Package: LandWebUtils 1.0.3.9048

Alex M Chubaty

LandWebUtils: Helper functions for the LandWeb project

Additional utilities for LandWeb analyses.

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

LandWebUtils_1.0.3.9048.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
LandWebUtils/json (API)

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

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

On CRAN:

Conda:

landscape-ecologysimulation-modeling

2.48 score 2 stars 3 scripts 121 exports 102 dependencies

Last updated from:1e0867afa9 (on development). Checks:7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develNOTE441
source / vignettesOK332
linux-releaseNOTE408
macos-releaseNOTE234
macos-oldrelNOTE288
windows-develNOTE418
windows-releaseNOTE259
windows-oldrelNOTE383
wasm-releaseOK194

Exports:.cleanLandWebStudyArea.doPlotBoxplotanalysesOutputsTimesbuild_studyarea_crosswalkbuildCaribouRangesbuildCrossedReportingPolygonsbuildLandbasePolygonsbuildReportingPolygonscaribouRangeLayersCASFRItoSpRastscc_age_compositecc_age_pct_missingcleanAreaNameextractFMAextractFMUfindOldSimFilesfindSimFilejoinReportingPolygonslandbaseLayerslandmine_area_burned_by_zonelandmine_area_sharelandmine_attach_identitylandmine_burn1landmine_draw_num_fireslandmine_estimate_kBestlandmine_fire_attainmentlandmine_fire_roslandmine_fri_metricslandmine_fri_summarylandmine_fri_verdictlandmine_fuel_typeslandmine_ignition_budgetlandmine_known_specieslandmine_optim_burnFunlandmine_optim_calibratelandmine_optim_clusterExportlandmine_optim_clusterSetuplandmine_optim_clusterWraplandmine_optim_fireSizeslandmine_optim_fitAndisonlandmine_optim_fitSNlandmine_optim_fitSN2landmine_optim_islandslandmine_optim_islandTargetlandmine_optim_islandWeightlandmine_optim_landscapelandmine_optim_params_appendlandmine_optim_params_readlandmine_optim_shapeIndexlandmine_optim_shapeTargetlandmine_optim_unpacklandmine_plot_areaBurnedOverTimelandmine_plot_calibConvergencelandmine_plot_calibDiscriminationlandmine_plot_calibIslandslandmine_plot_calibParamslandmine_plot_calibShapelandmine_plot_FRIlandmine_plot_fri_driverslandmine_plot_fri_zoneslandmine_plot_LTHFClandmine_reburn_budgetlandmine_reburn_ceilinglandmine_ros_tablelandmine_sizes_to_pixelslandweb_add_report_columnlandweb_anpp_arealandweb_arealandweb_bec_zoneslandweb_damage_codeslandweb_dominant_sppEquivlandweb_growth_sppEquivlandweb_growth_trait_frequencylandweb_growth_traitslandweb_lthfclandweb_member_coverlandweb_report_colourslandweb_report_groupslandweb_report_maplandweb_require_specieslandweb_resample_psplandweb_species_maplandweb_species_sppEquivlandweb_species_unitslandweb_sppEquivlandweb_sum_layerslandweb_unit_growth_traitsLandWebCRSLandWebStudyAreasLargePatcheslcc2020_classeslcc2020_remap_tableLeadingVegTypeByAgeClassloadCASFRImeanTruncParetoplotFMAplotGGplotLandWebpolygonCleanprepANSRsprepEcoprovinceLayerprepEcoregionLayerprepFMAsprepFMUsprepSpeciesLayers_CASFRIprepStudyAreaprepTestStudyArearasterListByPolyrecode_cohortsrefCodeForreportingPolygonLayersrunBoxPlotsVegCoverrunHistsLargePatchesrunHistsVegCovershortNameForsppEquiv_groupsstudyAreaCrosswalkstudyAreaInstudyAreaProvtenureShortNamesvalidateShortNames

Dependencies:amcaskpassbackportsbase64encBHbitopscallrcheckmateclassclassIntclicodetoolscpp11crayoncurldata.tableDBIdeldirdigestdismodplyre1071farverfasterizefilelockfpComparefsfuturefuture.applygarglegenericsggplot2globalsgluegoogledrivegtablehexbinhttrinterpisobandjpegjsonliteKernSmoothlabelinglatticelatticeExtralifecyclelistenvlobstrmagrittrmapMASSmimenabornngeoopensslotelpakparallellypemiscpeutilspillarpkgconfigpngprettyunitsprocessxproxypspurrrR6rappdirsrasterrasterVisRColorBrewerRcppRcppArmadilloRcppEigenRCurlreproducibleRequirerlangs2S7scalessfspSpaDES.toolsspatialutilssysterratibbletidyselecttilerunitsutf8uuidvctrsviridisLitewithrwkworkflowtoolszoo

Readme and manuals

Help Manual

Help pageTopics
Clean up the LandWeb LTHFCs.cleanLandWebStudyArea
Simulation timesteps for analysesanalysesOutputsTimes
Build the LandWeb study-area grouping crosswalkbuild_studyarea_crosswalk
Assemble the caribou range reporting layerbuildCaribouRanges
Build the tenure x sub-region crossed reporting polygonsbuildCrossedReportingPolygons
Build the active/passive landbase-status reporting polygonsbuildLandbasePolygons
Build the reporting-polygons named listbuildReportingPolygons
Jurisdictional caribou range source layerscaribouRangeLayers
'CASFRItoSpRasts'CASFRItoSpRasts
Composite current-condition stand age, filling gaps from a second sourcecc_age_composite
Percent of forest with no current-condition stand agecc_age_pct_missing
Extract study area name from run namecleanAreaName
Extract boundary polygon(s) for LandWeb forest management area(s)extractFMA
Extract boundary polygon(s) for Alberta forest management unit(s)extractFMU
Find LandWeb simulation output filesfindOldSimFiles findSimFile
Join reporting polygons and intersect their featuresjoinReportingPolygons
Candidate active/passive landbase-status source layerslandbaseLayers
Area burned per FRI zone in a single yearlandmine_area_burned_by_zone
Share of total area carried by the largest fireslandmine_area_share
Attach fire identity to a burn resultlandmine_attach_identity
Core Burn function for Andison's LandMine Fire Modulelandmine_burn landmine_burn1
LandMine calibration diagnostic plotslandmine_calibration_plots landmine_plot_calibConvergence landmine_plot_calibDiscrimination landmine_plot_calibIslands landmine_plot_calibParams landmine_plot_calibShape
Draw the number of fires per FRI zone for one periodlandmine_draw_num_fires
Fit the truncated-Pareto shape for the fire-size distributionlandmine_estimate_kBest
Per-fire target attainment from a LandMine 'fireSizes' tablelandmine_fire_attainment
Assign a rate of spread to every pixellandmine_fire_ros
Per-zone fire-return-interval diagnosticslandmine_fri_metrics
Summarize achieved fire return interval by FRI zonelandmine_fri_summary
One-line verdict on fire-return-interval attainmentlandmine_fri_verdict
Reporting group to fuel type, for LandMinelandmine_fuel_types
Ignition budget per FRI zonelandmine_ignition_budget
Leading-species to fuel-type lookup used by LandMinelandmine_known_species
LandMine burn optimization functionlandmine_optim_burnFun
Run the LandMine fire-spread calibrationlandmine_optim_calibrate
Export objects used for optimization and load packages on clusterlandmine_optim_clusterExport
Setup a cluster for LandMine optimizationlandmine_optim_clusterSetup
Wrapper function to setup cluster, export objects and load packageslandmine_optim_clusterWrap
Fire sizes for calibration, in pixels, from areas in hectareslandmine_optim_fireSizes
Andison-constrained objective for the LandMine fire-spread calibrationlandmine_optim_fitAndison
LandMine objective functionslandmine_optim_fitSN landmine_optim_fitSN2
Remnant islands within a simulated firelandmine_optim_islands
Andison island-remnant targetlandmine_optim_islandTarget
Resolution-dependent weight for the remnant-island termlandmine_optim_islandWeight
Build the synthetic landscape used for LandMine calibrationlandmine_optim_landscape
Andison's shape indexlandmine_optim_shapeIndex
Andison's expected shape index for a given fire arealandmine_optim_shapeTarget
Unpack LandMine fire-spread calibration parameterslandmine_optim_params_append landmine_optim_params_read landmine_optim_unpack
Plot what separates the failing zones from the restlandmine_plot_fri_drivers
Map fire-return-interval zones and their attainmentlandmine_plot_fri_zones
LandMine diagnostic plotslandmine_plots landmine_plot_areaBurnedOverTime landmine_plot_FRI landmine_plot_LTHFC
Rebuild the per-zone fire budget for the next reburn roundlandmine_reburn_budget
Summarize FRI zones still short of target at the reburn ceilinglandmine_reburn_ceiling
LandMine's rate-of-spread tablelandmine_ros_table
Convert fire sizes in hectares to whole pixels, preserving the expectationlandmine_sizes_to_pixels
Add the LandWeb reporting groups to a species equivalency tablelandweb_add_report_column
Ecological units that touch an area, for fitting growth curveslandweb_anpp_area
The outline of the LandWeb arealandweb_area
BC BEC zones over the BC plots of a growth-curve fitting arealandweb_bec_zones
Damage agent codes to exclude from growth-curve plots, by plot sourcelandweb_damage_codes
Give each merged LandWeb species group its dominant member's traitslandweb_dominant_sppEquiv
Species table for the shared growth-curve fitlandweb_growth_sppEquiv
How often refits on resampled plots chose each species' growth-curve traitslandweb_growth_trait_frequency
The growth-curve traits of each species, from the shared fitlandweb_growth_traits
The LandWeb long-term historic fire cycle (LTHFC) maplandweb_lthfc
Total SCANFI cover of each member species in a study arealandweb_member_cover
Colours for the LandWeb reporting groupslandweb_report_colours
LandWeb reporting groupslandweb_report_groups
Simulated species and groups to LandWeb reporting groupslandweb_report_map
Stop when a species input is emptylandweb_require_species
Resample the plots of a growth-curve fit, whole plots with replacementlandweb_resample_psp
SCANFI species to LandWeb species groupslandweb_species_map
SCANFI species to LandWeb species, one code per specieslandweb_species_sppEquiv
Which species LandWeb simulates on its own in a study arealandweb_species_units
Add the LandWeb species groups to a species equivalency tablelandweb_sppEquiv
Sum species cover layers into the units LandWeb simulateslandweb_sum_layers
Give each simulated unit the growth-curve traits of a member specieslandweb_unit_growth_traits
Target CRS (projection) to use with LandWebLandWebCRS
Study areas available for LandWeb simulationsLandWebStudyAreas studyAreaIn studyAreaProv
Calculate proportion of large patches in NRVLargePatches
Canada LCC 2020 class groups used by LandWeblcc2020_classes
Remap table for overlaying LCC 2020 onto the simulation land coverlcc2020_remap_table
Calculate proportion of landscape occupied by each vegetation classLeadingVegTypeByAgeClass
Load CASFRI data for LandWebloadCASFRI
Calculate the mean of a truncated Pareto distributionmeanTruncPareto
Plot boundary polygon(s) for forest management areasplotFMA plotGG plotLandWeb
Do an arbitrary set of operations on a polygonpolygonClean
Prepare reporting polygonsprepANSRs prepEcoprovinceLayer prepEcoregionLayer prepFMAs prepFMUs
Prepare species layers from CASFRI v4prepSpeciesLayers_CASFRI
Extract boundary polygon(s) for a LandWeb study areaprepStudyArea prepTestStudyArea
Create a list of rasters in each rep, at each timestep, for each polygon arearasterListByPoly
Recode cohorts' species to their groupsrecode_cohorts
Output key ('refCode') for one analysis kind and reporting layerrefCodeFor
Candidate reporting-polygon source layersreportingPolygonLayers
Generate box and whisker plots for leading vegetation coverrunBoxPlotsVegCover
Generate histograms for large patchesrunHistsLargePatches
Generate histograms for leading vegetation coverrunHistsVegCover
Look up curated short namesshortNameFor
Group the simulated species of a species tablesppEquiv_groups
Build (or load a cached) LandWeb study-area grouping crosswalkstudyAreaCrosswalk
Curated short names for the LandWeb tenurestenureShortNames
Validate a set of curated short namesvalidateShortNames