immediate todos [2/3]

[ ] direct interface with stdpopsim maps
[X] gwas
[X] variant result data structure

documentation todos [0/0]

Getting started

☑ installation

☑ quickstart

User Guide

☑ nuts and bolts

☑ indexes

☑ data structures

☑ submodule organization

☑ anatomy of a simulation

☑ founder data

☑ synthetic data

☑ working with real data

[X] example with vcf data
[X] example with vcf plink data

☑ recombination maps

☑ architectures

☑ architecture class

☑ components

☑ vertical components and founder initializations

☑ mating regimes

☑ choosing mates

☐ controlling population growth

☑ statistics and post-processors

☐ extending xftsim

[ ] Extending mating regimes
[ ] Extending phenogenetic architectures
[ ] Extending statistical estimators

Example gallery

[ ] random mating with variable population growth
[ ] linear cross-trait assortative mating
[ ] arbitrary cross-trait assortative mating
[ ] vertical tranmission and causal dependence
[ ] spatial assortment + environmental gradient

tutorials [1/4]

[X] quickstart
[X] random mating
[X] assortative mating
[X] transmission / causal dependences

major features [0/3]

[ ] support CV_only + tskit
[ ] spatial_module
[X] causal graph

features [0/2]

documentation

☐ replace duplicate descriptions

☐ module docstrings [2/13]

[ ] arch
[ ] data
[ ] effect
[ ] founders
[ ] io
[X] lsmate
[ ] mate
[ ] ped
[X] proc
[ ] reproduce
[ ] sim
[ ] stats
[ ] utils

☐ logging / profiling [1/3]

[X] basic timing
[ ] cpu use
[ ] memory use

submodule features

☐ arch [3/15]

[X] common index api
[X] DOCUMENT
[ ] add examples to documentation
[ ] add get_annotations methods
[ ] LDAK model
[X] GCTA model
[X] implement component types
[ ] auto add sum
[X] binary
[ ] binary + ruleout
[ ] misdiagnosis
[ ] GxG
[X] GxE
[X] causal graph methods
[ ] prettify __repr__

☐ data [0/1]

[ ] incorporate genetic maps from stdpopsim

☐ [#A] effect [4/6]

[X] common index api
[X] DOCUMENT
[ ] add get_annotations methods
[X] look into m_causal bug
[X] make scaled / standardized language intelligible/fix doc
[ ] prettify __repr__

☐ [#A] founders [1/8]

[ ] common index api
[X] DOCUMENT
[X] from_maf function
[ ] from_numpy
[X] from_vcf
[ ] from_plink
[X] from_zarr
[ ] prettify __repr__

☐ index [2/6]

[X] DOCUMENT
~ unify VariantIndex
[X] type field for components
[X] cleaner index creation
[X] make from_product etc staticmethods
[ ] allow vorigin specification via string
[ ] prettify __repr__

☐ [#A] ped [1/3]

[X] DOCUMENT
[ ] update from mating
[ ] prettify __repr__

☐ io [4/8]

[X] remove from gitignore
[ ] common index api
[X] DOCUMENT
[ ] from_vcf
[X] from_plink1
[ ] from_plink2
[X] from_zarr
[ ] prettify __repr__

☐ proc [1/3]

[X] DOCUMENT
[ ] to_disk
[ ] prettify __repr__

☐ [#A] reproduce [1/5]

[ ] common index api
[X] DOCUMENT
[ ] rmap from cM
[ ] rmap from hapmap
[ ] prettify __repr__

☐ [#A] mate [5/8]

[ ] common index api
[X] DOCUMENT
[X] random
[X] linear
[X] general xAM
[X] batched
[ ] spatial
[ ] prettify __repr__

☐ [#A] lsmate [1/3]

[ ] common index api
[X] DOCUMENT
[ ] prettify __repr__

☐ [#A] stats [3/12]

[ ] common index api
[ ] DOCUMENT
[ ] PCA
[X] sample
[X] mating
[X] HE regression
[ ] GWAS sumstats
[ ] LD scores
[ ] cross validation wrapper
[ ] PGS
[ ] REML
[ ] prettify __repr__

☐ struct [3/4]

[X] common index api
[X] constructors -> staticmethods
[X] DOCUMENT
[ ] prettify __repr__

☐ sim [1/3]

[X] DOCUMENT
[ ] Make it clear which args are optional for Simulation class
[ ] prettify __repr__

☐ utils [2/2]

[X] DOCUMENT - variable count
[X] DOCUMENT - everything else