R/niche_parameters.R
In agarciaEE/NINA: Niche Interaction Network Analyses
Defines functions
niche_parameters
Documented in
niche_parameters
#' @title NICHE PARAMETERS
#'
#' @param x NINA model
#' @param y Optional. NINA model
#' @param type String indicating the scale of the analysis. Default is "region"
#' @param centroid.w Logial to indicate if niche overlap estimate is to be weighted in relation to niche centroid
#' @param np.type If \code{centroid.w} is TRUE, type of centroid to estimate. Default is 'unimodal'. See \code{\link[NINA]{niche_position}}
#' @param np.metric If \code{centroid.w} is TRUE, statistic method to estimate the niche centroid. Default is 'median'. See \code{\link[NINA]{niche_position}}
#' @param quantile If \code{centroid.w} is TRUE, quantle threshold to filter niche densities. Default is 0.5. See \code{\link[NINA]{niche_position}}
#' @param centroid.w logical whether to weight niche overlap by distance to niche centroid
#' @param cor Logical whether to use environmentally corrected densites
#' @param rep Number of random samples to carry out the statistic tests
#' @param rand Directions of the comparisons. 1 performs all tests with argument 'x' as base of all comparisons. 2 uses argument 'y'. Default is 1.
#' @param alternative String indicating the alternative hypothesis. Default is "greater".
#' @param rnd.test Logical to indicate if randomization tests are to be estimated
#'
#' @description Estimates niche parameters
#'
#' @return Data frame.
#'
#' @details Returns an error if \code{filename} does not exist.
#'
#'
#' @importFrom stats quantile
#' @importFrom ecospat ecospat.niche.overlap
#' @importFrom raster extent compareRaster maxValue values
#' @importFrom plyr ldply
#'
#' @export
niche_parameters <- function(x, y, type = c("region", "global"), centroid.w = F, rnd.test = F,
quantile = 0.75, np.type = "unimodal", np.metric = c("median", "mean", "max"),
cor = F, rep = 100, rand = 1, alternative = c("greater", "lower")){
type = type[1]
np.metric = np.metric[1]
xW <- yW <- xG <- yG <- clus <- F
xmod = NULL
ymod = NULL
if (all(class(x) == c("NINA", "BCmodel"))) {
X = list(EnvSuit = x$z.mod,
EnvAcc = x$w)
xW = T
xmod = "BC"
}
else if (all(class(x) == c("NINA", "ECmodel"))) {
X = list(EnvSuit = x$z.mod,
EcoSuit = x$t.mod,
EcoAcc = x$g)
xG = T
xmod = "EC"
}
else if (all(class(x) == c("NINA", "ENmodel"))) {
X = list(EnvSuit = x$z.mod)
xmod = "EN"
if (missing(y)){ stop("Supplied model has nothing to compare to...\n\t...Provide another NINA model as 'y' argument")}
}
else{ stop("Object 'x' is not a NINA model")}
if(!is.null(x$clus)){clus = T}
if(!missing(y)){
if (all(class(y) == c("NINA", "BCmodel"))) {
Y = list(EnvSuit = y$z.mod,
EnvAcc = y$w)
yW = T
ymod = "BC"
}
else if (all(class(y) == c("NINA", "ECmodel"))) {
Y = list(EnvSuit = y$z.mod,
EcoSuit = y$t.mod,
EcoAcc = y$g)
yG = T
ymod = "EC"
}
else if (all(class(y) == c("NINA", "ENmodel"))) {
Y = list(EnvSuit = y$z.mod)
ymod = "EN"
}
else{ stop("Object 'y' is not a NINA model")}
if(!is.null(y$clus) != clus) {stop("Model 'x' and model 'y' have been estimated in different scales") }
if(!all(names(x$maps) %in% names(y$maps))) {
if(all(!names(x$maps) %in% names(y$maps))) {
stop("Species in model 'x' not found in model 'y'")
}
else {
sp.absent = names(x$maps)[!names(x$maps) %in% names(y$maps)]
warning(paste(sp.absent, "in model 'x' are not present in model 'y'"), immediate. = T)
}
}
}
out = list()
np = list()
p.values <- list()
simList <- list()
if (type == "region"){
if (clus){
for (e in names(X[[1]])){
message(paste("Estimating niche metrics of species in region", e, "..."))
np[[e]] = list()
p.values[[e]] <- list()
simList[[e]] <- list()
for (i in names(X[[1]][[e]])){
message(paste("Computing niche metrics of", i, "..."), appendLF = F)
if (xmod == "BC" && is.null(ymod)){
if(!is.null(X$EnvSuit[[e]][[i]]) && !is.null(X$EnvAcc[[e]][[i]])){
message("\n\t...between environmental niche and environmental accessibillity....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[e]][[i]], X$EnvAcc[[e]][[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[e]][[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Acc")
if (rnd.test){
simList[[e]][[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Acc")
p.values[[e]][[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Acc")
p.values[[e]][[i]] <- as.data.frame(p.values[[e]][[i]], row.names = rep("", nrow(p.values[[e]][[i]])))
}
message("...done.")
}
}
else if (xmod == "EC" && is.null(ymod)){
if(!is.null(X$EnvSuit[[e]][[i]]) && !is.null(X$EcoSuit[[e]][[i]])){
message("\n\t...between environmental niche and ecological niche...", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[e]][[i]], X$EcoSuit[[e]][[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[e]][[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Eco")
if (rnd.test){
simList[[e]][[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Eco")
p.values[[e]][[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Eco")
}
message("...done.")
}
if(!is.null(X$EcoSuit[[e]][[i]]) && !is.null(X$EcoAcc[[e]][[i]])){
message("\n\t...between ecological niche and ecological accessibillity....", appendLF = F)
ncomp <- niche_comparison(X$EcoSuit[[e]][[i]], X$EcoAcc[[e]][[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[e]][[i]] <- rbind(np[[e]][[i]], c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Eco2Acc"))
if (rnd.test){
simList[[e]][[i]] <- rbind(simList[[e]][[i]], cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Eco2Acc"))
p.values[[e]][[i]] <- rbind(p.values[[e]][[i]], cbind(alternative = alternative,
D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue, CS = ncomp$CS$pvalue,
ER = ncomp$ER$pvalue, ncomp$USE$pvalue,
comparison = "Eco2Acc"))
p.values[[e]][[i]] <- as.data.frame(p.values[[e]][[i]], row.names = rep("", nrow(p.values[[e]][[i]])))
}
message("...done.")
}
}
else if (!is.null(Y[[1]][[e]][[i]])){
if (xmod == "EN" && ymod == "EN"){
if(!is.null(X$EnvSuit[[e]][[i]]) && !is.null(Y$EnvSuit[[e]][[i]])){
message("\n\t...between environmental niches....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[e]][[i]], Y$EnvSuit[[e]][[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[e]][[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Env")
if (rnd.test){
simList[[e]][[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Env")
p.values[[e]][[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Env")
p.values[[e]][[i]] <- as.data.frame(p.values[[e]][[i]], row.names = rep("", nrow(p.values[[e]][[i]])))
}
message("...done.")
}
}
else if (xmod == "EN" && ymod == "BC"){
if(!is.null(X$EnvSuit[[e]][[i]]) && !is.null(Y$EnvSuit[[e]][[i]])){
message("\n\t...between environmental niches....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[e]][[i]], Y$EnvSuit[[e]][[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[e]][[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Env")
if (rnd.test){
simList[[e]][[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Env")
p.values[[e]][[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Env")
}
message("...done.")
}
if(!is.null(X$EnvSuit[[e]][[i]]) && !is.null(Y$EnvAcc[[e]][[i]])){
message("\n\t...between environmental niche and environmental accessibillity....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[e]][[i]], Y$EnvAcc[[e]][[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[e]][[i]] <- rbind(np[[e]][[i]], c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Acc"))
if (rnd.test){
simList[[e]][[i]] <- rbind(simList[[e]][[i]], cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Acc"))
p.values[[e]][[i]] <- rbind(p.values[[e]][[i]], cbind(alternative = alternative,
D = ncomp$D$pvalue, CS = ncomp$CS$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
ER = ncomp$ER$pvalue, ncomp$USE$pvalue,
comparison = "Env2Acc"))
p.values[[e]][[i]] <- as.data.frame(p.values[[e]][[i]], row.names = rep("", nrow(p.values[[e]][[i]])))
}
message("...done.")
}
}
else if (xmod == "EN" && ymod == "EC"){
if(!is.null(X$EnvSuit[[e]][[i]]) && !is.null(Y$EnvSuit[[e]][[i]])){
message("\n\t...between environmental niches....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[e]][[i]], Y$EnvSuit[[e]][[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[e]][[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Env")
if (rnd.test){
simList[[e]][[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Env")
p.values[[e]][[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Env")
p.values[[e]][[i]] <- as.data.frame(p.values[[e]][[i]], row.names = rep("", nrow(p.values[[e]][[i]])))
}
message("...done.")
}
}
else if (xmod == "BC" && ymod == "BC"){
if(!is.null(X$EnvSuit[[e]][[i]]) && !is.null(Y$EnvSuit[[e]][[i]])){
message("\n\t...between environmental niches....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[e]][[i]], Y$EnvSuit[[e]][[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[e]][[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Env")
if (rnd.test){
simList[[e]][[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Env")
p.values[[e]][[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Env")
}
message("...done.")
}
if(!is.null(X$EnvSuit[[e]][[i]]) && !is.null(Y$EnvAcc[[e]][[i]])){
message("\n\t...between environmental accessibilities...", appendLF = F)
ncomp <- niche_comparison(X$EnvAcc[[e]][[i]], Y$EnvAcc[[e]][[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[e]][[i]] <- rbind(np[[e]][[i]], c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Acc2Acc"))
if (rnd.test){
simList[[e]][[i]] <- rbind(simList[[e]][[i]], cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Acc2Acc"))
p.values[[e]][[i]] <- rbind(p.values[[e]][[i]], cbind(alternative = alternative,
D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue, CS = ncomp$CS$pvalue,
ER = ncomp$ER$pvalue, ncomp$USE$pvalue,
comparison = "Acc2Acc"))
p.values[[e]][[i]] <- as.data.frame(p.values[[e]][[i]], row.names = rep("", nrow(p.values[[e]][[i]])))
}
message("...done.")
}
}
else if (xmod == "BC" && ymod == "EC"){
if(!is.null(X$EnvSuit[[e]][[i]]) && !is.null(Y$EnvSuit[[e]][[i]])){
message("\n\t...between environmental niches....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[e]][[i]], Y$EnvSuit[[e]][[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[e]][[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Env")
if (rnd.test){
simList[[e]][[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Env")
p.values[[e]][[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Env")
}
message("...done.")
}
if(!is.null(X$EnvSuit[[e]][[i]]) && !is.null(Y$EcoSuit[[e]][[i]])){
message("\n\t...between environmental niche and ecological niche...", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[e]][[i]], Y$EcoSuit[[e]][[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[e]][[i]] <- rbind(np[[e]][[i]], c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Eco"))
if (rnd.test){
simList[[e]][[i]] <- rbind(simList[[e]][[i]], cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Eco"))
p.values[[e]][[i]] <- rbind(p.values[[e]][[i]], cbind(alternative = alternative,
D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue, CS = ncomp$CS$pvalue,
ER = ncomp$ER$pvalue, ncomp$USE$pvalue,
comparison = "Env2Eco"))
p.values[[e]][[i]] <- as.data.frame(p.values[[e]][[i]], row.names = rep("", nrow(p.values[[e]][[i]])))
}
message("...done.")
}
if(!is.null(X$EnvAcc[[e]][[i]]) && !is.null(Y$EcoAcc[[e]][[i]])){
message("\n\t...between environmental accessibility and ecological accessibility", appendLF = F)
ncomp <- niche_comparison(X$EnvAcc[[e]][[i]], Y$EcoAcc[[e]][[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[e]][[i]] <- rbind(np[[e]][[i]], c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Acc2Acc"))
if (rnd.test){
simList[[e]][[i]] <- rbind(simList[[e]][[i]], cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Acc2Acc"))
p.values[[e]][[i]] <- rbind(p.values[[e]][[i]], cbind(alternative = alternative,
D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue, CS = ncomp$CS$pvalue,
ER = ncomp$ER$pvalue, ncomp$USE$pvalue,
comparison = "Acc2Acc"))
p.values[[e]][[i]] <- as.data.frame(p.values[[e]][[i]], row.names = rep("", nrow(p.values[[e]][[i]])))
}
message("...done.")
}
}
else if (xmod == "EC" && ymod == "EC"){
if(!is.null(X$EnvSuit[[e]][[i]]) && !is.null(Y$EnvSuit[[e]][[i]])){
message("\n\t...between environmental niches....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[e]][[i]], Y$EnvSuit[[e]][[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[e]][[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Env")
if (rnd.test){
simList[[e]][[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Env")
p.values[[e]][[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Env")
}
message("...done.")
}
if(!is.null(X$EcoSuit[[e]][[i]]) && !is.null(Y$EcoSuit[[e]][[i]])){
message("\n\t...between ecological niches....", appendLF = F)
ncomp <- niche_comparison(X$EcoSuit[[e]][[i]], Y$EcoSuit[[e]][[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[e]][[i]] <- rbind(np[[e]][[i]], c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Eco2Eco"))
if (rnd.test){
simList[[e]][[i]] <- rbind(simList[[e]][[i]], cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Eco2Eco"))
p.values[[e]][[i]] <- rbind(p.values[[e]][[i]], cbind(alternative = alternative,
D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue, CS = ncomp$CS$pvalue,
ER = ncomp$ER$pvalue, ncomp$USE$pvalue,
comparison = "Eco2Eco"))
p.values[[e]][[i]] <- as.data.frame(p.values[[e]][[i]], row.names = rep("", nrow(p.values[[e]][[i]])))
}
message("...done.")
}
if(!is.null(X$EcoAcc[[e]][[i]]) && !is.null(Y$EnvAcc[[e]][[i]])){
message("\n\t...between environmental acessibilities...", appendLF = F)
ncomp <- niche_comparison(X$EcoAcc[[e]][[i]], Y$EnvAcc[[e]][[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[e]][[i]] <- rbind(np[[e]][[i]], c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Acc2Acc"))
if (rnd.test){
simList[[e]][[i]] <- rbind(simList[[e]][[i]], cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Acc2Acc"))
p.values[[e]][[i]] <- rbind(p.values[[e]][[i]], cbind(alternative = alternative,
D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue, CS = ncomp$CS$pvalue,
ER = ncomp$ER$pvalue, ncomp$USE$pvalue,
comparison = "Acc2Acc"))
p.values[[e]][[i]] <- as.data.frame(p.values[[e]][[i]], row.names = rep("", nrow(p.values[[e]][[i]])))
}
message("...done.")
}
}
else if (xmod == "BC" && ymod == "EN"){
if(!is.null(X$EnvSuit[[e]][[i]]) && !is.null(Y$EnvSuit[[e]][[i]])){
message("\n\t...between environmental niches....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[e]][[i]], Y$EnvSuit[[e]][[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[e]][[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Env")
if (rnd.test){
simList[[e]][[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Env")
p.values[[e]][[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Env")
}
message("...done.")
}
if(!is.null(X$EnvAcc[[e]][[i]]) && !is.null(Y$EnvSuit[[e]][[i]])){
message("\n\t...between environmental acccessiibiliity and environmental niche....", appendLF = F)
ncomp <- niche_comparison(X$EnvAcc[[e]][[i]], Y$EnvSuit[[e]][[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[e]][[i]] <- rbind(np[[e]][[i]], c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Acc2Env"))
if (rnd.test){
simList[[e]][[i]] <- rbind(simList[[e]][[i]], cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Acc2Env"))
p.values[[e]][[i]] <- rbind(p.values[[e]][[i]], cbind(alternative = alternative,
D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue, CS = ncomp$CS$pvalue,
ER = ncomp$ER$pvalue, ncomp$USE$pvalue,
comparison = "Acc2Env"))
p.values[[e]][[i]] <- as.data.frame(p.values[[e]][[i]], row.names = rep("", nrow(p.values[[e]][[i]])))
}
message("...done.")
}
}
else if (xmod == "EC" && ymod == "EN"){
if(!is.null(X$EnvSuit[[e]][[i]]) && !is.null(Y$EnvSuit[[e]][[i]])){
message("\n\t...between environmental niches....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[e]][[i]], Y$EnvSuit[[e]][[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[e]][[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Env")
if (rnd.test){
simList[[e]][[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Env")
p.values[[e]][[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Env")
p.values[[e]][[i]] <- as.data.frame(p.values[[e]][[i]], row.names = rep("", nrow(p.values[[e]][[i]])))
}
message("...done.")
}
}
else if (xmod == "EC" && ymod == "BC"){
if(!is.null(X$EnvSuit[[e]][[i]]) && !is.null(Y$EnvSuit[[e]][[i]])){
message("\n\t...between environmental niches....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[e]][[i]], Y$EnvSuit[[e]][[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[e]][[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Env")
if (rnd.test){
simList[[e]][[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Env")
p.values[[e]][[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Env")
}
message("...done.")
}
if(!is.null(X$EcoSuit[[e]][[i]]) && !is.null(Y$EnvSuit[[e]][[i]])){
message("\n\t...between ecological niche and environmental niche....", appendLF = F)
ncomp <- niche_comparison(X$EcoSuit[[e]][[i]], Y$EnvSuit[[e]][[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[e]][[i]] <- rbind(np[[e]][[i]], c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Eco2Env"))
if (rnd.test){
simList[[e]][[i]] <- rbind(simList[[e]][[i]], cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Eco2Env"))
p.values[[e]][[i]] <- rbind(p.values[[e]][[i]], cbind(alternative = alternative,
D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue, CS = ncomp$CS$pvalue,
ER = ncomp$ER$pvalue, ncomp$USE$pvalue,
comparison = "Eco2Env"))
p.values[[e]][[i]] <- as.data.frame(p.values[[e]][[i]], row.names = rep("", nrow(p.values[[e]][[i]])))
}
message("...done.")
}
if(!is.null(X$EcoAcc[[e]][[i]]) && !is.null(Y$EnvAcc[[e]][[i]])){
message("\n\t...between ecological accessibillity and environmental accessibillity....", appendLF = F)
ncomp <- niche_comparison(X$EcoAcc[[e]][[i]], Y$EnvAcc[[e]][[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[e]][[i]] <- rbind(np[[e]][[i]], c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Acc2Acc"))
if (rnd.test){
simList[[e]][[i]] <- rbind(simList[[e]][[i]], cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Acc2Acc"))
p.values[[e]][[i]] <- rbind(p.values[[e]][[i]], cbind(alternative = alternative,
D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue, CS = ncomp$CS$pvalue,
ER = ncomp$ER$pvalue, ncomp$USE$pvalue,
comparison = "Acc2Acc"))
p.values[[e]][[i]] <- as.data.frame(p.values[[e]][[i]], row.names = rep("", nrow(p.values[[e]][[i]])))
}
message("...done.")
}
}
}
else{
message(paste("...nothing to analyze."))
}
}
np[[e]] <- plyr::ldply(np[[e]], .id = "species")
}
if (rnd.test){
simList <- reverse_list(simList)
p.values <- reverse_list(p.values)
out$np <- plyr::ldply(np, .id = "region")
out$sim <- lapply(simList, function(i) ldply(i, .id = "region"))
out$pvalue <- lapply(p.values, function(i) ldply(i, .id = "region"))
} else {
out <- plyr::ldply(np, .id = "region")
}
}
else {
stop("Regional models not found")
}
}
if (type == "global"){
if(clus){
if(!is.null(x$z.mod.global)){
if(xmod == "EN"){
X = list(EnvSuit = x$z.mod.global)
} else if (xmod == "BC") {
X = list(EnvSuit = x$z.mod.global,
EnvAcc = x$w.global)
} else if (xmod == "EC") {
X = list(EnvSuit = x$z.mod.global,
EcoSuit = x$t.mod.global,
EcoAcc = x$g.global)
}
} else {
stop("Global models of argument 'x' not found")
}
if (!missing(y)){
if(!is.null(y$z.mod.global)){
if(ymod == "EN"){
Y = list(EnvSuit = y$z.mod.global)
} else if (ymod == "BC") {
Y = list(EnvSuit = y$z.mod.global,
EnvAcc = y$w.global)
} else if (ymod == "EC") {
Y = list(EnvSuit = y$z.mod.global,
EcoSuit = y$t.mod.global,
EcoAcc = y$g.global)
}
} else {
stop("Global models of argument 'y' not found")
}
}
}
np = list()
p.values <- list()
simList <- list()
for (i in names(X[[1]])){
message(paste("Computing niche metrics of", i, "..."), appendLF = F)
if (xmod == "BC" && is.null(ymod)){
if(!is.null(X$EnvSuit[[i]]) && !is.null(X$EnvAcc[[i]])){
message("\n\t...between environmental niche and environmental accessibillity....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[i]], X$EnvAcc[[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Acc")
if (rnd.test){
simList[[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Acc")
p.values[[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Acc")
p.values[[i]] <- as.data.frame(p.values[[i]], row.names = rep("", nrow(p.values[[i]])))
}
message("...done.")
}
}
else if (xmod == "EC" && is.null(ymod)){
if(!is.null(X$EnvSuit[[i]]) && !is.null(X$EcoSuit[[i]])){
message("\n\t...between environmental niche and ecological niche...", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[i]], X$EcoSuit[[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Eco")
if (rnd.test){
simList[[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Eco")
p.values[[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Eco")
}
message("...done.")
}
if(!is.null(X$EcoSuit[[i]]) && !is.null(X$EcoAcc[[i]])){
message("\n\t...between ecological niche and ecological accessibillity....", appendLF = F)
ncomp <- niche_comparison(X$EcoSuit[[i]], X$EcoAcc[[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[i]] <- rbind(np[[i]], c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Eco2Acc"))
if (rnd.test){
simList[[i]] <- rbind(simList[[i]], cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Eco2Acc"))
p.values[[i]] <- rbind(p.values[[i]], cbind(alternative = alternative,
D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue, CS = ncomp$CS$pvalue,
ER = ncomp$ER$pvalue, ncomp$USE$pvalue,
comparison = "Eco2Acc"))
p.values[[i]] <- as.data.frame(p.values[[i]], row.names = rep("", nrow(p.values[[i]])))
}
message("...done.")
}
}
else if (!is.null(Y[[1]][[i]])){
if (xmod == "EN" && ymod == "EN"){
if(!is.null(X$EnvSuit[[i]]) && !is.null(Y$EnvSuit[[i]])){
message("\n\t...between environmental niches....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[i]], Y$EnvSuit[[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Env")
if (rnd.test){
simList[[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Env")
p.values[[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Env")
p.values[[i]] <- as.data.frame(p.values[[i]], row.names = rep("", nrow(p.values[[i]])))
}
message("...done.")
}
}
else if (xmod == "EN" && ymod == "BC"){
if(!is.null(X$EnvSuit[[i]]) && !is.null(Y$EnvSuit[[i]])){
message("\n\t...between environmental niches....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[i]], Y$EnvSuit[[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Env")
if (rnd.test){
simList[[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Env")
p.values[[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Env")
}
message("...done.")
}
if(!is.null(X$EnvSuit[[i]]) && !is.null(Y$EnvAcc[[i]])){
message("\n\t...between environmental niche and environmental accessibillity....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[i]], Y$EnvAcc[[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[i]] <- rbind(np[[i]], c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Acc"))
if (rnd.test){
simList[[i]] <- rbind(simList[[i]], cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Acc"))
p.values[[i]] <- rbind(p.values[[i]], cbind(alternative = alternative,
D = ncomp$D$pvalue, CS = ncomp$CS$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
ER = ncomp$ER$pvalue, ncomp$USE$pvalue,
comparison = "Env2Acc"))
p.values[[i]] <- as.data.frame(p.values[[i]], row.names = rep("", nrow(p.values[[i]])))
}
message("...done.")
}
}
else if (xmod == "EN" && ymod == "EC"){
if(!is.null(X$EnvSuit[[i]]) && !is.null(Y$EnvSuit[[i]])){
message("\n\t...between environmental niches....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[i]], Y$EnvSuit[[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Env")
if (rnd.test){
simList[[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Env")
p.values[[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Env")
p.values[[i]] <- as.data.frame(p.values[[i]], row.names = rep("", nrow(p.values[[i]])))
}
message("...done.")
}
}
else if (xmod == "BC" && ymod == "BC"){
if(!is.null(X$EnvSuit[[i]]) && !is.null(Y$EnvSuit[[i]])){
message("\n\t...between environmental niches....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[i]], Y$EnvSuit[[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Env")
if (rnd.test){
simList[[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Env")
p.values[[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Env")
}
message("...done.")
}
if(!is.null(X$EnvSuit[[i]]) && !is.null(Y$EnvAcc[[i]])){
message("\n\t...between environmental accessibilities...", appendLF = F)
ncomp <- niche_comparison(X$EnvAcc[[i]], Y$EnvAcc[[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[i]] <- rbind(np[[i]], c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Acc2Acc"))
if (rnd.test){
simList[[i]] <- rbind(simList[[i]], cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Acc2Acc"))
p.values[[i]] <- rbind(p.values[[i]], cbind(alternative = alternative,
D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue, CS = ncomp$CS$pvalue,
ER = ncomp$ER$pvalue, ncomp$USE$pvalue,
comparison = "Acc2Acc"))
p.values[[i]] <- as.data.frame(p.values[[i]], row.names = rep("", nrow(p.values[[i]])))
}
message("...done.")
}
}
else if (xmod == "BC" && ymod == "EC"){
if(!is.null(X$EnvSuit[[i]]) && !is.null(Y$EnvSuit[[i]])){
message("\n\t...between environmental niches....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[i]], Y$EnvSuit[[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Env")
if (rnd.test){
simList[[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Env")
p.values[[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Env")
}
message("...done.")
}
if(!is.null(X$EnvSuit[[i]]) && !is.null(Y$EcoSuit[[i]])){
message("\n\t...between environmental niche and ecological niche...", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[i]], Y$EcoSuit[[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[i]] <- rbind(np[[i]], c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Eco"))
if (rnd.test){
simList[[i]] <- rbind(simList[[i]], cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Eco"))
p.values[[i]] <- rbind(p.values[[i]], cbind(alternative = alternative,
D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue, CS = ncomp$CS$pvalue,
ER = ncomp$ER$pvalue, ncomp$USE$pvalue,
comparison = "Env2Eco"))
p.values[[i]] <- as.data.frame(p.values[[i]], row.names = rep("", nrow(p.values[[i]])))
}
message("...done.")
}
if(!is.null(X$EnvAcc[[i]]) && !is.null(Y$EcoAcc[[i]])){
message("\n\t...between environmental accessibility and ecological accessibility", appendLF = F)
ncomp <- niche_comparison(X$EnvAcc[[i]], Y$EcoAcc[[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[i]] <- rbind(np[[i]], c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Acc2Acc"))
if (rnd.test){
simList[[i]] <- rbind(simList[[i]], cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Acc2Acc"))
p.values[[i]] <- rbind(p.values[[i]], cbind(alternative = alternative,
D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue, CS = ncomp$CS$pvalue,
ER = ncomp$ER$pvalue, ncomp$USE$pvalue,
comparison = "Acc2Acc"))
p.values[[i]] <- as.data.frame(p.values[[i]], row.names = rep("", nrow(p.values[[i]])))
}
message("...done.")
}
}
else if (xmod == "EC" && ymod == "EC"){
if(!is.null(X$EnvSuit[[i]]) && !is.null(Y$EnvSuit[[i]])){
message("\n\t...between environmental niches....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[i]], Y$EnvSuit[[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Env")
if (rnd.test){
simList[[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Env")
p.values[[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Env")
}
message("...done.")
}
if(!is.null(X$EcoSuit[[i]]) && !is.null(Y$EcoSuit[[i]])){
message("\n\t...between ecological niches....", appendLF = F)
ncomp <- niche_comparison(X$EcoSuit[[i]], Y$EcoSuit[[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[i]] <- rbind(np[[i]], c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Eco2Eco"))
if (rnd.test){
simList[[i]] <- rbind(simList[[i]], cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Eco2Eco"))
p.values[[i]] <- rbind(p.values[[i]], cbind(alternative = alternative,
D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue, CS = ncomp$CS$pvalue,
ER = ncomp$ER$pvalue, ncomp$USE$pvalue,
comparison = "Eco2Eco"))
p.values[[i]] <- as.data.frame(p.values[[i]], row.names = rep("", nrow(p.values[[i]])))
}
message("...done.")
}
if(!is.null(X$EcoAcc[[i]]) && !is.null(Y$EnvAcc[[i]])){
message("\n\t...between environmental acessibilities...", appendLF = F)
ncomp <- niche_comparison(X$EcoAcc[[i]], Y$EnvAcc[[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[i]] <- rbind(np[[i]], c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Acc2Acc"))
if (rnd.test){
simList[[i]] <- rbind(simList[[i]], cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Acc2Acc"))
p.values[[i]] <- rbind(p.values[[i]], cbind(alternative = alternative,
D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue, CS = ncomp$CS$pvalue,
ER = ncomp$ER$pvalue, ncomp$USE$pvalue,
comparison = "Acc2Acc"))
p.values[[i]] <- as.data.frame(p.values[[i]], row.names = rep("", nrow(p.values[[i]])))
}
message("...done.")
}
}
else if (xmod == "BC" && ymod == "EN"){
if(!is.null(X$EnvSuit[[i]]) && !is.null(Y$EnvSuit[[i]])){
message("\n\t...between environmental niches....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[i]], Y$EnvSuit[[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Env")
if (rnd.test){
simList[[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Env")
p.values[[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Env")
}
message("...done.")
}
if(!is.null(X$EnvAcc[[i]]) && !is.null(Y$EnvSuit[[i]])){
message("\n\t...between environmental acccessiibiliity and environmental niche....", appendLF = F)
ncomp <- niche_comparison(X$EnvAcc[[i]], Y$EnvSuit[[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[i]] <- rbind(np[[i]], c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Acc2Env"))
if (rnd.test){
simList[[i]] <- rbind(simList[[i]], cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Acc2Env"))
p.values[[i]] <- rbind(p.values[[i]], cbind(alternative = alternative,
D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue, CS = ncomp$CS$pvalue,
ER = ncomp$ER$pvalue, ncomp$USE$pvalue,
comparison = "Acc2Env"))
p.values[[i]] <- as.data.frame(p.values[[i]], row.names = rep("", nrow(p.values[[i]])))
}
message("...done.")
}
}
else if (xmod == "EC" && ymod == "EN"){
if(!is.null(X$EnvSuit[[i]]) && !is.null(Y$EnvSuit[[i]])){
message("\n\t...between environmental niches....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[i]], Y$EnvSuit[[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Env")
if (rnd.test){
simList[[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Env")
p.values[[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Env")
p.values[[i]] <- as.data.frame(p.values[[i]], row.names = rep("", nrow(p.values[[i]])))
}
message("...done.")
}
}
else if (xmod == "EC" && ymod == "BC"){
if(!is.null(X$EnvSuit[[i]]) && !is.null(Y$EnvSuit[[i]])){
message("\n\t...between environmental niches....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[i]], Y$EnvSuit[[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Env")
if (rnd.test){
simList[[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Env")
p.values[[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Env")
}
message("...done.")
}
if(!is.null(X$EcoSuit[[i]]) && !is.null(Y$EnvSuit[[i]])){
message("\n\t...between ecological niche and environmental niche....", appendLF = F)
ncomp <- niche_comparison(X$EcoSuit[[i]], Y$EnvSuit[[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[i]] <- rbind(np[[i]], c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Eco2Env"))
if (rnd.test){
simList[[i]] <- rbind(simList[[i]], cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Eco2Env"))
p.values[[i]] <- rbind(p.values[[i]], cbind(alternative = alternative,
D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue, CS = ncomp$CS$pvalue,
ER = ncomp$ER$pvalue, ncomp$USE$pvalue,
comparison = "Eco2Env"))
p.values[[i]] <- as.data.frame(p.values[[i]], row.names = rep("", nrow(p.values[[i]])))
}
message("...done.")
}
if(!is.null(X$EcoAcc[[i]]) && !is.null(Y$EnvAcc[[i]])){
message("\n\t...between ecological accessibillity and environmental accessibillity....", appendLF = F)
ncomp <- niche_comparison(X$EcoAcc[[i]], Y$EnvAcc[[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[i]] <- rbind(np[[i]], c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Acc2Acc"))
if (rnd.test){
simList[[i]] <- rbind(simList[[i]], cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Acc2Acc"))
p.values[[i]] <- rbind(p.values[[i]], cbind(alternative = alternative,
D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue, CS = ncomp$CS$pvalue,
ER = ncomp$ER$pvalue, ncomp$USE$pvalue,
comparison = "Acc2Acc"))
p.values[[i]] <- as.data.frame(p.values[[i]], row.names = rep("", nrow(p.values[[i]])))
}
message("...done.")
}
}
}
else{
message(paste("...nothing to analyze."))
}
}
if (rnd.test){
out$np <- plyr::ldply(np, .id = "species")
out$sim <- simList
out$pvalues <- p.values
} else {
out <- plyr::ldply(np, .id = "species")
}
}
message("DONE")
return(out)
}
agarciaEE/NINA documentation built on Jan. 9, 2025, 10:09 a.m.
R Package Documentation
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Defines functions niche_parameters
Documented in niche_parameters
#' @title NICHE PARAMETERS
#'
#' @param x NINA model
#' @param y Optional. NINA model
#' @param type String indicating the scale of the analysis. Default is "region"
#' @param centroid.w Logial to indicate if niche overlap estimate is to be weighted in relation to niche centroid
#' @param np.type If \code{centroid.w} is TRUE, type of centroid to estimate. Default is 'unimodal'. See \code{\link[NINA]{niche_position}}
#' @param np.metric If \code{centroid.w} is TRUE, statistic method to estimate the niche centroid. Default is 'median'. See \code{\link[NINA]{niche_position}}
#' @param quantile If \code{centroid.w} is TRUE, quantle threshold to filter niche densities. Default is 0.5. See \code{\link[NINA]{niche_position}}
#' @param centroid.w logical whether to weight niche overlap by distance to niche centroid
#' @param cor Logical whether to use environmentally corrected densites
#' @param rep Number of random samples to carry out the statistic tests
#' @param rand Directions of the comparisons. 1 performs all tests with argument 'x' as base of all comparisons. 2 uses argument 'y'. Default is 1.
#' @param alternative String indicating the alternative hypothesis. Default is "greater".
#' @param rnd.test Logical to indicate if randomization tests are to be estimated
#'
#' @description Estimates niche parameters
#'
#' @return Data frame.
#'
#' @details Returns an error if \code{filename} does not exist.
#'
#'
#' @importFrom stats quantile
#' @importFrom ecospat ecospat.niche.overlap
#' @importFrom raster extent compareRaster maxValue values
#' @importFrom plyr ldply
#'
#' @export
niche_parameters <- function(x, y, type = c("region", "global"), centroid.w = F, rnd.test = F,
quantile = 0.75, np.type = "unimodal", np.metric = c("median", "mean", "max"),
cor = F, rep = 100, rand = 1, alternative = c("greater", "lower")){
type = type[1]
np.metric = np.metric[1]
xW <- yW <- xG <- yG <- clus <- F
xmod = NULL
ymod = NULL
if (all(class(x) == c("NINA", "BCmodel"))) {
X = list(EnvSuit = x$z.mod,
EnvAcc = x$w)
xW = T
xmod = "BC"
}
else if (all(class(x) == c("NINA", "ECmodel"))) {
X = list(EnvSuit = x$z.mod,
EcoSuit = x$t.mod,
EcoAcc = x$g)
xG = T
xmod = "EC"
}
else if (all(class(x) == c("NINA", "ENmodel"))) {
X = list(EnvSuit = x$z.mod)
xmod = "EN"
if (missing(y)){ stop("Supplied model has nothing to compare to...\n\t...Provide another NINA model as 'y' argument")}
}
else{ stop("Object 'x' is not a NINA model")}
if(!is.null(x$clus)){clus = T}
if(!missing(y)){
if (all(class(y) == c("NINA", "BCmodel"))) {
Y = list(EnvSuit = y$z.mod,
EnvAcc = y$w)
yW = T
ymod = "BC"
}
else if (all(class(y) == c("NINA", "ECmodel"))) {
Y = list(EnvSuit = y$z.mod,
EcoSuit = y$t.mod,
EcoAcc = y$g)
yG = T
ymod = "EC"
}
else if (all(class(y) == c("NINA", "ENmodel"))) {
Y = list(EnvSuit = y$z.mod)
ymod = "EN"
}
else{ stop("Object 'y' is not a NINA model")}
if(!is.null(y$clus) != clus) {stop("Model 'x' and model 'y' have been estimated in different scales") }
if(!all(names(x$maps) %in% names(y$maps))) {
if(all(!names(x$maps) %in% names(y$maps))) {
stop("Species in model 'x' not found in model 'y'")
}
else {
sp.absent = names(x$maps)[!names(x$maps) %in% names(y$maps)]
warning(paste(sp.absent, "in model 'x' are not present in model 'y'"), immediate. = T)
}
}
}
out = list()
np = list()
p.values <- list()
simList <- list()
if (type == "region"){
if (clus){
for (e in names(X[[1]])){
message(paste("Estimating niche metrics of species in region", e, "..."))
np[[e]] = list()
p.values[[e]] <- list()
simList[[e]] <- list()
for (i in names(X[[1]][[e]])){
message(paste("Computing niche metrics of", i, "..."), appendLF = F)
if (xmod == "BC" && is.null(ymod)){
if(!is.null(X$EnvSuit[[e]][[i]]) && !is.null(X$EnvAcc[[e]][[i]])){
message("\n\t...between environmental niche and environmental accessibillity....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[e]][[i]], X$EnvAcc[[e]][[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[e]][[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Acc")
if (rnd.test){
simList[[e]][[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Acc")
p.values[[e]][[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Acc")
p.values[[e]][[i]] <- as.data.frame(p.values[[e]][[i]], row.names = rep("", nrow(p.values[[e]][[i]])))
}
message("...done.")
}
}
else if (xmod == "EC" && is.null(ymod)){
if(!is.null(X$EnvSuit[[e]][[i]]) && !is.null(X$EcoSuit[[e]][[i]])){
message("\n\t...between environmental niche and ecological niche...", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[e]][[i]], X$EcoSuit[[e]][[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[e]][[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Eco")
if (rnd.test){
simList[[e]][[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Eco")
p.values[[e]][[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Eco")
}
message("...done.")
}
if(!is.null(X$EcoSuit[[e]][[i]]) && !is.null(X$EcoAcc[[e]][[i]])){
message("\n\t...between ecological niche and ecological accessibillity....", appendLF = F)
ncomp <- niche_comparison(X$EcoSuit[[e]][[i]], X$EcoAcc[[e]][[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[e]][[i]] <- rbind(np[[e]][[i]], c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Eco2Acc"))
if (rnd.test){
simList[[e]][[i]] <- rbind(simList[[e]][[i]], cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Eco2Acc"))
p.values[[e]][[i]] <- rbind(p.values[[e]][[i]], cbind(alternative = alternative,
D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue, CS = ncomp$CS$pvalue,
ER = ncomp$ER$pvalue, ncomp$USE$pvalue,
comparison = "Eco2Acc"))
p.values[[e]][[i]] <- as.data.frame(p.values[[e]][[i]], row.names = rep("", nrow(p.values[[e]][[i]])))
}
message("...done.")
}
}
else if (!is.null(Y[[1]][[e]][[i]])){
if (xmod == "EN" && ymod == "EN"){
if(!is.null(X$EnvSuit[[e]][[i]]) && !is.null(Y$EnvSuit[[e]][[i]])){
message("\n\t...between environmental niches....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[e]][[i]], Y$EnvSuit[[e]][[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[e]][[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Env")
if (rnd.test){
simList[[e]][[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Env")
p.values[[e]][[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Env")
p.values[[e]][[i]] <- as.data.frame(p.values[[e]][[i]], row.names = rep("", nrow(p.values[[e]][[i]])))
}
message("...done.")
}
}
else if (xmod == "EN" && ymod == "BC"){
if(!is.null(X$EnvSuit[[e]][[i]]) && !is.null(Y$EnvSuit[[e]][[i]])){
message("\n\t...between environmental niches....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[e]][[i]], Y$EnvSuit[[e]][[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[e]][[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Env")
if (rnd.test){
simList[[e]][[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Env")
p.values[[e]][[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Env")
}
message("...done.")
}
if(!is.null(X$EnvSuit[[e]][[i]]) && !is.null(Y$EnvAcc[[e]][[i]])){
message("\n\t...between environmental niche and environmental accessibillity....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[e]][[i]], Y$EnvAcc[[e]][[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[e]][[i]] <- rbind(np[[e]][[i]], c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Acc"))
if (rnd.test){
simList[[e]][[i]] <- rbind(simList[[e]][[i]], cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Acc"))
p.values[[e]][[i]] <- rbind(p.values[[e]][[i]], cbind(alternative = alternative,
D = ncomp$D$pvalue, CS = ncomp$CS$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
ER = ncomp$ER$pvalue, ncomp$USE$pvalue,
comparison = "Env2Acc"))
p.values[[e]][[i]] <- as.data.frame(p.values[[e]][[i]], row.names = rep("", nrow(p.values[[e]][[i]])))
}
message("...done.")
}
}
else if (xmod == "EN" && ymod == "EC"){
if(!is.null(X$EnvSuit[[e]][[i]]) && !is.null(Y$EnvSuit[[e]][[i]])){
message("\n\t...between environmental niches....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[e]][[i]], Y$EnvSuit[[e]][[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[e]][[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Env")
if (rnd.test){
simList[[e]][[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Env")
p.values[[e]][[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Env")
p.values[[e]][[i]] <- as.data.frame(p.values[[e]][[i]], row.names = rep("", nrow(p.values[[e]][[i]])))
}
message("...done.")
}
}
else if (xmod == "BC" && ymod == "BC"){
if(!is.null(X$EnvSuit[[e]][[i]]) && !is.null(Y$EnvSuit[[e]][[i]])){
message("\n\t...between environmental niches....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[e]][[i]], Y$EnvSuit[[e]][[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[e]][[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Env")
if (rnd.test){
simList[[e]][[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Env")
p.values[[e]][[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Env")
}
message("...done.")
}
if(!is.null(X$EnvSuit[[e]][[i]]) && !is.null(Y$EnvAcc[[e]][[i]])){
message("\n\t...between environmental accessibilities...", appendLF = F)
ncomp <- niche_comparison(X$EnvAcc[[e]][[i]], Y$EnvAcc[[e]][[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[e]][[i]] <- rbind(np[[e]][[i]], c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Acc2Acc"))
if (rnd.test){
simList[[e]][[i]] <- rbind(simList[[e]][[i]], cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Acc2Acc"))
p.values[[e]][[i]] <- rbind(p.values[[e]][[i]], cbind(alternative = alternative,
D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue, CS = ncomp$CS$pvalue,
ER = ncomp$ER$pvalue, ncomp$USE$pvalue,
comparison = "Acc2Acc"))
p.values[[e]][[i]] <- as.data.frame(p.values[[e]][[i]], row.names = rep("", nrow(p.values[[e]][[i]])))
}
message("...done.")
}
}
else if (xmod == "BC" && ymod == "EC"){
if(!is.null(X$EnvSuit[[e]][[i]]) && !is.null(Y$EnvSuit[[e]][[i]])){
message("\n\t...between environmental niches....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[e]][[i]], Y$EnvSuit[[e]][[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[e]][[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Env")
if (rnd.test){
simList[[e]][[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Env")
p.values[[e]][[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Env")
}
message("...done.")
}
if(!is.null(X$EnvSuit[[e]][[i]]) && !is.null(Y$EcoSuit[[e]][[i]])){
message("\n\t...between environmental niche and ecological niche...", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[e]][[i]], Y$EcoSuit[[e]][[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[e]][[i]] <- rbind(np[[e]][[i]], c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Eco"))
if (rnd.test){
simList[[e]][[i]] <- rbind(simList[[e]][[i]], cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Eco"))
p.values[[e]][[i]] <- rbind(p.values[[e]][[i]], cbind(alternative = alternative,
D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue, CS = ncomp$CS$pvalue,
ER = ncomp$ER$pvalue, ncomp$USE$pvalue,
comparison = "Env2Eco"))
p.values[[e]][[i]] <- as.data.frame(p.values[[e]][[i]], row.names = rep("", nrow(p.values[[e]][[i]])))
}
message("...done.")
}
if(!is.null(X$EnvAcc[[e]][[i]]) && !is.null(Y$EcoAcc[[e]][[i]])){
message("\n\t...between environmental accessibility and ecological accessibility", appendLF = F)
ncomp <- niche_comparison(X$EnvAcc[[e]][[i]], Y$EcoAcc[[e]][[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[e]][[i]] <- rbind(np[[e]][[i]], c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Acc2Acc"))
if (rnd.test){
simList[[e]][[i]] <- rbind(simList[[e]][[i]], cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Acc2Acc"))
p.values[[e]][[i]] <- rbind(p.values[[e]][[i]], cbind(alternative = alternative,
D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue, CS = ncomp$CS$pvalue,
ER = ncomp$ER$pvalue, ncomp$USE$pvalue,
comparison = "Acc2Acc"))
p.values[[e]][[i]] <- as.data.frame(p.values[[e]][[i]], row.names = rep("", nrow(p.values[[e]][[i]])))
}
message("...done.")
}
}
else if (xmod == "EC" && ymod == "EC"){
if(!is.null(X$EnvSuit[[e]][[i]]) && !is.null(Y$EnvSuit[[e]][[i]])){
message("\n\t...between environmental niches....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[e]][[i]], Y$EnvSuit[[e]][[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[e]][[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Env")
if (rnd.test){
simList[[e]][[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Env")
p.values[[e]][[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Env")
}
message("...done.")
}
if(!is.null(X$EcoSuit[[e]][[i]]) && !is.null(Y$EcoSuit[[e]][[i]])){
message("\n\t...between ecological niches....", appendLF = F)
ncomp <- niche_comparison(X$EcoSuit[[e]][[i]], Y$EcoSuit[[e]][[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[e]][[i]] <- rbind(np[[e]][[i]], c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Eco2Eco"))
if (rnd.test){
simList[[e]][[i]] <- rbind(simList[[e]][[i]], cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Eco2Eco"))
p.values[[e]][[i]] <- rbind(p.values[[e]][[i]], cbind(alternative = alternative,
D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue, CS = ncomp$CS$pvalue,
ER = ncomp$ER$pvalue, ncomp$USE$pvalue,
comparison = "Eco2Eco"))
p.values[[e]][[i]] <- as.data.frame(p.values[[e]][[i]], row.names = rep("", nrow(p.values[[e]][[i]])))
}
message("...done.")
}
if(!is.null(X$EcoAcc[[e]][[i]]) && !is.null(Y$EnvAcc[[e]][[i]])){
message("\n\t...between environmental acessibilities...", appendLF = F)
ncomp <- niche_comparison(X$EcoAcc[[e]][[i]], Y$EnvAcc[[e]][[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[e]][[i]] <- rbind(np[[e]][[i]], c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Acc2Acc"))
if (rnd.test){
simList[[e]][[i]] <- rbind(simList[[e]][[i]], cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Acc2Acc"))
p.values[[e]][[i]] <- rbind(p.values[[e]][[i]], cbind(alternative = alternative,
D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue, CS = ncomp$CS$pvalue,
ER = ncomp$ER$pvalue, ncomp$USE$pvalue,
comparison = "Acc2Acc"))
p.values[[e]][[i]] <- as.data.frame(p.values[[e]][[i]], row.names = rep("", nrow(p.values[[e]][[i]])))
}
message("...done.")
}
}
else if (xmod == "BC" && ymod == "EN"){
if(!is.null(X$EnvSuit[[e]][[i]]) && !is.null(Y$EnvSuit[[e]][[i]])){
message("\n\t...between environmental niches....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[e]][[i]], Y$EnvSuit[[e]][[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[e]][[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Env")
if (rnd.test){
simList[[e]][[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Env")
p.values[[e]][[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Env")
}
message("...done.")
}
if(!is.null(X$EnvAcc[[e]][[i]]) && !is.null(Y$EnvSuit[[e]][[i]])){
message("\n\t...between environmental acccessiibiliity and environmental niche....", appendLF = F)
ncomp <- niche_comparison(X$EnvAcc[[e]][[i]], Y$EnvSuit[[e]][[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[e]][[i]] <- rbind(np[[e]][[i]], c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Acc2Env"))
if (rnd.test){
simList[[e]][[i]] <- rbind(simList[[e]][[i]], cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Acc2Env"))
p.values[[e]][[i]] <- rbind(p.values[[e]][[i]], cbind(alternative = alternative,
D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue, CS = ncomp$CS$pvalue,
ER = ncomp$ER$pvalue, ncomp$USE$pvalue,
comparison = "Acc2Env"))
p.values[[e]][[i]] <- as.data.frame(p.values[[e]][[i]], row.names = rep("", nrow(p.values[[e]][[i]])))
}
message("...done.")
}
}
else if (xmod == "EC" && ymod == "EN"){
if(!is.null(X$EnvSuit[[e]][[i]]) && !is.null(Y$EnvSuit[[e]][[i]])){
message("\n\t...between environmental niches....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[e]][[i]], Y$EnvSuit[[e]][[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[e]][[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Env")
if (rnd.test){
simList[[e]][[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Env")
p.values[[e]][[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Env")
p.values[[e]][[i]] <- as.data.frame(p.values[[e]][[i]], row.names = rep("", nrow(p.values[[e]][[i]])))
}
message("...done.")
}
}
else if (xmod == "EC" && ymod == "BC"){
if(!is.null(X$EnvSuit[[e]][[i]]) && !is.null(Y$EnvSuit[[e]][[i]])){
message("\n\t...between environmental niches....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[e]][[i]], Y$EnvSuit[[e]][[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[e]][[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Env")
if (rnd.test){
simList[[e]][[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Env")
p.values[[e]][[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Env")
}
message("...done.")
}
if(!is.null(X$EcoSuit[[e]][[i]]) && !is.null(Y$EnvSuit[[e]][[i]])){
message("\n\t...between ecological niche and environmental niche....", appendLF = F)
ncomp <- niche_comparison(X$EcoSuit[[e]][[i]], Y$EnvSuit[[e]][[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[e]][[i]] <- rbind(np[[e]][[i]], c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Eco2Env"))
if (rnd.test){
simList[[e]][[i]] <- rbind(simList[[e]][[i]], cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Eco2Env"))
p.values[[e]][[i]] <- rbind(p.values[[e]][[i]], cbind(alternative = alternative,
D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue, CS = ncomp$CS$pvalue,
ER = ncomp$ER$pvalue, ncomp$USE$pvalue,
comparison = "Eco2Env"))
p.values[[e]][[i]] <- as.data.frame(p.values[[e]][[i]], row.names = rep("", nrow(p.values[[e]][[i]])))
}
message("...done.")
}
if(!is.null(X$EcoAcc[[e]][[i]]) && !is.null(Y$EnvAcc[[e]][[i]])){
message("\n\t...between ecological accessibillity and environmental accessibillity....", appendLF = F)
ncomp <- niche_comparison(X$EcoAcc[[e]][[i]], Y$EnvAcc[[e]][[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[e]][[i]] <- rbind(np[[e]][[i]], c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Acc2Acc"))
if (rnd.test){
simList[[e]][[i]] <- rbind(simList[[e]][[i]], cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Acc2Acc"))
p.values[[e]][[i]] <- rbind(p.values[[e]][[i]], cbind(alternative = alternative,
D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue, CS = ncomp$CS$pvalue,
ER = ncomp$ER$pvalue, ncomp$USE$pvalue,
comparison = "Acc2Acc"))
p.values[[e]][[i]] <- as.data.frame(p.values[[e]][[i]], row.names = rep("", nrow(p.values[[e]][[i]])))
}
message("...done.")
}
}
}
else{
message(paste("...nothing to analyze."))
}
}
np[[e]] <- plyr::ldply(np[[e]], .id = "species")
}
if (rnd.test){
simList <- reverse_list(simList)
p.values <- reverse_list(p.values)
out$np <- plyr::ldply(np, .id = "region")
out$sim <- lapply(simList, function(i) ldply(i, .id = "region"))
out$pvalue <- lapply(p.values, function(i) ldply(i, .id = "region"))
} else {
out <- plyr::ldply(np, .id = "region")
}
}
else {
stop("Regional models not found")
}
}
if (type == "global"){
if(clus){
if(!is.null(x$z.mod.global)){
if(xmod == "EN"){
X = list(EnvSuit = x$z.mod.global)
} else if (xmod == "BC") {
X = list(EnvSuit = x$z.mod.global,
EnvAcc = x$w.global)
} else if (xmod == "EC") {
X = list(EnvSuit = x$z.mod.global,
EcoSuit = x$t.mod.global,
EcoAcc = x$g.global)
}
} else {
stop("Global models of argument 'x' not found")
}
if (!missing(y)){
if(!is.null(y$z.mod.global)){
if(ymod == "EN"){
Y = list(EnvSuit = y$z.mod.global)
} else if (ymod == "BC") {
Y = list(EnvSuit = y$z.mod.global,
EnvAcc = y$w.global)
} else if (ymod == "EC") {
Y = list(EnvSuit = y$z.mod.global,
EcoSuit = y$t.mod.global,
EcoAcc = y$g.global)
}
} else {
stop("Global models of argument 'y' not found")
}
}
}
np = list()
p.values <- list()
simList <- list()
for (i in names(X[[1]])){
message(paste("Computing niche metrics of", i, "..."), appendLF = F)
if (xmod == "BC" && is.null(ymod)){
if(!is.null(X$EnvSuit[[i]]) && !is.null(X$EnvAcc[[i]])){
message("\n\t...between environmental niche and environmental accessibillity....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[i]], X$EnvAcc[[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Acc")
if (rnd.test){
simList[[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Acc")
p.values[[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Acc")
p.values[[i]] <- as.data.frame(p.values[[i]], row.names = rep("", nrow(p.values[[i]])))
}
message("...done.")
}
}
else if (xmod == "EC" && is.null(ymod)){
if(!is.null(X$EnvSuit[[i]]) && !is.null(X$EcoSuit[[i]])){
message("\n\t...between environmental niche and ecological niche...", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[i]], X$EcoSuit[[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Eco")
if (rnd.test){
simList[[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Eco")
p.values[[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Eco")
}
message("...done.")
}
if(!is.null(X$EcoSuit[[i]]) && !is.null(X$EcoAcc[[i]])){
message("\n\t...between ecological niche and ecological accessibillity....", appendLF = F)
ncomp <- niche_comparison(X$EcoSuit[[i]], X$EcoAcc[[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[i]] <- rbind(np[[i]], c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Eco2Acc"))
if (rnd.test){
simList[[i]] <- rbind(simList[[i]], cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Eco2Acc"))
p.values[[i]] <- rbind(p.values[[i]], cbind(alternative = alternative,
D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue, CS = ncomp$CS$pvalue,
ER = ncomp$ER$pvalue, ncomp$USE$pvalue,
comparison = "Eco2Acc"))
p.values[[i]] <- as.data.frame(p.values[[i]], row.names = rep("", nrow(p.values[[i]])))
}
message("...done.")
}
}
else if (!is.null(Y[[1]][[i]])){
if (xmod == "EN" && ymod == "EN"){
if(!is.null(X$EnvSuit[[i]]) && !is.null(Y$EnvSuit[[i]])){
message("\n\t...between environmental niches....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[i]], Y$EnvSuit[[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Env")
if (rnd.test){
simList[[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Env")
p.values[[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Env")
p.values[[i]] <- as.data.frame(p.values[[i]], row.names = rep("", nrow(p.values[[i]])))
}
message("...done.")
}
}
else if (xmod == "EN" && ymod == "BC"){
if(!is.null(X$EnvSuit[[i]]) && !is.null(Y$EnvSuit[[i]])){
message("\n\t...between environmental niches....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[i]], Y$EnvSuit[[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Env")
if (rnd.test){
simList[[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Env")
p.values[[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Env")
}
message("...done.")
}
if(!is.null(X$EnvSuit[[i]]) && !is.null(Y$EnvAcc[[i]])){
message("\n\t...between environmental niche and environmental accessibillity....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[i]], Y$EnvAcc[[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[i]] <- rbind(np[[i]], c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Acc"))
if (rnd.test){
simList[[i]] <- rbind(simList[[i]], cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Acc"))
p.values[[i]] <- rbind(p.values[[i]], cbind(alternative = alternative,
D = ncomp$D$pvalue, CS = ncomp$CS$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
ER = ncomp$ER$pvalue, ncomp$USE$pvalue,
comparison = "Env2Acc"))
p.values[[i]] <- as.data.frame(p.values[[i]], row.names = rep("", nrow(p.values[[i]])))
}
message("...done.")
}
}
else if (xmod == "EN" && ymod == "EC"){
if(!is.null(X$EnvSuit[[i]]) && !is.null(Y$EnvSuit[[i]])){
message("\n\t...between environmental niches....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[i]], Y$EnvSuit[[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Env")
if (rnd.test){
simList[[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Env")
p.values[[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Env")
p.values[[i]] <- as.data.frame(p.values[[i]], row.names = rep("", nrow(p.values[[i]])))
}
message("...done.")
}
}
else if (xmod == "BC" && ymod == "BC"){
if(!is.null(X$EnvSuit[[i]]) && !is.null(Y$EnvSuit[[i]])){
message("\n\t...between environmental niches....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[i]], Y$EnvSuit[[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Env")
if (rnd.test){
simList[[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Env")
p.values[[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Env")
}
message("...done.")
}
if(!is.null(X$EnvSuit[[i]]) && !is.null(Y$EnvAcc[[i]])){
message("\n\t...between environmental accessibilities...", appendLF = F)
ncomp <- niche_comparison(X$EnvAcc[[i]], Y$EnvAcc[[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[i]] <- rbind(np[[i]], c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Acc2Acc"))
if (rnd.test){
simList[[i]] <- rbind(simList[[i]], cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Acc2Acc"))
p.values[[i]] <- rbind(p.values[[i]], cbind(alternative = alternative,
D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue, CS = ncomp$CS$pvalue,
ER = ncomp$ER$pvalue, ncomp$USE$pvalue,
comparison = "Acc2Acc"))
p.values[[i]] <- as.data.frame(p.values[[i]], row.names = rep("", nrow(p.values[[i]])))
}
message("...done.")
}
}
else if (xmod == "BC" && ymod == "EC"){
if(!is.null(X$EnvSuit[[i]]) && !is.null(Y$EnvSuit[[i]])){
message("\n\t...between environmental niches....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[i]], Y$EnvSuit[[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Env")
if (rnd.test){
simList[[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Env")
p.values[[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Env")
}
message("...done.")
}
if(!is.null(X$EnvSuit[[i]]) && !is.null(Y$EcoSuit[[i]])){
message("\n\t...between environmental niche and ecological niche...", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[i]], Y$EcoSuit[[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[i]] <- rbind(np[[i]], c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Eco"))
if (rnd.test){
simList[[i]] <- rbind(simList[[i]], cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Eco"))
p.values[[i]] <- rbind(p.values[[i]], cbind(alternative = alternative,
D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue, CS = ncomp$CS$pvalue,
ER = ncomp$ER$pvalue, ncomp$USE$pvalue,
comparison = "Env2Eco"))
p.values[[i]] <- as.data.frame(p.values[[i]], row.names = rep("", nrow(p.values[[i]])))
}
message("...done.")
}
if(!is.null(X$EnvAcc[[i]]) && !is.null(Y$EcoAcc[[i]])){
message("\n\t...between environmental accessibility and ecological accessibility", appendLF = F)
ncomp <- niche_comparison(X$EnvAcc[[i]], Y$EcoAcc[[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[i]] <- rbind(np[[i]], c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Acc2Acc"))
if (rnd.test){
simList[[i]] <- rbind(simList[[i]], cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Acc2Acc"))
p.values[[i]] <- rbind(p.values[[i]], cbind(alternative = alternative,
D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue, CS = ncomp$CS$pvalue,
ER = ncomp$ER$pvalue, ncomp$USE$pvalue,
comparison = "Acc2Acc"))
p.values[[i]] <- as.data.frame(p.values[[i]], row.names = rep("", nrow(p.values[[i]])))
}
message("...done.")
}
}
else if (xmod == "EC" && ymod == "EC"){
if(!is.null(X$EnvSuit[[i]]) && !is.null(Y$EnvSuit[[i]])){
message("\n\t...between environmental niches....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[i]], Y$EnvSuit[[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Env")
if (rnd.test){
simList[[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Env")
p.values[[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Env")
}
message("...done.")
}
if(!is.null(X$EcoSuit[[i]]) && !is.null(Y$EcoSuit[[i]])){
message("\n\t...between ecological niches....", appendLF = F)
ncomp <- niche_comparison(X$EcoSuit[[i]], Y$EcoSuit[[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[i]] <- rbind(np[[i]], c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Eco2Eco"))
if (rnd.test){
simList[[i]] <- rbind(simList[[i]], cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Eco2Eco"))
p.values[[i]] <- rbind(p.values[[i]], cbind(alternative = alternative,
D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue, CS = ncomp$CS$pvalue,
ER = ncomp$ER$pvalue, ncomp$USE$pvalue,
comparison = "Eco2Eco"))
p.values[[i]] <- as.data.frame(p.values[[i]], row.names = rep("", nrow(p.values[[i]])))
}
message("...done.")
}
if(!is.null(X$EcoAcc[[i]]) && !is.null(Y$EnvAcc[[i]])){
message("\n\t...between environmental acessibilities...", appendLF = F)
ncomp <- niche_comparison(X$EcoAcc[[i]], Y$EnvAcc[[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[i]] <- rbind(np[[i]], c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Acc2Acc"))
if (rnd.test){
simList[[i]] <- rbind(simList[[i]], cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Acc2Acc"))
p.values[[i]] <- rbind(p.values[[i]], cbind(alternative = alternative,
D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue, CS = ncomp$CS$pvalue,
ER = ncomp$ER$pvalue, ncomp$USE$pvalue,
comparison = "Acc2Acc"))
p.values[[i]] <- as.data.frame(p.values[[i]], row.names = rep("", nrow(p.values[[i]])))
}
message("...done.")
}
}
else if (xmod == "BC" && ymod == "EN"){
if(!is.null(X$EnvSuit[[i]]) && !is.null(Y$EnvSuit[[i]])){
message("\n\t...between environmental niches....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[i]], Y$EnvSuit[[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Env")
if (rnd.test){
simList[[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Env")
p.values[[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Env")
}
message("...done.")
}
if(!is.null(X$EnvAcc[[i]]) && !is.null(Y$EnvSuit[[i]])){
message("\n\t...between environmental acccessiibiliity and environmental niche....", appendLF = F)
ncomp <- niche_comparison(X$EnvAcc[[i]], Y$EnvSuit[[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[i]] <- rbind(np[[i]], c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Acc2Env"))
if (rnd.test){
simList[[i]] <- rbind(simList[[i]], cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Acc2Env"))
p.values[[i]] <- rbind(p.values[[i]], cbind(alternative = alternative,
D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue, CS = ncomp$CS$pvalue,
ER = ncomp$ER$pvalue, ncomp$USE$pvalue,
comparison = "Acc2Env"))
p.values[[i]] <- as.data.frame(p.values[[i]], row.names = rep("", nrow(p.values[[i]])))
}
message("...done.")
}
}
else if (xmod == "EC" && ymod == "EN"){
if(!is.null(X$EnvSuit[[i]]) && !is.null(Y$EnvSuit[[i]])){
message("\n\t...between environmental niches....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[i]], Y$EnvSuit[[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Env")
if (rnd.test){
simList[[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Env")
p.values[[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Env")
p.values[[i]] <- as.data.frame(p.values[[i]], row.names = rep("", nrow(p.values[[i]])))
}
message("...done.")
}
}
else if (xmod == "EC" && ymod == "BC"){
if(!is.null(X$EnvSuit[[i]]) && !is.null(Y$EnvSuit[[i]])){
message("\n\t...between environmental niches....", appendLF = F)
ncomp <- niche_comparison(X$EnvSuit[[i]], Y$EnvSuit[[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[i]] <- c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Env2Env")
if (rnd.test){
simList[[i]] <- cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Env2Env")
p.values[[i]] <- cbind(alternative = alternative, D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue,
CS = ncomp$CS$pvalue, ER = ncomp$ER$pvalue,
ncomp$USE$pvalue, comparison = "Env2Env")
}
message("...done.")
}
if(!is.null(X$EcoSuit[[i]]) && !is.null(Y$EnvSuit[[i]])){
message("\n\t...between ecological niche and environmental niche....", appendLF = F)
ncomp <- niche_comparison(X$EcoSuit[[i]], Y$EnvSuit[[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[i]] <- rbind(np[[i]], c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Eco2Env"))
if (rnd.test){
simList[[i]] <- rbind(simList[[i]], cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Eco2Env"))
p.values[[i]] <- rbind(p.values[[i]], cbind(alternative = alternative,
D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue, CS = ncomp$CS$pvalue,
ER = ncomp$ER$pvalue, ncomp$USE$pvalue,
comparison = "Eco2Env"))
p.values[[i]] <- as.data.frame(p.values[[i]], row.names = rep("", nrow(p.values[[i]])))
}
message("...done.")
}
if(!is.null(X$EcoAcc[[i]]) && !is.null(Y$EnvAcc[[i]])){
message("\n\t...between ecological accessibillity and environmental accessibillity....", appendLF = F)
ncomp <- niche_comparison(X$EcoAcc[[i]], Y$EnvAcc[[i]], centroid.w = centroid.w, rnd.test = rnd.test,
quantile = quantile, np.type = np.type, np.metric = np.metric,
cor = cor, rep = rep, rand = rand, alternative = alternative)
np[[i]] <- rbind(np[[i]], c(unlist(c(D = ncomp$D$obs, breadth.diff = ncomp$breadth.diff$obs, CS = ncomp$CS$obs,
ER = ncomp$ER$obs, ncomp$CS$weights, ncomp$USE$obs)),
comparison = "Acc2Acc"))
if (rnd.test){
simList[[i]] <- rbind(simList[[i]], cbind(D = ncomp$D$sim, breadth.diff = ncomp$breadth.diff$sim, CS = ncomp$CS$sim,
ER = ncomp$ER$sim, ncomp$USE$sim,
comparison = "Acc2Acc"))
p.values[[i]] <- rbind(p.values[[i]], cbind(alternative = alternative,
D = ncomp$D$pvalue, breadth.diff = ncomp$breadth.diff$pvalue, CS = ncomp$CS$pvalue,
ER = ncomp$ER$pvalue, ncomp$USE$pvalue,
comparison = "Acc2Acc"))
p.values[[i]] <- as.data.frame(p.values[[i]], row.names = rep("", nrow(p.values[[i]])))
}
message("...done.")
}
}
}
else{
message(paste("...nothing to analyze."))
}
}
if (rnd.test){
out$np <- plyr::ldply(np, .id = "species")
out$sim <- simList
out$pvalues <- p.values
} else {
out <- plyr::ldply(np, .id = "species")
}
}
message("DONE")
return(out)
}
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