Package: LandR 1.1.5.9018

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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NEWS

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

Peer review:

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

Datasets:

On CRAN:

ecological-modellinglandscape-ecosystem-modellingspades

153 exports 17 stars 3.14 score 120 dependencies 3 dependents 12 scripts

Last updated 15 days agofrom:ff6378a73e (on development). Checks:OK: 1 ERROR: 1 WARNING: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 24 2024
R-4.5-winWARNINGAug 24 2024
R-4.5-linuxERRORAug 26 2024
R-4.4-winWARNINGAug 24 2024
R-4.4-macWARNINGAug 15 2024
R-4.3-winWARNINGAug 24 2024

Exports:.compareCRS.compareRas.stackaddNoPixel2CohortDataaddPixels2CohortDataaggregateRasByDTasIntasIntegerassert1assert2assertCohortDataassertCohortDataAttrassertColumnsassertERGsassertFireToleranceDifassertPixelCohortDataassertPixelCohortDataValidassertPostPartialDistassertRepsAllCohortDataassertRstLCChangeassertSpeciesEcoregionCohortDataMatchassertSpeciesLayersassertSpeciesPlotLabelsassertSpeciesTableassertSpeciesTableRawassertSppMaxBMaxANPPassertSppVectorsassertStandAgeMapAttrassertUniqueCohortDataassignLightProbbiomodEnsembleFrcstWrapperbiomodEnsembleProjMapsbiomodEnsembleWrapperbiomodModelingWrapperbiomodProjWrapperBioSIM_extractPointsBioSIM_getMPBSLRBioSIM_getWindAnnualBioSIM_getWindMonthlycalcSeverityBcalcSiteShadecalculateClimateEffectCASFRItoSpRastscheckSpeciesTraitscohortDefinitionColsColorscolumnsForPixelGroupsconvertUnwantedLCCconvertUnwantedLCC2defineFlammabledescribeCohortDatadoResproutingdoSerotinydropTermecoregionProducerequivalentNameequivalentNameColumnextractMaxBfasterizeFromSpFireDisturbanceFireDisturbancePMfitNLMModelsgeneratePixelGroupsgenericExtractgenPGsPostDisturbancegetSpeciesTablegetWildfire_NFIinstallBioSIMisIntLANDISDisploadCASFRIloadkNNSpeciesLayersloadkNNSpeciesLayersValidationmakeAndCleanInitialCohortDatamakeBiomassMapmakeCohortDataFilesmakeDummyEcoregionFilesmakeDummyEcoregionMapmakeDummyRawBiomassMapmakeDummyRstLCCmakeDummyStandAgeMapmakeEcoregionDTmakeEcoregionMapmakeMinRelativeBmakePickellStackmakePixelGroupMapmakePixelTablemakeSpeciesEcoregionmakeVegTypeMapminRelativeBDefaultsmodifySpeciesAndSpeciesEcoregionTableNAcover2zerononForestedPixelsoverlayLCCsoverlayStackspartialggplotMLL_maxBpartitionBiomassPeatlandThermokarstpixelFateplantNewCohortsplotLeadingSpeciesplotSpatialplotVegTransitionsplotVTMprepEcoregionsprepEcozonesRstprepInputs_NTEMS_LCC_FAOprepInputs_NTEMS_NonforestprepInputsCanDEMprepInputsEcoregionprepInputsFireYearprepInputsLCCprepInputsMainInputprepInputsSpeciesprepInputsSpeciesEcoregionprepInputsStandAgeMapprepRasterToMatchprepRawBiomassMapprepSpeciesLayers_CASFRIprepSpeciesLayers_ForestInventoryprepSpeciesLayers_KNNprepSpeciesLayers_KNN2011prepSpeciesLayers_MBFRIprepSpeciesLayers_ONFRIprepSpeciesLayers_PickellprepSpeciesTablerandomStudyAreareclassreplaceAgeInFiresrescalermMissingCohortsscheduleDisturbancespeciesEcoregionLatestYearspeciesInStudyAreaspeciesPresentFromKNNspeciesTableUpdatesppColorssppEquivChecksppHarmonizestandAgeMapGeneratorstatsModelsubsetDTsumRastersBySpeciesuniqueCohortDefinitionuniqueSpeciesEcoregionDefinitionupdateCohortDataupdateCohortDataPostHarvestupdateSpeciesTablevegTransitionsvegTypeGeneratorvegTypeMapGeneratorvtm2conifdecidWard

Dependencies:abindamcaskpassbackportsbase64encbitopsbootbroomcarcarDatacheckmateclassclassIntclicolorspacecorrplotcowplotcpp11crayoncurldata.tableDBIDerivdigestdismodoBydplyre1071fansifarverfasterizefilelockfpComparefsgenericsggplot2ggpubrggrepelggsciggsignifggspatialgluegridExtragtablehmshttrinsightisobandjpegjsonliteKernSmoothlabelinglatticelifecyclelme4lobstrmagrittrMASSMatrixMatrixModelsmgcvmicrobenchmarkmimeminqamodelrMuMInmunsellnlmenloptrnnetnumDerivopensslparallellypbkrtestpemiscpeutilspillarpkgconfigpngpolynomprettyunitsprogressproxypurrrquantregquickPlotR6rasterRColorBrewerRcppRcppArmadilloRcppEigenRCurlreproducibleRequirerlangrosmrstatixs2scalessfspSpaDES.toolsSparseMstringistringrsurvivalsysterratibbletidyrtidyselecttidyterraunitsutf8vctrsviridisviridisLitewithrwk

Readme and manuals

Help Manual

Help pageTopics
'LandR' packageLandR-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
Aggregate a rasteraggregateRasByDT
Convert numeric values to rounded integersasInteger
Assertionsassert1 assert2 assertCohortData assertCohortDataAttr assertColumns assertERGs assertFireToleranceDif assertPixelCohortData assertPixelCohortDataValid assertRepsAllCohortData assertRstLCChange assertSpeciesEcoregionCohortDataMatch assertSpeciesLayers assertSpeciesPlotLabels assertSpeciesTable assertSpeciesTableRaw assertSppMaxBMaxANPP assertSppVectors assertStandAgeMapAttr assertUniqueCohortData
Assert post-fire disturbance mortality and regenerationassertPostPartialDist
Assign light probabilityassignLightProb
Simple wrapper around 'biomod2::BIOMOD_EnsembleForecasting()'biomodEnsembleFrcstWrapper
Make maps from 'BIOMOD_EnsembleForecasting()' resultsbiomodEnsembleProjMaps
BIOMOD_EnsembleModeling wrapperbiomodEnsembleWrapper
BIOMOD_Modeling wrapperbiomodModelingWrapper
BIOMOD_Projection wrapperbiomodProjWrapper
Extract point locations from DEM raster to pass to 'BioSIM' functionsBioSIM_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
Calculate fire severitycalcSeverityB
Calculate site shadecalcSiteShade
Null climate effectcalculateClimateEffect
'CASFRItoSpRasts'CASFRItoSpRasts
Check if all species in have trait valuescheckSpeciesTraits
Default columns that define cohortscohortDefinitionCols
Helper for setting Raster or 'SpatRaster' colorsColors
Default columns that define pixel groupscolumnsForPixelGroups
Convert Land Cover Classes (LCC) to another value in its neighbourhoodconvertUnwantedLCC
Convert Land Cover Classes (LCC) to another value in its neighbourhoodconvertUnwantedLCC2
Define flammability mapdefineFlammable
Summary for 'cohortData'describeCohortData
Activate resprouting after a (fire) disturbancedoResprouting
Activate serotiny after a (fire) disturbancedoSerotiny
Drop factor term including interactions from a model formuladropTerm
Make 'ecoregionMap' and 'ecoregion' tableecoregionProducer
Return equivalent name from a 'data.frame' of equivalenciesequivalentName equivalentNameColumn
Maximum biomass estimatorextractMaxB
Rasterize polygons using 'fasterize'fasterizeFromSp
Disturbance functionsFireDisturbance FireDisturbancePM PeatlandThermokarst
FUNCTIONS TO FIT NON-LINEAR MODELS TO ESTIMATE MAXB Wrapper function to fit non-linear growth model per species.fitNLMModels
Add the correct 'pixelGroups' to a 'pixelDataTable' objectgeneratePixelGroups
Generic extract pointsgenericExtract
Re-generate new 'pixelGroup's in partially disturbed pixels.genPGsPostDisturbance
Download and prepare a species traits table for use with 'Biomass_core' modulegetSpeciesTable prepSpeciesTable
Download and prepare raster fire data from NFIgetWildfire_NFI
Plot estimated maximum biomass by ageggplotMLL_maxB
Install 'BioSIM' to retrieve climate and other projections using 'BioSIM'installBioSIM
Simulate a LANDIS-II dispersal process on a landscape.LANDISDisp
Load CASFRI dataloadCASFRI
Load kNN species layers from online data repositoryloadkNNSpeciesLayers
Generate initial 'cohortData' tablemakeAndCleanInitialCohortData
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 simulationsmakeDummyEcoregionFiles makeDummyEcoregionMap makeDummyRawBiomassMap makeDummyRstLCC makeDummyStandAgeMap
Make the 'ecoregion' tablemakeEcoregionDT
Make the 'ecoregionMap' rastermakeEcoregionMap
Create 'minRelativeB' tablemakeMinRelativeB
'makePickellStack'makePickellStack
Create 'makePixelGroupMap'makePixelGroupMap
Make 'pixelTable' from biomass, age, land-cover and species cover datamakePixelTable
Create 'speciesEcoregion'makeSpeciesEcoregion
Make a vegetation type map from a stack of species abundancesloadkNNSpeciesLayersValidation makeVegTypeMap prepSpeciesLayers_KNN2011
minRelativeB defaults for Western Boreal Forest CanadaminRelativeBDefaults
Update 'species' and 'speciesEcoregion' tablesmodifySpeciesAndSpeciesEcoregionTable
Convert 'NA' values in 'speciesLayers' to zerosNAcover2zero
Assess non-forested pixels based on species cover data and land-covernonForestedPixels
Overlay different LCC data sourcesoverlayLCCs
Overlay layers within raster stacksoverlayStacks
Partial effect plots of maximum biomass estimates by agepartialggplotMLL_maxB
Partition biomass according to cover estimatespartitionBiomass
Create or amend data to a 'pixelFateDT' objectpixelFate
Create new cohorts based on provenance table with unique 'pixelGroup' and add to 'cohortData'plantNewCohorts
Leading species plotsplotLeadingSpecies
Create a 'ggplot' of a raster or 'sf' object.plotSpatial
Summary plots of leading vegetation typesplotVTM
Prepare ecoregions objectsprepEcoregions
Prepare ecozones rasterprepEcozonesRst
Obtain an LCC layer for a given year from NTEMS, with forest matching the FAO definitionprepInputs_NTEMS_LCC_FAO
Reclassify non-flammable pixels that become flammable - herbaceous or shrubby - vegetationprepInputs_NTEMS_Nonforest
Get digital elevation map of CanadaprepInputsCanDEM
Prepare ecoregion tableprepInputsEcoregion
Create a raster of fire perimetersprepInputsFireYear
Simple 'prepInputs' for Canadian LCC dataprepInputsLCC
Download and prepare a species traits table for use with 'Biomass_core' moduleprepInputsMainInput prepInputsSpecies
Prepare species ecoregion tableprepInputsSpeciesEcoregion
Create 'standAgeMap'prepInputsStandAgeMap
Create 'rasterToMatch' and 'rasterToMatchLarge'prepRasterToMatch
Create 'rawBiomassMap'prepRawBiomassMap
Prepare species layersprepSpeciesLayers_CASFRI prepSpeciesLayers_ForestInventory prepSpeciesLayers_KNN prepSpeciesLayers_MBFRI prepSpeciesLayers_ONFRI prepSpeciesLayers_Pickell
Create default study areas for use with LandR modulesrandomStudyArea
Replace stand age with time since last firereplaceAgeInFires
Rescale function (as in 'scales::rescale')rescale
Remove missing cohorts from 'cohortData' based on 'pixelGroupMap'rmMissingCohorts
Test whether disturbance should be scheduledscheduleDisturbance
Pull out the values from 'speciesEcoregion' table for current timespeciesEcoregionLatestYear
Create Stacks of the 'speciesEcoregion' contentspeciesEcoregionStack
Make a species factor rasterspeciesInStudyArea speciesPresentFromKNN
Change species table of parameters/traitsspeciesTableUpdate
Create species colour vector from a 'sppEquiv' tablesppColors
Table of species name equivalencies for Canadian treessppEquivalencies_CA
Check and expand 'sppEquiv'sppEquivCheck
Harmonize the three components that bring species into Biomass_** modulessppHarmonize
Produce stand age map based on 'cohortData'standAgeMapGenerator
The generic statistical model to run ('lmer' or 'glmer')statsModel
Subset a 'data.table' with random subsampling within 'by' groupssubsetDT
Function to sum rasters of species layerssumRastersBySpecies
The columns in a 'cohortData' that define "unique"uniqueCohortDefinition uniqueSpeciesEcoregionDefinition
Add cohorts to 'cohortData' and 'pixelGroupMap'.initiateNewCohorts updateCohortData
Add cohorts to 'cohortData' and 'pixelGroupMap'updateCohortDataPostHarvest
Customize species trait table valuesupdateSpeciesTable
Generate and add vegetation type column to 'cohortData'vegTypeGenerator
Generate vegetation type mapvegTypeMapGenerator vegTypeMapGenerator.data.table vegTypeMapGenerator.default
Create a summaries of vegetation type transitionsplotVegTransitions vegTransitions vtm2conifdecid
Ward Dispersal Kernel - vectorized, optimized for speedWard WardKernel