From 17823ad4b44b0feb9ae99ec648df34bdcc3f3939 Mon Sep 17 00:00:00 2001
From: Francesco Sabatini <francesco.sabatini@idiv.de>
Date: Wed, 29 Apr 2020 16:29:16 +0200
Subject: [PATCH] Changed 01b to set relax round
---
01b_MesobromionCluster.R | 20 +++++++++++++--
cli_01b.r | 55 +++++++++++++++++++++++-----------------
submit_01b.sh | 3 ++-
3 files changed, 52 insertions(+), 26 deletions(-)
diff --git a/01b_MesobromionCluster.R b/01b_MesobromionCluster.R
index 2a73aff..74c33e5 100644
--- a/01b_MesobromionCluster.R
+++ b/01b_MesobromionCluster.R
@@ -55,7 +55,7 @@ get.best <- function(x, N){
Mesobromion <- function(species.path, traits.path, output, myfunction="get.corXY.bootstrap",
- combinations=c("all", "sequential"), start.round=NA, max.inter.t,
+ combinations=c("all", "sequential"), start.round=NA, relax.round=NA, max.inter.t,
chunkn, chunk.i, nperm=199, ncores){
if(ncores>1){
@@ -196,7 +196,7 @@ Mesobromion <- function(species.path, traits.path, output, myfunction="get.corXY
print(paste("new best at nround=", nround, "is trait combination", best))
}
- if(nround>1){
+ if(nround>1 & nround < relax.round){
better <- corXY.ci %>%
filter(ntraits==nround) %>%
filter(q025>upper) %>%
@@ -219,6 +219,22 @@ Mesobromion <- function(species.path, traits.path, output, myfunction="get.corXY
print(paste("new best at round=", nround, "is trait combination", best))
} else {print(paste("no new best at round=", nround))}
}
+
+ if(nround>1 & nround > relax.round){
+ better <- corXY.ci %>%
+ filter(ntraits==nround) %>%
+ arrange(desc(Coef.obs)) %>%
+ slice(1) %>%
+ pull(Trait.comb)
+
+ new.best.row <- corXY.ci %>%
+ filter(Trait.comb==better)
+ upper <- new.best.row$q975
+ lower <- new.best.row$q025
+ best <- better
+ print(paste("Assumptions relaxed - new best at round=", nround, "is trait combination", best))
+ }
+
print(paste("save intermediate results at round", nround))
save(corXY.output, best, traits.sign.alone, corXY.ci, file = paste(output, "_round_",nround, ".RData", sep=""))
}
diff --git a/cli_01b.r b/cli_01b.r
index 37e3175..587a2e1 100644
--- a/cli_01b.r
+++ b/cli_01b.r
@@ -12,7 +12,7 @@ default.ncores <- 1
# ------------------------------------------------------------------------------
options <- list (
-
+
make_option(
opt_str = c("-c", "--ncores"),
dest = "ncores",
@@ -31,23 +31,23 @@ options <- list (
metavar = "4"
),
- make_option(
- opt_str = c("-n", "--chunkn"),
- dest = "chunkn",
- type = "integer",
- default = 1,
- help = "How many chunks?",
- metavar = "4"
- ),
-
- make_option(
- opt_str = c("-i", "--chunk.i"),
- dest = "chunk.i",
- type = "integer",
- default = NA,
- help = "Which chunk?",
- metavar = "4"
- ),
+ make_option(
+ opt_str = c("-n", "--chunkn"),
+ dest = "chunkn",
+ type = "integer",
+ default = 1,
+ help = "How many chunks?",
+ metavar = "4"
+ ),
+
+ make_option(
+ opt_str = c("-i", "--chunk.i"),
+ dest = "chunk.i",
+ type = "integer",
+ default = NA,
+ help = "Which chunk?",
+ metavar = "4"
+ ),
make_option(
opt_str = c("-p", "--nperm"),
dest = "nperm",
@@ -63,14 +63,22 @@ options <- list (
default = NA,
help = "Which start round?",
metavar = "4"
+ ),
+ make_option(
+ opt_str = c("-x", "--relax.round"),
+ dest = "relax.round",
+ type = "integer",
+ default = NA,
+ help = "After what round should the selection of new best combos stop being based on c.i.?",
+ metavar = "4"
)
)
parser <- OptionParser(
- usage = "Rscript %prog [options] data dt_beals header output",
- option_list = options,
- description = "\nan awesome R script",
- epilogue = "use with caution, the awesomeness might slap you in the face!"
+ usage = "Rscript %prog [options] data dt_beals header output",
+ option_list = options,
+ description = "\nan awesome R script",
+ epilogue = "use with caution, the awesomeness might slap you in the face!"
)
cli <- parse_args(parser, positional_arguments = 5)
@@ -85,6 +93,7 @@ output <- cli$args[3]
myfunction <- cli$args[4]
combinations <- cli$args[5]
start.round <- cli$options$start.round
+start.round <- cli$options$relax.round
max.inter.t <- cli$options$max.inter.t
chunkn <- cli$options$chunkn
chunk.i <- cli$options$chunk.i
@@ -97,5 +106,5 @@ ncores <- cli$options$ncores
source("01b_MesobromionCluster.R")
-Mesobromion(species.path, traits.path, output, myfunction, combinations, start.round
+Mesobromion(species.path, traits.path, output, myfunction, combinations, start.round, relax.round,
max.inter.t, chunkn, chunk.i, nperm, ncores)
diff --git a/submit_01b.sh b/submit_01b.sh
index 9f3f613..6184a13 100644
--- a/submit_01b.sh
+++ b/submit_01b.sh
@@ -22,10 +22,11 @@ Rscript \
cli_01b.r \
--max.inter.t 20 \
--chunk.i NA \
- --chunkn 32 \
+ --chunkn NA \
--nperm 999 \
--ncores ${NSLOTS:-1} \
--start.round 4 \
+ --relax.round 7 \
/data/splot/HIDDEN/species.out.10perc.txt \
/data/splot/HIDDEN/traits.out.10perc.txt \
"$output" \
--
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