From f1611e6b01e1055531659d91be506cc7c2a818ac Mon Sep 17 00:00:00 2001
From: Francesco Sabatini <francesco.sabatini@idiv.de>
Date: Mon, 17 Aug 2020 17:31:34 +0200
Subject: [PATCH] Aligned
---
01b_MesobromionCluster.R | 19 +++++++++----------
cli_01b.r | 2 +-
2 files changed, 10 insertions(+), 11 deletions(-)
diff --git a/01b_MesobromionCluster.R b/01b_MesobromionCluster.R
index 223f6cd..2d822d4 100644
--- a/01b_MesobromionCluster.R
+++ b/01b_MesobromionCluster.R
@@ -82,18 +82,17 @@ Mesobromion <- function(species.path, traits.path, output, myfunction="get.corXY
traits <- traits %>%
rename_all(.funs=~gsub(pattern=".mean$", replacement="", x=.)) %>%
mutate_if(~is.character(.), .funs=~as.factor(.)) %>%
+ filter(complete.cases(.)) %>% ## TEMPORARY ! only species without any NA
column_to_rownames("species0")
-
-#temporary ### Use only a subset of traits
- #dplyr::select(LeafArea:Disp.unit.leng)
- print("TEMPORARY - delete species with any NA in traits")
- traits <- traits %>%
- filter(complete.cases(.))
+ print("TEMPORARY - only species without any NA")
species <- species %>%
- dplyr::select(rownames(traits))
+ dplyr::select(rownames(traits))
- print("TEMPORARY - revert back species to pa")
+ print("TEMPORARY - revert abundances back to pa")
species <- (species>0)*1
+
+#temporary ### Use only a subset of traits
+ #dplyr::select(LeafArea:Disp.unit.leng)
if(combinations=="all") {
## create list of indices for each combination of traits up to a max number of interactions
@@ -119,10 +118,10 @@ Mesobromion <- function(species.path, traits.path, output, myfunction="get.corXY
corXY.output <- foreach(i=1:length(allcomb.t), .combine=rbind) %myinfix% {
tt <- unlist(allcomb.t[i])
corXY.output <- rbind(corXY.output,
- get.corXY.bootstrap(comm=species, trait=traits,
+ myfunction(comm=species, trait=traits,
trait.sel=tt, bootstrap=nperm))
}
- save(corXY.output, file = paste(output, "_.RData", sep=""))
+ save(corXY.output, file = paste(output,"_", chunk.i, "_.RData", sep=""))
}
diff --git a/cli_01b.r b/cli_01b.r
index 65f8ff1..b795568 100644
--- a/cli_01b.r
+++ b/cli_01b.r
@@ -105,4 +105,4 @@ ncores <- cli$options$ncores
# ------------------------------------------------------------------------------
source("01b_MesobromionCluster.R")
-Mesobromion(species.path, traits.path, output, myfunction, combinations, start.round, relax.round, max.inter.t, chunk.n, chunk.i, nperm, ncores)
+Mesobromion(species.path, traits.path, output, myfunction, combinations, start.round, relax.round, max.inter.t, chunkn, chunk.i, nperm, ncores)
--
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