diff --git a/Biomass_core.R b/Biomass_core.R
index 2df908f..f69fe27 100644
--- a/Biomass_core.R
+++ b/Biomass_core.R
@@ -13,7 +13,7 @@ defineModule(sim, list(
person("Jean", "Marchal", email = "jean.d.marchal@gmail.com", role = "ctb")
),
childModules = character(0),
- version = list(Biomass_core = numeric_version("1.3.10")),
+ version = list(Biomass_core = numeric_version("1.4.0")),
timeframe = as.POSIXlt(c(NA, NA)),
timeunit = "year",
citation = list("citation.bib"),
@@ -25,7 +25,7 @@ defineModule(sim, list(
"R.utils", "scales", "terra", "tidyr",
# "curl", "httr", ## called directly by this module, but pulled in by LandR (Sep 6th 2022).
## Excluded because loading is not necessary (just installation)
- "PredictiveEcology/LandR@development (>= 1.1.0.9006)",
+ "PredictiveEcology/LandR@development (>= 1.1.1)",
"PredictiveEcology/pemisc@development",
"PredictiveEcology/reproducible@development",
"PredictiveEcology/SpaDES.core@development (>= 2.0.2.9004)",
@@ -576,17 +576,8 @@ Init <- function(sim, verbose = getOption("LandR.verbose", TRUE)) {
if (is.null(sim$species))
stop("'species' object must be provided")
species <- as.data.table(sim$species) # The former setDT actually changed the vector
+ LandR::assertSpeciesTable(species)
set(species, NULL, "speciesCode", factor(species$species, levels = unique(species$species))) # supply levels for speed
- LandR::assertColumns(species,
- c(species = "character", Area = "factor", longevity = "integer",
- sexualmature = "integer", shadetolerance = "numeric",
- firetolerance = "integer", seeddistance_eff = "integer",
- seeddistance_max = "integer", resproutprob = "numeric",
- resproutage_min = "integer", resproutage_max = "integer",
- postfireregen = "factor", leaflongevity = "integer",
- wooddecayrate = "numeric", mortalityshape = "integer",
- growthcurve = "numeric", leafLignin = "numeric",
- hardsoft = "factor", speciesCode = "factor"))
sim$species <- setkey(species, speciesCode)
## prepare dummy versions if not supplied --------------------------
@@ -1302,7 +1293,6 @@ MortalityAndGrowth <- compiler::cmpfun(function(sim) {
})
Dispersal <- function(sim) {
-
treedFirePixelTableCurYr <- sim$treedFirePixelTableSinceLastDisp[burnTime == time(sim)]
pixelsFromCurYrBurn <- treedFirePixelTableCurYr$pixelIndex
tempActivePixel <- sim$activePixelIndex[!(sim$activePixelIndex %in% pixelsFromCurYrBurn)]
diff --git a/Biomass_core.html b/Biomass_core.html
index 05c4d13..488b21d 100644
--- a/Biomass_core.html
+++ b/Biomass_core.html
@@ -2995,7 +2995,7 @@
LandR Biomass_core Manual
-Last updated: 2024-04-19
+Last updated: 2024-05-10
@@ -3011,7 +3011,7 @@ Last updated: 2024-04-19
-
+
Authors:
@@ -4364,7 +4364,7 @@ List of input objects
data.table
-data.table with cohort-level information on age and biomass, by pixelGroup and ecolocation (i.e., ecoregionGroup). If supplied, it must have the following columns: pixelGroup (integer), ecoregionGroup (factor), speciesCode (factor), B (integer in latex2b27a1ad385d16c73646cd918252c6d2), age (integer in years)
+data.table with cohort-level information on age and biomass, by pixelGroup and ecolocation (i.e., ecoregionGroup). If supplied, it must have the following columns: pixelGroup (integer), ecoregionGroup (factor), speciesCode (factor), B (integer in latex2b27a1ad385d16c73646cd918252c6d2), age (integer in years)
|
NA
|