NEWS

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LandR 1.2.0.9003

Breaking changes

• drop support for R 4.2 due to changes in dependency packages;
• remove rasterRead() to use version from reproducible;
• columnsForPixelGroups is now a function (i.e., use columnsForPixelGroups() for consistent pixelGroup definitions);

Dependency changes

• now requires reproducible (>= 3.1.1.9063) following non-backwards-compatible changes to the reproducible API: options("reproducible.gdalwarp") was removed, and reproducible.inputPaths was renamed to reproducible.destinationPathShared (the old name remains as a deprecated alias);
• remove deprecated package crayon in favour of cli instead;
• remove deprecated package qs in favour of qs2 instead;
• move ggpubr to Suggests;
• add arrow to Suggests;

New features

• add functions to visualize vegetation type transitions;
• new function cohortDefinitionCols() to ensure consistent cohort definitions;
• new function lccMapGenerator() to calculate landcover classes from cohortData and pixelGroupMap;
• add new prepInputs_NTEMS_DominantSpecies function for importing dominant species layers from NTEMS website;
• add new speciesPresentFromNTEMS function to import dominant species layer from NTEMS and create factor raster to be hosted on Google drive;
• add loadSCANFISpeciesLayers and prepSpeciesLayers_SCANFI functions for loading SCANFI species data from Google drive;
• add adjustAgeToLongevity to adjust initial cohort ages based on longevity for each species;
• add studyAreaEco function to extend studyArea to ecological boundaries;
  • studyAreaEco allows studyArea = NULL, uses type = "ecozone" by default;
• add plot_raster_stats and calc_raster_counts for generating summaries of numeric rasters in Canada;

Enhancements

• LANDISDisp() spiral seed dispersal loop ported to C++ via Rcpp (~3.5–5.7× faster end-to-end depending on input size; ~5× on landscape-scale fixtures of 9 M cells). Memory use also drops dramatically: the per-cell-by-species source matrix is replaced with a per-pixelGroup species bitmask. Bit-identical to the previous R implementation under a fixed seed — guarded by 196 seed-locked / parity expectations (209 with LANDR_SLOW_TESTS=1). Default behaviour is unchanged for callers; the new path is on by default and can be opted out with LANDISDisp(..., useCpp = FALSE) or options(LandR.LANDISDisp.useCpp = FALSE). Rcpp (>= 1.0.10) added to Imports and LinkingTo; digest added to Suggests (used by the golden-output hash manifest in tests);
• calc_raster_stats() now derives min/mean/max/quantiles/proportion-zero from the value-frequency table produced by calc_raster_counts() instead of reading every pixel via exactextractr, keeping memory bounded on very large rasters; it gains a counts_df argument to reuse a precomputed table. plot_raster_stats() now honours supplied counts_df/stats_df instead of recomputing them, and fetches the Canada inset once, omitting it gracefully when the source is unavailable. zonal removed from Suggests;
• makeAndCleanInitialCohortData() now stop()s with an informative message naming the species that cannot be age-imputed, instead of the cryptic predict.merMod() "non-conformable arguments": a species with cohorts needing age imputation but no usable known-age rows to fit the age model (all dropped for zero biomass and/or cover) is absent from the model fit yet present in the prediction set, so its fixed-effect speciesCode has no coefficient. A TODO in the code outlines fix options (see #195);
• SCANFI and 2020 now default data source and year for stand age and biomass functions;
• use writeTo instead of filename2 in prepInputs() and related calls, following changes in reproducible;
• minRelativeB defaults updated based on discussion surrounding over-representation of shade tolerant species establishing and generating unreasonably high levels of understory cohorts;
• update speciesInStudyArea function to create dataSource parameter to direct function to download KNN or NTEMS factor raster from google drive and create associated species list;
• update prepRawBiomassMap function to allow for incorporation of NTEMS or SCANFI biomass;
• update prepInputsStandAgeMap function to allow for incorporation of SCANFI age map;
• update documentation and citations for prepSpeciesLayers_* functions;
• standardized sppEquivalencies_CA naming convention for provincial forestry columns with <province>_forestry ;
• remove undifferentiated tree species variants from provincial forestry columns in sppEquivalencies_CA;
• plotVTM now does not use Plot internally (with #140);
• several minor updates to loadSCANFISpeciesLayers, prepSpeciesLayers_SCANFI to address more edge cases;
• prepSpeciesLayers_SCANFI updates to improve join sppEquiv so "multiple - to - one" can be used;
• improved transition plots, use arrow datasets to minimize memory use (important for large study areas);

Bug fixes

• dropTerm now can deal with random effects better (#105);
• prepRawBiomassMap - needed overwrite = TRUE for cases where download was corrupt;
• prepRawBiomassMap needs httr2 package as remote site is failing with download.file;
• don't delete CA_forest_VLCE2 raster in prepInputs_NTEMS_LCC_FAO() (#110);
• corrected some BC forestry tree species entries;
• minor bug fixes to prepInputsFireYear pertaining to file structure of NFDB data;

LandR 1.1.5

• use INT2U instead of INT1U when writing rasters in .overlay() to avoid warning with larger values;

LandR 1.1.4

• fix bug in vegTypeMapGenerator() when mixedType = 1;
• allow mixedType = 0 in vegTypeMapGenerator();

LandR 1.1.3

• fixed an assertion;

LandR 1.1.2

• delete NTEMS file (24 GB) after use in prepInputs_NTEMS_LCC_FAO();
• update Quebec PSP column in speciesEquivalencies_CA;

LandR 1.1.1

• more conversion from raster to terra throughout;
• remove gdalUtilities dependency;
• fix bug in prepInputLCC: orig argument no longer accepted by terra::compareGeom;
• fix bug in calcSeverityB: output table was missing the proportion of B killed;
• new functions used to estimate maximum biomass (maxB) and species establishment probabilities (SEP);
• new function to update the speciesEcoregion table (brought over from Biomass_speciesParameters module), using estimated inflationFactor and mANPPproportion to adjust maxB and maxANPP, respectively;
• new functions to simulate disturbances - FireDisturbance and FireDisturbancePM pulled from; Biomass_regeneration and Biomass_regenerationPM modules, respectively;
• overlayLCCs() now works correctly with terra (#99);
• fixed partial argument match warnings (#100);
• new function standAgeMapGenerator() to produce standAgeMap from cohortData;
• new functions prepInputs_NTEMS_Nonforest() and prepInputs_NTEMS_LCC_FAO();
• add new assertions: assertSpeciesTable() and assertSpeciesTableRaw();

LandR 1.1.0

• move LandWeb-specific functions to LandWebUtils package (#86)
• Colors -- new function to help with terra migration.
• prepInputsFireYear can now handle rasterToMatch that is a SpatRaster
• drop support for R < 4.2 due to change in dependency package MuMIn (Sept 2022)
• new functions to download a set of default biogeoclimatic variables used across several modules, and subset data layers from different time periods according to a year. These functions may only be here temporarily.
• new raster/terra utility and plotting functions
• new functions related to producing default permafrost input data for modules. These functions may only be here temporarily.

LandR 1.0.9

• new function: nonForestedPixels used to detect pixels without species cover or a non-forested land-cover class;
• new function: prepRawBiomassMap used to create rawBiomassMap;
• new function: prepRasterToMatch used to create RasterToMatch and RasterToMatchLarge;

LandR 1.0.8

• drop support for R 3.6
• prepInputsStandAgeMapcan now accept firePerimeters layer, avoiding inner download if layer is present;
• new assertion (assertSppVectors) to check that species match between vectors (e.g. tables, colours and species list vector);
• new function sppHarmonize that deals with the 3 potential ways for a user to input the sim$sppEquiv, P(sim)$sppEquivCol, and sim$sppNameVector;
• update Eliot's email address;
• new functions: speciesInStudyArea and `species;
• remove undeclared dependency package Require;
• age imputation in makeAndCleanInitialCohortData can now be turned off;
• fix bug in LANDISDisp(): skip dispersal when src or rcv data.tables are empty;
• initial cohort biomass (calculated in .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);
• fix bug in prepInputsFireYear();
• drop single-level factor terms in statsModel;

LandR 1.0.7

• Several changes to accommodate the tracking and optional removal of pixels; data suffered data imputation in 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.

LandR 1.0.5

• Support for refitting modelBiomass (see Biomass_boreaDataPrep) with scaled data or different optimizer;
• Changes to loadkNNSpeciesLayers and prepSpeciesLayers_KNN prevent issues when default URL is down, or working offline (but layers are present locally);
• Several changes to accommodate LCC 2010 dataset;
• New columns to sppEquivalenciesCA (PSP, BC_Forestry and FuelClass);
• Lowered values of dummy rawBiomassMap;
• passing fireURL = NULL to prepStandAgeMap() bypasses age imputation;

LandR 1.0.4

• New assertion for validation data;
• New function sppEquivCheck;
• loadKNNSpeciesLayers can accept a sppEquiv table with one column
• Improved documentation for speciesEquivalencies_CA data;

LandR 1.0.3

• new function to calculate fire severity as biomass loss;
• bug fixes and improvements to to speciesTableUpdate;

LandR 1.0.2

• Fixes and further speed improvements to seed dispersal functions and general code cleaning;

LandR 1.0.1

• Complete rewrite of 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);
• add new function prepSpeciesLayers_ONFRI;

Bugfixes

• LANDISDisp did not correctly handle speciesCode when it is a factor. This is a common possibility. It now handles these correctly.

LandR 0.0.5

• new function updateSpeciesTable (moved from LandWebUtils) to allow user to update species parameters by passing a named list.

LandR 0.0.4

• 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.

LandR 0.0.3

• rounding of age classes and biomass now occurs only inside makeCohortDataFiles, as it is the last thing to do before making cohortData
• rounding of age and biomass has been taken out of 3 other functions -- .createCohortData, makeAndCleanInitialCohortData , and a hard coded bit in Biomass_borealDataPrep
• updated source for kNN databases (now using v1, instead of v0) - this involved changes in the URLs and how the data is downloaded;
• statsModel function has a new argument to improve caching with reproducible::Cache (i.e. not used internally);
• function arguments that where previously called time, are now called currentTime - these changes are matched in LandR Biomass modules
• minor code clean-ups/bugfixes and improved clarity

LandR 0.0.2

• Bug fixes in imports (DESCRIPTION)
• new function overlayLCCs which will help with overlaying more than one land cover classification raster.
• major revisions to convertUnwantedLCC to accommodate more cases and eliminate redundant arguments.
• prepInputsLCC() now works with "LCC10"