diff --git a/99_HIDDEN_functions.R b/99_HIDDEN_functions.R index 222457151b4639742eb03bd76452cc4ca87d9742..8ca71e6b29097ddc929d6b0882ad053de63575b2 100644 --- a/99_HIDDEN_functions.R +++ b/99_HIDDEN_functions.R @@ -50,11 +50,6 @@ get.corXY <- function(comm, traits, trait.sel="all", stat=c("mantel", "RV", "pro #### Function 1b - CorXY bootstrap#### get.corXY.bootstrap <- function(comm, traits, trait.sel="all", bootstrap=199){ - ## caution - ## ALL columns with only 0-1 values are AUTOMATICALLY considered as asym.bin sensu FD:gowdis - ##get all columns with binary variables - binary.traits <- which( (traits %>% summarize_all( ~all(na.omit(.) %in% 0:1) )) ==T) - if(identical(trait.sel, "all")) {trait.sel <- 1:ncol(traits)} ii <- trait.sel lab.tmp <- paste(ii, collapse="_") @@ -67,11 +62,18 @@ get.corXY.bootstrap <- function(comm, traits, trait.sel="all", bootstrap=199){ #Calculate correlations on full data n.sites <- nrow(comm) n.species <- ncol(comm) + + ## caution + ## ALL columns with only 0-1 values are AUTOMATICALLY considered as asym.bin sensu FD:gowdis + ##get all columns with binary variables + binary.traits <- which(apply(traits[,ii,drop=F], MARGIN=2, function(x)( all(na.omit(x) %in% 0:1) ))==T) + syn.out.tmp <- matrix.x(comm=comm, traits=traits[,ii,drop=F], scale=T, asym.bin=binary.traits)$matrix.X W.beals <- as.data.frame(beals(comm, include=T, type=2)) # permtute traits index.traits <- lapply(1:(bootstrap+1), function(x){sample(1:n.species, replace=F)}) - syn.out.perm.tmp <- matrix.x(comm=comm, traits=traits[index.traits[[bootstrap+1]],ii,drop=F], scale=T)$matrix.X + syn.out.perm.tmp <- matrix.x(comm=comm, traits=traits[index.traits[[bootstrap+1]],ii,drop=F], + scale=T, asym.bin=binary.traits)$matrix.X corXY <- NULL #RD.tmp <- RV.rtest(W.beals, as.data.frame(syn.out.tmp), nrepet = 0)