From 4fa25d73e83f612f5f7cf0e670c27e1041892d0e Mon Sep 17 00:00:00 2001
From: Francesco Sabatini <francesco.sabatini@idiv.de>
Date: Fri, 21 Aug 2020 08:35:08 +0200
Subject: [PATCH] Fix 99 for NAs in traits
---
99_HIDDEN_functions.R | 19 ++++++++-----------
1 file changed, 8 insertions(+), 11 deletions(-)
diff --git a/99_HIDDEN_functions.R b/99_HIDDEN_functions.R
index c5c919a..cb45b92 100644
--- a/99_HIDDEN_functions.R
+++ b/99_HIDDEN_functions.R
@@ -33,12 +33,6 @@ 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
- ## CAUTION - function below doesn't work as expected
-# 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)$matrix.X #, asym.bin=binary.traits
- W.beals <- as.data.frame(beals(comm, include=T, type=2))
# permute traits
### Create vector of species to resample from, which exclude species with NAs
traits.ii <- traits[,ii, drop=F]
@@ -53,12 +47,15 @@ get.corXY.bootstrap <- function(comm, traits, trait.sel="all", bootstrap=199){
out[is.na(out)] <- sample(toresample, replace=F)
return(out)
})
- #index.traits <- lapply(1:(bootstrap+1), function(x){sample(1:nrow(traits), replace=F)})
- syn.out.perm.tmp <- matrix.x(comm=comm, traits=traits[index.traits[[bootstrap+1]],ii,drop=F],
- scale=T)$matrix.X #, asym.bin=binary.traits
-
+ ##calculate corXY on observed values using all plots
+ syn.out.tmp <- matrix.x(comm=comm, traits=traits.ii, scale=T)$matrix.X #, asym.bin=binary.traits
+ W.beals <- as.data.frame(beals(comm, include=T, type=2))
(RD.tmp <- dcor(W.beals, as.data.frame(syn.out.tmp))^2)
+ ##calculate corresponding permuted corXY using all plots
+ syn.out.perm.tmp <- matrix.x(comm=comm, traits=traits.ii[index.traits[[bootstrap+1]],],
+ scale=T)$matrix.X #, asym.bin=binary.traits
(RD.perm.tmp <- dcor(W.beals, as.data.frame(syn.out.perm.tmp))^2)
+ ## calculate corXY for each bootstrap run
corXY <- NULL
corXY <- data.frame(Trait.comb=lab.tmp, bootstr.n=0, Test="RD",
Coef.obs=RD.tmp, Coef.perm=RD.perm.tmp)
@@ -66,7 +63,7 @@ get.corXY.bootstrap <- function(comm, traits, trait.sel="all", bootstrap=199){
index.bootstr <- lapply(1:bootstrap, function(x){sample(1:n.sites, replace=T)})
for(b in 1:bootstrap){
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[[b]],ii,drop=F],
+ syn.out.perm.tmp <- matrix.x(comm=comm, traits=traits.ii[index.traits[[b]],],
scale=T)$matrix.X #, asym.bin=binary.traits
RD.perm.tmp <- dcor(W.beals[index.bootstr[[b]],], as.data.frame(syn.out.perm.tmp)[index.bootstr[[b]],])^2
corXY <- rbind(corXY,
--
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