From 5d8a58e196afde89f100230360a7a65c4c3fae90 Mon Sep 17 00:00:00 2001
From: Francesco Sabatini <francesco.sabatini@idiv.de>
Date: Wed, 22 Apr 2020 18:53:48 +0200
Subject: [PATCH] Adjusted get.corXY.bootstrap to account for asymmetric binary
traits in FD:gowdis
---
99_HIDDEN_functions.R | 13 +++++++++++--
1 file changed, 11 insertions(+), 2 deletions(-)
diff --git a/99_HIDDEN_functions.R b/99_HIDDEN_functions.R
index 7d5580d..0f7dfce 100644
--- a/99_HIDDEN_functions.R
+++ b/99_HIDDEN_functions.R
@@ -50,6 +50,11 @@ 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(is.bin)) ==T)
+
if(identical(trait.sel, "all")) {trait.sel <- 1:ncol(traits)}
ii <- trait.sel
lab.tmp <- paste(ii, collapse="_")
@@ -62,7 +67,7 @@ get.corXY.bootstrap <- function(comm, traits, trait.sel="all", bootstrap=199){
#Calculate correlations on full data
n.sites <- nrow(comm)
n.species <- ncol(comm)
- syn.out.tmp <- matrix.x(comm=comm, traits=traits[,ii,drop=F], scale=T)$matrix.X
+ syn.out.tmp <- matrix.x(comm=comm, traits=traits[,ii,drop=F], scale=T, asym.bin=binary.traits)$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)})
@@ -81,7 +86,8 @@ get.corXY.bootstrap <- function(comm, traits, trait.sel="all", bootstrap=199){
for(b in 1:bootstrap){
#RV.tmp <- RV.rtest(W.beals[index.bootstr[[b]],], as.data.frame(syn.out.tmp)[index.bootstr[[b]],])
RD.tmp <- dcor(W.beals[index.bootstr[[b]],], as.data.frame(syn.out.tmp)[index.bootstr[[b]],])^2
- syn.out.perm.tmp <- matrix.x(comm=comm, traits=traits[index.traits[[bootstrap]],ii,drop=F], scale=T)$matrix.X
+ syn.out.perm.tmp <- matrix.x(comm=comm, traits=traits[index.traits[[bootstrap]],ii,drop=F],
+ scale=T, asym.bin=binary.traits)$matrix.X
#RV.perm.tmp <- RV.rtest(W.beals[index.bootstr[[b]],], as.data.frame(syn.out.perm.tmp)[index.bootstr[[b]],])
RD.perm.tmp <- dcor(W.beals[index.bootstr[[b]],], as.data.frame(syn.out.perm.tmp)[index.bootstr[[b]],])^2
corXY <- rbind(corXY,
@@ -210,4 +216,7 @@ get.SES <- function(obs.df, perm.df, stat="RV") {
+## Cracked version of matrix.x from SYNCSA to account for asymmetric binary variables in gowdis
+
+
--
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