Package: fireSenseUtils 0.2.3

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.tar.gz
fireSenseUtils_0.2.3.zip(r-4.7)fireSenseUtils_0.2.3.zip(r-4.6)fireSenseUtils_0.2.3.zip(r-4.5)
fireSenseUtils_0.2.3.tgz(r-4.6-any)fireSenseUtils_0.2.3.tgz(r-4.5-any)
fireSenseUtils_0.2.3.tar.gz(r-4.7-any)fireSenseUtils_0.2.3.tar.gz(r-4.6-any)
fireSenseUtils_0.2.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
fireSenseUtils/json (API)
NEWS

# 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:

3.70 score 1 stars 3 scripts 92 exports 161 dependencies

Last updated from:1d843b8172 (on development). Checks:7 WARNING, 1 ERROR, 1 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	WARNING	456
source / vignettes	ERROR	404
linux-release-x86_64	WARNING	395
macos-release-arm64	WARNING	263
macos-oldrel-arm64	WARNING	186
windows-devel	WARNING	404
windows-release	WARNING	340
windows-oldrel	WARNING	360
wasm-release	OK	206

Exports:.doDataChecks .objFunIgnition .objFunIgnitionPW .objfunSpreadFit annualStackToDTx1000 assessFuelClasses bufferIgnitionPoints bufferToArea bufferToAreaRast burnClassGenerator burnClassPredict burnClassSummary burnProbFromClass calcNonForestYoungAge calcYoungAge castCohortData chk_duplicatedStartPixels cleanUpSpreadFirePoints climateRasterToDataTable cohortsToFuelClasses compareClimate compareMDC covsX1000AndSetDF DEoptimIterative dtReplaceNAwith0 ELFsInStudyArea ELFtemplateRaster escapesTxt extractSpecial fireSenseCloudParameters fireSenseCloudParametersMap fireSenseCovariatesCreate fuelClassPrep getFirePoints_NFDB getFirePoints_NFDB_V2 getFirePolygons harmonizeBufferAndPoints harmonizeFireData ignitionsTxt igOrEscNames latestNBACUrl logistic2p logistic3p logistic4p logistic5p logisticAll logisticParamNames logMinB makeELFs makeFireIDs makeFireSenseLCC makeLandcoverDT makeLociList makeMutuallyExclusive makeTSD mergePreparedCovs multiplier nonNFColNamesTxt objNlminb oom paramsSeparate plotBurnSummary plotCumulativeBurns plotELFs plotHistoricFires polygonIDTxt predictIgnition prepare_FuelCovsCoarse prepare_ignitionClimate prepare_LightningData prepareCovariatesOuter putBackIntoRaster pw rasterFireBufferDT rasterFireSpreadPoints rbetaBetween readLightningData removeBufferedFiresOutsideRTM rescaleCovariates rescaleKnown2 rescaleVarsByMagnitude runDEoptim runELFs spreadFitAdditionalColNamesTxt spreadProbFromIntegerCovs stackAndExtract termsInDEoptim toX1000 updateStackYearNames visualizeDE yearTxt youngAgeTxt

Dependencies:abind amc askpass backports base64enc bitops boot broom callr car carData checkmate class classInt cli clusters codetools colorspace corrplot cowplot cpp11 crayon curl data.table DBI DEoptim Deriv digest dismo doBy dplyr e1071 EnvStats farver fastDummies fasterize filelock forecast Formula fpCompare fracdiff fs gargle generics ggplot2 ggpubr ggrepel ggsci ggsignif ggspatial glue googledrive gridExtra gtable hms httr httr2 igraph insight isoband jpeg jsonlite KernSmooth kSamples labeling LandR lattice lifecycle lme4 lmtest lobstr magick magrittr MASS Matrix MatrixModels mclust mgcv microbenchmark mime minqa modelr MuMIn nlme nloptr nnet nortest numDeriv openssl pak parallelly patchwork pbkrtest pemisc peutils pillar pkgconfig png polynom prettyunits pROC processx progress proxy ps purrr qs2 quantreg quickPlot R6 rappdirs raster rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen RcppParallel RCurl Rdpack reformulas reproducible Require RhpcBLASctl rlang rosm rprojroot rstatix rstudioapi s2 S7 scales sf sp SpaDES.core SpaDES.project SpaDES.tools SparseM stringfish stringi stringr SuppDists survival sys terra tibble tidyr tidyselect tidyterra timeDate units urca utf8 uuid vctrs viridis viridisLite whisker withr wk zoo

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Development and contributors

Readme and manuals

Help Manual

Help page	Topics
'fireSenseUtils' package	fireSenseUtils-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
Abbreviate species names for fuel classes	abbreviateSpNames
Convert list of annual 'SpatRaster' to 'data.table'	annualStackToDTx1000 annualStackToDTx1000.list annualStackToDTx1000.Raster annualStackToDTx1000.SpatRaster
Semi-automated selection of fuel classed based on GLMs	assessFuelClasses
Buffer ignition points to create non-ignitions for model	bufferIgnitionPoints
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
Generate, Summarize, Predict Burn Classes from Covariates	burnClassGenerator burnClassPredict burnClassSummary burnProbFromClass
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
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 index	climateRasterToDataTable
Classify 'pixelGroups' by flammability	cohortsToFuelClasses
Merging and assignment of fuel classes	combine_fuel_classes
Plot the historical and projected climate values for flammable land surface	compareClimate
Plot the historical and projected MDC for a flammable land surface	compareMDC
Convert covariates to/from integers for smaller footprint; make 'data.frame'	covsX1000AndSetDF
Replace 'NA's in a 'data.table' with zeros	dtReplaceNAwith0
Identify and rasterize Ecologically-based Low Fractal-dimensional objects within a study area	ELFsInStudyArea
Build a Canada-wide raster template for ELF construction	ELFtemplateRaster
Extract the elements of the special terms, i.e. the variable and the knot value	extractSpecial
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
Hard-coded name/text constants	escapesTxt fireSenseUtils-constants ignitionsTxt nonNFColNamesTxt polygonIDTxt spreadFitAdditionalColNamesTxt yearTxt youngAgeTxt
Calculate proportional burn of landcover and tree species	fuelClassPrep
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
Construct standardized FireSense object names	igOrEscNames
Discover the URL of the most recent NBAC shapefile archive	latestNBACUrl
Multiple-parameter versions of logistic functions	logistic2p logistic3p 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
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
Build ignition covariates table by stacking/extracting rasters and joining lightning	mergePreparedCovs
Buffer-size multiplier for fire footprints	multiplier
'objNlminb'	objNlminb
Order of Magnitude	oom
Split the character vector of parameters into 'covPars' and 'logisticPars'	paramsSeparate
Plot burn summary	plotBurnSummary
Plot cumulative burn maps	plotCumulativeBurns
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
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
Handling piecewise terms in a formula	pw
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
Run 'DEoptim'	DEoptimIterative runDEoptim termsInDEoptim
Run ELFs modules and optionally update googledrive png	runELFs
Convert covariates from their 'x1000' integer to usable by spread	spreadProbFromIntegerCovs
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