From 4798a781507eed876d90886577c95fd70239a865 Mon Sep 17 00:00:00 2001
From: Francesco Sabatini <francesco.sabatini@idiv.de>
Date: Mon, 27 Apr 2020 10:32:22 +0200
Subject: [PATCH] Added new argument start.round
---
01b_MesobromionCluster.R | 17 +++++++++++------
cli_01b.r | 3 ++-
session.R | 5 +++--
submit_01b.sh | 3 ++-
4 files changed, 18 insertions(+), 10 deletions(-)
diff --git a/01b_MesobromionCluster.R b/01b_MesobromionCluster.R
index 8b07980..ba35464 100644
--- a/01b_MesobromionCluster.R
+++ b/01b_MesobromionCluster.R
@@ -55,7 +55,8 @@ get.best <- function(x, N){
Mesobromion <- function(species.path, traits.path, output, myfunction="get.corXY.bootstrap",
- combinations=c("all", "sequential"), max.inter.t, chunkn, chunk.i, nperm=199, ncores){
+ combinations=c("all", "sequential"), start.round=NA, max.inter.t,
+ chunkn, chunk.i, nperm=199, ncores){
if(ncores>1){
require(parallel)
@@ -72,9 +73,9 @@ Mesobromion <- function(species.path, traits.path, output, myfunction="get.corXY
species <- read_delim(species.path, delim="\t") %>%
as.data.frame()
traits <- read_delim(traits.path, delim="\t") %>%
- as.data.frame() %>%
+ as.data.frame() #%>%
### TEMPORARY FOR TESTING!
- dplyr::select(1:11)
+ #dplyr::select(1:11)
traits <- traits %>%
@@ -115,8 +116,11 @@ Mesobromion <- function(species.path, traits.path, output, myfunction="get.corXY
if(combinations=="sequential"){
- corXY.ci <- NULL
- for(nround in 1:max.inter.t){
+ if(!is.na(start.round)){
+ print(paste("Load data from previous round=", start.round-1))
+ load(file = paste(output, "_round_", start.round-1, ".RData", sep=""))
+ } else {corXY.ci <- NULL}
+ for(nround in start.round:max.inter.t){
corXY.output <- NULL
## select combination of traits based on best
if(nround==1) {
@@ -211,8 +215,9 @@ Mesobromion <- function(species.path, traits.path, output, myfunction="get.corXY
} else {print(paste("no new best at round=", nround))}
}
print(paste("save intermediate results at round", nround))
- save(corXY.output, file = paste(output, "_round_",nround, ".RData", sep=""))
+ save(corXY.output, best, traits.sign.alone, corXY.ci, file = paste(output, "_round_",nround, ".RData", sep=""))
}
}
if(ncores>1){stopCluster(cl)}
}
+
diff --git a/cli_01b.r b/cli_01b.r
index 51a65a6..912e036 100644
--- a/cli_01b.r
+++ b/cli_01b.r
@@ -65,7 +65,7 @@ parser <- OptionParser(
epilogue = "use with caution, the awesomeness might slap you in the face!"
)
-cli <- parse_args(parser, positional_arguments = 5)
+cli <- parse_args(parser, positional_arguments = 6)
# ------------------------------------------------------------------------------
# assign a few shortcuts
@@ -76,6 +76,7 @@ traits.path <- cli$args[2]
output <- cli$args[3]
myfunction <- cli$args[4]
combinations <- cli$args[5]
+start.round <- cli$args[6]
max.inter.t <- cli$options$max.inter.t
chunkn <- cli$options$chunkn
chunk.i <- cli$options$chunk.i
diff --git a/session.R b/session.R
index 722702f..c62e048 100644
--- a/session.R
+++ b/session.R
@@ -6,11 +6,12 @@ myfunction <- "get.corXY.bootstrap"
max.inter.t <- 3
chunk.i <- NA
nperm <- 20
-ncores <- 10
+ncores <- 1
chunkn <- 3*ncores
combinations <- "sequential"
+start.round <- 4
source("01b_MesobromionCluster.R")
#Mesobromion(species.path, traits.path, output, myfunction, max.inter.t, chunkn, chunk.i, nperm)
-Mesobromion(species.path, traits.path, output, myfunction, combinations, max.inter.t,
+Mesobromion(species.path, traits.path, output, myfunction, combinations, start.round, max.inter.t,
chunkn, chunk.i, nperm, ncores)
diff --git a/submit_01b.sh b/submit_01b.sh
index bfd8cec..56b0e11 100644
--- a/submit_01b.sh
+++ b/submit_01b.sh
@@ -29,4 +29,5 @@ Rscript \
/data/splot/HIDDEN/traits.out.10perc.txt \
"$output" \
"get.corXY.bootstrap" \
- "sequential"
+ "sequential" \
+ 4
--
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