Aligned submit to cover data

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

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!

session.R

 
-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

submit_01b.sh

 #!/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" \