R/bioclims_SpatRaster.r
In adamlilith/fasterRaster: Faster Raster and Spatial Vector Processing Using 'GRASS GIS'
Defines functions
.calcQuarterSR
#' @aliases bioclims
#' @rdname bioclims
#' @exportMethod bioclims
methods::setMethod(
f = "bioclims",
signature = c(ppt = "SpatRaster"),
function(
ppt,
tmin,
tmax,
tmean = NULL,
bios = NULL,
sample = TRUE,
quarter = 3,
pptDelta = 1,
verbose = TRUE
) {
# BIOCLIM numbers
classicBios <- 1L:19L
extendedBios <- 41L:60L
allBios <- c(classicBios, extendedBios)
meanTempBios <- c(1, 4, 8:11, 18:19, 41:46, 53:54, 57:60) # BIOCLIMs that require mean temp
quarterTempBios <- c(10, 11, 18, 19, 41:46, 53:54) # BIOCLIMs that require quarter temperatures
quarterPrecipBios <- c(8, 9, 16, 17, 16:19, 45:48, 55:56)
wettestQuarterBios <- c(8, 16, 46, 48, 55)
driestQuarterBios <- c(9, 17, 45, 47, 56)
warmestQuarterBios <- c(10, 18, 42, 44, 53)
coldestQuarterBios <- c(11, 19, 41, 43, 54)
if (is.null(bios)) {
bios <- classicBios
} else if (any(bios == "*")) {
bios <- allBios
} else if (any(bios == "+")) {
bios <- bios[bios != "+"]
bios <- c(bios, extendedBios)
}
bios <- unique(bios)
bios <- sort(bios)
bios <- as.integer(bios)
if (quarter <= 1) stop("Argument `quarter` must be > 1.")
nLayers <- terra::nlyr(ppt)
if (any(omnibus::notIn(bios, allBios))) stop("Argument `bios` has at least one invalid value. Valid values include:\n ", paste(allBios, collapse = " "))
if (nLayers != terra::nlyr(tmin) | nLayers != terra::nlyr(tmax)) stop("The input rasters must have the same number of layers.")
if (quarter > nLayers) stop("Argument `quarter` cannot be more than the number of raster layers in any input data.")
### number of tasks (used for progress bar
nTasks <- length(bios) +
(any(meanTempBios %in% bios) & !is.null(tmean)) +
any(bios %in% quarterTempBios) +
any(bios %in% quarterPrecipBios) +
(any(bios %in% warmestQuarterBios) & !(53 %in% warmestQuarterBios)) +
(any(bios %in% coldestQuarterBios) & !(54 %in% coldestQuarterBios)) +
(any(bios %in% wettestQuarterBios) & !(55 %in% wettestQuarterBios)) +
(any(bios %in% driestQuarterBios) & !(55 %in% driestQuarterBios))
if (verbose | faster("verbose")) {
pb <- utils::txtProgressBar(min = 0, max = nTasks, initial = 0, style = 3, width = 30)
}
tasks <- 0
### calculate tmean if needed
if (is.null(tmean) & any(bios %in% meanTempBios)) {
tmean <- (tmin + tmax) / 2
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
### quarter temperature rasters
if (any(bios %in% quarterTempBios)) {
tmeanByQuarter <- .calcQuarterSR(tmean, fun = "mean", quarter = quarter)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
### quarter precipitation rasters
if (any(bios %in% quarterPrecipBios)) {
pptByQuarter <- .calcQuarterSR(ppt, fun = "sum", quarter = quarter)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
### MAIN
########
out <- NULL
### BIO53 (warmest quarter)
if (any(bios %in% warmestQuarterBios)) {
bio53 <- app(tmeanByQuarter, which.max)
warmestQuarters <- terra::freq(bio53)$value
names(bio53) <- "bio53"
if (53 %in% bios) out <- c(out, bio53)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
### BIOCLIM 54 (coldest quarter)
if (any(bios %in% coldestQuarterBios)) {
bio54 <- app(tmeanByQuarter, which.min)
coldestQuarters <- terra::freq(bio54)$value
names(bio54) <- "bio54"
if (54 %in% bios) out <- c(out, bio54)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
### BIOCLIM 55 (wettest quarter)
if (any(bios %in% wettestQuarterBios)) {
bio55 <- app(pptByQuarter, which.max)
wettestQuarters <- terra::freq(bio55)$value
names(bio55) <- "bio55"
if (55 %in% bios) out <- c(out, bio55)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
### BIOCLIM 56 (driest quarter)
if (any(bios %in% driestQuarterBios)) {
bio56 <- app(pptByQuarter, which.min)
driestQuarters <- terra::freq(bio56)$value
names(bio56) <- "bio56"
if (56 %in% bios) out <- c(out, bio56)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
### BIOCLIM 1
if (any(1 %in% bios)) {
bio1 <- mean(tmean)
names(bio1) <- "bio1"
out <- c(out, bio1)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
### BIOCLIM 2
if (any(c(2, 3) %in% bios)) {
delta <- tmax - tmin
bio2 <- mean(delta)
names(bio2) <- "bio2"
if (2 %in% bios) out <- c(out, bio2)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
### BIOCLIM 5
if (any(c(3, 5, 7) %in% bios)) {
bio5 <- max(tmax)
names(bio5) <- "bio5"
if (5 %in% bios) out <- c(out, bio5)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
### BIOCLIM 6
if (any(c(3, 6, 7) %in% bios)) {
bio6 <- min(tmin)
names(bio6) <- "bio6"
if (6 %in% bios) out <- c(out, bio6)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
### BIOCLIM 7 (annual temp range)
if (any(c(3, 7) %in% bios)) {
bio7 <- bio5 - bio6
names(bio7) <- "bio7"
if (7 %in% bios) out <- c(out, bio7)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
### BIOCLIM 3 (100 * bio2 / bio7)
if (3 %in% bios) {
bio3 <- 100 * bio2 / bio7
names(bio3) <- "bio3"
out <- c(out, bio3)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
### BIOCLIM 4 (100 * sd of temp)
if (4 %in% bios) {
bio4 <- 100 * terra::stdev(tmean, pop = !sample)
names(bio4) <- "bio4"
out <- c(out, bio4)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIOCLIM 8 (mean temp of wettest quarter)
if (8 %in% bios) {
mm <- terra::minmax(tmeanByQuarter)
minVal <- -10 * abs(min(mm[1L, , drop = TRUE]))
bio8 <- tmean[[1L]] * 0 + minVal
for (i in wettestQuarters) {
bio8 <- max(bio8, (bio55 == i) * tmeanByQuarter[[i]])
}
names(bio8) <- "bio8"
out <- c(out, bio8)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIOCLIM 9 (mean temp of driest quarter)
if (9 %in% bios) {
mm <- terra::minmax(tmeanByQuarter)
minVal <- -10 * abs(min(mm[1L, , drop = TRUE]))
bio9 <- tmean[[1L]] * 0 + minVal
for (i in driestQuarters) {
bio9 <- max(bio9, (bio56 == i) * tmeanByQuarter[[i]])
}
names(bio9) <- "bio9"
out <- c(out, bio9)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIOCLIM 10 (mean temp of warmest quarter)
if (10 %in% bios) {
mm <- terra::minmax(tmeanByQuarter)
minVal <- -10 * abs(min(mm[1L, , drop = TRUE]))
bio10 <- tmean[[1L]] * 0 + minVal
for (i in warmestQuarters) {
bio10 <- max(bio10, (bio53 == i) * tmeanByQuarter[[i]])
}
names(bio10) <- "bio10"
out <- c(out, bio10)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIOCLIM 11 (mean temp of coldest quarter)
if (11 %in% bios) {
mm <- terra::minmax(tmeanByQuarter)
minVal <- -10 * abs(min(mm[1L, , drop = TRUE]))
bio11 <- tmean[[1L]] * 0 + minVal
for (i in coldestQuarters) {
bio11 <- max(bio11, (bio54 == i) * tmeanByQuarter[[i]])
}
bio11 <- max(bio11)
names(bio11) <- "bio11"
out <- c(out, bio11)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIOCLIM 12 (total precipitation)
if (12 %in% bios) {
bio12 <- sum(ppt)
names(bio12) <- "bio12"
if (12 %in% bios) out <- c(out, bio12)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIOCLIM 13 (wettest month precipitation)
if (13 %in% bios) {
bio13 <- max(ppt)
names(bio13) <- "bio13"
out <- c(out, bio13)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIOCLIM 14 (driest month precipitation)
if (14 %in% bios) {
bio14 <- min(ppt)
names(bio14) <- "bio14"
out <- c(out, bio14)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
### BIOCLIM 15 (CV of precipitation)
if (15 %in% bios) {
sd <- terra::stdev(ppt + pptDelta, pop = !sample)
bio15 <- 100 * sd / mean(ppt + pptDelta)
names(bio15) <- "bio15"
out <- c(out, bio15)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIOCLIM 16 (precipitation of the wettest quarter)
if (16 %in% bios) {
bio16 <- ppt[[1L]] * 0
for (i in wettestQuarters) {
bio16 <- c(bio16, (bio55 == i) * pptByQuarter[[i]])
}
bio16 <- sum(bio16)
names(bio16) <- "bio16"
out <- c(out, bio16)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIO17: Precipitation of the driest quarter
if (17 %in% bios) {
bio17 <- ppt[[1L]] * 0
for (i in driestQuarters) {
bio17 <- c(bio17, (bio56 == i) * pptByQuarter[[i]])
}
bio17 <- sum(bio17)
names(bio17) <- "bio17"
out <- c(out, bio17)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIO18: Precipitation of the warmest quarter (based on mean temperature)
if (18 %in% bios) {
bio18 <- ppt[[1L]] * 0
for (i in warmestQuarters) {
bio18 <- c(bio18, (bio53 == i) * pptByQuarter[[i]])
}
bio18 <- sum(bio18)
names(bio18) <- "bio18"
out <- c(out, bio18)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIO19: Precipitation of the coldest quarter (based on mean temperature)
if (19 %in% bios) {
bio19 <- ppt[[1L]] * 0
for (i in coldestQuarters) {
bio19 <- c(bio19, (bio54 == i) * pptByQuarter[[i]])
}
bio19 <- sum(bio19)
names(bio19) <- "bio19"
out <- c(out, bio19)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIO41: Temperature of the quarter following the coldest quarter (based on mean temperature)
if (41 %in% bios) {
mm <- terra::minmax(tmeanByQuarter)
minVal <- -10 * abs(min(mm[1L, , drop = TRUE]))
bio41 <- tmean[[1L]] * 0 + minVal
for (i in coldestQuarters) {
if (i + quarter <= nLayers) {
j <- i + quarter
} else {
j <- i + quarter - nLayers
}
bio41 <- max(bio41, (bio54 == i) * tmeanByQuarter[[j]])
}
names(bio41) <- "bio41"
out <- c(out, bio41)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIO42: Temperature of the quarter following the warmest quarter (based on mean temperature)
if (42 %in% bios) {
mm <- terra::minmax(tmeanByQuarter)
minVal <- -10 * abs(min(mm[1L, , drop = TRUE]))
bio42 <- tmean[[1L]] * 0 + minVal
for (i in warmestQuarters) {
if (i + quarter <= nLayers) {
j <- i + quarter
} else {
j <- i + quarter - nLayers
}
bio42 <- max(bio42, (bio53 == i) * tmeanByQuarter[[j]])
}
names(bio42) <- "bio42"
out <- c(out, bio42)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIO43: Precipitation of the quarter following the coldest quarter (based on mean temperature; mm)
if (43 %in% bios) {
bio43 <- ppt[[1L]] * 0
for (i in coldestQuarters) {
if (i + quarter <= nLayers) {
j <- i + quarter
} else {
j <- i + quarter - nLayers
}
bio43 <- max(bio43, (bio54 == i) * pptByQuarter[[j]])
}
names(bio43) <- "bio43"
out <- c(out, bio43)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIO44: Precipitation of the quarter following the warmest quarter (based on mean temperature; mm)
if (44 %in% bios) {
bio44 <- ppt[[1L]] * 0
for (i in warmestQuarters) {
if (i + quarter <= nLayers) {
j <- i + quarter
} else {
j <- i + quarter - nLayers
}
bio44 <- max(bio44, (bio53 == i) * pptByQuarter[[j]])
}
names(bio44) <- "bio44"
out <- c(out, bio44)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIO45: Temperature of the quarter following the driest quarter (based on mean temperature; deg C)
if (45 %in% bios) {
mm <- terra::minmax(tmeanByQuarter)
minVal <- -10 * abs(min(mm[2L, , drop = TRUE]))
bio45 <- tmean[[1L]] * 0 + minVal
for (i in driestQuarters) {
if (i + quarter <= nLayers) {
j <- i + quarter
} else {
j <- i + quarter - nLayers
}
bio45 <- max(bio45, (bio56 == i) * tmeanByQuarter[[j]])
}
names(bio45) <- "bio45"
out <- c(out, bio45)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIO46: Temperature of the quarter following the wettest quarter (based on mean temperature; deg C)
if (46 %in% bios) {
mm <- terra::minmax(tmeanByQuarter)
minVal <- -10 * abs(min(mm[2L, , drop = TRUE]))
bio46 <- tmean[[1L]] * 0 + minVal
for (i in wettestQuarters) {
if (i + quarter <= nLayers) {
j <- i + quarter
} else {
j <- i + quarter - nLayers
}
bio46 <- max(bio46, (bio55 == i) * tmeanByQuarter[[j]])
}
names(bio46) <- "bio46"
out <- c(out, bio46)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIO47: Precipitation of the quarter following the driest quarter (based on mean temperature; mm)
if (47 %in% bios) {
bio47 <- ppt[[1L]] * 0
for (i in driestQuarters) {
if (i + quarter <= nLayers) {
j <- i + quarter
} else {
j <- i + quarter - nLayers
}
bio47 <- max(bio47, (bio56 == i) * pptByQuarter[[j]])
}
names(bio47) <- "bio47"
out <- c(out, bio47)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIO48: Precipitation of the quarter following the wettest quarter (based on mean temperature; mm)
if (48 %in% bios) {
bio48 <- ppt[[1L]] * 0
for (i in wettestQuarters) {
if (i + quarter <= nLayers) {
j <- i + quarter
} else {
j <- i + quarter - nLayers
}
bio48 <- max(bio48, (bio55 == i) * pptByQuarter[[j]])
}
names(bio48) <- "bio48"
out <- c(out, bio48)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIO49: Hottest month
if (49 %in% bios) {
bio49 <- terra::app(tmax, which.max)
names(bio49) <- "bio49"
out <- c(out, bio49)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIO50: Coldest month
if (50 %in% bios) {
bio50 <- terra::app(tmin, which.min)
names(bio50) <- "bio50"
out <- c(out, bio50)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIO51: Wettest month
if (51 %in% bios) {
bio51 <- terra::app(ppt, which.max)
names(bio51) <- "bio51"
out <- c(out, bio51)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIO52: Driest month
if (52 %in% bios) {
bio52 <- terra::app(ppt, which.min)
names(bio52) <- "bio52"
out <- c(out, bio52)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIO57: The largest decrease in temperature from one month to the next (deg C).
# BIO58: The largest increase in temperature from one month to the next (deg C).
if (any(c(57, 58) %in% bios)) {
deltas <- tmean
for (i in 1:nLayers) {
if (i + quarter <= nLayers) {
target <- i + 1
} else {
target <- 1
}
deltas[[i]] <- tmean[[i]] - tmean[[target]]
}
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
if (57 %in% bios) {
bio57 <- max(deltas)
names(bio57) <- "bio57"
out <- c(out, bio57)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
if (58 %in% bios) {
bio58 <- abs(min(deltas))
names(bio58) <- "bio58"
out <- c(out, bio58)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
}
# BIO59: The largest decrease in precipitation from one month to the next.
# BIO60: The largest increase in precipitation from one month to the next.
if (any(c(59, 60) %in% bios)) {
deltas <- ppt
for (i in 1:nLayers) {
if (i + quarter <= nLayers) {
target <- i + 1
} else {
target <- 1
}
deltas[[i]] <- ppt[[i]] - ppt[[target]]
}
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
if (59 %in% bios) {
bio59 <- max(deltas)
names(bio59) <- "bio59"
out <- c(out, bio59)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
if (60 %in% bios) {
bio60 <- abs(min(deltas))
names(bio60) <- "bio60"
out <- c(out, bio60)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
}
out <- do.call(c, out)
outNames <- names(out)
nc <- nchar(outNames)
if (any(nc == 4L)) {
shorts <- out[[nc == 4L]]
shorts <- shorts[[order(names(shorts))]]
} else { shorts <- NULL }
if (any(nc == 5L)) {
longs <- out[[nc == 5L]]
longs <- longs[[order(names(longs))]]
} else { longs <- NULL }
if (is.null(shorts)) {
out <- longs
} else if (is.null(longs)) {
out <- shorts
} else {
out <- c(shorts, longs)
}
if (verbose | faster("verbose")) close(pb)
out
} # EOF
)
#' Calculate a series of "quarter" rasters and return their [sources()] names. A quarter can be summarized using
#'
#' x A "stack" of `SpatRaster`s
#' fun Character: Name of function to summarize across a quarter ("sum", "min", "max", or "mean").
#' quarter Numeric: Length of a quarter
#'
#' @noRd
.calcQuarterSR <- function(x, fun, quarter) {
out <- x
qs <- c(x, x[[1L:(quarter - 1L)]])
n <- nlyr(x)
for (i in seq_len(n)) {
select <- i:(i + quarter - 1L)
quart <- qs[[select]]
args <- list(x = quart)
out[[i]] <- do.call(fun, args)
} # next quarter
names(out) <- paste0("q", 1L:n)
out
}
adamlilith/fasterRaster documentation built on Sept. 23, 2024, 1:28 a.m.
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Defines functions .calcQuarterSR
#' @aliases bioclims
#' @rdname bioclims
#' @exportMethod bioclims
methods::setMethod(
f = "bioclims",
signature = c(ppt = "SpatRaster"),
function(
ppt,
tmin,
tmax,
tmean = NULL,
bios = NULL,
sample = TRUE,
quarter = 3,
pptDelta = 1,
verbose = TRUE
) {
# BIOCLIM numbers
classicBios <- 1L:19L
extendedBios <- 41L:60L
allBios <- c(classicBios, extendedBios)
meanTempBios <- c(1, 4, 8:11, 18:19, 41:46, 53:54, 57:60) # BIOCLIMs that require mean temp
quarterTempBios <- c(10, 11, 18, 19, 41:46, 53:54) # BIOCLIMs that require quarter temperatures
quarterPrecipBios <- c(8, 9, 16, 17, 16:19, 45:48, 55:56)
wettestQuarterBios <- c(8, 16, 46, 48, 55)
driestQuarterBios <- c(9, 17, 45, 47, 56)
warmestQuarterBios <- c(10, 18, 42, 44, 53)
coldestQuarterBios <- c(11, 19, 41, 43, 54)
if (is.null(bios)) {
bios <- classicBios
} else if (any(bios == "*")) {
bios <- allBios
} else if (any(bios == "+")) {
bios <- bios[bios != "+"]
bios <- c(bios, extendedBios)
}
bios <- unique(bios)
bios <- sort(bios)
bios <- as.integer(bios)
if (quarter <= 1) stop("Argument `quarter` must be > 1.")
nLayers <- terra::nlyr(ppt)
if (any(omnibus::notIn(bios, allBios))) stop("Argument `bios` has at least one invalid value. Valid values include:\n ", paste(allBios, collapse = " "))
if (nLayers != terra::nlyr(tmin) | nLayers != terra::nlyr(tmax)) stop("The input rasters must have the same number of layers.")
if (quarter > nLayers) stop("Argument `quarter` cannot be more than the number of raster layers in any input data.")
### number of tasks (used for progress bar
nTasks <- length(bios) +
(any(meanTempBios %in% bios) & !is.null(tmean)) +
any(bios %in% quarterTempBios) +
any(bios %in% quarterPrecipBios) +
(any(bios %in% warmestQuarterBios) & !(53 %in% warmestQuarterBios)) +
(any(bios %in% coldestQuarterBios) & !(54 %in% coldestQuarterBios)) +
(any(bios %in% wettestQuarterBios) & !(55 %in% wettestQuarterBios)) +
(any(bios %in% driestQuarterBios) & !(55 %in% driestQuarterBios))
if (verbose | faster("verbose")) {
pb <- utils::txtProgressBar(min = 0, max = nTasks, initial = 0, style = 3, width = 30)
}
tasks <- 0
### calculate tmean if needed
if (is.null(tmean) & any(bios %in% meanTempBios)) {
tmean <- (tmin + tmax) / 2
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
### quarter temperature rasters
if (any(bios %in% quarterTempBios)) {
tmeanByQuarter <- .calcQuarterSR(tmean, fun = "mean", quarter = quarter)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
### quarter precipitation rasters
if (any(bios %in% quarterPrecipBios)) {
pptByQuarter <- .calcQuarterSR(ppt, fun = "sum", quarter = quarter)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
### MAIN
########
out <- NULL
### BIO53 (warmest quarter)
if (any(bios %in% warmestQuarterBios)) {
bio53 <- app(tmeanByQuarter, which.max)
warmestQuarters <- terra::freq(bio53)$value
names(bio53) <- "bio53"
if (53 %in% bios) out <- c(out, bio53)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
### BIOCLIM 54 (coldest quarter)
if (any(bios %in% coldestQuarterBios)) {
bio54 <- app(tmeanByQuarter, which.min)
coldestQuarters <- terra::freq(bio54)$value
names(bio54) <- "bio54"
if (54 %in% bios) out <- c(out, bio54)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
### BIOCLIM 55 (wettest quarter)
if (any(bios %in% wettestQuarterBios)) {
bio55 <- app(pptByQuarter, which.max)
wettestQuarters <- terra::freq(bio55)$value
names(bio55) <- "bio55"
if (55 %in% bios) out <- c(out, bio55)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
### BIOCLIM 56 (driest quarter)
if (any(bios %in% driestQuarterBios)) {
bio56 <- app(pptByQuarter, which.min)
driestQuarters <- terra::freq(bio56)$value
names(bio56) <- "bio56"
if (56 %in% bios) out <- c(out, bio56)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
### BIOCLIM 1
if (any(1 %in% bios)) {
bio1 <- mean(tmean)
names(bio1) <- "bio1"
out <- c(out, bio1)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
### BIOCLIM 2
if (any(c(2, 3) %in% bios)) {
delta <- tmax - tmin
bio2 <- mean(delta)
names(bio2) <- "bio2"
if (2 %in% bios) out <- c(out, bio2)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
### BIOCLIM 5
if (any(c(3, 5, 7) %in% bios)) {
bio5 <- max(tmax)
names(bio5) <- "bio5"
if (5 %in% bios) out <- c(out, bio5)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
### BIOCLIM 6
if (any(c(3, 6, 7) %in% bios)) {
bio6 <- min(tmin)
names(bio6) <- "bio6"
if (6 %in% bios) out <- c(out, bio6)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
### BIOCLIM 7 (annual temp range)
if (any(c(3, 7) %in% bios)) {
bio7 <- bio5 - bio6
names(bio7) <- "bio7"
if (7 %in% bios) out <- c(out, bio7)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
### BIOCLIM 3 (100 * bio2 / bio7)
if (3 %in% bios) {
bio3 <- 100 * bio2 / bio7
names(bio3) <- "bio3"
out <- c(out, bio3)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
### BIOCLIM 4 (100 * sd of temp)
if (4 %in% bios) {
bio4 <- 100 * terra::stdev(tmean, pop = !sample)
names(bio4) <- "bio4"
out <- c(out, bio4)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIOCLIM 8 (mean temp of wettest quarter)
if (8 %in% bios) {
mm <- terra::minmax(tmeanByQuarter)
minVal <- -10 * abs(min(mm[1L, , drop = TRUE]))
bio8 <- tmean[[1L]] * 0 + minVal
for (i in wettestQuarters) {
bio8 <- max(bio8, (bio55 == i) * tmeanByQuarter[[i]])
}
names(bio8) <- "bio8"
out <- c(out, bio8)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIOCLIM 9 (mean temp of driest quarter)
if (9 %in% bios) {
mm <- terra::minmax(tmeanByQuarter)
minVal <- -10 * abs(min(mm[1L, , drop = TRUE]))
bio9 <- tmean[[1L]] * 0 + minVal
for (i in driestQuarters) {
bio9 <- max(bio9, (bio56 == i) * tmeanByQuarter[[i]])
}
names(bio9) <- "bio9"
out <- c(out, bio9)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIOCLIM 10 (mean temp of warmest quarter)
if (10 %in% bios) {
mm <- terra::minmax(tmeanByQuarter)
minVal <- -10 * abs(min(mm[1L, , drop = TRUE]))
bio10 <- tmean[[1L]] * 0 + minVal
for (i in warmestQuarters) {
bio10 <- max(bio10, (bio53 == i) * tmeanByQuarter[[i]])
}
names(bio10) <- "bio10"
out <- c(out, bio10)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIOCLIM 11 (mean temp of coldest quarter)
if (11 %in% bios) {
mm <- terra::minmax(tmeanByQuarter)
minVal <- -10 * abs(min(mm[1L, , drop = TRUE]))
bio11 <- tmean[[1L]] * 0 + minVal
for (i in coldestQuarters) {
bio11 <- max(bio11, (bio54 == i) * tmeanByQuarter[[i]])
}
bio11 <- max(bio11)
names(bio11) <- "bio11"
out <- c(out, bio11)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIOCLIM 12 (total precipitation)
if (12 %in% bios) {
bio12 <- sum(ppt)
names(bio12) <- "bio12"
if (12 %in% bios) out <- c(out, bio12)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIOCLIM 13 (wettest month precipitation)
if (13 %in% bios) {
bio13 <- max(ppt)
names(bio13) <- "bio13"
out <- c(out, bio13)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIOCLIM 14 (driest month precipitation)
if (14 %in% bios) {
bio14 <- min(ppt)
names(bio14) <- "bio14"
out <- c(out, bio14)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
### BIOCLIM 15 (CV of precipitation)
if (15 %in% bios) {
sd <- terra::stdev(ppt + pptDelta, pop = !sample)
bio15 <- 100 * sd / mean(ppt + pptDelta)
names(bio15) <- "bio15"
out <- c(out, bio15)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIOCLIM 16 (precipitation of the wettest quarter)
if (16 %in% bios) {
bio16 <- ppt[[1L]] * 0
for (i in wettestQuarters) {
bio16 <- c(bio16, (bio55 == i) * pptByQuarter[[i]])
}
bio16 <- sum(bio16)
names(bio16) <- "bio16"
out <- c(out, bio16)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIO17: Precipitation of the driest quarter
if (17 %in% bios) {
bio17 <- ppt[[1L]] * 0
for (i in driestQuarters) {
bio17 <- c(bio17, (bio56 == i) * pptByQuarter[[i]])
}
bio17 <- sum(bio17)
names(bio17) <- "bio17"
out <- c(out, bio17)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIO18: Precipitation of the warmest quarter (based on mean temperature)
if (18 %in% bios) {
bio18 <- ppt[[1L]] * 0
for (i in warmestQuarters) {
bio18 <- c(bio18, (bio53 == i) * pptByQuarter[[i]])
}
bio18 <- sum(bio18)
names(bio18) <- "bio18"
out <- c(out, bio18)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIO19: Precipitation of the coldest quarter (based on mean temperature)
if (19 %in% bios) {
bio19 <- ppt[[1L]] * 0
for (i in coldestQuarters) {
bio19 <- c(bio19, (bio54 == i) * pptByQuarter[[i]])
}
bio19 <- sum(bio19)
names(bio19) <- "bio19"
out <- c(out, bio19)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIO41: Temperature of the quarter following the coldest quarter (based on mean temperature)
if (41 %in% bios) {
mm <- terra::minmax(tmeanByQuarter)
minVal <- -10 * abs(min(mm[1L, , drop = TRUE]))
bio41 <- tmean[[1L]] * 0 + minVal
for (i in coldestQuarters) {
if (i + quarter <= nLayers) {
j <- i + quarter
} else {
j <- i + quarter - nLayers
}
bio41 <- max(bio41, (bio54 == i) * tmeanByQuarter[[j]])
}
names(bio41) <- "bio41"
out <- c(out, bio41)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIO42: Temperature of the quarter following the warmest quarter (based on mean temperature)
if (42 %in% bios) {
mm <- terra::minmax(tmeanByQuarter)
minVal <- -10 * abs(min(mm[1L, , drop = TRUE]))
bio42 <- tmean[[1L]] * 0 + minVal
for (i in warmestQuarters) {
if (i + quarter <= nLayers) {
j <- i + quarter
} else {
j <- i + quarter - nLayers
}
bio42 <- max(bio42, (bio53 == i) * tmeanByQuarter[[j]])
}
names(bio42) <- "bio42"
out <- c(out, bio42)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIO43: Precipitation of the quarter following the coldest quarter (based on mean temperature; mm)
if (43 %in% bios) {
bio43 <- ppt[[1L]] * 0
for (i in coldestQuarters) {
if (i + quarter <= nLayers) {
j <- i + quarter
} else {
j <- i + quarter - nLayers
}
bio43 <- max(bio43, (bio54 == i) * pptByQuarter[[j]])
}
names(bio43) <- "bio43"
out <- c(out, bio43)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIO44: Precipitation of the quarter following the warmest quarter (based on mean temperature; mm)
if (44 %in% bios) {
bio44 <- ppt[[1L]] * 0
for (i in warmestQuarters) {
if (i + quarter <= nLayers) {
j <- i + quarter
} else {
j <- i + quarter - nLayers
}
bio44 <- max(bio44, (bio53 == i) * pptByQuarter[[j]])
}
names(bio44) <- "bio44"
out <- c(out, bio44)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIO45: Temperature of the quarter following the driest quarter (based on mean temperature; deg C)
if (45 %in% bios) {
mm <- terra::minmax(tmeanByQuarter)
minVal <- -10 * abs(min(mm[2L, , drop = TRUE]))
bio45 <- tmean[[1L]] * 0 + minVal
for (i in driestQuarters) {
if (i + quarter <= nLayers) {
j <- i + quarter
} else {
j <- i + quarter - nLayers
}
bio45 <- max(bio45, (bio56 == i) * tmeanByQuarter[[j]])
}
names(bio45) <- "bio45"
out <- c(out, bio45)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIO46: Temperature of the quarter following the wettest quarter (based on mean temperature; deg C)
if (46 %in% bios) {
mm <- terra::minmax(tmeanByQuarter)
minVal <- -10 * abs(min(mm[2L, , drop = TRUE]))
bio46 <- tmean[[1L]] * 0 + minVal
for (i in wettestQuarters) {
if (i + quarter <= nLayers) {
j <- i + quarter
} else {
j <- i + quarter - nLayers
}
bio46 <- max(bio46, (bio55 == i) * tmeanByQuarter[[j]])
}
names(bio46) <- "bio46"
out <- c(out, bio46)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIO47: Precipitation of the quarter following the driest quarter (based on mean temperature; mm)
if (47 %in% bios) {
bio47 <- ppt[[1L]] * 0
for (i in driestQuarters) {
if (i + quarter <= nLayers) {
j <- i + quarter
} else {
j <- i + quarter - nLayers
}
bio47 <- max(bio47, (bio56 == i) * pptByQuarter[[j]])
}
names(bio47) <- "bio47"
out <- c(out, bio47)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIO48: Precipitation of the quarter following the wettest quarter (based on mean temperature; mm)
if (48 %in% bios) {
bio48 <- ppt[[1L]] * 0
for (i in wettestQuarters) {
if (i + quarter <= nLayers) {
j <- i + quarter
} else {
j <- i + quarter - nLayers
}
bio48 <- max(bio48, (bio55 == i) * pptByQuarter[[j]])
}
names(bio48) <- "bio48"
out <- c(out, bio48)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIO49: Hottest month
if (49 %in% bios) {
bio49 <- terra::app(tmax, which.max)
names(bio49) <- "bio49"
out <- c(out, bio49)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIO50: Coldest month
if (50 %in% bios) {
bio50 <- terra::app(tmin, which.min)
names(bio50) <- "bio50"
out <- c(out, bio50)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIO51: Wettest month
if (51 %in% bios) {
bio51 <- terra::app(ppt, which.max)
names(bio51) <- "bio51"
out <- c(out, bio51)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIO52: Driest month
if (52 %in% bios) {
bio52 <- terra::app(ppt, which.min)
names(bio52) <- "bio52"
out <- c(out, bio52)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
# BIO57: The largest decrease in temperature from one month to the next (deg C).
# BIO58: The largest increase in temperature from one month to the next (deg C).
if (any(c(57, 58) %in% bios)) {
deltas <- tmean
for (i in 1:nLayers) {
if (i + quarter <= nLayers) {
target <- i + 1
} else {
target <- 1
}
deltas[[i]] <- tmean[[i]] - tmean[[target]]
}
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
if (57 %in% bios) {
bio57 <- max(deltas)
names(bio57) <- "bio57"
out <- c(out, bio57)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
if (58 %in% bios) {
bio58 <- abs(min(deltas))
names(bio58) <- "bio58"
out <- c(out, bio58)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
}
# BIO59: The largest decrease in precipitation from one month to the next.
# BIO60: The largest increase in precipitation from one month to the next.
if (any(c(59, 60) %in% bios)) {
deltas <- ppt
for (i in 1:nLayers) {
if (i + quarter <= nLayers) {
target <- i + 1
} else {
target <- 1
}
deltas[[i]] <- ppt[[i]] - ppt[[target]]
}
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
if (59 %in% bios) {
bio59 <- max(deltas)
names(bio59) <- "bio59"
out <- c(out, bio59)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
if (60 %in% bios) {
bio60 <- abs(min(deltas))
names(bio60) <- "bio60"
out <- c(out, bio60)
tasks <- tasks + 1
if (verbose | faster("verbose")) utils::setTxtProgressBar(pb, tasks)
}
}
out <- do.call(c, out)
outNames <- names(out)
nc <- nchar(outNames)
if (any(nc == 4L)) {
shorts <- out[[nc == 4L]]
shorts <- shorts[[order(names(shorts))]]
} else { shorts <- NULL }
if (any(nc == 5L)) {
longs <- out[[nc == 5L]]
longs <- longs[[order(names(longs))]]
} else { longs <- NULL }
if (is.null(shorts)) {
out <- longs
} else if (is.null(longs)) {
out <- shorts
} else {
out <- c(shorts, longs)
}
if (verbose | faster("verbose")) close(pb)
out
} # EOF
)
#' Calculate a series of "quarter" rasters and return their [sources()] names. A quarter can be summarized using
#'
#' x A "stack" of `SpatRaster`s
#' fun Character: Name of function to summarize across a quarter ("sum", "min", "max", or "mean").
#' quarter Numeric: Length of a quarter
#'
#' @noRd
.calcQuarterSR <- function(x, fun, quarter) {
out <- x
qs <- c(x, x[[1L:(quarter - 1L)]])
n <- nlyr(x)
for (i in seq_len(n)) {
select <- i:(i + quarter - 1L)
quart <- qs[[select]]
args <- list(x = quart)
out[[i]] <- do.call(fun, args)
} # next quarter
names(out) <- paste0("q", 1L:n)
out
}
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