
-format (str) – The format of the output file. Either “yaml” or “json”.
-simplified (bool) – If True, the output file follows the Human Data Model, +
format (str) – The format of the output file. Either “yaml” or “json”.
+simplified (bool) – If True, the output file follows the Human Data Model, which has many fields omitted and is thus more compact. If False, the output file is fully-resolved and follows the -Machine Data Model.
+Machine Data Model.
Loading and saving Demes graphsdemes.dumps(graph, *, format='yaml', simplified=True)[source]¶
Dump the specified graph to a YAML or JSON string.
The keywords and structure of the output are defined by the
-Specification.
+Specification.
- Parameters:
graph (demes.Graph) – The graph to dump.
format (str) – The format of the output file. Either “yaml” or “json”.
simplified (bool) – If True, returns a string following the Human Data Model,
+
format (str) – The format of the output file. Either “yaml” or “json”.
simplified (bool) – If True, returns a string following the Human Data Model,
which has many fields omitted and is thus more compact.
If False, returns a string that is fully-resolved following the
-Machine Data Model.
- Returns:
The YAML or JSON string.
- Return type:
--
+
-
Dump the specified graph to a YAML or JSON string. The keywords and structure of the output are defined by the -Specification.
+Specification.- Parameters:
graph (demes.Graph) – The graph to dump.
-format (str) – The format of the output file. Either “yaml” or “json”.
-simplified (bool) – If True, returns a string following the Human Data Model, +
format (str) – The format of the output file. Either “yaml” or “json”.
+simplified (bool) – If True, returns a string following the Human Data Model, which has many fields omitted and is thus more compact. If False, returns a string that is fully-resolved following the -Machine Data Model.
+Machine Data Model.
- Returns:
The YAML or JSON string.
- Return type: -
-
+
graphs – An iterable of graphs to dump.
-filename (Union[str, os.PathLike, FileLike]) – Path to the output file, or a file-like object with a +
filename (Union[str, os.PathLike, FileLike]) – Path to the output file, or a file-like object with a
write()method.
-simplified (bool) – If True, the output file follows the Human Data Model, +
simplified (bool) – If True, the output file follows the Human Data Model, which has many fields omitted and is thus more compact. If False, the output file is fully-resolved and follows the -Machine Data Model.
+Machine Data Model.
Building Demes graphsThe Builder class provides a set of convenient methods for
incrementally constructing a demographic model.
The state of the demographic model is stored internally as a dictionary
-of objects following Demes’ Human Data Model.
+of objects following Demes’ Human Data Model.
The content of this dictionary is not resolved and is not verified.
The Builder object may be converted into a resolved and validated
Graph object using the resolve() method.
- Variables:
-data (dict) –
The data dictionary of the demographic model’s current state.
+
data (dict) –
The data dictionary of the demographic model’s current state.
The objects nested within this dictionary should follow
-Demes’ data model, as described in the Human Data Model schema.
+Demes’ data model, as described in the Human Data Model schema.
Note
Users may freely modify the data dictionary, such as temporarily
-adding or deleting fields, as long as the Human Data Model
+adding or deleting fields, as long as the Human Data Model
is not violated when the resolve() method is called.
@@ -395,16 +395,16 @@ Building Demes graphs
- Parameters:
-description (str) – A human readable description of the demography.
time_units (str) – The units of time used for the demography. This is
+
description (str) – A human readable description of the demography.
time_units (str) – The units of time used for the demography. This is
commonly years or generations, but can be any string.
generation_time (float) – The generation time of demes, in units given
+
generation_time (float) – The generation time of demes, in units given
by the time_units parameter.
doi (list[str]) – If the graph describes a published demography, the DOI(s)
+
doi (list[str]) – If the graph describes a published demography, the DOI(s)
should be be given here as a list.
defaults (dict) – A dictionary of default values, following the
-Human Data Model schema for defaults.
metadata (dict) – A dictionary of arbitrary additional data.
defaults (dict) – A dictionary of default values, following the
+Human Data Model schema for defaults.
metadata (dict) – A dictionary of arbitrary additional data.
@@ -419,16 +419,16 @@ Building Demes graphs
- Parameters:
-name (str) – A string identifier for the deme.
description (str) – A description of the deme.
ancestors (list[str]) – List of deme names for the deme’s ancestors.
proportions (list[float]) – The proportions of ancestry from each ancestor.
+
name (str) – A string identifier for the deme.
description (str) – A description of the deme.
ancestors (list[str]) – List of deme names for the deme’s ancestors.
proportions (list[float]) – The proportions of ancestry from each ancestor.
This list has the same length as ancestors, and must sum to 1.
start_time (float) – The deme’s start time.
epochs (list[dict]) – List of epoch dictionaries. Each dictionary
-follows the Human Data Model schema for an epoch object.
defaults (dict) – A dictionary of default deme values, following the
-Human Data Model schema for deme defaults.
start_time (float) – The deme’s start time.
epochs (list[dict]) – List of epoch dictionaries. Each dictionary
+follows the Human Data Model schema for an epoch object.
defaults (dict) – A dictionary of default deme values, following the
+Human Data Model schema for deme defaults.
@@ -452,15 +452,15 @@ Building Demes graphs
Parameters:
-demes (list[str]) – List of deme names. If specified, migration is symmetric
+
demes (list[str]) – List of deme names. If specified, migration is symmetric
between all pairs of demes in this list.
source (str) – The name of the source deme. If specified, migration is asymmetric
+
source (str) – The name of the source deme. If specified, migration is asymmetric
from this deme.
dest (str) – The name of the destination deme. If specified, migration is
+
dest (str) – The name of the destination deme. If specified, migration is
asymmetric into this deme.
rate (float) – The rate of migration per generation.
start_time (float) – The time at which the migration rate is enabled.
end_time (float) – The time at which the migration rate is disabled.
rate (float) – The rate of migration per generation.
start_time (float) – The time at which the migration rate is enabled.
end_time (float) – The time at which the migration rate is disabled.
Building Demes graphs
Parameters:
-sources (list(str)) – A list of names of the source deme(s).
dest (str) – The name of the destination deme.
proportion (list(float)) – At the instant after migration, this is the expected proportion(s)
+
sources (list(str)) – A list of names of the source deme(s).
dest (str) – The name of the destination deme.
proportion (list(float)) – At the instant after migration, this is the expected proportion(s)
of individuals in the destination deme made up
of individuals from the source deme(s).
time (float) – The time at which migrations occur.
time (float) – The time at which migrations occur.
Building Demes graphsParameters:
data (MutableMapping) – The data dictionary to initialise the Builder’s state.
The objects nested within this dictionary should follow
-Demes’ Human Data Model, but see the note for
+Demes’ Human Data Model, but see the note for
Builder.data.
Returns:
@@ -533,7 +533,7 @@ Working with Demes graphsclass demes.Graph(*, description='', time_units, generation_time=None, doi=_Nothing.NOTHING, metadata=_Nothing.NOTHING)[source]¶
The Graph class is a resolved and validated representation of a
demographic model.
-A Graph object matches Demes’ Machine Data Model, with a small number of
+
A Graph object matches Demes’ Machine Data Model, with a small number of
additional redundant attributes that make the Graph a more convenient
object to use when inspecting a model’s properties.
Graph objects are not intended to be constructed directly—demographic
@@ -547,21 +547,21 @@
Working with Demes graphs
Variables:
-description (str) – A human readable description of the demography.
time_units (str) – The units of time used for the demography. This is
+
description (str) – A human readable description of the demography.
time_units (str) – The units of time used for the demography. This is
commonly years or generations, but can be any string.
This field is intended to be useful for documenting a demography,
but the actual value provided here should not be relied upon.
generation_time (float) – The generation time of demes, in units given
+
generation_time (float) – The generation time of demes, in units given
by the time_units parameter. Concretely, dividing all times
by generation_time will convert the graph to have time
units in generations.
See also: in_generations().
doi (list[str]) – A list of publications that describe the demographic model.
metadata (dict) – A dictionary of arbitrary additional data.
migrations (list[AsymmetricMigration]) – The continuous asymmetric migrations for the demographic model.
pulses (list[Pulse]) – The instantaneous pulse migrations for the demographic model.
doi (list[str]) – A list of publications that describe the demographic model.
metadata (dict) – A dictionary of arbitrary additional data.
migrations (list[AsymmetricMigration]) – The continuous asymmetric migrations for the demographic model.
pulses (list[Pulse]) – The instantaneous pulse migrations for the demographic model.
Working with Demes graphs
Parameters:
-deme_name (str) – The name of the deme.
+deme_name (str) – The name of the deme.
Return type:
-
+
Returns:
True if the deme is in the graph, False otherwise.
@@ -598,7 +598,7 @@ Working with Demes graphs
Parameters:
-deme_name (str) – The name of the deme.
+deme_name (str) – The name of the deme.
Return type:
@@ -615,10 +615,10 @@ Working with Demes graphs
Returns:
-A data dictionary following the Machine Data Model.
+A data dictionary following the Machine Data Model.
Return type:
-
+
@@ -629,10 +629,10 @@ Working with Demes graphs
Returns:
-A data dictionary following the Human Data Model.
+A data dictionary following the Human Data Model.
Return type:
-
+
@@ -656,10 +656,10 @@ Working with Demes graphsParameters:
other (Graph) – The graph to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Working with Demes graphsMerge, and Admix objects.
Return type:
-
+
@@ -701,8 +701,8 @@ Working with Demes graphs
Parameters:
-data (dict) – A data dictionary following either the
-Human Data Model or the Machine Data Model.
+data (dict) – A data dictionary following either the
+Human Data Model or the Machine Data Model.
Returns:
A resolved and validated demographic model.
@@ -732,7 +732,7 @@ Working with Demes graphsisclose(other, *, rel_tol=1e-09, abs_tol=1e-12)[source]¶
Returns true if the graph and other implement essentially
the same demographic model. Numerical values are compared using the
-math.isclose() function, from which this method takes its name.
+math.isclose() function, from which this method takes its name.
Furthermore, the following implementation details are ignored during
the comparison:
@@ -747,17 +747,17 @@ Working with Demes graphsParameters:
other (Graph) – The graph to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Returns:
True if the two graphs implement the same model, False otherwise.
Return type:
-
+
@@ -807,7 +807,7 @@ Working with Demes graphsend_times are a list of end times for each matrix.
Return type:
-tuple[list[list[list[float]]], list[float]]
+
Working with Demes graphsA NetworkX compatible dict-of-lists graph of the demes’ predecessors.
Return type:
-
+
@@ -842,7 +842,7 @@ Working with Demes graphs
Parameters:
-names (dict) – A dictionary with deme names and new names.
+names (dict) – A dictionary with deme names and new names.
Returns:
A demographic model with renamed demes.
@@ -872,7 +872,7 @@ Working with Demes graphsA NetworkX compatible dict-of-lists graph of the demes’ successors.
Return type:
-
+
@@ -887,15 +887,15 @@ Working with Demes graphs
Variables:
-name (str) – A concise string that identifies the deme.
description (str) – A description of the deme.
start_time (float) – The time at which the deme begins to exist.
ancestors (list[str]) – List of deme names for the deme’s ancestors.
proportions (list[float]) – The proportions of ancestry from each ancestor,
+
name (str) – A concise string that identifies the deme.
description (str) – A description of the deme.
start_time (float) – The time at which the deme begins to exist.
ancestors (list[str]) – List of deme names for the deme’s ancestors.
proportions (list[float]) – The proportions of ancestry from each ancestor,
ordered to correspond with the same order as the ancestors
list.
If there are one or more ancestors, the proportions sum to 1.
epochs (list[Epoch]) – A list of epochs that span the time interval over which the
+
epochs (list[Epoch]) – A list of epochs that span the time interval over which the
deme exists. Epoch time intervals are non-overlapping,
completely cover the deme’s existence time interval,
and are listed in time-descending order (from the past
@@ -914,10 +914,10 @@
Working with Demes graphsParameters:
other (Deme) – The deme to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Working with Demes graphs
- Return type:
--
+
-
@@ -943,17 +943,17 @@ Working with Demes graphsParameters:
other (Deme) – The deme to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two demes are equivalent, False otherwise.
- Return type:
--
+
-
@@ -967,13 +967,13 @@ Working with Demes graphs
- Parameters:
-time (float) – The time at which the size should be calculated.
+time (float) – The time at which the size should be calculated.
- Returns:
The deme size.
- Return type:
--
+
-
@@ -984,7 +984,7 @@ Working with Demes graphs
- Return type:
--
+
-
@@ -1004,16 +1004,16 @@ Working with Demes graphs
- Variables:
-start_time (float) – The start time of the epoch.
+
start_time (float) – The start time of the epoch.
This value is greater than zero and may be infinity.
end_time (float) – The end time of the epoch.
+
end_time (float) – The end time of the epoch.
This value is greater than or equal to zero and finite.
start_size (float) – Population size at start_time.
end_size (float) – Population size at end_time.
+
start_size (float) – Population size at start_time.
end_size (float) – Population size at end_time.
If start_size != end_size, the population size changes
between the start and end times according to the
size_function.
size_function (str) –
The size change function. This is either
+
size_function (str) –
The size change function. This is either
constant, exponential or linear, though it is possible
that additional values will be added in the future.
@@ -1041,8 +1041,8 @@ Working with Demes graphsfloat) – The selfing rate for this epoch.
cloning_rate (float) – The cloning rate for this epoch.
selfing_rate (float) – The selfing rate for this epoch.
cloning_rate (float) – The cloning rate for this epoch.
Working with Demes graphsParameters:
other (Epoch) – The epoch to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Working with Demes graphsParameters:
other (Epoch) – The epoch to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two epochs are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1097,7 +1097,7 @@ Working with Demes graphs
- Return type:
--
+
-
@@ -1118,11 +1118,11 @@ Continuous demographic events
- Variables:
-source (str) – The source deme for asymmetric migration.
dest (str) – The destination deme for asymmetric migration.
start_time (float) – The time at which the migration rate is activated.
end_time (float) – The time at which the migration rate is deactivated.
rate (float) – The rate of migration per generation.
source (str) – The source deme for asymmetric migration.
dest (str) – The destination deme for asymmetric migration.
start_time (float) – The time at which the migration rate is activated.
end_time (float) – The time at which the migration rate is deactivated.
rate (float) – The rate of migration per generation.
Continuous demographic eventsParameters:
other (AsymmetricMigration) – The migration to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Continuous demographic eventsParameters:
other (AsymmetricMigration) – The migration to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two epochs are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1188,10 +1188,10 @@ Discrete demographic events
- Variables:
-dest (str) – The destination deme.
time (float) – The time of migration.
proportions (list(float)) – Immediately following migration, the proportion(s)
+
dest (str) – The destination deme.
time (float) – The time of migration.
proportions (list(float)) – Immediately following migration, the proportion(s)
of individuals in the destination deme made up of migrant individuals or
having parents from the source deme(s).
@@ -1208,10 +1208,10 @@ Discrete demographic eventsParameters:
other (Pulse) – The pulse to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Discrete demographic eventsParameters:
other (Pulse) – The pulse to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two pulses are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1254,9 +1254,9 @@ Discrete demographic events
- Variables:
-
@@ -1271,10 +1271,10 @@ Discrete demographic eventsParameters:
other (Split) – The split to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Discrete demographic eventsParameters:
other (Split) – The split to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two splits are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1316,9 +1316,9 @@ Discrete demographic events
- Variables:
-
@@ -1333,10 +1333,10 @@ Discrete demographic eventsParameters:
other (Branch) – The branch to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Discrete demographic eventsParameters:
other (Branch) – The branch to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two branches are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1377,11 +1377,11 @@ Discrete demographic events
- Variables:
-
@@ -1396,10 +1396,10 @@ Discrete demographic eventsParameters:
other (Merge) – The merge to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Discrete demographic eventsParameters:
other (Merge) – The merge to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two merges are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1440,11 +1440,11 @@ Discrete demographic events
- Variables:
-
@@ -1459,10 +1459,10 @@ Discrete demographic eventsParameters:
other (Admix) – The admixture to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Discrete demographic eventsParameters:
other (Admix) – The admixture to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two admixtures are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1530,14 +1530,14 @@ Conversion functions
- Parameters:
-command (str) – The ms command line.
N0 (float) – The reference population size (\(N_0\)) used to translate
+
command (str) – The ms command line.
N0 (float) – The reference population size (\(N_0\)) used to translate
from coalescent units. For a command that specifies a
\(\theta\) value with the -t theta option,
this can be calculated as \(N_0 = \theta / (4 \mu L)\),
where \(\mu\) is the per-generation mutation rate and
\(L\) is the length of the sequence being simulated.
deme_names (list[str]) – A list of names to use for the demes.
+
deme_names (list[str]) – A list of names to use for the demes.
If not specified, demes will be named deme1, deme2, etc.
Conversion functions
- Parameters:
-N0 (float) – The reference population size used to translate into coalescent units.
+
N0 (float) – The reference population size used to translate into coalescent units.
See from_ms() for details.
samples (list(int)) – A list of haploid sample numbers, one for each deme, in the same
+
samples (list(int)) – A list of haploid sample numbers, one for each deme, in the same
order as the order of demes in the graph.
The parameter is ignored for demographic models with only one deme.
The given sampling scheme will be used with the -I argument.
@@ -1576,7 +1576,7 @@
Conversion functionsThe ms command line.
- Return type:
--
+
-
diff --git a/main/introduction.html b/main/introduction.html
index b84f08d..20a45cd 100644
--- a/main/introduction.html
+++ b/main/introduction.html
@@ -175,8 +175,8 @@ Quick search
Introduction¶
The demes Python package provides an API for defining, parsing, and sharing
-Demes demographic models. Applications can use
-demes to parse human-readable Demes YAML files
+Demes demographic models. Applications can use
+demes to parse human-readable Demes YAML files
into fully-resolved demographic models. In addition, demes provides
convenient data structures to simplify manipulation of demographic models.
If you find an error in the documentation or a bug in the software,
@@ -192,7 +192,7 @@
MotivationDemes Specification aims to make defining demographic
+
The Demes Specification aims to make defining demographic
models more intuitive, less prone to error or ambiguity, and readily
interchangeable between simulation platforms.
Demographic models, which define populations (or demes), their properties,
@@ -203,7 +203,7 @@
Motivation¶
The following YAML file implements a two-epoch demographic
history for a single deme, where the deme doubles in size 100 generations ago.
-See the Demes tutorial for a detailed introduction to
+See the Demes tutorial for a detailed introduction to
writing Demes YAML files.
description: Single-population two-epoch demography.
time_units: generations
@@ -233,7 +233,7 @@ Example<Axes: ylabel='time ago (generations)'>
-
+
diff --git a/main/quickstart.html b/main/quickstart.html
index 9f74fc2..1161bba 100644
--- a/main/quickstart.html
+++ b/main/quickstart.html
@@ -231,7 +231,7 @@ Loading a Demes graph
-
+
This YAML file can be loaded into Python with the load() function,
to obtain a Graph instance (modify the filename as appropriate).
@@ -402,7 +402,7 @@ Plotting a Demes graph<Axes: ylabel='time ago (generations)'>
-
+
Graph object using the resolve() method.data (dict) –
The data dictionary of the demographic model’s current state. +
data (dict) –
The data dictionary of the demographic model’s current state. The objects nested within this dictionary should follow -Demes’ data model, as described in the Human Data Model schema.
+Demes’ data model, as described in the Human Data Model schema.Note
Users may freely modify the data dictionary, such as temporarily
-adding or deleting fields, as long as the Human Data Model
+adding or deleting fields, as long as the Human Data Model
is not violated when the resolve() method is called.
Building Demes graphs
- Parameters:
-description (str) – A human readable description of the demography.
time_units (str) – The units of time used for the demography. This is
+
description (str) – A human readable description of the demography.
time_units (str) – The units of time used for the demography. This is
commonly years or generations, but can be any string.
generation_time (float) – The generation time of demes, in units given
+
generation_time (float) – The generation time of demes, in units given
by the time_units parameter.
doi (list[str]) – If the graph describes a published demography, the DOI(s)
+
doi (list[str]) – If the graph describes a published demography, the DOI(s)
should be be given here as a list.
defaults (dict) – A dictionary of default values, following the
-Human Data Model schema for defaults.
metadata (dict) – A dictionary of arbitrary additional data.
defaults (dict) – A dictionary of default values, following the
+Human Data Model schema for defaults.
metadata (dict) – A dictionary of arbitrary additional data.
@@ -419,16 +419,16 @@ Building Demes graphs
- Parameters:
-name (str) – A string identifier for the deme.
description (str) – A description of the deme.
ancestors (list[str]) – List of deme names for the deme’s ancestors.
proportions (list[float]) – The proportions of ancestry from each ancestor.
+
name (str) – A string identifier for the deme.
description (str) – A description of the deme.
ancestors (list[str]) – List of deme names for the deme’s ancestors.
proportions (list[float]) – The proportions of ancestry from each ancestor.
This list has the same length as ancestors, and must sum to 1.
start_time (float) – The deme’s start time.
epochs (list[dict]) – List of epoch dictionaries. Each dictionary
-follows the Human Data Model schema for an epoch object.
defaults (dict) – A dictionary of default deme values, following the
-Human Data Model schema for deme defaults.
start_time (float) – The deme’s start time.
epochs (list[dict]) – List of epoch dictionaries. Each dictionary
+follows the Human Data Model schema for an epoch object.
defaults (dict) – A dictionary of default deme values, following the
+Human Data Model schema for deme defaults.
-
-
description (str) – A human readable description of the demography.
-time_units (str) – The units of time used for the demography. This is +
description (str) – A human readable description of the demography.
+time_units (str) – The units of time used for the demography. This is commonly
yearsorgenerations, but can be any string.
-generation_time (float) – The generation time of demes, in units given +
generation_time (float) – The generation time of demes, in units given by the
time_unitsparameter.
-doi (list[str]) – If the graph describes a published demography, the DOI(s) +
doi (list[str]) – If the graph describes a published demography, the DOI(s) should be be given here as a list.
-defaults (dict) – A dictionary of default values, following the -Human Data Model schema for defaults.
-metadata (dict) – A dictionary of arbitrary additional data.
+defaults (dict) – A dictionary of default values, following the +Human Data Model schema for defaults.
+metadata (dict) – A dictionary of arbitrary additional data.
-
-
name (str) – A string identifier for the deme.
-description (str) – A description of the deme.
-ancestors (list[str]) – List of deme names for the deme’s ancestors.
-proportions (list[float]) – The proportions of ancestry from each ancestor. +
name (str) – A string identifier for the deme.
+description (str) – A description of the deme.
+ancestors (list[str]) – List of deme names for the deme’s ancestors.
+proportions (list[float]) – The proportions of ancestry from each ancestor. This list has the same length as
ancestors, and must sum to 1.
-start_time (float) – The deme’s start time.
-epochs (list[dict]) – List of epoch dictionaries. Each dictionary -follows the Human Data Model schema for an epoch object.
-defaults (dict) – A dictionary of default deme values, following the -Human Data Model schema for deme defaults.
+start_time (float) – The deme’s start time.
+epochs (list[dict]) – List of epoch dictionaries. Each dictionary +follows the Human Data Model schema for an epoch object.
+defaults (dict) – A dictionary of default deme values, following the +Human Data Model schema for deme defaults.
-
-
demes (list[str]) – List of deme names. If specified, migration is symmetric +
demes (list[str]) – List of deme names. If specified, migration is symmetric between all pairs of demes in this list.
-source (str) – The name of the source deme. If specified, migration is asymmetric +
source (str) – The name of the source deme. If specified, migration is asymmetric from this deme.
-dest (str) – The name of the destination deme. If specified, migration is +
dest (str) – The name of the destination deme. If specified, migration is asymmetric into this deme.
-rate (float) – The rate of migration per generation.
-start_time (float) – The time at which the migration rate is enabled.
-end_time (float) – The time at which the migration rate is disabled.
+rate (float) – The rate of migration per generation.
+start_time (float) – The time at which the migration rate is enabled.
+end_time (float) – The time at which the migration rate is disabled.
Building Demes graphs
Parameters:
-sources (list(str)) – A list of names of the source deme(s).
dest (str) – The name of the destination deme.
proportion (list(float)) – At the instant after migration, this is the expected proportion(s)
+
sources (list(str)) – A list of names of the source deme(s).
dest (str) – The name of the destination deme.
proportion (list(float)) – At the instant after migration, this is the expected proportion(s)
of individuals in the destination deme made up
of individuals from the source deme(s).
time (float) – The time at which migrations occur.
time (float) – The time at which migrations occur.
Building Demes graphsParameters:
data (MutableMapping) – The data dictionary to initialise the Builder’s state.
The objects nested within this dictionary should follow
-Demes’ Human Data Model, but see the note for
+Demes’ Human Data Model, but see the note for
Builder.data.
Returns:
@@ -533,7 +533,7 @@ Working with Demes graphsclass demes.Graph(*, description='', time_units, generation_time=None, doi=_Nothing.NOTHING, metadata=_Nothing.NOTHING)[source]¶
The Graph class is a resolved and validated representation of a
demographic model.
-A Graph object matches Demes’ Machine Data Model, with a small number of
+
A Graph object matches Demes’ Machine Data Model, with a small number of
additional redundant attributes that make the Graph a more convenient
object to use when inspecting a model’s properties.
Graph objects are not intended to be constructed directly—demographic
@@ -547,21 +547,21 @@
Working with Demes graphs
Variables:
-description (str) – A human readable description of the demography.
time_units (str) – The units of time used for the demography. This is
+
description (str) – A human readable description of the demography.
time_units (str) – The units of time used for the demography. This is
commonly years or generations, but can be any string.
This field is intended to be useful for documenting a demography,
but the actual value provided here should not be relied upon.
generation_time (float) – The generation time of demes, in units given
+
generation_time (float) – The generation time of demes, in units given
by the time_units parameter. Concretely, dividing all times
by generation_time will convert the graph to have time
units in generations.
See also: in_generations().
doi (list[str]) – A list of publications that describe the demographic model.
metadata (dict) – A dictionary of arbitrary additional data.
migrations (list[AsymmetricMigration]) – The continuous asymmetric migrations for the demographic model.
pulses (list[Pulse]) – The instantaneous pulse migrations for the demographic model.
doi (list[str]) – A list of publications that describe the demographic model.
metadata (dict) – A dictionary of arbitrary additional data.
migrations (list[AsymmetricMigration]) – The continuous asymmetric migrations for the demographic model.
pulses (list[Pulse]) – The instantaneous pulse migrations for the demographic model.
Working with Demes graphs
Parameters:
-deme_name (str) – The name of the deme.
+deme_name (str) – The name of the deme.
Return type:
-
+
Returns:
True if the deme is in the graph, False otherwise.
@@ -598,7 +598,7 @@ Working with Demes graphs
Parameters:
-deme_name (str) – The name of the deme.
+deme_name (str) – The name of the deme.
Return type:
@@ -615,10 +615,10 @@ Working with Demes graphs
Returns:
-A data dictionary following the Machine Data Model.
+A data dictionary following the Machine Data Model.
Return type:
-
+
@@ -629,10 +629,10 @@ Working with Demes graphs
Returns:
-A data dictionary following the Human Data Model.
+A data dictionary following the Human Data Model.
Return type:
-
+
@@ -656,10 +656,10 @@ Working with Demes graphsParameters:
other (Graph) – The graph to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Working with Demes graphsMerge, and Admix objects.
Return type:
-
+
@@ -701,8 +701,8 @@ Working with Demes graphs
Parameters:
-data (dict) – A data dictionary following either the
-Human Data Model or the Machine Data Model.
+data (dict) – A data dictionary following either the
+Human Data Model or the Machine Data Model.
Returns:
A resolved and validated demographic model.
@@ -732,7 +732,7 @@ Working with Demes graphsisclose(other, *, rel_tol=1e-09, abs_tol=1e-12)[source]¶
Returns true if the graph and other implement essentially
the same demographic model. Numerical values are compared using the
-math.isclose() function, from which this method takes its name.
+math.isclose() function, from which this method takes its name.
Furthermore, the following implementation details are ignored during
the comparison:
@@ -747,17 +747,17 @@ Working with Demes graphsParameters:
other (Graph) – The graph to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Returns:
True if the two graphs implement the same model, False otherwise.
Return type:
-
+
@@ -807,7 +807,7 @@ Working with Demes graphsend_times are a list of end times for each matrix.
Return type:
-tuple[list[list[list[float]]], list[float]]
+
Working with Demes graphsA NetworkX compatible dict-of-lists graph of the demes’ predecessors.
Return type:
-
+
@@ -842,7 +842,7 @@ Working with Demes graphs
Parameters:
-names (dict) – A dictionary with deme names and new names.
+names (dict) – A dictionary with deme names and new names.
Returns:
A demographic model with renamed demes.
@@ -872,7 +872,7 @@ Working with Demes graphsA NetworkX compatible dict-of-lists graph of the demes’ successors.
Return type:
-
+
@@ -887,15 +887,15 @@ Working with Demes graphs
Variables:
-name (str) – A concise string that identifies the deme.
description (str) – A description of the deme.
start_time (float) – The time at which the deme begins to exist.
ancestors (list[str]) – List of deme names for the deme’s ancestors.
proportions (list[float]) – The proportions of ancestry from each ancestor,
+
name (str) – A concise string that identifies the deme.
description (str) – A description of the deme.
start_time (float) – The time at which the deme begins to exist.
ancestors (list[str]) – List of deme names for the deme’s ancestors.
proportions (list[float]) – The proportions of ancestry from each ancestor,
ordered to correspond with the same order as the ancestors
list.
If there are one or more ancestors, the proportions sum to 1.
epochs (list[Epoch]) – A list of epochs that span the time interval over which the
+
epochs (list[Epoch]) – A list of epochs that span the time interval over which the
deme exists. Epoch time intervals are non-overlapping,
completely cover the deme’s existence time interval,
and are listed in time-descending order (from the past
@@ -914,10 +914,10 @@
Working with Demes graphsParameters:
other (Deme) – The deme to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Working with Demes graphs
- Return type:
--
+
-
@@ -943,17 +943,17 @@ Working with Demes graphsParameters:
other (Deme) – The deme to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two demes are equivalent, False otherwise.
- Return type:
--
+
-
@@ -967,13 +967,13 @@ Working with Demes graphs
- Parameters:
-time (float) – The time at which the size should be calculated.
+time (float) – The time at which the size should be calculated.
- Returns:
The deme size.
- Return type:
--
+
-
@@ -984,7 +984,7 @@ Working with Demes graphs
- Return type:
--
+
-
@@ -1004,16 +1004,16 @@ Working with Demes graphs
- Variables:
-start_time (float) – The start time of the epoch.
+
start_time (float) – The start time of the epoch.
This value is greater than zero and may be infinity.
end_time (float) – The end time of the epoch.
+
end_time (float) – The end time of the epoch.
This value is greater than or equal to zero and finite.
start_size (float) – Population size at start_time.
end_size (float) – Population size at end_time.
+
start_size (float) – Population size at start_time.
end_size (float) – Population size at end_time.
If start_size != end_size, the population size changes
between the start and end times according to the
size_function.
size_function (str) –
The size change function. This is either
+
size_function (str) –
The size change function. This is either
constant, exponential or linear, though it is possible
that additional values will be added in the future.
@@ -1041,8 +1041,8 @@ Working with Demes graphsfloat) – The selfing rate for this epoch.
cloning_rate (float) – The cloning rate for this epoch.
selfing_rate (float) – The selfing rate for this epoch.
cloning_rate (float) – The cloning rate for this epoch.
Working with Demes graphsParameters:
other (Epoch) – The epoch to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Working with Demes graphsParameters:
other (Epoch) – The epoch to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two epochs are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1097,7 +1097,7 @@ Working with Demes graphs
- Return type:
--
+
-
@@ -1118,11 +1118,11 @@ Continuous demographic events
- Variables:
-source (str) – The source deme for asymmetric migration.
dest (str) – The destination deme for asymmetric migration.
start_time (float) – The time at which the migration rate is activated.
end_time (float) – The time at which the migration rate is deactivated.
rate (float) – The rate of migration per generation.
source (str) – The source deme for asymmetric migration.
dest (str) – The destination deme for asymmetric migration.
start_time (float) – The time at which the migration rate is activated.
end_time (float) – The time at which the migration rate is deactivated.
rate (float) – The rate of migration per generation.
Continuous demographic eventsParameters:
other (AsymmetricMigration) – The migration to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Continuous demographic eventsParameters:
other (AsymmetricMigration) – The migration to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two epochs are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1188,10 +1188,10 @@ Discrete demographic events
- Variables:
-dest (str) – The destination deme.
time (float) – The time of migration.
proportions (list(float)) – Immediately following migration, the proportion(s)
+
dest (str) – The destination deme.
time (float) – The time of migration.
proportions (list(float)) – Immediately following migration, the proportion(s)
of individuals in the destination deme made up of migrant individuals or
having parents from the source deme(s).
@@ -1208,10 +1208,10 @@ Discrete demographic eventsParameters:
other (Pulse) – The pulse to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Discrete demographic eventsParameters:
other (Pulse) – The pulse to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two pulses are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1254,9 +1254,9 @@ Discrete demographic events
- Variables:
-
@@ -1271,10 +1271,10 @@ Discrete demographic eventsParameters:
other (Split) – The split to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Discrete demographic eventsParameters:
other (Split) – The split to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two splits are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1316,9 +1316,9 @@ Discrete demographic events
- Variables:
-
@@ -1333,10 +1333,10 @@ Discrete demographic eventsParameters:
other (Branch) – The branch to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Discrete demographic eventsParameters:
other (Branch) – The branch to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two branches are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1377,11 +1377,11 @@ Discrete demographic events
- Variables:
-
@@ -1396,10 +1396,10 @@ Discrete demographic eventsParameters:
other (Merge) – The merge to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Discrete demographic eventsParameters:
other (Merge) – The merge to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two merges are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1440,11 +1440,11 @@ Discrete demographic events
- Variables:
-
@@ -1459,10 +1459,10 @@ Discrete demographic eventsParameters:
other (Admix) – The admixture to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Discrete demographic eventsParameters:
other (Admix) – The admixture to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two admixtures are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1530,14 +1530,14 @@ Conversion functions
- Parameters:
-command (str) – The ms command line.
N0 (float) – The reference population size (\(N_0\)) used to translate
+
command (str) – The ms command line.
N0 (float) – The reference population size (\(N_0\)) used to translate
from coalescent units. For a command that specifies a
\(\theta\) value with the -t theta option,
this can be calculated as \(N_0 = \theta / (4 \mu L)\),
where \(\mu\) is the per-generation mutation rate and
\(L\) is the length of the sequence being simulated.
deme_names (list[str]) – A list of names to use for the demes.
+
deme_names (list[str]) – A list of names to use for the demes.
If not specified, demes will be named deme1, deme2, etc.
Conversion functions
- Parameters:
-N0 (float) – The reference population size used to translate into coalescent units.
+
N0 (float) – The reference population size used to translate into coalescent units.
See from_ms() for details.
samples (list(int)) – A list of haploid sample numbers, one for each deme, in the same
+
samples (list(int)) – A list of haploid sample numbers, one for each deme, in the same
order as the order of demes in the graph.
The parameter is ignored for demographic models with only one deme.
The given sampling scheme will be used with the -I argument.
@@ -1576,7 +1576,7 @@
Conversion functionsThe ms command line.
- Return type:
--
+
-
diff --git a/main/introduction.html b/main/introduction.html
index b84f08d..20a45cd 100644
--- a/main/introduction.html
+++ b/main/introduction.html
@@ -175,8 +175,8 @@ Quick search
Introduction¶
The demes Python package provides an API for defining, parsing, and sharing
-Demes demographic models. Applications can use
-demes to parse human-readable Demes YAML files
+Demes demographic models. Applications can use
+demes to parse human-readable Demes YAML files
into fully-resolved demographic models. In addition, demes provides
convenient data structures to simplify manipulation of demographic models.
If you find an error in the documentation or a bug in the software,
@@ -192,7 +192,7 @@
MotivationDemes Specification aims to make defining demographic
+
The Demes Specification aims to make defining demographic
models more intuitive, less prone to error or ambiguity, and readily
interchangeable between simulation platforms.
Demographic models, which define populations (or demes), their properties,
@@ -203,7 +203,7 @@
Motivation¶
The following YAML file implements a two-epoch demographic
history for a single deme, where the deme doubles in size 100 generations ago.
-See the Demes tutorial for a detailed introduction to
+See the Demes tutorial for a detailed introduction to
writing Demes YAML files.
description: Single-population two-epoch demography.
time_units: generations
@@ -233,7 +233,7 @@ Example<Axes: ylabel='time ago (generations)'>
-
+
diff --git a/main/quickstart.html b/main/quickstart.html
index 9f74fc2..1161bba 100644
--- a/main/quickstart.html
+++ b/main/quickstart.html
@@ -231,7 +231,7 @@ Loading a Demes graph
-
+
This YAML file can be loaded into Python with the load() function,
to obtain a Graph instance (modify the filename as appropriate).
@@ -402,7 +402,7 @@ Plotting a Demes graph<Axes: ylabel='time ago (generations)'>
-
+
-
-
sources (list(str)) – A list of names of the source deme(s).
-dest (str) – The name of the destination deme.
-proportion (list(float)) – At the instant after migration, this is the expected proportion(s) +
sources (list(str)) – A list of names of the source deme(s).
+dest (str) – The name of the destination deme.
+proportion (list(float)) – At the instant after migration, this is the expected proportion(s) of individuals in the destination deme made up of individuals from the source deme(s).
-time (float) – The time at which migrations occur.
+time (float) – The time at which migrations occur.
data (MutableMapping) – The data dictionary to initialise the Builder’s state.
The objects nested within this dictionary should follow
-Demes’ Human Data Model, but see the note for
+Demes’ Human Data Model, but see the note for
Builder.data.
Working with Demes graphsclass demes.Graph(*, description='', time_units, generation_time=None, doi=_Nothing.NOTHING, metadata=_Nothing.NOTHING)[source]¶
The Graph class is a resolved and validated representation of a
demographic model.
-A Graph object matches Demes’ Machine Data Model, with a small number of
+
A Graph object matches Demes’ Machine Data Model, with a small number of
additional redundant attributes that make the Graph a more convenient
object to use when inspecting a model’s properties.
Graph objects are not intended to be constructed directly—demographic
@@ -547,21 +547,21 @@
Working with Demes graphs
Variables:
-description (str) – A human readable description of the demography.
time_units (str) – The units of time used for the demography. This is
+
description (str) – A human readable description of the demography.
time_units (str) – The units of time used for the demography. This is
commonly years or generations, but can be any string.
This field is intended to be useful for documenting a demography,
but the actual value provided here should not be relied upon.
generation_time (float) – The generation time of demes, in units given
+
generation_time (float) – The generation time of demes, in units given
by the time_units parameter. Concretely, dividing all times
by generation_time will convert the graph to have time
units in generations.
See also: in_generations().
doi (list[str]) – A list of publications that describe the demographic model.
metadata (dict) – A dictionary of arbitrary additional data.
migrations (list[AsymmetricMigration]) – The continuous asymmetric migrations for the demographic model.
pulses (list[Pulse]) – The instantaneous pulse migrations for the demographic model.
doi (list[str]) – A list of publications that describe the demographic model.
metadata (dict) – A dictionary of arbitrary additional data.
migrations (list[AsymmetricMigration]) – The continuous asymmetric migrations for the demographic model.
pulses (list[Pulse]) – The instantaneous pulse migrations for the demographic model.
Working with Demes graphs
Parameters:
-deme_name (str) – The name of the deme.
+deme_name (str) – The name of the deme.
Return type:
-
+
Returns:
True if the deme is in the graph, False otherwise.
@@ -598,7 +598,7 @@ Working with Demes graphs
Parameters:
-deme_name (str) – The name of the deme.
+deme_name (str) – The name of the deme.
Return type:
@@ -615,10 +615,10 @@ Working with Demes graphs
Returns:
-A data dictionary following the Machine Data Model.
+A data dictionary following the Machine Data Model.
Return type:
-
+
@@ -629,10 +629,10 @@ Working with Demes graphs
Returns:
-A data dictionary following the Human Data Model.
+A data dictionary following the Human Data Model.
Return type:
-
+
@@ -656,10 +656,10 @@ Working with Demes graphsParameters:
other (Graph) – The graph to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Working with Demes graphsMerge, and Admix objects.
Return type:
-
+
@@ -701,8 +701,8 @@ Working with Demes graphs
Parameters:
-data (dict) – A data dictionary following either the
-Human Data Model or the Machine Data Model.
+data (dict) – A data dictionary following either the
+Human Data Model or the Machine Data Model.
Returns:
A resolved and validated demographic model.
@@ -732,7 +732,7 @@ Working with Demes graphsisclose(other, *, rel_tol=1e-09, abs_tol=1e-12)[source]¶
Returns true if the graph and other implement essentially
the same demographic model. Numerical values are compared using the
-math.isclose() function, from which this method takes its name.
+math.isclose() function, from which this method takes its name.
Furthermore, the following implementation details are ignored during
the comparison:
@@ -747,17 +747,17 @@ Working with Demes graphsParameters:
other (Graph) – The graph to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Returns:
True if the two graphs implement the same model, False otherwise.
Return type:
-
+
@@ -807,7 +807,7 @@ Working with Demes graphsend_times are a list of end times for each matrix.
Return type:
-tuple[list[list[list[float]]], list[float]]
+
Working with Demes graphsA NetworkX compatible dict-of-lists graph of the demes’ predecessors.
Return type:
-
+
@@ -842,7 +842,7 @@ Working with Demes graphs
Parameters:
-names (dict) – A dictionary with deme names and new names.
+names (dict) – A dictionary with deme names and new names.
Returns:
A demographic model with renamed demes.
@@ -872,7 +872,7 @@ Working with Demes graphsA NetworkX compatible dict-of-lists graph of the demes’ successors.
Return type:
-
+
@@ -887,15 +887,15 @@ Working with Demes graphs
Variables:
-name (str) – A concise string that identifies the deme.
description (str) – A description of the deme.
start_time (float) – The time at which the deme begins to exist.
ancestors (list[str]) – List of deme names for the deme’s ancestors.
proportions (list[float]) – The proportions of ancestry from each ancestor,
+
name (str) – A concise string that identifies the deme.
description (str) – A description of the deme.
start_time (float) – The time at which the deme begins to exist.
ancestors (list[str]) – List of deme names for the deme’s ancestors.
proportions (list[float]) – The proportions of ancestry from each ancestor,
ordered to correspond with the same order as the ancestors
list.
If there are one or more ancestors, the proportions sum to 1.
epochs (list[Epoch]) – A list of epochs that span the time interval over which the
+
epochs (list[Epoch]) – A list of epochs that span the time interval over which the
deme exists. Epoch time intervals are non-overlapping,
completely cover the deme’s existence time interval,
and are listed in time-descending order (from the past
@@ -914,10 +914,10 @@
Working with Demes graphsParameters:
other (Deme) – The deme to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Working with Demes graphs
- Return type:
--
+
-
@@ -943,17 +943,17 @@ Working with Demes graphsParameters:
other (Deme) – The deme to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two demes are equivalent, False otherwise.
- Return type:
--
+
-
@@ -967,13 +967,13 @@ Working with Demes graphs
- Parameters:
-time (float) – The time at which the size should be calculated.
+time (float) – The time at which the size should be calculated.
- Returns:
The deme size.
- Return type:
--
+
-
@@ -984,7 +984,7 @@ Working with Demes graphs
- Return type:
--
+
-
@@ -1004,16 +1004,16 @@ Working with Demes graphs
- Variables:
-start_time (float) – The start time of the epoch.
+
start_time (float) – The start time of the epoch.
This value is greater than zero and may be infinity.
end_time (float) – The end time of the epoch.
+
end_time (float) – The end time of the epoch.
This value is greater than or equal to zero and finite.
start_size (float) – Population size at start_time.
end_size (float) – Population size at end_time.
+
start_size (float) – Population size at start_time.
end_size (float) – Population size at end_time.
If start_size != end_size, the population size changes
between the start and end times according to the
size_function.
size_function (str) –
The size change function. This is either
+
size_function (str) –
The size change function. This is either
constant, exponential or linear, though it is possible
that additional values will be added in the future.
@@ -1041,8 +1041,8 @@ Working with Demes graphsfloat) – The selfing rate for this epoch.
cloning_rate (float) – The cloning rate for this epoch.
selfing_rate (float) – The selfing rate for this epoch.
cloning_rate (float) – The cloning rate for this epoch.
Working with Demes graphsParameters:
other (Epoch) – The epoch to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Working with Demes graphsParameters:
other (Epoch) – The epoch to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two epochs are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1097,7 +1097,7 @@ Working with Demes graphs
- Return type:
--
+
-
@@ -1118,11 +1118,11 @@ Continuous demographic events
- Variables:
-source (str) – The source deme for asymmetric migration.
dest (str) – The destination deme for asymmetric migration.
start_time (float) – The time at which the migration rate is activated.
end_time (float) – The time at which the migration rate is deactivated.
rate (float) – The rate of migration per generation.
source (str) – The source deme for asymmetric migration.
dest (str) – The destination deme for asymmetric migration.
start_time (float) – The time at which the migration rate is activated.
end_time (float) – The time at which the migration rate is deactivated.
rate (float) – The rate of migration per generation.
Continuous demographic eventsParameters:
other (AsymmetricMigration) – The migration to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Continuous demographic eventsParameters:
other (AsymmetricMigration) – The migration to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two epochs are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1188,10 +1188,10 @@ Discrete demographic events
- Variables:
-dest (str) – The destination deme.
time (float) – The time of migration.
proportions (list(float)) – Immediately following migration, the proportion(s)
+
dest (str) – The destination deme.
time (float) – The time of migration.
proportions (list(float)) – Immediately following migration, the proportion(s)
of individuals in the destination deme made up of migrant individuals or
having parents from the source deme(s).
@@ -1208,10 +1208,10 @@ Discrete demographic eventsParameters:
other (Pulse) – The pulse to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Discrete demographic eventsParameters:
other (Pulse) – The pulse to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two pulses are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1254,9 +1254,9 @@ Discrete demographic events
- Variables:
-
@@ -1271,10 +1271,10 @@ Discrete demographic eventsParameters:
other (Split) – The split to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Discrete demographic eventsParameters:
other (Split) – The split to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two splits are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1316,9 +1316,9 @@ Discrete demographic events
- Variables:
-
@@ -1333,10 +1333,10 @@ Discrete demographic eventsParameters:
other (Branch) – The branch to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Discrete demographic eventsParameters:
other (Branch) – The branch to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two branches are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1377,11 +1377,11 @@ Discrete demographic events
- Variables:
-
@@ -1396,10 +1396,10 @@ Discrete demographic eventsParameters:
other (Merge) – The merge to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Discrete demographic eventsParameters:
other (Merge) – The merge to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two merges are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1440,11 +1440,11 @@ Discrete demographic events
- Variables:
-
@@ -1459,10 +1459,10 @@ Discrete demographic eventsParameters:
other (Admix) – The admixture to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Discrete demographic eventsParameters:
other (Admix) – The admixture to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two admixtures are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1530,14 +1530,14 @@ Conversion functions
- Parameters:
-command (str) – The ms command line.
N0 (float) – The reference population size (\(N_0\)) used to translate
+
command (str) – The ms command line.
N0 (float) – The reference population size (\(N_0\)) used to translate
from coalescent units. For a command that specifies a
\(\theta\) value with the -t theta option,
this can be calculated as \(N_0 = \theta / (4 \mu L)\),
where \(\mu\) is the per-generation mutation rate and
\(L\) is the length of the sequence being simulated.
deme_names (list[str]) – A list of names to use for the demes.
+
deme_names (list[str]) – A list of names to use for the demes.
If not specified, demes will be named deme1, deme2, etc.
Conversion functions
- Parameters:
-N0 (float) – The reference population size used to translate into coalescent units.
+
N0 (float) – The reference population size used to translate into coalescent units.
See from_ms() for details.
samples (list(int)) – A list of haploid sample numbers, one for each deme, in the same
+
samples (list(int)) – A list of haploid sample numbers, one for each deme, in the same
order as the order of demes in the graph.
The parameter is ignored for demographic models with only one deme.
The given sampling scheme will be used with the -I argument.
@@ -1576,7 +1576,7 @@
Conversion functionsThe ms command line.
- Return type:
--
+
-
diff --git a/main/introduction.html b/main/introduction.html
index b84f08d..20a45cd 100644
--- a/main/introduction.html
+++ b/main/introduction.html
@@ -175,8 +175,8 @@ Quick search
Introduction¶
The demes Python package provides an API for defining, parsing, and sharing
-Demes demographic models. Applications can use
-demes to parse human-readable Demes YAML files
+Demes demographic models. Applications can use
+demes to parse human-readable Demes YAML files
into fully-resolved demographic models. In addition, demes provides
convenient data structures to simplify manipulation of demographic models.
If you find an error in the documentation or a bug in the software,
@@ -192,7 +192,7 @@
MotivationDemes Specification aims to make defining demographic
+
The Demes Specification aims to make defining demographic
models more intuitive, less prone to error or ambiguity, and readily
interchangeable between simulation platforms.
Demographic models, which define populations (or demes), their properties,
@@ -203,7 +203,7 @@
Motivation¶
The following YAML file implements a two-epoch demographic
history for a single deme, where the deme doubles in size 100 generations ago.
-See the Demes tutorial for a detailed introduction to
+See the Demes tutorial for a detailed introduction to
writing Demes YAML files.
description: Single-population two-epoch demography.
time_units: generations
@@ -233,7 +233,7 @@ Example<Axes: ylabel='time ago (generations)'>
-
+
diff --git a/main/quickstart.html b/main/quickstart.html
index 9f74fc2..1161bba 100644
--- a/main/quickstart.html
+++ b/main/quickstart.html
@@ -231,7 +231,7 @@ Loading a Demes graph
-
+
This YAML file can be loaded into Python with the load() function,
to obtain a Graph instance (modify the filename as appropriate).
@@ -402,7 +402,7 @@ Plotting a Demes graph<Axes: ylabel='time ago (generations)'>
-
+
The Graph class is a resolved and validated representation of a demographic model.
-A Graph object matches Demes’ Machine Data Model, with a small number of +
A Graph object matches Demes’ Machine Data Model, with a small number of additional redundant attributes that make the Graph a more convenient object to use when inspecting a model’s properties. Graph objects are not intended to be constructed directly—demographic @@ -547,21 +547,21 @@
Working with Demes graphs
Variables:
-description (str) – A human readable description of the demography.
time_units (str) – The units of time used for the demography. This is
+
description (str) – A human readable description of the demography.
time_units (str) – The units of time used for the demography. This is
commonly years or generations, but can be any string.
This field is intended to be useful for documenting a demography,
but the actual value provided here should not be relied upon.
generation_time (float) – The generation time of demes, in units given
+
generation_time (float) – The generation time of demes, in units given
by the time_units parameter. Concretely, dividing all times
by generation_time will convert the graph to have time
units in generations.
See also: in_generations().
doi (list[str]) – A list of publications that describe the demographic model.
metadata (dict) – A dictionary of arbitrary additional data.
migrations (list[AsymmetricMigration]) – The continuous asymmetric migrations for the demographic model.
pulses (list[Pulse]) – The instantaneous pulse migrations for the demographic model.
doi (list[str]) – A list of publications that describe the demographic model.
metadata (dict) – A dictionary of arbitrary additional data.
migrations (list[AsymmetricMigration]) – The continuous asymmetric migrations for the demographic model.
pulses (list[Pulse]) – The instantaneous pulse migrations for the demographic model.
Working with Demes graphs
Parameters:
-deme_name (str) – The name of the deme.
+deme_name (str) – The name of the deme.
Return type:
-
+
Returns:
True if the deme is in the graph, False otherwise.
@@ -598,7 +598,7 @@ Working with Demes graphs
Parameters:
-deme_name (str) – The name of the deme.
+deme_name (str) – The name of the deme.
Return type:
@@ -615,10 +615,10 @@ Working with Demes graphs
Returns:
-A data dictionary following the Machine Data Model.
+A data dictionary following the Machine Data Model.
Return type:
-
+
@@ -629,10 +629,10 @@ Working with Demes graphs
Returns:
-A data dictionary following the Human Data Model.
+A data dictionary following the Human Data Model.
Return type:
-
+
@@ -656,10 +656,10 @@ Working with Demes graphsParameters:
other (Graph) – The graph to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Working with Demes graphsMerge, and Admix objects.
Return type:
-
+
@@ -701,8 +701,8 @@ Working with Demes graphs
Parameters:
-data (dict) – A data dictionary following either the
-Human Data Model or the Machine Data Model.
+data (dict) – A data dictionary following either the
+Human Data Model or the Machine Data Model.
Returns:
A resolved and validated demographic model.
@@ -732,7 +732,7 @@ Working with Demes graphsisclose(other, *, rel_tol=1e-09, abs_tol=1e-12)[source]¶
Returns true if the graph and other implement essentially
the same demographic model. Numerical values are compared using the
-math.isclose() function, from which this method takes its name.
+math.isclose() function, from which this method takes its name.
Furthermore, the following implementation details are ignored during
the comparison:
@@ -747,17 +747,17 @@ Working with Demes graphsParameters:
other (Graph) – The graph to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Returns:
True if the two graphs implement the same model, False otherwise.
Return type:
-
+
@@ -807,7 +807,7 @@ Working with Demes graphsend_times are a list of end times for each matrix.
Return type:
-tuple[list[list[list[float]]], list[float]]
+
Working with Demes graphsA NetworkX compatible dict-of-lists graph of the demes’ predecessors.
Return type:
-
+
@@ -842,7 +842,7 @@ Working with Demes graphs
Parameters:
-names (dict) – A dictionary with deme names and new names.
+names (dict) – A dictionary with deme names and new names.
Returns:
A demographic model with renamed demes.
@@ -872,7 +872,7 @@ Working with Demes graphsA NetworkX compatible dict-of-lists graph of the demes’ successors.
Return type:
-
+
@@ -887,15 +887,15 @@ Working with Demes graphs
Variables:
-name (str) – A concise string that identifies the deme.
description (str) – A description of the deme.
start_time (float) – The time at which the deme begins to exist.
ancestors (list[str]) – List of deme names for the deme’s ancestors.
proportions (list[float]) – The proportions of ancestry from each ancestor,
+
name (str) – A concise string that identifies the deme.
description (str) – A description of the deme.
start_time (float) – The time at which the deme begins to exist.
ancestors (list[str]) – List of deme names for the deme’s ancestors.
proportions (list[float]) – The proportions of ancestry from each ancestor,
ordered to correspond with the same order as the ancestors
list.
If there are one or more ancestors, the proportions sum to 1.
epochs (list[Epoch]) – A list of epochs that span the time interval over which the
+
epochs (list[Epoch]) – A list of epochs that span the time interval over which the
deme exists. Epoch time intervals are non-overlapping,
completely cover the deme’s existence time interval,
and are listed in time-descending order (from the past
@@ -914,10 +914,10 @@
Working with Demes graphsParameters:
other (Deme) – The deme to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Working with Demes graphs
- Return type:
--
+
-
@@ -943,17 +943,17 @@ Working with Demes graphsParameters:
other (Deme) – The deme to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two demes are equivalent, False otherwise.
- Return type:
--
+
-
@@ -967,13 +967,13 @@ Working with Demes graphs
- Parameters:
-time (float) – The time at which the size should be calculated.
+time (float) – The time at which the size should be calculated.
- Returns:
The deme size.
- Return type:
--
+
-
@@ -984,7 +984,7 @@ Working with Demes graphs
- Return type:
--
+
-
@@ -1004,16 +1004,16 @@ Working with Demes graphs
- Variables:
-start_time (float) – The start time of the epoch.
+
start_time (float) – The start time of the epoch.
This value is greater than zero and may be infinity.
end_time (float) – The end time of the epoch.
+
end_time (float) – The end time of the epoch.
This value is greater than or equal to zero and finite.
start_size (float) – Population size at start_time.
end_size (float) – Population size at end_time.
+
start_size (float) – Population size at start_time.
end_size (float) – Population size at end_time.
If start_size != end_size, the population size changes
between the start and end times according to the
size_function.
size_function (str) –
The size change function. This is either
+
size_function (str) –
The size change function. This is either
constant, exponential or linear, though it is possible
that additional values will be added in the future.
@@ -1041,8 +1041,8 @@ Working with Demes graphsfloat) – The selfing rate for this epoch.
cloning_rate (float) – The cloning rate for this epoch.
selfing_rate (float) – The selfing rate for this epoch.
cloning_rate (float) – The cloning rate for this epoch.
Working with Demes graphsParameters:
other (Epoch) – The epoch to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Working with Demes graphsParameters:
other (Epoch) – The epoch to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two epochs are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1097,7 +1097,7 @@ Working with Demes graphs
- Return type:
--
+
-
@@ -1118,11 +1118,11 @@ Continuous demographic events
- Variables:
-source (str) – The source deme for asymmetric migration.
dest (str) – The destination deme for asymmetric migration.
start_time (float) – The time at which the migration rate is activated.
end_time (float) – The time at which the migration rate is deactivated.
rate (float) – The rate of migration per generation.
source (str) – The source deme for asymmetric migration.
dest (str) – The destination deme for asymmetric migration.
start_time (float) – The time at which the migration rate is activated.
end_time (float) – The time at which the migration rate is deactivated.
rate (float) – The rate of migration per generation.
Continuous demographic eventsParameters:
other (AsymmetricMigration) – The migration to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Continuous demographic eventsParameters:
other (AsymmetricMigration) – The migration to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two epochs are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1188,10 +1188,10 @@ Discrete demographic events
- Variables:
-dest (str) – The destination deme.
time (float) – The time of migration.
proportions (list(float)) – Immediately following migration, the proportion(s)
+
dest (str) – The destination deme.
time (float) – The time of migration.
proportions (list(float)) – Immediately following migration, the proportion(s)
of individuals in the destination deme made up of migrant individuals or
having parents from the source deme(s).
@@ -1208,10 +1208,10 @@ Discrete demographic eventsParameters:
other (Pulse) – The pulse to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Discrete demographic eventsParameters:
other (Pulse) – The pulse to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two pulses are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1254,9 +1254,9 @@ Discrete demographic events
- Variables:
-
@@ -1271,10 +1271,10 @@ Discrete demographic eventsParameters:
other (Split) – The split to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Discrete demographic eventsParameters:
other (Split) – The split to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two splits are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1316,9 +1316,9 @@ Discrete demographic events
- Variables:
-
@@ -1333,10 +1333,10 @@ Discrete demographic eventsParameters:
other (Branch) – The branch to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Discrete demographic eventsParameters:
other (Branch) – The branch to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two branches are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1377,11 +1377,11 @@ Discrete demographic events
- Variables:
-
@@ -1396,10 +1396,10 @@ Discrete demographic eventsParameters:
other (Merge) – The merge to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Discrete demographic eventsParameters:
other (Merge) – The merge to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two merges are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1440,11 +1440,11 @@ Discrete demographic events
- Variables:
-
@@ -1459,10 +1459,10 @@ Discrete demographic eventsParameters:
other (Admix) – The admixture to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Discrete demographic eventsParameters:
other (Admix) – The admixture to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two admixtures are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1530,14 +1530,14 @@ Conversion functions
- Parameters:
-command (str) – The ms command line.
N0 (float) – The reference population size (\(N_0\)) used to translate
+
command (str) – The ms command line.
N0 (float) – The reference population size (\(N_0\)) used to translate
from coalescent units. For a command that specifies a
\(\theta\) value with the -t theta option,
this can be calculated as \(N_0 = \theta / (4 \mu L)\),
where \(\mu\) is the per-generation mutation rate and
\(L\) is the length of the sequence being simulated.
deme_names (list[str]) – A list of names to use for the demes.
+
deme_names (list[str]) – A list of names to use for the demes.
If not specified, demes will be named deme1, deme2, etc.
Conversion functions
- Parameters:
-N0 (float) – The reference population size used to translate into coalescent units.
+
N0 (float) – The reference population size used to translate into coalescent units.
See from_ms() for details.
samples (list(int)) – A list of haploid sample numbers, one for each deme, in the same
+
samples (list(int)) – A list of haploid sample numbers, one for each deme, in the same
order as the order of demes in the graph.
The parameter is ignored for demographic models with only one deme.
The given sampling scheme will be used with the -I argument.
@@ -1576,7 +1576,7 @@
Conversion functionsThe ms command line.
- Return type:
--
+
-
diff --git a/main/introduction.html b/main/introduction.html
index b84f08d..20a45cd 100644
--- a/main/introduction.html
+++ b/main/introduction.html
@@ -175,8 +175,8 @@ Quick search
Introduction¶
The demes Python package provides an API for defining, parsing, and sharing
-Demes demographic models. Applications can use
-demes to parse human-readable Demes YAML files
+Demes demographic models. Applications can use
+demes to parse human-readable Demes YAML files
into fully-resolved demographic models. In addition, demes provides
convenient data structures to simplify manipulation of demographic models.
If you find an error in the documentation or a bug in the software,
@@ -192,7 +192,7 @@
MotivationDemes Specification aims to make defining demographic
+
The Demes Specification aims to make defining demographic
models more intuitive, less prone to error or ambiguity, and readily
interchangeable between simulation platforms.
Demographic models, which define populations (or demes), their properties,
@@ -203,7 +203,7 @@
Motivation¶
The following YAML file implements a two-epoch demographic
history for a single deme, where the deme doubles in size 100 generations ago.
-See the Demes tutorial for a detailed introduction to
+See the Demes tutorial for a detailed introduction to
writing Demes YAML files.
description: Single-population two-epoch demography.
time_units: generations
@@ -233,7 +233,7 @@ Example<Axes: ylabel='time ago (generations)'>
-
+
diff --git a/main/quickstart.html b/main/quickstart.html
index 9f74fc2..1161bba 100644
--- a/main/quickstart.html
+++ b/main/quickstart.html
@@ -231,7 +231,7 @@ Loading a Demes graph
-
+
This YAML file can be loaded into Python with the load() function,
to obtain a Graph instance (modify the filename as appropriate).
@@ -402,7 +402,7 @@ Plotting a Demes graph<Axes: ylabel='time ago (generations)'>
-
+
-
-
description (str) – A human readable description of the demography.
-time_units (str) – The units of time used for the demography. This is +
description (str) – A human readable description of the demography.
+time_units (str) – The units of time used for the demography. This is commonly
yearsorgenerations, but can be any string. This field is intended to be useful for documenting a demography, but the actual value provided here should not be relied upon.
-generation_time (float) – The generation time of demes, in units given +
generation_time (float) – The generation time of demes, in units given by the
time_unitsparameter. Concretely, dividing all times bygeneration_timewill convert the graph to have time units in generations. See also:in_generations().
-doi (list[str]) – A list of publications that describe the demographic model.
-metadata (dict) – A dictionary of arbitrary additional data.
-- -
migrations (list[AsymmetricMigration]) – The continuous asymmetric migrations for the demographic model.
-pulses (list[Pulse]) – The instantaneous pulse migrations for the demographic model.
+doi (list[str]) – A list of publications that describe the demographic model.
+metadata (dict) – A dictionary of arbitrary additional data.
+- +
migrations (list[AsymmetricMigration]) – The continuous asymmetric migrations for the demographic model.
+pulses (list[Pulse]) – The instantaneous pulse migrations for the demographic model.
deme_name (str) – The name of the deme.
+deme_name (str) – The name of the deme.
True if the deme is in the graph, False otherwise.
Working with Demes graphs
Parameters:
-deme_name (str) – The name of the deme.
+deme_name (str) – The name of the deme.
Return type:
@@ -615,10 +615,10 @@ Working with Demes graphs
Returns:
-A data dictionary following the Machine Data Model.
+A data dictionary following the Machine Data Model.
Return type:
-
+
@@ -629,10 +629,10 @@ Working with Demes graphs
Returns:
-A data dictionary following the Human Data Model.
+A data dictionary following the Human Data Model.
Return type:
-
+
@@ -656,10 +656,10 @@ Working with Demes graphsParameters:
other (Graph) – The graph to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Working with Demes graphsMerge, and Admix objects.
Return type:
-
+
@@ -701,8 +701,8 @@ Working with Demes graphs
Parameters:
-data (dict) – A data dictionary following either the
-Human Data Model or the Machine Data Model.
+data (dict) – A data dictionary following either the
+Human Data Model or the Machine Data Model.
Returns:
A resolved and validated demographic model.
@@ -732,7 +732,7 @@ Working with Demes graphsisclose(other, *, rel_tol=1e-09, abs_tol=1e-12)[source]¶
Returns true if the graph and other implement essentially
the same demographic model. Numerical values are compared using the
-math.isclose() function, from which this method takes its name.
+math.isclose() function, from which this method takes its name.
Furthermore, the following implementation details are ignored during
the comparison:
@@ -747,17 +747,17 @@ Working with Demes graphsParameters:
other (Graph) – The graph to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Returns:
True if the two graphs implement the same model, False otherwise.
Return type:
-
+
@@ -807,7 +807,7 @@ Working with Demes graphsend_times are a list of end times for each matrix.
Return type:
-tuple[list[list[list[float]]], list[float]]
+
Working with Demes graphsA NetworkX compatible dict-of-lists graph of the demes’ predecessors.
Return type:
-
+
@@ -842,7 +842,7 @@ Working with Demes graphs
Parameters:
-names (dict) – A dictionary with deme names and new names.
+names (dict) – A dictionary with deme names and new names.
Returns:
A demographic model with renamed demes.
@@ -872,7 +872,7 @@ Working with Demes graphsA NetworkX compatible dict-of-lists graph of the demes’ successors.
Return type:
-
+
@@ -887,15 +887,15 @@ Working with Demes graphs
Variables:
-name (str) – A concise string that identifies the deme.
description (str) – A description of the deme.
start_time (float) – The time at which the deme begins to exist.
ancestors (list[str]) – List of deme names for the deme’s ancestors.
proportions (list[float]) – The proportions of ancestry from each ancestor,
+
name (str) – A concise string that identifies the deme.
description (str) – A description of the deme.
start_time (float) – The time at which the deme begins to exist.
ancestors (list[str]) – List of deme names for the deme’s ancestors.
proportions (list[float]) – The proportions of ancestry from each ancestor,
ordered to correspond with the same order as the ancestors
list.
If there are one or more ancestors, the proportions sum to 1.
epochs (list[Epoch]) – A list of epochs that span the time interval over which the
+
epochs (list[Epoch]) – A list of epochs that span the time interval over which the
deme exists. Epoch time intervals are non-overlapping,
completely cover the deme’s existence time interval,
and are listed in time-descending order (from the past
@@ -914,10 +914,10 @@
Working with Demes graphsParameters:
other (Deme) – The deme to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Working with Demes graphs
- Return type:
--
+
-
@@ -943,17 +943,17 @@ Working with Demes graphsParameters:
other (Deme) – The deme to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two demes are equivalent, False otherwise.
- Return type:
--
+
-
@@ -967,13 +967,13 @@ Working with Demes graphs
- Parameters:
-time (float) – The time at which the size should be calculated.
+time (float) – The time at which the size should be calculated.
- Returns:
The deme size.
- Return type:
--
+
-
@@ -984,7 +984,7 @@ Working with Demes graphs
- Return type:
--
+
-
@@ -1004,16 +1004,16 @@ Working with Demes graphs
- Variables:
-start_time (float) – The start time of the epoch.
+
start_time (float) – The start time of the epoch.
This value is greater than zero and may be infinity.
end_time (float) – The end time of the epoch.
+
end_time (float) – The end time of the epoch.
This value is greater than or equal to zero and finite.
start_size (float) – Population size at start_time.
end_size (float) – Population size at end_time.
+
start_size (float) – Population size at start_time.
end_size (float) – Population size at end_time.
If start_size != end_size, the population size changes
between the start and end times according to the
size_function.
size_function (str) –
The size change function. This is either
+
size_function (str) –
The size change function. This is either
constant, exponential or linear, though it is possible
that additional values will be added in the future.
@@ -1041,8 +1041,8 @@ Working with Demes graphsfloat) – The selfing rate for this epoch.
cloning_rate (float) – The cloning rate for this epoch.
selfing_rate (float) – The selfing rate for this epoch.
cloning_rate (float) – The cloning rate for this epoch.
Working with Demes graphsParameters:
other (Epoch) – The epoch to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Working with Demes graphsParameters:
other (Epoch) – The epoch to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two epochs are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1097,7 +1097,7 @@ Working with Demes graphs
- Return type:
--
+
-
@@ -1118,11 +1118,11 @@ Continuous demographic events
- Variables:
-source (str) – The source deme for asymmetric migration.
dest (str) – The destination deme for asymmetric migration.
start_time (float) – The time at which the migration rate is activated.
end_time (float) – The time at which the migration rate is deactivated.
rate (float) – The rate of migration per generation.
source (str) – The source deme for asymmetric migration.
dest (str) – The destination deme for asymmetric migration.
start_time (float) – The time at which the migration rate is activated.
end_time (float) – The time at which the migration rate is deactivated.
rate (float) – The rate of migration per generation.
Continuous demographic eventsParameters:
other (AsymmetricMigration) – The migration to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Continuous demographic eventsParameters:
other (AsymmetricMigration) – The migration to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two epochs are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1188,10 +1188,10 @@ Discrete demographic events
- Variables:
-dest (str) – The destination deme.
time (float) – The time of migration.
proportions (list(float)) – Immediately following migration, the proportion(s)
+
dest (str) – The destination deme.
time (float) – The time of migration.
proportions (list(float)) – Immediately following migration, the proportion(s)
of individuals in the destination deme made up of migrant individuals or
having parents from the source deme(s).
@@ -1208,10 +1208,10 @@ Discrete demographic eventsParameters:
other (Pulse) – The pulse to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Discrete demographic eventsParameters:
other (Pulse) – The pulse to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two pulses are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1254,9 +1254,9 @@ Discrete demographic events
- Variables:
-
@@ -1271,10 +1271,10 @@ Discrete demographic eventsParameters:
other (Split) – The split to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Discrete demographic eventsParameters:
other (Split) – The split to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two splits are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1316,9 +1316,9 @@ Discrete demographic events
- Variables:
-
@@ -1333,10 +1333,10 @@ Discrete demographic eventsParameters:
other (Branch) – The branch to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Discrete demographic eventsParameters:
other (Branch) – The branch to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two branches are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1377,11 +1377,11 @@ Discrete demographic events
- Variables:
-
@@ -1396,10 +1396,10 @@ Discrete demographic eventsParameters:
other (Merge) – The merge to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Discrete demographic eventsParameters:
other (Merge) – The merge to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two merges are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1440,11 +1440,11 @@ Discrete demographic events
- Variables:
-
@@ -1459,10 +1459,10 @@ Discrete demographic eventsParameters:
other (Admix) – The admixture to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Discrete demographic eventsParameters:
other (Admix) – The admixture to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two admixtures are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1530,14 +1530,14 @@ Conversion functions
- Parameters:
-command (str) – The ms command line.
N0 (float) – The reference population size (\(N_0\)) used to translate
+
command (str) – The ms command line.
N0 (float) – The reference population size (\(N_0\)) used to translate
from coalescent units. For a command that specifies a
\(\theta\) value with the -t theta option,
this can be calculated as \(N_0 = \theta / (4 \mu L)\),
where \(\mu\) is the per-generation mutation rate and
\(L\) is the length of the sequence being simulated.
deme_names (list[str]) – A list of names to use for the demes.
+
deme_names (list[str]) – A list of names to use for the demes.
If not specified, demes will be named deme1, deme2, etc.
Conversion functions
- Parameters:
-N0 (float) – The reference population size used to translate into coalescent units.
+
N0 (float) – The reference population size used to translate into coalescent units.
See from_ms() for details.
samples (list(int)) – A list of haploid sample numbers, one for each deme, in the same
+
samples (list(int)) – A list of haploid sample numbers, one for each deme, in the same
order as the order of demes in the graph.
The parameter is ignored for demographic models with only one deme.
The given sampling scheme will be used with the -I argument.
@@ -1576,7 +1576,7 @@
Conversion functionsThe ms command line.
- Return type:
--
+
-
diff --git a/main/introduction.html b/main/introduction.html
index b84f08d..20a45cd 100644
--- a/main/introduction.html
+++ b/main/introduction.html
@@ -175,8 +175,8 @@ Quick search
Introduction¶
The demes Python package provides an API for defining, parsing, and sharing
-Demes demographic models. Applications can use
-demes to parse human-readable Demes YAML files
+Demes demographic models. Applications can use
+demes to parse human-readable Demes YAML files
into fully-resolved demographic models. In addition, demes provides
convenient data structures to simplify manipulation of demographic models.
If you find an error in the documentation or a bug in the software,
@@ -192,7 +192,7 @@
MotivationDemes Specification aims to make defining demographic
+
The Demes Specification aims to make defining demographic
models more intuitive, less prone to error or ambiguity, and readily
interchangeable between simulation platforms.
Demographic models, which define populations (or demes), their properties,
@@ -203,7 +203,7 @@
Motivation¶
The following YAML file implements a two-epoch demographic
history for a single deme, where the deme doubles in size 100 generations ago.
-See the Demes tutorial for a detailed introduction to
+See the Demes tutorial for a detailed introduction to
writing Demes YAML files.
description: Single-population two-epoch demography.
time_units: generations
@@ -233,7 +233,7 @@ Example<Axes: ylabel='time ago (generations)'>
-
+
diff --git a/main/quickstart.html b/main/quickstart.html
index 9f74fc2..1161bba 100644
--- a/main/quickstart.html
+++ b/main/quickstart.html
@@ -231,7 +231,7 @@ Loading a Demes graph
-
+
This YAML file can be loaded into Python with the load() function,
to obtain a Graph instance (modify the filename as appropriate).
@@ -402,7 +402,7 @@ Plotting a Demes graph<Axes: ylabel='time ago (generations)'>
-
+
deme_name (str) – The name of the deme.
+deme_name (str) – The name of the deme.
Working with Demes graphs
Returns:
-A data dictionary following the Machine Data Model.
+A data dictionary following the Machine Data Model.
Return type:
-
+
@@ -629,10 +629,10 @@ Working with Demes graphs
Returns:
-A data dictionary following the Human Data Model.
+A data dictionary following the Human Data Model.
Return type:
-
+
@@ -656,10 +656,10 @@ Working with Demes graphsParameters:
other (Graph) – The graph to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Working with Demes graphsMerge, and Admix objects.
A data dictionary following the Machine Data Model.
+A data dictionary following the Machine Data Model.
A data dictionary following the Human Data Model.
+A data dictionary following the Human Data Model.
Working with Demes graphsParameters:
other (Graph) – The graph to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Working with Demes graphsMerge, and Admix objects.
other (
Graph) – The graph to compare against.
-rel_tol (float) – The relative tolerance permitted for numerical -comparisons. See documentation for
math.isclose().
-abs_tol (float) – The absolute tolerance permitted for numerical -comparisons. See documentation for
math.isclose().
+rel_tol (float) – The relative tolerance permitted for numerical +comparisons. See documentation for
math.isclose().
+abs_tol (float) – The absolute tolerance permitted for numerical +comparisons. See documentation for
math.isclose().
Merge, and Admix objects.
data (dict) – A data dictionary following either the -Human Data Model or the Machine Data Model.
+data (dict) – A data dictionary following either the +Human Data Model or the Machine Data Model.
A resolved and validated demographic model.
@@ -732,7 +732,7 @@Working with Demes graphsisclose(other, *, rel_tol=1e-09, abs_tol=1e-12)[source]¶
Returns true if the graph and other implement essentially
the same demographic model. Numerical values are compared using the
-math.isclose() function, from which this method takes its name.
+math.isclose() function, from which this method takes its name.
Furthermore, the following implementation details are ignored during
the comparison:
@@ -747,17 +747,17 @@ Working with Demes graphsParameters:
other (Graph) – The graph to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Returns:
True if the two graphs implement the same model, False otherwise.
Return type:
-
+
@@ -807,7 +807,7 @@ Working with Demes graphsend_times are a list of end times for each matrix.
Return type:
-tuple[list[list[list[float]]], list[float]]
+
Working with Demes graphsA NetworkX compatible dict-of-lists graph of the demes’ predecessors.
Returns true if the graph and other implement essentially
the same demographic model. Numerical values are compared using the
-math.isclose() function, from which this method takes its name.
+math.isclose() function, from which this method takes its name.
Furthermore, the following implementation details are ignored during
the comparison:
@@ -747,17 +747,17 @@Working with Demes graphsParameters:
- -
other (
Graph) – The graph to compare against.- -
rel_tol (float) – The relative tolerance permitted for numerical -comparisons. See documentation for
math.isclose().- +
abs_tol (float) – The absolute tolerance permitted for numerical -comparisons. See documentation for
math.isclose().- +
rel_tol (float) – The relative tolerance permitted for numerical +comparisons. See documentation for
math.isclose().abs_tol (float) – The absolute tolerance permitted for numerical +comparisons. See documentation for
math.isclose().Returns: True if the two graphs implement the same model, False otherwise.
Return type: -+ @@ -807,7 +807,7 @@Working with Demes graphsend_times are a list of end times for each matrix.
tuple[list[list[list[float]]], list[float]]
+A NetworkX compatible dict-of-lists graph of the demes’ predecessors.
Working with Demes graphs
Parameters:
-names (dict) – A dictionary with deme names and new names.
+names (dict) – A dictionary with deme names and new names.
Returns:
A demographic model with renamed demes.
@@ -872,7 +872,7 @@ Working with Demes graphsA NetworkX compatible dict-of-lists graph of the demes’ successors.
Return type:
-
+
@@ -887,15 +887,15 @@ Working with Demes graphs
Variables:
-name (str) – A concise string that identifies the deme.
description (str) – A description of the deme.
start_time (float) – The time at which the deme begins to exist.
ancestors (list[str]) – List of deme names for the deme’s ancestors.
proportions (list[float]) – The proportions of ancestry from each ancestor,
+
name (str) – A concise string that identifies the deme.
description (str) – A description of the deme.
start_time (float) – The time at which the deme begins to exist.
ancestors (list[str]) – List of deme names for the deme’s ancestors.
proportions (list[float]) – The proportions of ancestry from each ancestor,
ordered to correspond with the same order as the ancestors
list.
If there are one or more ancestors, the proportions sum to 1.
epochs (list[Epoch]) – A list of epochs that span the time interval over which the
+
epochs (list[Epoch]) – A list of epochs that span the time interval over which the
deme exists. Epoch time intervals are non-overlapping,
completely cover the deme’s existence time interval,
and are listed in time-descending order (from the past
@@ -914,10 +914,10 @@
Working with Demes graphsParameters:
other (Deme) – The deme to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Working with Demes graphs
- Return type:
--
+
-
@@ -943,17 +943,17 @@ Working with Demes graphsParameters:
other (Deme) – The deme to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two demes are equivalent, False otherwise.
- Return type:
--
+
-
@@ -967,13 +967,13 @@ Working with Demes graphs
- Parameters:
-time (float) – The time at which the size should be calculated.
+time (float) – The time at which the size should be calculated.
- Returns:
The deme size.
- Return type:
--
+
-
@@ -984,7 +984,7 @@ Working with Demes graphs
- Return type:
--
+
-
@@ -1004,16 +1004,16 @@ Working with Demes graphs
- Variables:
-start_time (float) – The start time of the epoch.
+
start_time (float) – The start time of the epoch.
This value is greater than zero and may be infinity.
end_time (float) – The end time of the epoch.
+
end_time (float) – The end time of the epoch.
This value is greater than or equal to zero and finite.
start_size (float) – Population size at start_time.
end_size (float) – Population size at end_time.
+
start_size (float) – Population size at start_time.
end_size (float) – Population size at end_time.
If start_size != end_size, the population size changes
between the start and end times according to the
size_function.
size_function (str) –
The size change function. This is either
+
size_function (str) –
The size change function. This is either
constant, exponential or linear, though it is possible
that additional values will be added in the future.
@@ -1041,8 +1041,8 @@ Working with Demes graphsfloat) – The selfing rate for this epoch.
cloning_rate (float) – The cloning rate for this epoch.
selfing_rate (float) – The selfing rate for this epoch.
cloning_rate (float) – The cloning rate for this epoch.
Working with Demes graphsParameters:
other (Epoch) – The epoch to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Working with Demes graphsParameters:
other (Epoch) – The epoch to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two epochs are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1097,7 +1097,7 @@ Working with Demes graphs
- Return type:
--
+
-
@@ -1118,11 +1118,11 @@ Continuous demographic events
- Variables:
-source (str) – The source deme for asymmetric migration.
dest (str) – The destination deme for asymmetric migration.
start_time (float) – The time at which the migration rate is activated.
end_time (float) – The time at which the migration rate is deactivated.
rate (float) – The rate of migration per generation.
source (str) – The source deme for asymmetric migration.
dest (str) – The destination deme for asymmetric migration.
start_time (float) – The time at which the migration rate is activated.
end_time (float) – The time at which the migration rate is deactivated.
rate (float) – The rate of migration per generation.
Continuous demographic eventsParameters:
other (AsymmetricMigration) – The migration to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Continuous demographic eventsParameters:
other (AsymmetricMigration) – The migration to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two epochs are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1188,10 +1188,10 @@ Discrete demographic events
- Variables:
-dest (str) – The destination deme.
time (float) – The time of migration.
proportions (list(float)) – Immediately following migration, the proportion(s)
+
dest (str) – The destination deme.
time (float) – The time of migration.
proportions (list(float)) – Immediately following migration, the proportion(s)
of individuals in the destination deme made up of migrant individuals or
having parents from the source deme(s).
@@ -1208,10 +1208,10 @@ Discrete demographic eventsParameters:
other (Pulse) – The pulse to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Discrete demographic eventsParameters:
other (Pulse) – The pulse to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two pulses are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1254,9 +1254,9 @@ Discrete demographic events
- Variables:
-
@@ -1271,10 +1271,10 @@ Discrete demographic eventsParameters:
other (Split) – The split to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Discrete demographic eventsParameters:
other (Split) – The split to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two splits are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1316,9 +1316,9 @@ Discrete demographic events
- Variables:
-
@@ -1333,10 +1333,10 @@ Discrete demographic eventsParameters:
other (Branch) – The branch to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Discrete demographic eventsParameters:
other (Branch) – The branch to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two branches are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1377,11 +1377,11 @@ Discrete demographic events
- Variables:
-
@@ -1396,10 +1396,10 @@ Discrete demographic eventsParameters:
other (Merge) – The merge to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Discrete demographic eventsParameters:
other (Merge) – The merge to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two merges are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1440,11 +1440,11 @@ Discrete demographic events
- Variables:
-
@@ -1459,10 +1459,10 @@ Discrete demographic eventsParameters:
other (Admix) – The admixture to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
Discrete demographic eventsParameters:
other (Admix) – The admixture to compare against.
rel_tol (float) – The relative tolerance permitted for numerical
-comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
-comparisons. See documentation for math.isclose().
rel_tol (float) – The relative tolerance permitted for numerical
+comparisons. See documentation for math.isclose()
abs_tol (float) – The absolute tolerance permitted for numerical
+comparisons. See documentation for math.isclose().
- Returns:
True if the two admixtures are equivalent, False otherwise.
- Return type:
--
+
-
@@ -1530,14 +1530,14 @@ Conversion functions
- Parameters:
-command (str) – The ms command line.
N0 (float) – The reference population size (\(N_0\)) used to translate
+
command (str) – The ms command line.
N0 (float) – The reference population size (\(N_0\)) used to translate
from coalescent units. For a command that specifies a
\(\theta\) value with the -t theta option,
this can be calculated as \(N_0 = \theta / (4 \mu L)\),
where \(\mu\) is the per-generation mutation rate and
\(L\) is the length of the sequence being simulated.
deme_names (list[str]) – A list of names to use for the demes.
+
deme_names (list[str]) – A list of names to use for the demes.
If not specified, demes will be named deme1, deme2, etc.
Conversion functions
- Parameters:
-N0 (float) – The reference population size used to translate into coalescent units.
+
N0 (float) – The reference population size used to translate into coalescent units.
See from_ms() for details.
samples (list(int)) – A list of haploid sample numbers, one for each deme, in the same
+
samples (list(int)) – A list of haploid sample numbers, one for each deme, in the same
order as the order of demes in the graph.
The parameter is ignored for demographic models with only one deme.
The given sampling scheme will be used with the -I argument.
@@ -1576,7 +1576,7 @@
Conversion functionsThe ms command line.
- Return type:
--
+
-
diff --git a/main/introduction.html b/main/introduction.html
index b84f08d..20a45cd 100644
--- a/main/introduction.html
+++ b/main/introduction.html
@@ -175,8 +175,8 @@ Quick search
Introduction¶
The demes Python package provides an API for defining, parsing, and sharing
-Demes demographic models. Applications can use
-demes to parse human-readable Demes YAML files
+Demes demographic models. Applications can use
+demes to parse human-readable Demes YAML files
into fully-resolved demographic models. In addition, demes provides
convenient data structures to simplify manipulation of demographic models.
If you find an error in the documentation or a bug in the software,
@@ -192,7 +192,7 @@
MotivationDemes Specification aims to make defining demographic
+
The Demes Specification aims to make defining demographic
models more intuitive, less prone to error or ambiguity, and readily
interchangeable between simulation platforms.
Demographic models, which define populations (or demes), their properties,
@@ -203,7 +203,7 @@
Motivation¶
The following YAML file implements a two-epoch demographic
history for a single deme, where the deme doubles in size 100 generations ago.
-See the Demes tutorial for a detailed introduction to
+See the Demes tutorial for a detailed introduction to
writing Demes YAML files.
description: Single-population two-epoch demography.
time_units: generations
@@ -233,7 +233,7 @@ Example<Axes: ylabel='time ago (generations)'>
-
+
diff --git a/main/quickstart.html b/main/quickstart.html
index 9f74fc2..1161bba 100644
--- a/main/quickstart.html
+++ b/main/quickstart.html
@@ -231,7 +231,7 @@ Loading a Demes graph
-
+
This YAML file can be loaded into Python with the load() function,
to obtain a Graph instance (modify the filename as appropriate).
@@ -402,7 +402,7 @@ Plotting a Demes graph<Axes: ylabel='time ago (generations)'>
-
+
names (dict) – A dictionary with deme names and new names.
+names (dict) – A dictionary with deme names and new names.
A demographic model with renamed demes.
@@ -872,7 +872,7 @@Working with Demes graphsA NetworkX compatible dict-of-lists graph of the demes’ successors.
-
-
name (str) – A concise string that identifies the deme.
-description (str) – A description of the deme.
-start_time (float) – The time at which the deme begins to exist.
-ancestors (list[str]) – List of deme names for the deme’s ancestors.
-proportions (list[float]) – The proportions of ancestry from each ancestor, +
name (str) – A concise string that identifies the deme.
+description (str) – A description of the deme.
+start_time (float) – The time at which the deme begins to exist.
+ancestors (list[str]) – List of deme names for the deme’s ancestors.
+proportions (list[float]) – The proportions of ancestry from each ancestor, ordered to correspond with the same order as the ancestors list. If there are one or more ancestors, the proportions sum to 1.
-epochs (list[Epoch]) – A list of epochs that span the time interval over which the +
epochs (list[Epoch]) – A list of epochs that span the time interval over which the deme exists. Epoch time intervals are non-overlapping, completely cover the deme’s existence time interval, and are listed in time-descending order (from the past @@ -914,10 +914,10 @@
Working with Demes graphsParameters:
other (
Deme) – The deme to compare against.
-rel_tol (float) – The relative tolerance permitted for numerical -comparisons. See documentation for
math.isclose()
-abs_tol (float) – The absolute tolerance permitted for numerical -comparisons. See documentation for
math.isclose().
+rel_tol (float) – The relative tolerance permitted for numerical +comparisons. See documentation for
math.isclose()
+abs_tol (float) – The absolute tolerance permitted for numerical +comparisons. See documentation for
math.isclose().
Working with Demes graphs
- Return type:
-- +
@@ -943,17 +943,17 @@Working with Demes graphsParameters:
other (
Deme) – The deme to compare against.
-rel_tol (float) – The relative tolerance permitted for numerical -comparisons. See documentation for
math.isclose()
-abs_tol (float) – The absolute tolerance permitted for numerical -comparisons. See documentation for
math.isclose().
+rel_tol (float) – The relative tolerance permitted for numerical +comparisons. See documentation for
math.isclose()
+abs_tol (float) – The absolute tolerance permitted for numerical +comparisons. See documentation for
math.isclose().
- Returns:
True if the two demes are equivalent, False otherwise.
- Return type:
-- +
@@ -967,13 +967,13 @@Working with Demes graphs
- Parameters:
-time (float) – The time at which the size should be calculated.
+time (float) – The time at which the size should be calculated.
- Returns:
The deme size.
- Return type:
-- +
@@ -984,7 +984,7 @@Working with Demes graphs
- Return type:
-- +
@@ -1004,16 +1004,16 @@Working with Demes graphs
- Variables:
-
-
start_time (float) – The start time of the epoch. +
start_time (float) – The start time of the epoch. This value is greater than zero and may be infinity.
-end_time (float) – The end time of the epoch. +
end_time (float) – The end time of the epoch. This value is greater than or equal to zero and finite.
-start_size (float) – Population size at
start_time.
-end_size (float) – Population size at
end_time. +start_size (float) – Population size at
start_time.
+end_size (float) – Population size at
end_time. Ifstart_size != end_size, the population size changes between the start and end times according to thesize_function.
-size_function (str) –
The size change function. This is either +
size_function (str) –
The size change function. This is either
constant,exponentialorlinear, though it is possible that additional values will be added in the future.@@ -1041,8 +1041,8 @@
Working with Demes graphsfloat) – The selfing rate for this epoch.
-cloning_rate (float) – The cloning rate for this epoch.
+selfing_rate (float) – The selfing rate for this epoch.
+cloning_rate (float) – The cloning rate for this epoch.
Working with Demes graphsParameters:
other (
Epoch) – The epoch to compare against.
-rel_tol (float) – The relative tolerance permitted for numerical -comparisons. See documentation for
math.isclose()
-abs_tol (float) – The absolute tolerance permitted for numerical -comparisons. See documentation for
math.isclose().
+rel_tol (float) – The relative tolerance permitted for numerical +comparisons. See documentation for
math.isclose()
+abs_tol (float) – The absolute tolerance permitted for numerical +comparisons. See documentation for
math.isclose().
Working with Demes graphsParameters:
other (
Epoch) – The epoch to compare against.
-rel_tol (float) – The relative tolerance permitted for numerical -comparisons. See documentation for
math.isclose()
-abs_tol (float) – The absolute tolerance permitted for numerical -comparisons. See documentation for
math.isclose().
+rel_tol (float) – The relative tolerance permitted for numerical +comparisons. See documentation for
math.isclose()
+abs_tol (float) – The absolute tolerance permitted for numerical +comparisons. See documentation for
math.isclose().
- Returns:
True if the two epochs are equivalent, False otherwise.
- Return type:
-- +
@@ -1097,7 +1097,7 @@Working with Demes graphs
- Return type:
-- +
@@ -1118,11 +1118,11 @@Continuous demographic events
- Variables:
-
-
source (str) – The source deme for asymmetric migration.
-dest (str) – The destination deme for asymmetric migration.
-start_time (float) – The time at which the migration rate is activated.
-end_time (float) – The time at which the migration rate is deactivated.
-rate (float) – The rate of migration per generation.
+source (str) – The source deme for asymmetric migration.
+dest (str) – The destination deme for asymmetric migration.
+start_time (float) – The time at which the migration rate is activated.
+end_time (float) – The time at which the migration rate is deactivated.
+rate (float) – The rate of migration per generation.
Continuous demographic eventsParameters:
other (AsymmetricMigration) – The migration to compare against.
-rel_tol (float) – The relative tolerance permitted for numerical -comparisons. See documentation for
math.isclose()
-abs_tol (float) – The absolute tolerance permitted for numerical -comparisons. See documentation for
math.isclose().
+rel_tol (float) – The relative tolerance permitted for numerical +comparisons. See documentation for
math.isclose()
+abs_tol (float) – The absolute tolerance permitted for numerical +comparisons. See documentation for
math.isclose().
Continuous demographic eventsParameters:
other (AsymmetricMigration) – The migration to compare against.
-rel_tol (float) – The relative tolerance permitted for numerical -comparisons. See documentation for
math.isclose()
-abs_tol (float) – The absolute tolerance permitted for numerical -comparisons. See documentation for
math.isclose().
+rel_tol (float) – The relative tolerance permitted for numerical +comparisons. See documentation for
math.isclose()
+abs_tol (float) – The absolute tolerance permitted for numerical +comparisons. See documentation for
math.isclose().
- Returns:
True if the two epochs are equivalent, False otherwise.
- Return type:
-- +
@@ -1188,10 +1188,10 @@Discrete demographic events
- Variables:
-
-
- -
dest (str) – The destination deme.
-time (float) – The time of migration.
-proportions (list(float)) – Immediately following migration, the proportion(s) +
- +
dest (str) – The destination deme.
+time (float) – The time of migration.
+proportions (list(float)) – Immediately following migration, the proportion(s) of individuals in the destination deme made up of migrant individuals or having parents from the source deme(s).
Discrete demographic eventsParameters:
other (
Pulse) – The pulse to compare against.
-rel_tol (float) – The relative tolerance permitted for numerical -comparisons. See documentation for
math.isclose()
-abs_tol (float) – The absolute tolerance permitted for numerical -comparisons. See documentation for
math.isclose().
+rel_tol (float) – The relative tolerance permitted for numerical +comparisons. See documentation for
math.isclose()
+abs_tol (float) – The absolute tolerance permitted for numerical +comparisons. See documentation for
math.isclose().
Discrete demographic eventsParameters:
other (
Pulse) – The pulse to compare against.
-rel_tol (float) – The relative tolerance permitted for numerical -comparisons. See documentation for
math.isclose()
-abs_tol (float) – The absolute tolerance permitted for numerical -comparisons. See documentation for
math.isclose().
+rel_tol (float) – The relative tolerance permitted for numerical +comparisons. See documentation for
math.isclose()
+abs_tol (float) – The absolute tolerance permitted for numerical +comparisons. See documentation for
math.isclose().
- Returns:
True if the two pulses are equivalent, False otherwise.
- Return type:
-- +
@@ -1254,9 +1254,9 @@Discrete demographic events
- Variables:
Discrete demographic eventsParameters:
other (
Split) – The split to compare against.
-rel_tol (float) – The relative tolerance permitted for numerical -comparisons. See documentation for
math.isclose()
-abs_tol (float) – The absolute tolerance permitted for numerical -comparisons. See documentation for
math.isclose().
+rel_tol (float) – The relative tolerance permitted for numerical +comparisons. See documentation for
math.isclose()
+abs_tol (float) – The absolute tolerance permitted for numerical +comparisons. See documentation for
math.isclose().
Discrete demographic eventsParameters:
other (
Split) – The split to compare against.
-rel_tol (float) – The relative tolerance permitted for numerical -comparisons. See documentation for
math.isclose()
-abs_tol (float) – The absolute tolerance permitted for numerical -comparisons. See documentation for
math.isclose().
+rel_tol (float) – The relative tolerance permitted for numerical +comparisons. See documentation for
math.isclose()
+abs_tol (float) – The absolute tolerance permitted for numerical +comparisons. See documentation for
math.isclose().
- Returns:
True if the two splits are equivalent, False otherwise.
- Return type:
-- +
@@ -1316,9 +1316,9 @@Discrete demographic events
- Variables:
Discrete demographic eventsParameters:
other (
Branch) – The branch to compare against.
-rel_tol (float) – The relative tolerance permitted for numerical -comparisons. See documentation for
math.isclose()
-abs_tol (float) – The absolute tolerance permitted for numerical -comparisons. See documentation for
math.isclose().
+rel_tol (float) – The relative tolerance permitted for numerical +comparisons. See documentation for
math.isclose()
+abs_tol (float) – The absolute tolerance permitted for numerical +comparisons. See documentation for
math.isclose().
Discrete demographic eventsParameters:
other (
Branch) – The branch to compare against.
-rel_tol (float) – The relative tolerance permitted for numerical -comparisons. See documentation for
math.isclose()
-abs_tol (float) – The absolute tolerance permitted for numerical -comparisons. See documentation for
math.isclose().
+rel_tol (float) – The relative tolerance permitted for numerical +comparisons. See documentation for
math.isclose()
+abs_tol (float) – The absolute tolerance permitted for numerical +comparisons. See documentation for
math.isclose().
- Returns:
True if the two branches are equivalent, False otherwise.
- Return type:
-- +
@@ -1377,11 +1377,11 @@Discrete demographic events
- Variables:
Discrete demographic eventsParameters:
other (
Merge) – The merge to compare against.
-rel_tol (float) – The relative tolerance permitted for numerical -comparisons. See documentation for
math.isclose()
-abs_tol (float) – The absolute tolerance permitted for numerical -comparisons. See documentation for
math.isclose().
+rel_tol (float) – The relative tolerance permitted for numerical +comparisons. See documentation for
math.isclose()
+abs_tol (float) – The absolute tolerance permitted for numerical +comparisons. See documentation for
math.isclose().
Discrete demographic eventsParameters:
other (
Merge) – The merge to compare against.
-rel_tol (float) – The relative tolerance permitted for numerical -comparisons. See documentation for
math.isclose()
-abs_tol (float) – The absolute tolerance permitted for numerical -comparisons. See documentation for
math.isclose().
+rel_tol (float) – The relative tolerance permitted for numerical +comparisons. See documentation for
math.isclose()
+abs_tol (float) – The absolute tolerance permitted for numerical +comparisons. See documentation for
math.isclose().
- Returns:
True if the two merges are equivalent, False otherwise.
- Return type:
-- +
@@ -1440,11 +1440,11 @@Discrete demographic events
- Variables:
Discrete demographic eventsParameters:
other (
Admix) – The admixture to compare against.
-rel_tol (float) – The relative tolerance permitted for numerical -comparisons. See documentation for
math.isclose()
-abs_tol (float) – The absolute tolerance permitted for numerical -comparisons. See documentation for
math.isclose().
+rel_tol (float) – The relative tolerance permitted for numerical +comparisons. See documentation for
math.isclose()
+abs_tol (float) – The absolute tolerance permitted for numerical +comparisons. See documentation for
math.isclose().
Discrete demographic eventsParameters:
other (
Admix) – The admixture to compare against.
-rel_tol (float) – The relative tolerance permitted for numerical -comparisons. See documentation for
math.isclose()
-abs_tol (float) – The absolute tolerance permitted for numerical -comparisons. See documentation for
math.isclose().
+rel_tol (float) – The relative tolerance permitted for numerical +comparisons. See documentation for
math.isclose()
+abs_tol (float) – The absolute tolerance permitted for numerical +comparisons. See documentation for
math.isclose().
- Returns:
True if the two admixtures are equivalent, False otherwise.
- Return type:
-- +
@@ -1530,14 +1530,14 @@Conversion functions
- Parameters:
-
-
command (str) – The ms command line.
-N0 (float) – The reference population size (\(N_0\)) used to translate +
command (str) – The ms command line.
+N0 (float) – The reference population size (\(N_0\)) used to translate from coalescent units. For a
commandthat specifies a \(\theta\) value with the-t thetaoption, this can be calculated as \(N_0 = \theta / (4 \mu L)\), where \(\mu\) is the per-generation mutation rate and \(L\) is the length of the sequence being simulated.
-deme_names (list[str]) – A list of names to use for the demes. +
deme_names (list[str]) – A list of names to use for the demes. If not specified, demes will be named deme1, deme2, etc.
Conversion functions
- Parameters:
-
-
N0 (float) – The reference population size used to translate into coalescent units. +
N0 (float) – The reference population size used to translate into coalescent units. See
from_ms()for details.
-samples (list(int)) – A list of haploid sample numbers, one for each deme, in the same +
samples (list(int)) – A list of haploid sample numbers, one for each deme, in the same order as the order of demes in the graph. The parameter is ignored for demographic models with only one deme. The given sampling scheme will be used with the
-Iargument. @@ -1576,7 +1576,7 @@Conversion functions
The ms command line.
- Return type:
-- +
diff --git a/main/introduction.html b/main/introduction.html index b84f08d..20a45cd 100644 --- a/main/introduction.html +++ b/main/introduction.html @@ -175,8 +175,8 @@Quick search
Introduction¶
The
demesPython package provides an API for defining, parsing, and sharing -Demes demographic models. Applications can use -demesto parse human-readable Demes YAML files +Demes demographic models. Applications can use +demesto parse human-readable Demes YAML files into fully-resolved demographic models. In addition,demesprovides convenient data structures to simplify manipulation of demographic models. If you find an error in the documentation or a bug in the software, @@ -192,7 +192,7 @@MotivationDemes Specification aims to make defining demographic +
The Demes Specification aims to make defining demographic models more intuitive, less prone to error or ambiguity, and readily interchangeable between simulation platforms. Demographic models, which define populations (or demes), their properties, @@ -203,7 +203,7 @@
Motivation¶
The following YAML file implements a two-epoch demographic history for a single deme, where the deme doubles in size 100 generations ago. -See the Demes tutorial for a detailed introduction to +See the Demes tutorial for a detailed introduction to writing Demes YAML files.
+-description: Single-population two-epoch demography. time_units: generations @@ -233,7 +233,7 @@
Example
<Axes: ylabel='time ago (generations)'>
Loading a Demes graph
-+
This YAML file can be loaded into Python with the
@@ -402,7 +402,7 @@load()function, to obtain aGraphinstance (modify the filename as appropriate).Plotting a Demes graph
-<Axes: ylabel='time ago (generations)'>
+