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Merge branch 'development' of ssh://github.com/PredictiveEcology/Biom…
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -13,7 +13,7 @@ defineModule(sim, list( | |
| person("Jean", "Marchal", email = "[email protected]", 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"), | ||
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@@ -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)", | ||
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@@ -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$species <- setkey(species, speciesCode) | ||
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| ## prepare dummy versions if not supplied -------------------------- | ||
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@@ -1302,7 +1293,6 @@ MortalityAndGrowth <- compiler::cmpfun(function(sim) { | |
| }) | ||
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| Dispersal <- function(sim) { | ||
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| treedFirePixelTableCurYr <- sim$treedFirePixelTableSinceLastDisp[burnTime == time(sim)] | ||
| pixelsFromCurYrBurn <- treedFirePixelTableCurYr$pixelIndex | ||
| tempActivePixel <- sim$activePixelIndex[!(sim$activePixelIndex %in% pixelsFromCurYrBurn)] | ||
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