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stacking.R
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#' @include Ensemble.SDM.R checkargs.R
#' @importFrom sp Polygon Polygons SpatialPolygons SpatialPoints bbox
#' @importFrom raster raster stack reclassify mask calc overlay values rasterize rasterToPoints values<-
#' @importFrom stats lm
NULL
#'Stack different ensemble SDMs in an SSDM
#'
#'This is a function to stack several ensemble SDMs in an SSDM. The function
#'takes as inputs several S4 \linkS4class{Ensemble.SDM} class objects produced
#'with \code{\link{ensemble_modelling}} or \code{\link{ensemble}} functions. The
#'function returns an S4 \linkS4class{Stacked.SDM} class object containing the
#'local species richness map, the between-algorithm variance map, and all
#'evaluation tables coming with (model evaluation, algorithm evaluation,
#'algorithm correlation matrix and variable importance), and a list of ensemble
#'SDMs for each species (see \code{\link{ensemble_modelling}}).
#'
#'@param esdm,... character. Ensemble SDMs to be stacked.
#'@param name character. Optional name given to the final SSDM produced (by
#' default 'Species.SDM').
#'@param method character. Define the method used to create the local species
#' richness map (see details below).
#'@param rep.B integer. If the method used to create the local species richness
#' is the random bernoulli (\strong{Bernoulli}), rep.B parameter defines the number of
#' repetitions used to create binary maps for each species.
#'@param Env raster object. Stacked raster object of environmental variables
#' (can be processed first by \code{\link{load_var}}). Needed only for stacking
#' method using probability ranking from richness (\strong{PRR}).
#'@param range integer. Set a value of range restriction (in pixels) around
#' presences occurrences on habitat suitability maps (all further points will
#' have a null probability, see Crisp et al (2011) in references). If NULL, no
#' range restriction will be applied.
#'@param endemism character. Define the method used to create an endemism map
#' (see details below).
#'@param eval logical. If set to FALSE, disable stack evaluation.
#' @param uncertainty logical. If set to TRUE, generates an uncertainty map and
#' an algorithm correlation matrix.
#'@param verbose logical. If set to TRUE, allows the function to print text in
#' the console.
#'@param GUI logical. Don't take that argument into account (parameter for the
#' user interface).
#'
#'@return an S4 \linkS4class{Stacked.SDM} class object viewable with the
#' \code{\link{plot.model}} function.
#'
#'@details \strong{Methods:} Choice of the method used to compute the local
#' species richness map (see Calabrese et al. (2014) and D'Amen et al (2015) for
#' more informations, see reference below): \describe{\item{pSSDM}{sum
#' probabilities of habitat suitability maps}\item{Bernoulli}{draw repeatedly
#' from a Bernoulli distribution}\item{bSSDM}{sum the binary map obtained with
#' the thresholding (depending on the metric of the
#' ESDM).}\item{MaximumLikelihood}{adjust species richness of the model by
#' linear regression}\item{PRR.MEM}{model richness with a macroecological model
#' (MEM) and adjust each ESDM binary map by ranking habitat suitability and
#' keeping as much as predicted richness of the MEM}\item{PRR.pSSDM}{model
#' richness with a pSSDM and adjust each ESDM binary map by ranking habitat
#' suitability and keeping as much as predicted richness of the pSSDM}}
#'
#' \strong{Endemism:} Choice of the method used to compute the endemism map
#' (see Crisp et al. (2001) for more information, see reference below):
#' \describe{\item{NULL}{No endemism map}\item{WEI}{(Weighted Endemism Index)
#' Endemism map built by counting all species in each cell and weighting each
#' by the inverse of its range} \item{CWEI}{(Corrected Weighted Endemism Index)
#' Endemism map built by dividing the weighted endemism index by the total
#' count of species in the cell.}}First string of the character is the method
#' either WEI or CWEI, and in those cases second string of the vector is used
#' to precise range calculation, whether the total number of occurrences
#' \strong{'NbOcc'} whether the surface of the binary map species distribution
#' \strong{'Binary'}.
#'
#' @examples
#' \dontrun{
#' # Loading data
#' data(Env)
#' data(Occurrences)
#' Occ1 <- subset(Occurrences, Occurrences$SPECIES == 'elliptica')
#' Occ2 <- subset(Occurrences, Occurrences$SPECIES == 'gracilis')
#'
#' # SSDM building
#' ESDM1 <- ensemble_modelling(c('CTA', 'SVM'), Occ1, Env, rep = 1,
#' Xcol = 'LONGITUDE', Ycol = 'LATITUDE',
#' name = 'elliptica', ensemble.thresh = c(0.6))
#' ESDM2 <- ensemble_modelling(c('CTA', 'SVM'), Occ2, Env, rep = 1,
#' Xcol = 'LONGITUDE', Ycol = 'LATITUDE',
#' name = 'gracilis', ensemble.thresh = c(0.6))
#' SSDM <- stacking(ESDM1, ESDM2)
#'
#' # Results plotting
#' plot(SSDM)
#' }
#'
#'@seealso \code{\link{stack_modelling}} to build SSDMs.
#'
#'@references M. D'Amen, A. Dubuis, R. F. Fernandes, J. Pottier, L. Pelissier, &
#' A Guisan (2015) "Using species richness and functional traits prediction to
#' constrain assemblage predicitions from stacked species distribution models"
#' \emph{Journal of Biogeography} 42(7):1255-1266
#' \url{http://doc.rero.ch/record/235561/files/pel_usr.pdf}
#'
#' J.M. Calabrese, G. Certain, C. Kraan, & C.F. Dormann (2014) "Stacking
#' species distribution models and adjusting bias by linking them to
#' macroecological models." \emph{Global Ecology and Biogeography} 23:99-112
#' \url{http://portal.uni-freiburg.de/biometrie/mitarbeiter/dormann/calabrese2013globalecolbiogeogr.pdf}
#'
#' M. D. Crisp, S. Laffan, H. P. Linder & A. Monro (2001) "Endemism in the
#' Australian flora" \emph{Journal of Biogeography} 28:183-198
#' \url{http://biology-assets.anu.edu.au/hosted_sites/Crisp/pdfs/Crisp2001_endemism.pdf}
#'
#' C. Liu, P. M. Berry, T. P. Dawson, R. & G. Pearson (2005) "Selecting
#' thresholds of occurrence in the prediction of species distributions."
#' \emph{Ecography} 28:85-393
#' \url{http://www.researchgate.net/publication/230246974_Selecting_Thresholds_of_Occurrence_in_the_Prediction_of_Species_Distributions}
#'
#'@rdname stacking
#'@export
setGeneric('stacking', function(esdm, ..., name = NULL, method = 'pSSDM', rep.B = 1000,
Env = NULL, range = NULL, endemism = c('WEI','Binary'), eval = TRUE, uncertainty=TRUE,
verbose = TRUE, GUI = FALSE) {return(standardGeneric('stacking'))})
#' @rdname stacking
#' @export
setMethod('stacking', 'Ensemble.SDM', function(esdm, ..., name = NULL, method = 'pSSDM', rep.B = 1000,
Env = NULL, range = NULL, endemism = c('WEI','Binary'), eval = TRUE, uncertainty=TRUE,
verbose = TRUE, GUI = FALSE) {
# Check arguments
.checkargs(esdm = esdm, name = name, method = method, rep.B = rep.B, range = range,
endemism = endemism, eval = eval, verbose = verbose, GUI = GUI)
esdms <- list(esdm, ...)
if (length(esdms) < 2) {
stop("You neeed more than one ensemble SDM to do stackings")
}
names <- c()
for (i in seq_len(length(esdms))) {
if (esdms[[i]]@name %in% names) {
stop("Ensemble models can't have the same name, you need to rename one of ",
esdms[[i]]@name)
} else {
names <- c(names, esdms[[i]]@name)
}
}
if (verbose) {
cat("Stack creation... \n")
}
stack <- Stacked.SDM(diversity.map = reclassify(esdm@projection[[1]], c(-Inf,Inf, 0)),
endemism.map = reclassify(esdm@projection[[1]], c(-Inf, Inf, 0)),
uncertainty = if(!uncertainty){raster()}else{reclassify(esdm@uncertainty, c(-Inf, Inf, NA))},
parameters = esdm@parameters)
# ESDMs
for (i in seq_len(length(esdms))) {
suppressWarnings({
stack@esdms[esdms[[i]]@name] <- esdms[[i]]
})
}
# Name
if (verbose) {
cat(" naming...")
}
if (is.null(name)) {
name <- "Species"
}
stack@name <- paste0(name, ".SSDM")
if (verbose) {
cat(" done. \n")
}
# Range restriction
if (verbose) {
cat(" range restriction...")
}
if (!is.null(range)) {
for (j in seq_len(length(esdms))) {
nbocc <- length(as.factor(esdms[[j]]@data$Presence[esdms[[j]]@data$Presence ==
1]))/sum(esdms[[j]]@algorithm.evaluation$kept.model)
occ <- esdms[[j]]@data[1:nbocc, ]
occ <- occ[which(occ$Presence == 1), 1:2]
circles <- list()
for (i in seq_len(length(occ[, 1]))) {
x <- occ$X[i]
y <- occ$Y[i]
pts <- seq(0, 2 * pi, length.out = 100)
# xy = cbind(x + range/60 * sin(pts), y + range/60 * cos(pts))
res <- res(stack@endemism.map)[1]
xy <- cbind(x + range * res * sin(pts), y + range * res * cos(pts))
circle <- Polygon(xy)
circles[i] <- circle
}
sc <- SpatialPolygons(list(Polygons(circles, "Circles")))
esdms[[j]]@projection <- mask(esdms[[j]]@projection, sc, updatevalue = 0)
# thresh = esdms[[j]]@evaluation$threshold esdms[[j]]@projection =
# reclassify(esdms[[j]]@projection, c(-Inf,thresh,0, thresh,Inf,1))
}
}
if (verbose) {
cat(" done. \n")
}
# Diversity map
if (verbose)
cat(" diversity mapping...")
diversity <- mapDiversity(stack, method, rep.B, verbose, Env)
stack@diversity.map <- diversity$diversity.map
if(!is.null(diversity$esdms))
stack@esdms <- diversity$esdms
names(stack@diversity.map) <- "diversity"
if (verbose)
cat(" done. \n")
# uncertainty map
if(uncertainty){
if (verbose) {
cat(" uncertainty mapping...")
}
uncertainties <- stack()
for (i in seq_len(length(esdms))) {
a <- try(esdms[[i]]@uncertainty)
if (inherits(a, "try-error")) {
if (verbose) {
cat("Ensemble model", esdms[[i]]@name, "uncertainty map not computed")
}
} else {
b <- try(stack(uncertainties, a))
if (inherits(b, "try-error")) {
if (verbose) {
cat("Ensemble model", esdms[[i]]@name, ":", b)
}
} else {
uncertainties <- b
}
}
}
a <- try(calc(uncertainties, mean))
if (inherits(a, "try-error")) {
if (verbose) {
cat("No uncertainty map to do uncertainty mapping")
}
} else {
stack@uncertainty <- a
names(stack@uncertainty) <- "uncertainty"
}
if (verbose) {
cat(" done. \n")
}
}
# endemism map
if (verbose) {
cat(" endemism mapping...")
}
if (is.null(endemism)) {
"deactivated"
} else {
for (i in seq_len(length(esdms))) {
if (endemism[2] == "NbOcc") {
endweight <- length(as.factor(esdms[[i]]@data$Presence[esdms[[i]]@data$Presence ==
1]))/sum(esdms[[i]]@algorithm.evaluation$kept.model)
} else if (endemism[2] == "Binary") {
endweight <- sum(values(reclassify(esdms[[i]]@projection, c(-Inf,
esdms[[i]]@evaluation$threshold, 0, esdms[[i]]@evaluation$threshold,
Inf, 1))), na.rm = TRUE)
}
if (endemism[1] == "WEI") {
stack@endemism.map <- stack@endemism.map + esdms[[i]]@projection/endweight
} else if (endemism[1] == "CWEI") {
stack@endemism.map <- stack@endemism.map + overlay(esdms[[i]]@projection,
stack@diversity.map, fun = function(x, y) {
y <- round(y)
x[which(y > 0)] <- x[which(y > 0)]/endweight/y[which(y >
0)]
return(x)
})
}
}
stack@endemism.map <- stack@endemism.map/stack@endemism.map@data@max
}
if (verbose) {
cat(" done. \n")
}
# variable Importance
if (verbose) {
cat(" comparing variable importance...")
}
stack@variable.importance <- esdm@variable.importance
for (i in 2:length(esdms)) {
a <- try(rbind(stack@variable.importance, esdms[[i]]@variable.importance))
if (inherits(a, "try-error")) {
cat(a)
} else {
stack@variable.importance <- a
}
}
a <- stack@variable.importance[1:2, ]
row.names(a) <- c("Mean", "SD")
for (i in seq_len(length(stack@variable.importance))) {
a[i] <- c(mean(stack@variable.importance[, i]), sd(stack@variable.importance[,
i]))
}
stack@variable.importance <- a
if (verbose) {
cat(" done. \n")
}
# Algorithm Correlation
if (verbose) {
cat(" comparing algorithms correlation...")
}
algo <- c() # Listing all algorithms presents in esdms and renaming esdms row and columns
for (i in seq_len(length(esdms))) {
if (length(esdms[[i]]@algorithm.correlation) == 0) {
if (verbose) {
cat("\n", esdms[[i]]@name, "algorithms correlation has not been computed. \n")
}
} else {
for (j in seq_len(length(esdms[[i]]@algorithm.correlation))) {
if (length(strsplit(names(esdms[[i]]@algorithm.correlation)[j],
".", fixed = TRUE)[[1]]) > 1) {
a <- strsplit(row.names(esdms[[i]]@algorithm.correlation)[j],
".SDM", fixed = TRUE)[[1]][1]
a <- tail(strsplit(a, ".", fixed = TRUE)[[1]], n = 1)
names(esdms[[i]]@algorithm.correlation)[j] <- a
row.names(esdms[[i]]@algorithm.correlation)[j] <- a
}
if (!(names(esdms[[i]]@algorithm.correlation)[j] %in% algo)) {
algo <- c(algo, names(esdms[[i]]@algorithm.correlation)[j])
}
}
}
}
mcorr <- data.frame(matrix(nrow = length(algo), ncol = length(algo)))
names(mcorr) <- algo
row.names(mcorr) <- algo
if (length(algo) > 0) {
for (i in seq_len(length(algo))) {
for (j in seq_len(length(algo))) {
if (i > j) {
corr <- c()
for (k in seq_len(length(esdms))) {
if (length(esdms[[k]]@algorithm.correlation) != 0) {
row <- which(row.names(esdms[[k]]@algorithm.correlation) ==
row.names(mcorr)[j])
col <- which(names(esdms[[k]]@algorithm.correlation) ==
names(mcorr)[i])
if (length(row) > 0 && length(col) > 0) {
corr <- c(corr, esdms[[k]]@algorithm.correlation[row,
col])
}
}
mcorr[i, j] <- mean(corr, na.rm = TRUE)
}
}
}
}
}
stack@algorithm.correlation <- mcorr
if (verbose) {
cat(" done. \n")
}
# Algorithm Evaluation
if (verbose) {
cat(" comparing algorithms evaluation")
}
stack@algorithm.evaluation <- esdm@algorithm.evaluation
for (i in 2:length(esdms)) {
stack@algorithm.evaluation <- rbind(stack@algorithm.evaluation, esdms[[i]]@algorithm.evaluation)
}
# stack@algorithm.evaluation$algo <- "algo"
stack@algorithm.evaluation$algo <- unlist(regmatches(row.names(stack@algorithm.evaluation), gregexpr("ANN|CTA|GAM|GBM|GLM|MARS|MAXENT|RF|SVM", row.names(stack@algorithm.evaluation))))
# for (i in seq_len(length(row.names(stack@algorithm.evaluation)))) {
# stack@algorithm.evaluation$algo[i] <- strsplit(row.names(stack@algorithm.evaluation),
# ".", fixed = TRUE)[[i]][2]
# }
stack@algorithm.evaluation <- aggregate.data.frame(stack@algorithm.evaluation[-which(names(stack@algorithm.evaluation) ==
"algo")],
by = list(stack@algorithm.evaluation[, which(names(stack@algorithm.evaluation) ==
"algo")]), FUN = mean)
row.names(stack@algorithm.evaluation) <- stack@algorithm.evaluation$Group.1
stack@algorithm.evaluation <- stack@algorithm.evaluation[-1]
if (verbose) {
cat(" done. \n")
}
# Evaluation
if (eval){
if (verbose)
cat(" evaluating...")
stack@evaluation <- evaluate(stack)
}
# Parameters
stack@parameters$method <- method
if (method == "B") {
stack@parameters$rep.B <- rep.B
}
stack@parameters$range <- range
stack@parameters$endemism <- paste0(endemism[1], "|", endemism[2])
return(stack)
})