Package: fireSenseUtils 0.0.5.9084

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]

# 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:

4.51 score 1 stars 2 scripts 56 exports 145 dependencies

Last updated 2 days agofrom:29c10c9c3b (on development). Checks:1 OK, 7 WARNING. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Jan 31 2025
R-4.5-win	WARNING	Jan 31 2025
R-4.5-mac	WARNING	Jan 31 2025
R-4.5-linux	WARNING	Jan 31 2025
R-4.4-win	WARNING	Jan 31 2025
R-4.4-mac	WARNING	Jan 31 2025
R-4.3-win	WARNING	Jan 31 2025
R-4.3-mac	WARNING	Jan 31 2025

Exports:.doDataChecks .objFunIgnition .objFunIgnitionPW .objfunSpreadFit annualStackToDTx1000 assessFuelClasses bufferIgnitionPoints bufferToArea bufferToAreaRast burnClassGenerator burnClassPredict burnClassSummary burnProbFromClass calcYoungAge castCohortData chk_duplicatedStartPixels cleanUpSpreadFirePoints climateRasterToDataTable cohortsToFuelClasses compareMDC DEoptimIterative dtReplaceNAwith0 extractSpecial fuelClassPrep getFirePoints_NFDB getFirePoints_NFDB_V2 getFirePolygons harmonizeBufferAndPoints harmonizeFireData logistic2p logistic3p logistic4p logistic5p makeFireIDs makeLandcoverDT makeLociList makeMutuallyExclusive makeTSD multiplier objNlminb oom plotBurnSummary plotCumulativeBurns plotHistoricFires predictIgnition pw rasterFireBufferDT rasterFireSpreadPoints rbetaBetween removeBufferedFiresOutsideRTM rescaleKnown2 runDEoptim stackAndExtract termsInDEoptim updateStackYearNames visualizeDE

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

fireSense LCC flammability analysis

Ian Eddy, Eliot McIntire, Steve Cumming, Alex Chubaty

Rendered fromFiresense_LCC_flammability.Rmdusingknitr::rmarkdownon Jan 31 2025.

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

fireSense tutorial

Jean Marchal, Eliot McIntire, Tati Micheletti, Alex Chubaty

Rendered fromfireSense-tutorial.Rmdusingknitr::rmarkdownon Jan 31 2025.

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

Citation

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
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
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
Download and prepare fire data from National Fire Database	compareMDC
Replace 'NA's in a 'data.table' with zeros	dtReplaceNAwith0
Extract the elements of the special terms, i.e. the variable and the knot value	extractSpecial
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
Four- and five-parameter logistic functions	logistic2p logistic3p logistic4p logistic5p
identify each year's individual fires and buffer them accordingly	makeFireIDs
wrapper on GLM that creates separate GLMs for each item in fuel	makeGLM
Create landcoverDT object to classify and track non-forest lcc	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
preparing a time since disturbance map from stand age and fire data	makeTSD
multiplier	multiplier
'objNlminb'	objNlminb
Order of Magnitude	oom
Plot burn summary	plotBurnSummary
Plot cumulative burn maps	plotCumulativeBurns
Plot historic ignitions, escapes, and area burned	plotHistoricFires
Predictions from ignition model	predictIgnition
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
remove buffered fires in fireBufferedListDT that are outside RTM	removeBufferedFiresOutsideRTM
rescale function no.2	rescaleKnown2
Wrapper around 'DEoptim' call	DEoptimIterative runDEoptim termsInDEoptim
prepare covariate table with ignition year, fuel class, climate value, and land cover	stackAndExtract
Update name of layers in a climate raster stack	updateStackYearNames
Make histograms of 'DEoptim' object 'pars'	visualizeDE