Changes in version 1.2.0.9002                      

  - 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);
  - drop support for R 4.2 due to changes in dependency packages;
  - 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;
  - SCANFI and 2020 now default data source and year for stand age and
    biomass functions;
  - 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;
  - add functions to visualize vegetation type transitions;
  - use writeTo instead of filename2 in prepInputs() and related calls,
    following changes in reproducible;
  - remove rasterRead() to use version from reproducible;
  - columnsForPixelGroups is now a function (i.e., use
    columnsForPixelGroups() for consistent pixelGroup definitions);
  - new function cohortDefinitionCols() to ensure consistent cohort
    definitions;
  - new function lccMapGenerator() to calculate landcover classes from
    cohortData and pixelGroupMap;
  - don't delete CA_forest_VLCE2 raster in prepInputs_NTEMS_LCC_FAO()
    (#110);
  - minRelativeB defaults updated based on discussion surrounding
    over-representation of shade tolerant species establishing and
    generating unreasonably high levels of understory cohorts;
  - 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;
  - 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;
  - 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;
  - update documentation and citations for prepSpeciesLayers_*
    functions;
  - corrected some BC forestry tree species entries;
  - 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;
  - add plot_raster_stats and calc_raster_counts for generating
    summaries of numeric rasters in Canada;
  - minor bug fixes to prepInputsFireYear pertaining to file structure
    of NFDB data;
  - improved transition plots, use arrow datasets to minimize memory use
    (important for large study areas);

                        Changes in version 1.1.5                        

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

                        Changes in version 1.1.4                        

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

                        Changes in version 1.1.3                        

  - fixed an assertion;

                        Changes in version 1.1.2                        

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

                        Changes in version 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();

                        Changes in version 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.

                        Changes in version 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;

                        Changes in version 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;

                        Changes in version 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.

                        Changes in version 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;

                        Changes in version 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;

                        Changes in version 1.0.3                        

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

                        Changes in version 1.0.2                        

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

                        Changes in version 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.

                        Changes in version 0.0.5                        

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

                        Changes in version 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.

                        Changes in version 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

                        Changes in version 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"