NEWS.md
vegTypeMapGenerator() when mixedType = 1;mixedType = 0 in vegTypeMapGenerator();prepInputs_NTEMS_LCC_FAO();speciesEquivalencies_CA;raster to terra throughout;gdalUtilities dependency;prepInputLCC: orig argument no longer accepted by terra::compareGeom;calcSeverityB: output table was missing the proportion of B killed;maxB) and species establishment probabilities (SEP);speciesEcoregion table (brought over from Biomass_speciesParameters module), using estimated inflationFactor and mANPPproportion to adjust maxB and maxANPP, respectively;FireDisturbance and FireDisturbancePM pulled from; Biomass_regeneration and Biomass_regenerationPM modules, respectively;overlayLCCs() now works correctly with terra (#99);standAgeMapGenerator() to produce standAgeMap from cohortData;prepInputs_NTEMS_Nonforest() and prepInputs_NTEMS_LCC_FAO();assertSpeciesTable() and assertSpeciesTableRaw();LandWebUtils package (#86)Colors – new function to help with terra migration.prepInputsFireYear can now handle rasterToMatch that is a SpatRaster
MuMIn (Sept 2022)raster/terra utility and plotting functionsnonForestedPixels used to detect pixels without species cover or a non-forested land-cover class;prepRawBiomassMap used to create rawBiomassMap;prepRasterToMatch used to create RasterToMatch and RasterToMatchLarge;prepInputsStandAgeMapcan now accept firePerimeters layer, avoiding inner download if layer is present;assertSppVectors) to check that species match between vectors (e.g. tables, colours and species list vector);sppHarmonize that deals with the 3 potential ways for a user to input the sim$sppEquiv, P(sim)$sppEquivCol, and sim$sppNameVector;speciesInStudyArea and `species;Require;makeAndCleanInitialCohortData can now be turned off;LANDISDisp(): skip dispersal when src or rcv data.tables are empty;.initiateNewCohorts) can now be a fixed integer or, as before, calculated using the LANDIS-II Biomass Succession Extension v3.2.1 approach (Scheller & Miranda 2015);prepInputsFireYear();statsModel;Biomass_borealDataPrep;assertColumns gives better message for which columns are incorrect/missing;minRelativeBDefaults is now a function so they are more easily accessible ;statsModel was pulling along with it all the data, 5x. Now it does not. The Caching of this should be fast and small now.modelBiomass (see Biomass_boreaDataPrep) with scaled data or different optimizer;loadkNNSpeciesLayers and prepSpeciesLayers_KNN prevent issues when default URL is down, or working offline (but layers are present locally);sppEquivalenciesCA (PSP, BC_Forestry and FuelClass);rawBiomassMap;fireURL = NULL to prepStandAgeMap() bypasses age imputation;sppEquivCheck;loadKNNSpeciesLayers can accept a sppEquiv table with one columnspeciesEquivalencies_CA data;speciesTableUpdate;LANDISDisp now (back to) native R. It is about 15x faster than the Rcpp implementation, and much simpler, with about 30% of the number of lines of code. It was inspired by the “spiral” approach as was used in the Rcpp in the pre-1.0.0 version of LandR, but much more efficiently as it is now correctly identifies every pixel outward from a centre pixel using raster::focalWeight, with the maximum of the seeddispersal_max across all species. RAM use appears under control, even for large problems (tested on 50M pixel Raster with 8M potential Source pixels and 500,000 Receiving pixels, with a peak additional RAM of 3 GB during LANDISDisp); LANDISDisp now accommodates sub-cellSize dispersal distances, using the original Ward Dispersal equation. Previously, the sub-pixel dispersal was treated as if it was starting from the centre of the pixel. So, if less than a full pixel, then very little horizontal transfer. This has the effect that there will be a large increase in horizontal transfer for the species that have small seeddistance_max (i.e., less than cell size);prepSpeciesLayers_ONFRI;updateSpeciesTable (moved from LandWebUtils) to allow user to update species parameters by passing a named list.assignLightProb now allows interpolating germination probability between species shade tolerance levels for any given stand shade value. This allows for for decimal values in species shade tolerance traits and greater fine tuning of shade-related germination probabilities.makeCohortDataFiles, as it is the last thing to do before making cohortData
.createCohortData, makeAndCleanInitialCohortData , and a hard coded bit in Biomass_borealDataPrep
statsModel function has a new argument to improve caching with reproducible::Cache (i.e. not used internally);time, are now called currentTime - these changes are matched in LandR Biomass modulesoverlayLCCs which will help with overlaying more than one land cover classification raster.convertUnwantedLCC to accommodate more cases and eliminate redundant arguments.prepInputsLCC() now works with “LCC10”