From 5f7c220c9a7ac8330b12fb03c34d75e1c13e01c3 Mon Sep 17 00:00:00 2001
From: Francesco Sabatini <francesco.sabatini@idiv.de>
Date: Tue, 4 Aug 2020 16:01:35 +0200
Subject: [PATCH] Aligned submit to cover data
---
00_Mesobromion_DataPreparation.R | 4 ++--
01b_MesobromionCluster.R | 3 ++-
session.R | 4 ++--
submit_01b.sh | 6 +++---
4 files changed, 9 insertions(+), 8 deletions(-)
diff --git a/00_Mesobromion_DataPreparation.R b/00_Mesobromion_DataPreparation.R
index e825207..3386d0f 100644
--- a/00_Mesobromion_DataPreparation.R
+++ b/00_Mesobromion_DataPreparation.R
@@ -297,7 +297,7 @@ species_nozero <- species[,-(empty+1)]
write_delim(species_nozero , path="_data/Mesobromion/species.out.10perc_nozero.txt", delim="\t")
write_delim(traits_nozero, path="_data/Mesobromion/traits.out.10perc_nozero.txt", delim="\t")
-
+### create list of relevées
write_delim(species %>%
dplyr::select(RELEVE_NR),
path="_derived/Mesobromion/ReleveList.txt", delim="\t")
@@ -345,7 +345,7 @@ traits.proz %>%
filter_at(.vars=vars(-"species0"),
all_vars(is.na(.))) %>%
dim() ## [1] 16 53 # species with no trait info
-write_delim(traits.cov, path="_data/Mesobromion/traits.out.10perc.cov.txt", delim="\t")
+write_delim(traits.proz, path="_data/Mesobromion/traits.out.10perc.cov.txt", delim="\t")
#### CORRELATION BETWEEN FUZZY WEIGHTED AND BEALS MATRICES
#### WAS RUN IN THE CLUSTER WITH THE SCRIPT 01b_MesobromionCluster.R
diff --git a/01b_MesobromionCluster.R b/01b_MesobromionCluster.R
index 03a024d..79bf597 100644
--- a/01b_MesobromionCluster.R
+++ b/01b_MesobromionCluster.R
@@ -71,7 +71,8 @@ Mesobromion <- function(species.path, traits.path, output, myfunction="get.corXY
myfunction <- get(myfunction)
## calculate corr between species composition matrix and traits
species <- read_delim(species.path, delim="\t") %>%
- as.data.frame()
+ as.data.frame() %>%
+ column_to_rownames("RELEVE_NR")
traits <- read_delim(traits.path, delim="\t") %>%
as.data.frame() #%>%
### TEMPORARY FOR TESTING!
diff --git a/session.R b/session.R
index 0c16f8d..07dc7d3 100644
--- a/session.R
+++ b/session.R
@@ -1,6 +1,6 @@
-species.path <- "_data/Mesobromion/species.out.10perc.txt"
-traits.path <- "_data/Mesobromion/traits.out.10perc.txt"
+species.path <- "_data/Mesobromion/species.out.10perc.cov.txt"
+traits.path <- "_data/Mesobromion/traits.out.10perc.cov.txt"
output <- "_derived/Mesobromion/HIDDEN"
myfunction <- "get.corXY.bootstrap"
max.inter.t <- 2
diff --git a/submit_01b.sh b/submit_01b.sh
index 0e50834..5e24dff 100644
--- a/submit_01b.sh
+++ b/submit_01b.sh
@@ -1,7 +1,7 @@
#!/bin/bash
#$ -S /bin/bash
-#$ -N HIDDEN
+#$ -N HIDDENcov
#$ -o /work/$USER/$JOB_NAME-$JOB_ID.log
#$ -j y
@@ -27,8 +27,8 @@ Rscript \
--ncores ${NSLOTS:-1} \
--start.round 1 \
--relax.round 4 \
- /data/splot/HIDDEN/species.out.10perc.txt \
- /data/splot/HIDDEN/traits.out.10perc.txt \
+ /data/splot/HIDDEN/species.out.10perc.cov.txt \
+ /data/splot/HIDDEN/traits.out.10perc.cov.txt \
"$output" \
"get.corXY.bootstrap" \
"sequential" \
--
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