Package: fireSenseUtils 0.2.3.9097

Eliot J B McIntire

fireSenseUtils: Utilities for Working With the 'fireSense' Group of 'SpaDES' Modules

Utilities for working with the 'fireSense' group of 'SpaDES' modules.

Authors:Jean Marchal [aut], Eliot J B McIntire [aut, cre], Alex M Chubaty [aut], Ian Eddy [aut]

fireSenseUtils_0.2.3.9097.tar.gz
fireSenseUtils_0.2.3.9060.zip(r-4.7-any)fireSenseUtils_0.2.3.9060.zip(r-4.6-any)fireSenseUtils_0.2.3.9060.zip(r-4.5-any)
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fireSenseUtils_0.2.3.9097.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
fireSenseUtils/json (API)

# Install 'fireSenseUtils' in R:

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

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

On CRAN:

5.03 score 1 stars 5 scripts 178 exports 128 dependencies

Last updated from:95f8d319e4 (on development). Checks:7 FAIL, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel	FAIL	177
source / vignettes	OK	770
linux-release	FAIL	203
macos-release	FAIL	167
macos-oldrel	FAIL	226
windows-devel	FAIL	126
windows-release	FAIL	152
windows-oldrel	FAIL	132
wasm-release	OK	225

Exports:.doDataChecks .objfunSpreadFit addBufferEdge adWeightAuto annualStackToDTx1000 assertCovariateRange assessFuelClasses bestByReplicatedMean bufferEdge bufferToArea bufferToAreaRast calcNonForestYoungAge calcYoungAge castCohortData chk_duplicatedStartPixels chooseDomSecFuelClasses cleanUpSpreadFirePoints climateCovRanges climateRasterToDataTable coefIdentifiability cohortsToFuelClasses combinePlans combineSpreadProbSummaries covsX1000AndSetDF dataYearElement dataYearFor defaultFireYears deoptimPopulationSize dtReplaceNAwith0 ELFfireCounts ELFfireOverlay ELFfitStatus ELFflammableArea elfLabels ELFmergedName ELFmergePlan ELFneighbours ELFregionStats ELFrunName ELFsArctic ELFsExcluded ELFsInStudyArea ELFsizePlan ELFsSkipped ELFtemplateRaster emptySpreadCovariates escapedFires escapeSizePixels escapesTxt fewFireELFs firePixelsByYear fireRecordShapefile fireSenseCloudParameters fireSenseCloudParametersMap fireSenseCovariatesCreate fireSenseFlammabilityThreshold fireSenseForestedLCC fireSenseFuelClassCol fireSenseIgAggFactor fireSenseNonflammableLCC fireSenseNonForestCanBeYoungAge fireSenseRunawayEdgeFrac fireSenseRunawayEdgeMin fireSenseSCANFIVersion fireSenseYoungAgeCutoff fitConvergence fixedLogisticPars fuelClassPrep fuelLinearRange fuelLogToLinear getFirePoints_NFDB getFirePoints_NFDB_V2 getFirePolygons harmonizeBufferAndPoints harmonizeFireData harmonizeFireDataDeps hindcastObserved hindcastSimulated identifiedInIsolation ignitionFitAdditionalColNamesTxt ignitionFitFilenameFor ignitionFitFileTag ignitionFitLedgerFolder ignitionsTxt igOrEscNames isLinearFuelRange isYoungAge latestIgnitionFits latestNBACUrl latestSpreadFits lccFlammableShare linkSaturation logistic2p logistic3p logistic3pUpper logistic4p logistic5p logisticAll logisticParamNames logMinB makeELFs makeFireIDs makeFireSenseLCC makeFireSenseLCCDeps makeLandcoverDT makeLociList makeMutuallyExclusive makeTSD mergeELFs mergePreparedCovs multiplier nfdbPointUrl nonNFColNamesTxt omitNullArgs paramsSeparate plotBurnSummary plotCumulativeBurns plotELFs plotHindcastDistributions plotHindcastMap plotHindcastSizes plotHistoricFires plotSpreadFitResponse plotSpreadFitValidation polygonIDTxt predictIgnition prepare_FuelCovsCoarse prepare_FuelCovsCoarseByYear prepare_ignitionClimate prepare_LightningData prepareCovariatesOuter profileCoefficients putBackIntoRaster rasterFireBufferDT rasterFireSpreadPoints rbetaBetween readLightningData removeBufferedFiresOutsideRTM rescaleCovariates rescaleKnown2 rescaleVarsByMagnitude rescorePopulation runDEoptim runELFs scoreFireSizes simulateFireSizes sizeRuleLandCover spreadCovCentre spreadCovCols spreadDesignCols spreadFitAdditionalColNames spreadFitAdditionalColNamesTxt spreadFitCovCentreTxt spreadFitFilenameFor spreadFitFileTag spreadFitLedgerFolder spreadFitValidationData spreadFitWorkerMemoryGB spreadIndicatorCols spreadIndicatorRanges spreadInterceptTxt spreadProbCeiling spreadProbFloor spreadProbFromIntegerCovs spreadProbGates spreadProbGateTest spreadProbSummary stackAndExtract termsInDEoptim toX1000 treedWetlandAgbTxt treedWetlandTxt updateStackYearNames visualizeDE yearTxt youngAgeAtYear youngAgeExclusiveCols youngAgeTxt

Dependencies:abind amc askpass backports base64enc bitops boot callr checkmate class classInt cli climateData clusters codetools cowplot cpp11 crayon curl data.table DBI DEoptim digest dismo dplyr e1071 EnvStats farver fastDummies fasterize filelock fireregimetools Formula fpCompare fs gargle generics ggplot2 ggspatial glue googledrive gridExtra gtable hms httr httr2 igraph insight isoband jpeg jsonlite KernSmooth labeling LandR lattice lifecycle lme4 lobstr magrittr MASS Matrix mime minqa MuMIn nlme nloptr nortest openssl otel pak parallelly patchwork pemisc peutils pillar pkgconfig png prettyunits processx progress proxy ps purrr qs2 quickPlot R6 rappdirs raster rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen RcppParallel RCurl Rdpack reformulas reproducible Require RhpcBLASctl rlang rosm rstudioapi s2 S7 scales sf sp SpaDES.core SpaDES.tools stringfish stringi stringr sys terra tibble tidyr tidyselect tidyterra units utf8 uuid vctrs viridis viridisLite whisker withr wk

fireSense tutorial

Rendered fromfireSense-tutorial.Rmdusingknitr::rmarkdown

Last update: 2026-09-29
Started: 2020-04-03

fireSense LCC flammability analysis

Compare LCC and fire data | Plot

Rendered fromFiresense_LCC_flammability.Rmdusingknitr::rmarkdown

Last update: 2026-09-01
Started: 2020-11-24

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
'fireSenseUtils' package	fireSenseUtils-package fireSenseUtils
Objective function for 'fireSense_spreadFit' module	.objfunSpreadFit
Abbreviate species names for fuel classes	abbreviateSpNames
Automatic weight for the Anderson-Darling term	adWeightAuto
Convert list of annual 'SpatRaster' to 'data.table'	annualStackToDTx1000 annualStackToDTx1000.list annualStackToDTx1000.Raster annualStackToDTx1000.SpatRaster
Assert that rescaled spread covariates are usable	assertCovariateRange
Semi-automated selection of fuel classed based on GLMs	assessFuelClasses
The edge ring of each fire's buffer	addBufferEdge bufferEdge
Create buffers around polygons based on area target for buffer	bufferToArea bufferToArea.list bufferToArea.sf bufferToArea.SpatialPolygons
Create a variable sized buffer around a set of pixels belonging to the same fire ID	bufferToAreaRast
Modify 'cohortData' with burn column	buildCohortBurnHistory
Zero-out young non-forest pixels across LCC layers and add a 'youngAge' mask	calcNonForestYoungAge
Iteratively calculate 'youngAge' column in FS covariates	calcYoungAge
preparing covariates for fitting modules	castCohortData
Data checks and assertions for 'spreadFitRun'	.doDataChecks chk_duplicatedStartPixels
Choose an ELF's dominant and secondary fuel classes	chooseDomSecFuelClasses
Ensure fire points are located on flammable pixels inside a fire polygon Intended to be run using 'Map'	cleanUpSpreadFirePoints
Fixed ranges of the spread covariates	climateCovRanges
Converts stacks of climate rasters to data.table and optionally subsets to index	climateRasterToDataTable
Classify 'pixelGroups' by flammability	cohortsToFuelClasses
Merging and assignment of fuel classes	combine_fuel_classes
Add the size merges to the fire-count plan	combinePlans
Convert covariates to/from integers for smaller footprint; make 'data.frame'	covsX1000AndSetDF
The data year a year's vegetation comes from	dataYearElement dataYearFor
Default fire years for the fireSense modules	defaultFireYears
Default DEoptim population size for a fit	deoptimPopulationSize
Replace 'NA's in a 'data.table' with zeros	dtReplaceNAwith0
Count fires in each ELF	ELFfireCounts
Clip fire polygons to each ELF, once	ELFfireOverlay
Classify each ELF as zero, few or ok on its fire counts	ELFfitStatus
Measure flammable area in each ELF	ELFflammableArea
Text to print on ELFs	elfLabels
Name of a merged ELF	ELFmergedName
Decide which ELFs with too few fires to merge, and which not to fit	ELFmergePlan
Shared core borders between ELFs	ELFneighbours
Area, land cover and burn rate of each region	ELFregionStats
The ELF to run for an ELF id	ELFrunName
ELFs permanently left out of fireSense	ELFsArctic
ELFs that cannot be fitted	ELFsExcluded
Identify and rasterize Ecologically-based Low Fractal-dimensional objects within a study area	ELFsInStudyArea
Merge regions that are too small with a similar neighbour	ELFsizePlan
ELFs not fitted after merging	ELFsSkipped
Build a Canada-wide raster template for ELF construction	ELFtemplateRaster
Spread covariates that carry no information	emptySpreadCovariates
Fires that escaped	escapedFires
Pixels a fire must burn to count as escaped	escapeSizePixels
Count fires per ELF and merge ELFs with too few	fewFireELFs
Pixel IDs burned in each year	firePixelsByYear
Path to the shapefile in a fire-record archive	fireRecordShapefile
Get current state of FireSense Fit parameters as a map	fireSenseCloudParameters
Get current state of FireSense Fit parameters as a map	fireSenseCloudParametersMap
Create FireSense Input Covariates	fireSenseCovariatesCreate
Non-flammable land-cover codes for the FireSense land cover	fireSenseNonflammableLCC
Defaults shared by the fireSense modules and functions	fireSenseFlammabilityThreshold fireSenseForestedLCC fireSenseFuelClassCol fireSenseIgAggFactor fireSenseNonForestCanBeYoungAge fireSenseRunawayEdgeFrac fireSenseRunawayEdgeMin fireSenseSCANFIVersion fireSenseSharedDefaults fireSenseYoungAgeCutoff
Hard-coded name/text constants	escapesTxt fireSenseUtils-constants ignitionFitAdditionalColNamesTxt ignitionsTxt nonNFColNamesTxt polygonIDTxt spreadFitAdditionalColNamesTxt spreadFitCovCentreTxt spreadInterceptTxt treedWetlandAgbTxt treedWetlandTxt yearTxt youngAgeTxt
Diagnostics of a fitted spread model	coefIdentifiability combineSpreadProbSummaries fitConvergence fitDiagnostics identifiedInIsolation linkSaturation profileCoefficients scoreFireSizes simulateFireSizes spreadProbSummary
The Google Drive folder of the shared fit ledgers	fitLedgerFolders ignitionFitLedgerFolder spreadFitLedgerFolder
The logistic parameters fixed at 1, not fitted	fixedLogisticPars
Calculate proportional burn of landcover and tree species	fuelClassPrep
Range that puts linear fuel biomass on the scale the spread fit uses	fuelLinearRange
Fuel biomass from the log scale back to the linear scale	fuelLogToLinear
Get Fire 'SpatialPoints' from Canadian Fire Database	getFirePoints_NFDB
Get Fire 'SpatialPoints' from Canadian Fire Database	getFirePoints_NFDB_V2
Download and prepare fire data from National Fire Database	getFirePolygons
Cleaning up the polygon points	harmonizeBufferAndPoints
Harmonize fire data	harmonizeFireData
Functions whose code affects what 'harmonizeFireData()' returns	harmonizeFireDataDeps
Observed fire in an ELF core in one year	hindcastObserved
One simulated year in an ELF core	hindcastSimulated
The shared IgnitionFit ledger files	ignitionFitFilenameFor ignitionFitFileTag latestIgnitionFits
Construct standardized FireSense object names	igOrEscNames
Was this covariate rescaled as linear fuel biomass?	isLinearFuelRange
Is an age young?	isYoungAge
Discover the URL of the most recent NBAC shapefile archive	latestNBACUrl
Each land-cover class's share of an ELF's flammable pixels	lccFlammableShare
Multiple-parameter versions of logistic functions	logistic2p logistic3p logistic3pUpper logistic4p logistic5p logisticAll
Logistic parameter names	logisticParamNames
Log with a minimum	logMinB
Make Ecologically-based Low Fractal-Dimensional polygons	makeELFs plotELFs
Identify each year's individual fires and buffer them accordingly	makeFireIDs
Prepare NTEMS Land Cover Data for Fire Simulation Models	makeFireSenseLCC
Functions whose code affects what 'makeFireSenseLCC()' returns	makeFireSenseLCCDeps
Wrapper on 'glm' that creates separate GLMs for each item in fuel	makeGLM
Create 'landcoverDT' object to classify and track non-forest land cover classes	makeLandcoverDT
Convert a list of 'SpatialPointsDataFrame' object to a list of 'data.table' objects	makeLociList
guarantees mutually exclusive values in a data table	makeMutuallyExclusive
Put 'cohortData' back into a 'SpatRaster' with some extra details	makeRastersFromCD
Prepare a time since disturbance map from stand age and fire data	makeTSD
Merge ELF maps as planned	mergeELFs
Build ignition covariates table by stacking/extracting rasters and joining lightning	mergePreparedCovs
Buffer-size multiplier for fire footprints	multiplier
URL of the National Fire Database point archive	nfdbPointUrl
Names of the arguments that are 'NULL', to give to 'Cache(omitArgs =)'	omitNullArgs
Split the character vector of parameters into 'covPars' and 'logisticPars'	paramsSeparate
Plot burn summary	plotBurnSummary
Plot cumulative burn maps	plotCumulativeBurns
Simulated rep-years beside the observed year	plotHindcastDistributions
Burn-frequency map with the observed fires on top	plotHindcastMap
Fire-size distribution, simulated and observed	plotHindcastSizes
Plot historic ignitions, escapes, and area burned	plotHistoricFires
Predictions from ignition model	predictIgnition
Create and aggregate fuel covariate rasters to a coarse resolution	prepare_FuelCovsCoarse
Fuel covariate rasters at a coarse resolution, with 'youngAge' resolved for each fire year	prepare_FuelCovsCoarseByYear
Aggregate and cache ignition-related climate rasters	prepare_ignitionClimate
Prepare and cache lightning rasters from Google Drive sources	prepare_LightningData
Prepare and (optionally) cache scaled covariates for modeling	prepareCovariatesOuter
Rebuild land cover layers back into a SpatRastser	putBackIntoRaster
this is a wrapper to simplify caching of 'lapply' with 'bufferForFireRaster'. Years are iteratively processed by 'makeFireID'.	rasterFireBufferDT
Create a list of annual ignition points based on fire raster	rasterFireSpreadPoints
Generate random beta variates between 2 values and a mean	rbetaBetween
Read lightning data	readLightningData
Remove buffered fires in 'fireBufferedListDT' that are outside 'flammableRTM'	removeBufferedFiresOutsideRTM
Rescale/standardize covariates for modeling	rescaleCovariates
rescale function no.2	rescaleKnown2
Rescale a 'data.table' according to a named vector of rescalers	rescaleVarsByMagnitude
Re-score a population with replication, and pick the best members by their mean	bestByReplicatedMean rescorePopulation
Run 'DEoptim'	runDEoptim termsInDEoptim
Run the ELFs module and return the ELF names or maps	runELFs
Path to the land-cover map the size rule uses	sizeRuleLandCover
The centre of each covariate of a spread fit: its mean over the data the objective uses	spreadCovCentre
The columns of the spread model's design, in the order of its coefficients	spreadCovCols spreadDesignCols
Default values for various things	spreadFitAdditionalColNames
The shared SpreadFit ledger files	latestSpreadFits spreadFitFilenameFor spreadFitFileTag
Compare a spread fit with the data it was fitted to	plotSpreadFitResponse plotSpreadFitValidation spreadFitValidationData
Memory (GB) assumed per DEoptim worker before a fit has a memory record	spreadFitWorkerMemoryGB
Indicator covariates of the spread model	spreadIndicatorCols spreadIndicatorRanges
The spread-probability ceiling and floor	spreadProbBounds spreadProbCeiling spreadProbFloor
Convert covariates from their 'x1000' integer to usable by spread	spreadProbFromIntegerCovs
Would parameter sets pass the objective's spreadProb gates in its first block of years?	spreadProbGates
The objective's spread-probability gates, on one year's spreadProb	spreadProbGateTest
Prepare covariate table with ignition year, fuel class, climate value, and land cover	stackAndExtract
Convert numeric values to integers x 1000	toX1000
Update name of layers in a climate raster stack	updateStackYearNames
Make histograms of 'DEoptim' object 'pars'	visualizeDE
'youngAge' of pixels at one fire year	youngAgeAtYear
Columns 'youngAge' is mutually exclusive with	youngAgeExclusiveCols