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#' @rdname pcps.sig
#' @encoding UTF-8
#' @export
matrix.p.sig <- function (comm, phylodist, envir, checkdata = TRUE, FUN, runs = 999, parallel = NULL, newname = "pcps", ...)
{
res <- list(call = match.call())
if (inherits(comm, "metacommunity.data")) {
if (!missing(phylodist)) {
stop("\n When you use an object of class metacommunity.data the argument phylodist must not be specified. \n")
}
phylodist <- comm$phylodist
envir <- comm$environmental
comm <- comm$community
}
list.warning <- list()
if(checkdata){
organize.temp <- organize.pcps(comm, phylodist = phylodist, envir = envir, check.comm = TRUE)
if(!is.null(organize.temp$stop)){
organize.temp$call <- match.call()
return(organize.temp)
}
list.warning <- organize.temp$list.warning
comm <- organize.temp$community
phylodist <- organize.temp$phylodist
envir <- organize.temp$environmental
# envir nao conferido
}
if(length(list.warning)>0){
res$list.warning <- list.warning
}
res.pcps.null <- matrix.p.null(comm, phylodist, runs = runs, calcpcps = FALSE)
res.pcps.null <- mutate.names.matrix.p.null(res.pcps.null, "pcps", newname)
res$P.obs <- res.pcps.null$P.obs
statistic.obs <- sapply(list(res.pcps.null$P.obs), FUN = FUN, simplify = FALSE, return.model = TRUE, envir = envir, ...)
res$model <- statistic.obs[[1]]$mod.obs
res$fun <- FUN
res$obs.statistic <- statistic.obs[[1]]$statistic.obs
newClusters <- FALSE
if (is.numeric(parallel)) {
parallel <- parallel::makeCluster(parallel, type = "PSOCK")
newClusters <- TRUE
}
if (!inherits(parallel, "cluster")) {
statistic.null.taxa <- sapply(res.pcps.null$P.null.taxa, FUN = FUN, simplify = FALSE, envir = envir, ...)
statistic.null.site <- sapply(res.pcps.null$P.null.site, FUN = FUN, simplify = FALSE, envir = envir, ...)
}
else {
statistic.null.taxa <- parallel::parLapply(parallel, res.pcps.null$P.null.taxa, fun = FUN, envir = envir, ...)
statistic.null.site <- parallel::parLapply(parallel, res.pcps.null$P.null.site, fun = FUN, envir = envir, ...)
}
if (newClusters) {
parallel::stopCluster(parallel)
}
res$statistic.null.site <- do.call("rbind", statistic.null.site)
res$statistic.null.taxa <- do.call("rbind", statistic.null.taxa)
res$p.site.shuffle <- as.vector(rbind((apply(sweep(res$statistic.null.site, 2, res$obs.statistic, ">="), 2, sum)+1)/(runs + 1)))
res$p.taxa.shuffle <- as.vector(rbind((apply(sweep(res$statistic.null.taxa, 2, res$obs.statistic, ">="), 2, sum)+1)/(runs + 1)))
class(res) <- "pcpssig"
return(res)
}
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