Package: LandR 1.2.0.9054

Eliot J B McIntire

LandR: Landscape Ecosystem Modelling in R

Utilities for 'LandR' suite of landscape simulation models. These models simulate forest vegetation dynamics based on LANDIS-II, and incorporate fire and insect disturbance, as well as other important ecological processes. Models are implemented as 'SpaDES' modules.

Authors:Eliot J B McIntire [aut, cre], Alex M Chubaty [aut], Ceres Barros [aut], Ian M S Eddy [aut], His Majesty the King in Right of Canada, as represented by the Minister of Natural Resources Canada [cph]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
LandR/json (API)

# Install 'LandR' in R:

install.packages('LandR', repos = c('https://predictiveecology.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/predictiveecology/landr/issues

Pkgdown/docs site:https://landr.predictiveecology.org

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

sppEquivalencies_CA - Species equivalencies table ('sppEquiv') and 'sppEquivalencies_CA'

On CRAN:

ecological-modelling landscape-ecosystem-modelling spades cpp

6.75 score 20 stars 1 packages 15 scripts 183 exports 105 dependencies

Last updated from:04bfdcd873 (on development). Checks:13 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	NOTE	519
linux-devel-x86_64	NOTE	599
source / vignettes	OK	711
linux-release-arm64	NOTE	635
linux-release-x86_64	NOTE	627
macos-release-arm64	NOTE	452
macos-release-x86_64	NOTE	1356
macos-oldrel-arm64	NOTE	754
macos-oldrel-x86_64	NOTE	1026
windows-devel-arm64	NOTE	663
windows-devel-x86_64	NOTE	723
windows-release-arm64	NOTE	659
windows-release-x86_64	NOTE	634
windows-oldrel-x86_64	NOTE	613
wasm-release	OK	243

Exports:.compareCRS .compareRas .stack addNoPixel2CohortData addPixels2CohortData adjustAgeToLongevity aggregateRasByDT asInt asInteger assert1 assert2 assertCohortData assertCohortDataAttr assertCohortDataERG assertColumns assertERGs assertFireToleranceDif assertPixelCohortData assertPixelCohortDataValid assertPostFireDist assertPostPartialDist assertRepsAllCohortData assertRstLCChange assertSpeciesEcoregionCohortDataMatch assertSpeciesLayers assertSpeciesPlotLabels assertSpeciesTable assertSpeciesTableRaw assertSppMaxBMaxANPP assertSppVectors assertStandAgeMapAttr assertUniqueCohortData assignLightProb biomodEnsembleFrcstWrapper biomodEnsembleProjMaps biomodEnsembleWrapper biomodModelingWrapper biomodProjWrapper BioSIM_extractPoints BioSIM_getMPBSLR BioSIM_getWindAnnual BioSIM_getWindMonthly calc_raster_counts calc_raster_stats calcSeverityB calcSiteShade calculateClimateEffect CASFRItoSpRasts checkSpeciesTraits cohortDefinitionCols Colors columnsForPixelGroups convert_SCANFI_LCC_codes convertUnwantedLCC convertUnwantedLCC2 defineFlammable describeCohortData doResprouting doSerotiny dropTerm ecoregionProducer equivalentName equivalentNameColumn extractMaxB fasterizeFromSp FireDisturbance FireDisturbancePM fitNLMModels forestLandMask gadm_canada generatePixelGroups genericExtract genPGsPostDisturbance getSpeciesTable getWildfire_NFI imputeBadAgeModelDefault installBioSIM isInt LANDISDisp LandROptions lccMapGenerator leadingByPixelGroup leadingSpeciesProp loadCASFRI loadkNNSpeciesLayers loadkNNSpeciesLayersValidation loadSCANFISpeciesLayers makeAndCleanInitialCohortData makeBiomassMap makeCohortDataFiles makeDummyEcoregionFiles makeDummyEcoregionMap makeDummyRawBiomassMap makeDummyRstLCC makeDummyStandAgeMap makeEcoregionDT makeEcoregionMap makeMinRelativeB makePickellStack makePixelGroupMap makePixelTable makeSpeciesEcoregion makeVegTypeMap minRelativeBDefaults mixedwoodProp modifySpeciesAndSpeciesEcoregionTable NAcover2zero nonForestedPixels overlayLCCs overlayStacks partialggplotMLL_maxB partitionBiomass PeatlandThermokarst pixelFate plantNewCohorts plot_raster plot_raster_stats plotLeadingSpecies plotSpatial plotVegTransitions plotVTM prepEcoregions prepEcozonesRst prepInputs_CWIM prepInputs_FAO_forest prepInputs_NTEMS_DominantSpecies prepInputs_NTEMS_LCC_FAO prepInputs_NTEMS_Nonforest prepInputs_SCANFI_LCC_FAO prepInputs_SCANFI_structure prepInputsCanDEM prepInputsEcoregion prepInputsFireYear prepInputsLCC prepInputsMainInput prepInputsSpecies prepInputsSpeciesEcoregion prepInputsStandAgeMap prepRasterToMatch prepRawBiomassMap prepSpeciesLayers_CASFRI prepSpeciesLayers_ForestInventory prepSpeciesLayers_KNN prepSpeciesLayers_KNN2011 prepSpeciesLayers_MBFRI prepSpeciesLayers_NTEMS prepSpeciesLayers_ONFRI prepSpeciesLayers_Pickell prepSpeciesLayers_SCANFI prepSpeciesTable randomStudyArea reclass replaceAgeInFires rescale rmMissingCohorts scanfiUrlRemap scheduleDisturbance speciesEcoregionLatestYear speciesInStudyArea speciesPresentFromKNN speciesPresentFromNTEMS speciesPresentFromSCANFI speciesTableUpdate sppColors sppEquivCheck sppHarmonize standAgeMapGenerator statsModel studyAreaEco subsetDataSize subsetDT sumRastersBySpecies uniqueCohortDefinition uniqueSpeciesEcoregionDefinition updateCohortData updateCohortDataPostHarvest updateSpeciesTable vegTransitions vegTypeGenerator vegTypeMapGenerator vtm2conifdecid Ward wetlandToLCC

Dependencies:abind amc askpass backports base64enc bitops boot callr checkmate class classInt cli cpp11 crayon curl data.table DBI digest dismo dplyr e1071 farver fasterize filelock Formula fpCompare fs generics ggplot2 ggspatial glue gridExtra gtable hms httr httr2 insight isoband jpeg jsonlite KernSmooth labeling lattice lifecycle lme4 lobstr magrittr MASS Matrix mime minqa MuMIn nlme nloptr openssl otel pak parallelly patchwork pemisc peutils pillar pkgconfig png prettyunits processx progress proxy ps purrr R6 raster rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl Rdpack reformulas reproducible Require rlang rosm s2 S7 scales sf sp SpaDES.tools stringi stringr sys terra tibble tidyr tidyselect tidyterra units utf8 vctrs viridis viridisLite withr wk

National forest raster summaries by ecozone

Rendered fromscanfi-summary.Rmdusingknitr::rmarkdown

Last update: 2026-09-18
Started: 2026-08-24

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
'LandR' package	LandR-package LandR
Compare raster properties	.compareCRS .compareRas
Fit non-linear growth model under various starting conditions	.fitNLMwCovariates
Get maximum biomass coefficient names	.getMaxBCoefs
Find interpolated value of light probability	.interpolateLightProb
Prepare data for model plotting	.MLLMaxBPartialPlotData
Prepare data for model plotting	.MLLMaxBplotData
Set NA values in 'Raster' or 'SpatRaster'	.NAvalueFlag .projectExtent .stack asInt isInt reclass
Add number of pixels per 'pixelGroup' and add it has a new column to 'cohortData'	addNoPixel2CohortData
Generate 'cohortData' table per pixel:	addPixels2CohortData
Reduces the age of cohorts that exceed their longevity x adjustmentFactor	adjustAgeToLongevity
Aggregate a raster	aggregateRasByDT
Convert numeric values to rounded integers	asInteger
Assertions	assert1 assert2 assertCohortData assertCohortDataAttr assertCohortDataERG assertColumns assertERGs assertFireToleranceDif assertions assertPixelCohortData assertPixelCohortDataValid assertPostFireDist assertRepsAllCohortData assertRstLCChange assertSpeciesEcoregionCohortDataMatch assertSpeciesLayers assertSpeciesPlotLabels assertSpeciesTable assertSpeciesTableRaw assertSppMaxBMaxANPP assertSppVectors assertStandAgeMapAttr assertUniqueCohortData
Assert post-fire disturbance mortality and regeneration	assertPostPartialDist
Assign light probability	assignLightProb
Simple wrapper around 'biomod2::BIOMOD_EnsembleForecasting()'	biomodEnsembleFrcstWrapper
Make maps from 'BIOMOD_EnsembleForecasting()' results	biomodEnsembleProjMaps
BIOMOD_EnsembleModeling wrapper	biomodEnsembleWrapper
BIOMOD_Modeling wrapper	biomodModelingWrapper
BIOMOD_Projection wrapper	biomodProjWrapper
Extract point locations from DEM raster to pass to 'BioSIM' functions	BioSIM_extractPoints
Get annual historic and projected MPB climate suitability maps from 'BioSIM'	BioSIM_getMPBSLR
Get annual historic and projected wind maps from 'BioSIM'	BioSIM_getWindAnnual
Get monthly historic and projected wind maps from 'BioSIM'	BioSIM_getWindMonthly
Raster summary statistics and maps by polygon	calc_raster_counts calc_raster_stats plot_raster_stats raster_stats
Calculate fire severity	calcSeverityB
Calculate site shade	calcSiteShade
Null climate effect	calculateClimateEffect
'CASFRItoSpRasts'	CASFRItoSpRasts
Check if all species in have trait values	checkSpeciesTraits
Default columns that define cohorts	cohortDefinitionCols
Helper for setting Raster or 'SpatRaster' colors	Colors Colours
Default columns that define pixel groups	columnsForPixelGroups
Convert SCANFI Landcover layers from 1-8 codes to typical Canada LCC codes (0-230)	convert_SCANFI_LCC_codes
Convert Land Cover Classes (LCC) to another value in its neighbourhood	convertUnwantedLCC
Convert Land Cover Classes (LCC) to another value in its neighbourhood	convertUnwantedLCC2
Define flammability map	defineFlammable
Summary for 'cohortData'	describeCohortData
Activate resprouting after a (fire) disturbance	doResprouting
Activate serotiny after a (fire) disturbance	doSerotiny
Drop factor term including interactions from a model formula	dropTerm
Make 'ecoregionMap' and 'ecoregion' table	ecoregionProducer
Return equivalent name from a 'data.frame' of equivalencies	equivalentName equivalentNameColumn
Maximum biomass estimator	extractMaxB
Rasterize polygons using 'fasterize'	fasterizeFromSp
Disturbance functions	Disturbances FireDisturbance FireDisturbancePM PeatlandThermokarst
FUNCTIONS TO FIT NON-LINEAR MODELS TO ESTIMATE MAXB Wrapper function to fit non-linear growth model per species.	fitNLMModels
Is a pixel forest land?	forestLandMask
Canada administrative boundaries	gadm_canada
Add the correct 'pixelGroups' to a 'pixelDataTable' object	generatePixelGroups
Generic extract points	genericExtract
Re-generate new 'pixelGroup's in partially disturbed pixels.	genPGsPostDisturbance
Download and prepare a species traits table for use with 'Biomass_core' module	getSpeciesTable prepSpeciesTable speciesTable
Download and prepare raster fire data from NFI	getWildfire_NFI
Plot estimated maximum biomass by age	ggplotMLL_maxB
Default model for imputing missing stand ages	imputeBadAgeModelDefault
Install 'BioSIM' to retrieve climate and other projections using 'BioSIM'	installBioSIM
Simulate a LANDIS-II dispersal process on a landscape.	LANDISDisp
'LandR' options	LandROptions opts.LandR
Calculate landcover classes based on species cohorts	lccMapGenerator
Leading species of each 'pixelGroup'	leadingByPixelGroup
Load CASFRI data	loadCASFRI
Load kNN species layers from online data repository	loadkNNSpeciesLayers
Load SCANFI species layers from online data repository	loadSCANFISpeciesLayers
Generate initial 'cohortData' table	makeAndCleanInitialCohortData
Create 'biomassMap'	makeBiomassMap
Make the 'cohortData' table, while modifying the temporary 'pixelCohortData' that will be used to prepare other files.	makeCohortDataFiles
Create dummy inputs for test simulations	dummy-inputs dummyInputs makeDummyEcoregionFiles makeDummyEcoregionMap makeDummyRawBiomassMap makeDummyRstLCC makeDummyStandAgeMap
Make the 'ecoregion' table	makeEcoregionDT
Make the 'ecoregionMap' raster	makeEcoregionMap
Create 'minRelativeB' table	makeMinRelativeB
'makePickellStack'	makePickellStack
Create 'makePixelGroupMap'	makePixelGroupMap
Make 'pixelTable' from biomass, age, land-cover and species cover data	makePixelTable
Create 'speciesEcoregion'	makeSpeciesEcoregion
Make a vegetation type map from a stack of species abundances	LandR-deprecated loadkNNSpeciesLayersValidation makeVegTypeMap prepSpeciesLayers_KNN2011
minRelativeB defaults for Western Boreal Forest Canada	minRelativeBDefaults
Leading-species and mixedwood proportion thresholds	leadingProportions leadingSpeciesProp mixedwoodProp
Update 'species' and 'speciesEcoregion' tables	modifySpeciesAndSpeciesEcoregionTable
Convert 'NA' values in 'speciesLayers' to zeros	NAcover2zero
Assess non-forested pixels based on species cover data and land-cover	nonForestedPixels
Overlay different LCC data sources	overlayLCCs
Overlay layers within raster stacks	overlayStacks
Partial effect plots of maximum biomass estimates by age	partialggplotMLL_maxB
Partition biomass according to cover estimates	partitionBiomass
Create or amend data to a 'pixelFateDT' object	pixelFate
Create new cohorts based on provenance table with unique 'pixelGroup' and add to 'cohortData'	plantNewCohorts
Plot raster objects using ggplot	plot_raster
Leading species plots	plotLeadingSpecies
Create a 'ggplot' of a raster or 'sf' object.	plotSpatial
Summary plots of leading vegetation types	plotVTM
Prepare ecoregions objects	prepEcoregions
Prepare ecozones raster	prepEcozonesRst
Wetland (site) layer from the Canadian Wetland Inventory Map	prepInputs_CWIM
Obtain the NFIS FAO forest layer	prepInputs_FAO_forest
Obtain an Dominant species layer for a given year from NTEMS	prepInputs_NTEMS_DominantSpecies
Obtain an LCC layer for a given year from NTEMS, with forest matching the FAO definition	prepInputs_NTEMS_LCC_FAO
Reclassify non-flammable pixels that become flammable - herbaceous or shrubby - vegetation	prepInputs_NTEMS_Nonforest
Obtain an LCC layer for a given year from SCANFI, with forest matching the FAO definition	prepInputs_SCANFI_LCC_FAO
Obtain a SCANFI structural attribute layer	prepInputs_SCANFI_structure
Get digital elevation map of Canada	prepInputsCanDEM
Prepare ecoregion table	prepInputsEcoregion
Create a raster of fire perimeters	prepInputsFireYear
Simple 'prepInputs' for Canadian LCC data	prepInputsLCC
Download and prepare a species traits table for use with 'Biomass_core' module	prepInputsMainInput prepInputsSpecies
Prepare species ecoregion table	prepInputsSpeciesEcoregion
Create 'standAgeMap'	prepInputsStandAgeMap
Create 'rasterToMatch' and 'rasterToMatchLarge'	prepRasterToMatch
Create 'rawBiomassMap'	prepRawBiomassMap
Prepare species layers	prepSpeciesLayers prepSpeciesLayers_CASFRI prepSpeciesLayers_ForestInventory prepSpeciesLayers_KNN prepSpeciesLayers_MBFRI prepSpeciesLayers_NTEMS prepSpeciesLayers_ONFRI prepSpeciesLayers_Pickell prepSpeciesLayers_SCANFI
Create default study areas for use with LandR modules	randomStudyArea
Replace stand age with time since last fire	replaceAgeInFires
Rescale function (as in 'scales::rescale')	rescale
Remove missing cohorts from 'cohortData' based on 'pixelGroupMap'	rmMissingCohorts
Resolve SCANFI Google Drive ids to the PredictiveEcology mirror	scanfiUrlRemap
Test whether disturbance should be scheduled	scheduleDisturbance
Pull out the values from 'speciesEcoregion' table for current time	speciesEcoregionLatestYear
Create Stacks of the 'speciesEcoregion' content	speciesEcoregionStack
Get species list in a given study area for a forest in Canada	speciesInStudyArea
Make a species factor raster from KNN	speciesPresentFromKNN
Make a species factor raster based on NTEMS Data	speciesPresentFromNTEMS
Make a species factor raster based on SCANFI Data	speciesPresentFromSCANFI
Change species table of parameters/traits	speciesTableUpdate
Create species colour vector from a 'sppEquiv' table	sppColors sppColours
Species equivalencies table ('sppEquiv') and 'sppEquivalencies_CA'	sppEquiv sppEquivalencies_CA
Check and expand 'sppEquiv'	sppEquivCheck
Harmonize the three components that bring species into Biomass_** modules	sppHarmonize
Produce stand age map based on 'cohortData'	standAgeMapGenerator
The generic statistical model to run ('lmer' or 'glmer')	statsModel
Ecological boundaries within a study area	studyAreaEco
How many rows to keep per group when subsampling for model fitting	subsetDataSize
Subset a 'data.table' with random subsampling within 'by' groups	subsetDT
Function to sum rasters of species layers	sumRastersBySpecies
The columns in a 'cohortData' that define "unique"	uniqueCohortDefinition uniqueDefinitions uniqueSpeciesEcoregionDefinition
Add cohorts to 'cohortData' and 'pixelGroupMap'	.initiateNewCohorts updateCohortData
Add cohorts to 'cohortData' and 'pixelGroupMap'	updateCohortDataPostHarvest
Customize species trait table values	updateSpeciesTable
Generate and add vegetation type column to 'cohortData'	vegTypeGenerator
Generate vegetation type map	vegTypeMapGenerator vegTypeMapGenerator.data.table vegTypeMapGenerator.default
Create a summaries of vegetation type transitions	plotVegTransitions vegetation-transitions vegetationTransitions vegTransitions vtm2conifdecid
Ward Dispersal Kernel - vectorized, optimized for speed	Ward WardKernel
Add wetland classes to a land-cover map	wetlandToLCC