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refactor: follow renamed fireSenseUtils constants (Txt suffix) #8

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refactor: follow renamed fireSenseUtils constants (Txt suffix) #8

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58 changes: 29 additions & 29 deletions fireSense_dataPrepFit.R
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Original file line number Diff line number Diff line change
Expand Up @@ -358,9 +358,9 @@ Init <- function(sim) {


FuelNames <- c(sim$sppEquiv$FuelClass, names(sim$nonForestedLCCGroups))
hasYoungAge <- youngAgeName %in% colnames(pars)
hasYoungAge <- youngAgeTxt %in% colnames(pars)
if (isTRUE(hasYoungAge))
FuelNames <- c(youngAgeName, FuelNames)
FuelNames <- c(youngAgeTxt, FuelNames)

ClimateNames <- setdiff(setdiff(colnames(pars), lpn[[whLogistic]]), FuelNames)

Expand Down Expand Up @@ -678,8 +678,8 @@ prepare_SpreadFit <- function(sim) {

indices <- Map(yrs = mod$allYears, function(yrs) {
dt <- rbindlist(sim$fireBufferedListDT[yrs], idcol = "fireYear")
yrsNum <- gsub(fireSenseUtils::yearChar, "", yrs) |> as.integer()
vegData[, year := gsub(fireSenseUtils::yearChar, "", year) |> as.integer()] # need for next inequality check
yrsNum <- gsub(fireSenseUtils::yearTxt, "", yrs) |> as.integer()
vegData[, year := gsub(fireSenseUtils::yearTxt, "", year) |> as.integer()] # need for next inequality check

dt2 <- dt[vegData[min(yrsNum) >= year & year < max(yrsNum)], on = c("pixelID")]
dt2[!is.na(buffer)]
Expand All @@ -696,7 +696,7 @@ prepare_SpreadFit <- function(sim) {
#because they can be burned or unburned, or in >1 fire years that are < 10 years apart
setnames(fireSenseVegData, "buffer", "burned")

nonVegColnames <- c("pixelID", "burned", "ids", grep(fireSenseUtils::yearChar, ignore.case = TRUE, colnames(fireSenseVegData), value = TRUE))
nonVegColnames <- c("pixelID", "burned", "ids", grep(fireSenseUtils::yearTxt, ignore.case = TRUE, colnames(fireSenseVegData), value = TRUE))
vegCols <- setdiff(names(fireSenseVegData),
nonVegColnames)
dropCols <- names(which(colSums(fireSenseVegData[, ..vegCols], na.rm = TRUE) == 0))
Expand All @@ -719,7 +719,7 @@ prepare_SpreadFit <- function(sim) {
}
}

RHS <- paste(paste0(sim$climateVariablesForFire$spread, collapse = " + "), youngAgeName,
RHS <- paste(paste0(sim$climateVariablesForFire$spread, collapse = " + "), youngAgeTxt,
paste0(vegCols, collapse = " + "), sep = " + ")

## this is a funny way to get years but avoids years with 0 fires
Expand All @@ -733,18 +733,18 @@ prepare_SpreadFit <- function(sim) {
spreadClimate <- sim$historicalClimateRasters[sim$climateVariablesForFire$spread]
#don't need climate data for years outside fire years
spreadClimate <- lapply(spreadClimate, FUN = function(x){
x <- terra::subset(x, subset = names(x) %in% paste0(fireSenseUtils::yearChar, P(sim)$fireYears))
x <- terra::subset(x, subset = names(x) %in% paste0(fireSenseUtils::yearTxt, P(sim)$fireYears))
})

climateDT <- climateRasterToDataTable(historicalClimateRasters = spreadClimate) |>
Cache(userTags = c("climateRasterToDataTable", names(spreadClimate)))

fbl <- rbindlist(sim$fireBufferedListDT, idcol = fireSenseUtils::yearChar)
rmCols <- setdiff(colnames(fbl), c("pixelID", fireSenseUtils::yearChar))
fbl <- rbindlist(sim$fireBufferedListDT, idcol = fireSenseUtils::yearTxt)
rmCols <- setdiff(colnames(fbl), c("pixelID", fireSenseUtils::yearTxt))
set(fbl, NULL, rmCols, NULL)
fbl <- climateDT[fbl, on = c(fireSenseUtils::yearChar, "pixelID"), nomatch = NULL]
fbl <- climateDT[fbl, on = c(fireSenseUtils::yearTxt, "pixelID"), nomatch = NULL]

fireSense_annualSpreadFitCovariates <- split(fbl, by = fireSenseUtils::yearChar, keep.by = FALSE)
fireSense_annualSpreadFitCovariates <- split(fbl, by = fireSenseUtils::yearTxt, keep.by = FALSE)

## prepare non-annual spread fit covariates by getting the youngAge
# have to remove years that have no fires and so no climate data needed
Expand All @@ -770,7 +770,7 @@ prepare_SpreadFit <- function(sim) {
annualCovariates <- Map(ac = annualCovariates, yrNum = names(annualCovariates),
function(ac,
yrNum) {
yrChar <- paste0(fireSenseUtils::yearChar, yrNum)
yrChar <- paste0(fireSenseUtils::yearTxt, yrNum)
lapply(ac, function(x) {
x[pixelID %in% sim$landcoverDTs[[yrChar]]$pixelID, ]
})
Expand All @@ -790,11 +790,11 @@ prepare_SpreadFit <- function(sim) {

if (!P(sim)$nonForestCanBeYoungAge) {
## TODO: test this inversion of makeMutuallyExclusive's regular use
args <- as.list(rep(youngAgeName, length = length(sim$nonForestedLCCGroups)))
args <- as.list(rep(youngAgeTxt, length = length(sim$nonForestedLCCGroups)))
names(args) <- names(sim$nonForestedLCCGroups)
} else {
## this is done later in spreadFit - but done here for accuracy of outputs
args <- list(names(sim$nonForestedLCCGroups)) |> setNames(youngAgeName)
args <- list(names(sim$nonForestedLCCGroups)) |> setNames(youngAgeTxt)
}

annualCovariates <- lapply(annualCovariates, makeMutuallyExclusive, mutuallyExclusiveCols = args)
Expand Down Expand Up @@ -858,7 +858,7 @@ prepare_SpreadFitFire_Raster <- function(sim) {
flammableRTM = sim$flammableRTM)

## TODO: this is temporary while we migrate out of spatial/raster constructs
## the fireSenseUtils::yearChar prefix is added by fireSenseUtils::makeLociList - discuss what to do
## the fireSenseUtils::yearTxt prefix is added by fireSenseUtils::makeLociList - discuss what to do
tempFun <- function(pts, year){
pts$YEAR <- year
return(pts)
Expand Down Expand Up @@ -1057,7 +1057,7 @@ prepare_IgnitionFit <- function(sim) {
## ignition won't have same years as spread so we do not use names of init objects
## The reason is some years may have ignitions but no fires, e.g. 2010 in RIA
years <- yearGroups(Par$dataYears, Par$fireYears, FALSE)
years <- Map(y = years, function(y) paste0(fireSenseUtils::yearChar, y))
years <- Map(y = years, function(y) paste0(fireSenseUtils::yearTxt, y))
mod$allYears <- years
allYearsVect <- unlist(mod$allYears)
#assume that if multiple climate variables are present, they are of equal length
Expand All @@ -1072,7 +1072,7 @@ prepare_IgnitionFit <- function(sim) {
"\ntruncating P(sim)$fireYears to: ",
paste0(min(yearsInClimateRast), ":", max(yearsInClimateRast)))
years <- Map(y = years, function(y) intersect(y, yearsInClimateRast))
P(sim)$fireYears <- intersect(as.numeric(gsub(fireSenseUtils::yearChar, "", yearsInClimateRast)),
P(sim)$fireYears <- intersect(as.numeric(gsub(fireSenseUtils::yearTxt, "", yearsInClimateRast)),
P(sim)$fireYears)
}

Expand Down Expand Up @@ -1103,7 +1103,7 @@ prepare_IgnitionFit <- function(sim) {
igCovariates <- names(sim$fireSense_ignitionCovariates)
igCovariates <- igCovariates[!igCovariates %in%
c(names(ignitionClimate),
fireSenseUtils::yearChar, "ignitions", "ignitionsNoGT1", "pixelID")]
fireSenseUtils::yearTxt, "ignitions", "ignitionsNoGT1", "pixelID")]
## this is safer for multiple climate variables
interactionsDF <- as.data.table(expand.grid(igCovariates, sim$climateVariablesForFire$ignition))
interactionsDF[, interaction := do.call(paste, c(.SD, sep = ":")), .SDcols = names(interactionsDF)]
Expand Down Expand Up @@ -1150,15 +1150,15 @@ prepare_EscapeFit <- function(sim) {
}
escapeCells <- cellFromXY(aggregatedRas, coords)
escapeDT <- as.data.table(escapes)
setnames(escapeDT, "YEAR", fireSenseUtils::yearChar)
setnames(escapeDT, "YEAR", fireSenseUtils::yearTxt)
escapeDT[, pixelID := escapeCells]
escapeDT <- escapeDT[, .(year, pixelID)]
escapeDT <- escapeDT[, .(escapes = .N), .(year, pixelID)]
escapeDT[, year := as.numeric(year)]
escapeDT <- escapeDT[sim$fireSense_ignitionCovariates, on = c("pixelID", fireSenseUtils::yearChar)]
escapeDT <- escapeDT[sim$fireSense_ignitionCovariates, on = c("pixelID", fireSenseUtils::yearTxt)]
escapeDT[is.na(escapes), escapes := 0]

escapeVars <- names(escapeDT)[!names(escapeDT) %in% c(fireSenseUtils::yearChar, "pixelID", "escapes",
escapeVars <- names(escapeDT)[!names(escapeDT) %in% c(fireSenseUtils::yearTxt, "pixelID", "escapes",
sim$climateVariablesForFire$ignition,
"ignitions", ranEffsLabel)]

Expand Down Expand Up @@ -1205,9 +1205,9 @@ plotAndMessage <- function(sim) {
}

rmMissingPixels <- function(fbldt, pixelIDsAllowed) {
fbldt <- rbindlist(fbldt, idcol = fireSenseUtils::yearChar)
fbldt <- rbindlist(fbldt, idcol = fireSenseUtils::yearTxt)
fbldt <- fbldt[pixelID %in% unique(pixelIDsAllowed)]
fireBufferedListDT <- split(fbldt, by = fireSenseUtils::yearChar, keep.by = FALSE)
fireBufferedListDT <- split(fbldt, by = fireSenseUtils::yearTxt, keep.by = FALSE)
}

runBorealDP_forCohortData <- function(sim) {
Expand Down Expand Up @@ -1362,7 +1362,7 @@ runBorealDP_forCohortData <- function(sim) {
doRstLCCs <- !suppliedElsewhere("rstLCCs", sim)
doStandAgeMaps <- !suppliedElsewhere("standAgeMaps", sim)

dyChars <- paste0(fireSenseUtils::yearChar, mod$dys)
dyChars <- paste0(fireSenseUtils::yearTxt, mod$dys)
outs <- Map(dyChar = dyChars, dy = mod$dys, function(dyChar, dy) {
if (doRstLCCs) {
#use a threshold to to assign non-flammable cover (e.g. if < 10% flammable cover)
Expand Down Expand Up @@ -1463,10 +1463,10 @@ runBorealDP_forCohortData <- function(sim) {
}

if (!suppliedElsewhere("firePolys", sim)) {
sim$firePolys <- allFirePolys[names(allFirePolys) %in% paste0(fireSenseUtils::yearChar, P(sim)$fireYears)]
sim$firePolys <- allFirePolys[names(allFirePolys) %in% paste0(fireSenseUtils::yearTxt, P(sim)$fireYears)]
if (sum(lengths(sim$firePolys)) == 0) {
stop("There are no fires in this study area during these years:\n",
paste(paste0(fireSenseUtils::yearChar, P(sim)$fireYears), collapse = ", "))
paste(paste0(fireSenseUtils::yearTxt, P(sim)$fireYears), collapse = ", "))
}
}

Expand Down Expand Up @@ -1556,14 +1556,14 @@ runBorealDP_forCohortData <- function(sim) {
}

if (!suppliedElsewhere("spreadFitAdditionalColNames")) {
sim$spreadFitAdditionalColNames <- fireSenseUtils::spreadFitAdditionalColNames
sim$spreadFitAdditionalColNames <- fireSenseUtils::spreadFitAdditionalColNamesTxt
}

return(invisible(sim))
}

youngAgeName <- fireSenseUtils::youngAgeName
ranEffsLabel <- fireSenseUtils::yearChar
youngAgeTxt <- fireSenseUtils::youngAgeTxt
ranEffsLabel <- fireSenseUtils::yearTxt
cohDat <- "cohortData"
pixGM <- "pixelGroupMap"
saMap <- "standAgeMap"
Expand Down
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