From bb7f73f56a2c7c1e3396b7e16755edf714879680 Mon Sep 17 00:00:00 2001
From: Francesco Sabatini <francesco.sabatini@idiv.de>
Date: Tue, 5 May 2020 19:04:53 +0200
Subject: [PATCH] Relaxed round - fixed
---
01b_MesobromionCluster.R | 47 ++++++++++++++++++++--------------------
session.R | 12 +++++-----
2 files changed, 30 insertions(+), 29 deletions(-)
diff --git a/01b_MesobromionCluster.R b/01b_MesobromionCluster.R
index 74c33e5..bf025d4 100644
--- a/01b_MesobromionCluster.R
+++ b/01b_MesobromionCluster.R
@@ -116,6 +116,7 @@ Mesobromion <- function(species.path, traits.path, output, myfunction="get.corXY
if(combinations=="sequential"){
+
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=""))
@@ -127,23 +128,37 @@ Mesobromion <- function(species.path, traits.path, output, myfunction="get.corXY
allcomb.t <- lapply(1:ncol(traits), function(x){return(x)})
nall <- length(allcomb.t)
} else {
- best.row <- corXY.ci %>%
- filter(Trait.comb==best)
- upper <- best.row$q975
- lower <- best.row$q025
+ if(nround >= relax.round){
+ best <- corXY.ci %>%
+ filter(ntraits==(nround-1)) %>%
+ arrange(desc(Coef.obs)) %>%
+ slice(1) %>%
+ pull(Trait.comb)
+
+ new.best.row <- corXY.ci %>%
+ filter(Trait.comb==best)
+ upper <- new.best.row$q975
+ lower <- new.best.row$q025
+ print(paste("Assumptions relaxed - new best at round=", nround, "is trait combination", best))
+ } else {
+ best.row <- corXY.ci %>%
+ filter(Trait.comb==best)
+ upper <- best.row$q975
+ lower <- best.row$q025
+ }
best.split <- as.numeric(unlist(strsplit(best, "_")))
- max.inter.t <- nround-length(best.split)
+ max.inter.ti <- nround-length(best.split)
#n.traits <- ncol(traits)
list.traits <- as.numeric(traits.sign.alone)
list.traits <- list.traits[-which(list.traits %in% best.split)] ## list of remaining traits without best
- if(length(list.traits) < max.inter.t) {
+ if(length(list.traits) < max.inter.ti) {
save(corXY.output, file = paste(output, ".RData", sep=""))
if(ncores>1) {stopCluster(cl)}
stop("Tested all combo of significant traits")
}
allcomb.t <- NULL
#for(n.inter in 1:max.inter.t){
- allcomb.t <- c(allcomb.t, combn(list.traits, max.inter.t, simplify=F))
+ allcomb.t <- c(allcomb.t, combn(list.traits, max.inter.ti, simplify=F))
#}
#add best to all combo
allcomb.t <- lapply(allcomb.t, function(x){return(c(best.split, x))})
@@ -196,7 +211,7 @@ Mesobromion <- function(species.path, traits.path, output, myfunction="get.corXY
print(paste("new best at nround=", nround, "is trait combination", best))
}
- if(nround>1 & nround < relax.round){
+ if(nround>1){
better <- corXY.ci %>%
filter(ntraits==nround) %>%
filter(q025>upper) %>%
@@ -219,22 +234,6 @@ 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/session.R b/session.R
index c62e048..f17c1c5 100644
--- a/session.R
+++ b/session.R
@@ -1,17 +1,19 @@
species.path <- "_data/Mesobromion/species.out.10perc.txt"
traits.path <- "_data/Mesobromion/traits.out.10perc.txt"
-output <- "test99"
+output <- "_derived/Mesobromion/HIDDEN"
myfunction <- "get.corXY.bootstrap"
-max.inter.t <- 3
+max.inter.t <- 7
chunk.i <- NA
-nperm <- 20
+nperm <- 2
ncores <- 1
chunkn <- 3*ncores
combinations <- "sequential"
-start.round <- 4
+start.round <- 6
+relax.round <- 6
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, start.round, max.inter.t,
+Mesobromion(species.path, traits.path, output, myfunction,
+ combinations, start.round, relax.round, max.inter.t,
chunkn, chunk.i, nperm, ncores)
--
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