Package: fireSenseUtils 0.0.5.9073

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]

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fireSenseUtils.pdf |fireSenseUtils.html✨
fireSenseUtils/json (API)
NEWS

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

Peer review:

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

On CRAN:

4.48 score 1 stars 2 scripts 53 exports 137 dependencies

Last updated 3 months agofrom:492560cf40 (on development). Checks:OK: 5 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 02 2024
R-4.5-winNOTEOct 02 2024
R-4.5-linuxNOTEOct 02 2024
R-4.4-winOKOct 02 2024
R-4.4-macOKOct 02 2024
R-4.3-winOKOct 02 2024
R-4.3-macOKOct 02 2024

Exports:.doDataChecks.objFunIgnition.objFunIgnitionPW.objfunSpreadFitannualStackToDTx1000bufferIgnitionPointsbufferToAreabufferToAreaRastburnClassGeneratorburnClassPredictburnClassSummaryburnProbFromClasscalcYoungAgecastCohortDatachk_duplicatedStartPixelscleanUpSpreadFirePointsclimateRasterToDataTablecohortsToFuelClassescompareMDCDEoptimIterativedtReplaceNAwith0extractSpecialgetFirePoints_NFDBgetFirePoints_NFDB_V2getFirePolygonsharmonizeBufferAndPointsharmonizeFireDatalogistic2plogistic3plogistic4plogistic5pmakeFireIDsmakeLandcoverDTmakeLociListmakeMutuallyExclusivemakeTSDmultiplierobjNlminboomplotBurnSummaryplotCumulativeBurnsplotHistoricFirespredictIgnitionpwrasterFireBufferDTrasterFireSpreadPointsrbetaBetweenremoveBufferedFiresOutsideRTMrescaleKnown2runDEoptimstackAndExtractupdateStackYearNamesvisualizeDE

Dependencies:abindamcaskpassbackportsbase64encBHbitopsbootbroomcarcarDatacheckmateclassclassIntclicolorspacecorrplotcowplotcpp11crayoncurldata.tableDBIDEoptimDerivdigestdismodoBydplyre1071EnvStatsfansifarverfastDummiesfasterizefilelockFormulafpComparefsgenericsggplot2ggpubrggrepelggsciggsignifggspatialgluegridExtragtablehmshttrinsightisobandjpegjsonliteKernSmoothkSampleslabelingLandRlatticelifecyclelme4lobstrmagrittrMASSMatrixMatrixModelsmclustmgcvmicrobenchmarkmimeminqamodelrMuMInmunsellnlmenloptrnnetnortestnumDerivopensslparallellypbkrtestpemiscpeutilspillarpkgconfigplyrpngpolynomprettyunitspROCprogressproxypurrrqsquantregquickPlotR6RApiSerializerasterRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelRCurlreproducibleRequireRhpcBLASctlrlangrosmrstatixs2scalessfspSpaDES.toolsSparseMstringfishstringistringrSuppDistssurvivalsysterratibbletidyrtidyselecttidyterraunitsutf8vctrsviridisviridisLitewithrwk

fireSense LCC flammability analysis

Ian Eddy, Eliot McIntire, Steve Cumming, Alex Chubaty

Rendered fromFiresense_LCC_flammability.Rmdusingknitr::rmarkdownon Oct 02 2024.

Last update: 2024-05-01
Started: 2020-11-24

fireSense tutorial

Jean Marchal, Eliot McIntire, Tati Micheletti, Alex Chubaty

Rendered fromfireSense-tutorial.Rmdusingknitr::rmarkdownon Oct 02 2024.

Last update: 2024-05-01
Started: 2020-04-03

Readme and manuals

Help Manual

Help pageTopics
'fireSenseUtils' packagefireSenseUtils-package fireSenseUtils
Objective function when no piecewise model is used.objFunIgnition
Function to pass to the optimizer - Piece-wise version.objFunIgnitionPW
Objective function for 'fireSense_spreadFit' module.objfunSpreadFit
Convert list of annual SpatRaster to 'data.table'annualStackToDTx1000 annualStackToDTx1000.list annualStackToDTx1000.Raster annualStackToDTx1000.SpatRaster
buffer ignition points to create non-ignitions for modelbufferIgnitionPoints
Create buffers around polygons based on area target for bufferbufferToArea bufferToArea.list bufferToArea.sf bufferToArea.SpatialPolygons
create a variable sized buffer around a set of pixels belonging to the same fire IDbufferToAreaRast
Modify cohortData with burn columnbuildCohortBurnHistory
Generate, Summarize, Predict Burn Classes from CovariatesburnClassGenerator burnClassPredict burnClassSummary burnProbFromClass
Iteratively calculate 'youngAge' column in FS covariatescalcYoungAge
preparing covariates for fitting modulescastCohortData
Data checks and assertions for 'spreadFitRun'.doDataChecks chk_duplicatedStartPixels
Ensure fire points are located on flammable pixels inside a fire polygon Intended to be run using 'Map'cleanUpSpreadFirePoints
Converts stacks of climate rasters to data.table and optionally subsets to indexclimateRasterToDataTable
Classify 'pixelGroups' by flammabilitycohortsToFuelClasses
Download and prepare fire data from National Fire DatabasecompareMDC
Replace 'NA's in a 'data.table' with zerosdtReplaceNAwith0
Extract the elements of the special terms, i.e. the variable and the knot valueextractSpecial
Get Fire 'SpatialPoints' from Canadian Fire DatabasegetFirePoints_NFDB
Get Fire 'SpatialPoints' from Canadian Fire DatabasegetFirePoints_NFDB_V2
Download and prepare fire data from National Fire DatabasegetFirePolygons
Cleaning up the polygon pointsharmonizeBufferAndPoints
Outer wrapper on spread fire polygon data munging that does several things: 1. ensure buffered fires are entirely in studyArea 2. ensure every fire has a corresponding ignition point, and vice versa 3. ensure these points are flammableharmonizeFireData
Four- and five-parameter logistic functionslogistic2p logistic3p logistic4p logistic5p
identify each year's individual fires and buffer them accordinglymakeFireIDs
Create landcoverDT object to classify and track non-forest lccmakeLandcoverDT
Convert a list of 'SpatialPointsDataFrame' object to a list of 'data.table' objectsmakeLociList
guarantees mutually exclusive values in a data tablemakeMutuallyExclusive
Put 'cohortData' back into a 'SpatRaster' with some extra detailsmakeRastersFromCD
preparing a time since disturbance map from stand age and fire datamakeTSD
multipliermultiplier
'objNlminb'objNlminb
Order of Magnitudeoom
Plot burn summaryplotBurnSummary
Plot cumulative burn mapsplotCumulativeBurns
Plot historic ignitions, escapes, and area burnedplotHistoricFires
Predictions from ignition modelpredictIgnition
Handling piecewise terms in a formulapw
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 rasterrasterFireSpreadPoints
Generate random beta variates between 2 values and a meanrbetaBetween
remove buffered fires in fireBufferedListDT that are outside RTMremoveBufferedFiresOutsideRTM
rescale function no.2rescaleKnown2
Wrapper around 'DEoptim' callDEoptimIterative runDEoptim
prepare covariate table with ignition year, fuel class, climate value, and land coverstackAndExtract
Update name of layers in a climate raster stackupdateStackYearNames
Make histograms of 'DEoptim' object 'pars'visualizeDE