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Commit 6fd5b3c4 authored by Georges Kunstler's avatar Georges Kunstler
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run with cat

parent dedc93b2
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Makefile
View file @ 6fd5b3c4
......@@ -4,7 +4,7 @@ D3 := output/processed
D4 := figs/test.format.tree
D5 := figs/test.traits
D6 := figs/test.CWM
sites:= Fushan Paracou BCI Mbaiki Luquillo Japan Spain Sweden Canada France Swiss NSW NVS US
sites:= Fushan Paracou BCI Mbaiki Luquillo Japan Spain Sweden Canada France Swiss NSW NVS
D3Done := $(addsuffix /Done.txt,$(addprefix $(D3)/, $(sites) ))
D2traits := $(addsuffix /traits.csv,$(addprefix $(D2)/, $(sites) ))
D2tree := $(addsuffix /tree.csv,$(addprefix $(D2)/, $(sites) ))
......@@ -71,7 +71,7 @@ $(D2)/Luquillo/tree.csv: R/format.data/Luquillo.R $(shell find $(D1)/Luquillo -t
Mbaiki: $(D3)/Mbaiki/Done.txt
$(D3)/Mbaiki/Done.txt: R/process.data/process-fun.R $(D2)/Mbaiki/traits.csv
Rscript -e "source('$<'); process_bigplot_dataset('Mbaiki', Rlim=15,std.traits='no'); process_bigplot_dataset('Mbaiki', Rlim=15,std.traits='global');"
Rscript -e "source('$<'); process_bigplot_dataset('Mbaiki', Rlim=15,std.traits='global');"
$(D2)/Mbaiki/traits.csv: R/find.trait/Mbaiki.R R/find.trait/trait-fun.R $(D2)/Mbaiki/tree.csv
Rscript $< ; rm -f $(D5)/Done.txt
......@@ -84,7 +84,7 @@ $(D2)/Mbaiki/tree.csv: R/format.data/Mbaiki.R $(shell find $(D1)/Mbaiki -type f)
Canada: $(D3)/Canada/Done.txt
$(D3)/Canada/Done.txt: R/process.data/process-fun.R $(D2)/Canada/traits.csv
Rscript -e "source('$<'); process_inventory_dataset('Canada',std.traits='no'); process_inventory_dataset('Canada',std.traits='global');"
Rscript -e "source('$<'); process_inventory_dataset('Canada',std.traits='global');"
$(D2)/Canada/traits.csv: R/find.trait/Canada.R R/find.trait/trait-fun.R $(D2)/Canada/tree.csv $(D2)/TRY/data.TRY.std.rds
Rscript $< ; rm -f $(D5)/Done.txt
......@@ -96,7 +96,7 @@ $(D2)/Canada/tree.csv: R/format.data/Canada.R $(shell find $(D1)/Canada -type f)
France: $(D3)/France/Done.txt
$(D3)/France/Done.txt: R/process.data/process-fun.R $(D2)/France/traits.csv
Rscript -e "source('$<'); process_inventory_dataset('France',std.traits='no'); process_inventory_dataset('France',std.traits='global');"
Rscript -e "source('$<'); process_inventory_dataset('France',std.traits='global');"
$(D2)/France/traits.csv: R/find.trait/France.R R/find.trait/trait-fun.R $(D2)/France/tree.csv $(D2)/TRY/data.TRY.std.rds
Rscript $< ; rm -f $(D5)/Done.txt
......@@ -109,7 +109,7 @@ $(D2)/France/tree.csv: R/format.data/France.R $(shell find $(D1)/France -type f)
Fushan: $(D3)/Fushan/Done.txt
$(D3)/Fushan/Done.txt: R/process.data/process-fun.R $(D2)/Fushan/traits.csv
Rscript -e "source('$<'); process_bigplot_dataset('Fushan', Rlim=15,std.traits='no'); process_bigplot_dataset('Fushan', Rlim=15,std.traits='global');"
Rscript -e "source('$<'); process_bigplot_dataset('Fushan', Rlim=15,std.traits='global');"
$(D2)/Fushan/traits.csv: R/find.trait/Fushan.R R/find.trait/trait-fun.R $(D2)/Fushan/tree.csv
......@@ -123,7 +123,7 @@ $(D2)/Fushan/tree.csv: R/format.data/Fushan.R $(shell find $(D1)/Fushan -type f)
NSW: $(D3)/NSW/Done.txt
$(D3)/NSW/Done.txt: R/process.data/process-fun.R $(D2)/NSW/traits.csv
Rscript -e "source('$<'); process_inventory_dataset('NSW',std.traits='no'); process_inventory_dataset('NSW',std.traits='global');"
Rscript -e "source('$<'); process_inventory_dataset('NSW',std.traits='global');"
$(D2)/NSW/traits.csv: R/find.trait/NSW.R R/find.trait/trait-fun.R $(D2)/NSW/tree.csv $(D2)/TRY/data.TRY.std.rds
Rscript $< ; rm -f $(D5)/Done.txt
......@@ -136,7 +136,7 @@ $(D2)/NSW/tree.csv: R/format.data/NSW.R $(shell find $(D1)/NSW -type f)
NVS: $(D3)/NVS/Done.txt
$(D3)/NVS/Done.txt: R/process.data/process-fun.R $(D2)/NVS/traits.csv
Rscript -e "source('$<'); process_inventory_dataset('NVS',std.traits='no'); process_inventory_dataset('NVS',std.traits='global');"
Rscript -e "source('$<'); process_inventory_dataset('NVS',std.traits='global');"
$(D2)/NVS/traits.csv: R/find.trait/NVS.R R/find.trait/trait-fun.R $(D2)/NVS/tree.csv
Rscript $< ; rm -f $(D5)/Done.txt
......@@ -149,7 +149,7 @@ $(D2)/NVS/tree.csv: R/format.data/NVS.R $(shell find $(D1)/NVS -type f)
Paracou: $(D3)/Paracou/Done.txt
$(D3)/Paracou/Done.txt: R/process.data/process-fun.R $(D2)/Paracou/traits.csv
Rscript -e "source('$<'); process_bigplot_dataset('Paracou', Rlim=15,std.traits='no'); process_bigplot_dataset('Paracou', Rlim=15,std.traits='global');"
Rscript -e "source('$<'); process_bigplot_dataset('Paracou', Rlim=15,std.traits='global');"
$(D2)/Paracou/traits.csv: R/find.trait/Paracou.R R/find.trait/trait-fun.R $(D2)/Paracou/tree.csv
Rscript $< ; rm -f $(D5)/Done.txt
......@@ -162,7 +162,7 @@ $(D2)/Paracou/tree.csv: R/format.data/Paracou.R $(shell find $(D1)/Paracou -type
Spain: $(D3)/Spain/Done.txt
$(D3)/Spain/Done.txt: R/process.data/process-fun.R $(D2)/Spain/traits.csv
Rscript -e "source('$<'); process_inventory_dataset('Spain',std.traits='no'); process_inventory_dataset('Spain',std.traits='global');"
Rscript -e "source('$<'); process_inventory_dataset('Spain',std.traits='global');"
$(D2)/Spain/traits.csv: R/find.trait/Spain.R R/find.trait/trait-fun.R $(D2)/Spain/tree.csv $(D2)/TRY/data.TRY.std.rds
Rscript $< ; rm -f $(D5)/Done.txt
......@@ -175,7 +175,7 @@ $(D2)/Spain/tree.csv: R/format.data/Spain.R $(shell find $(D1)/Spain -type f)
Sweden: $(D3)/Sweden/Done.txt
$(D3)/Sweden/Done.txt: R/process.data/process-fun.R $(D2)/Sweden/traits.csv
Rscript -e "source('$<'); process_inventory_dataset('Sweden',std.traits='no'); process_inventory_dataset('Sweden',std.traits='global');"
Rscript -e "source('$<'); process_inventory_dataset('Sweden',std.traits='global');"
$(D2)/Sweden/traits.csv: R/find.trait/Sweden.R R/find.trait/trait-fun.R $(D2)/Sweden/tree.csv $(D2)/TRY/data.TRY.std.rds
Rscript $< ; rm -f $(D5)/Done.txt
......@@ -188,7 +188,7 @@ $(D2)/Sweden/tree.csv: R/format.data/Sweden.R $(shell find $(D1)/Sweden -type f)
Swiss: $(D3)/Swiss/Done.txt
$(D3)/Swiss/Done.txt: R/process.data/process-fun.R $(D2)/Swiss/traits.csv
Rscript -e "source('$<'); process_inventory_dataset('Swiss',std.traits='no'); process_inventory_dataset('Swiss',std.traits='global');"
Rscript -e "source('$<'); process_inventory_dataset('Swiss',std.traits='global');"
$(D2)/Swiss/traits.csv: R/find.trait/Swiss.R R/find.trait/trait-fun.R $(D2)/Swiss/tree.csv $(D2)/TRY/data.TRY.std.rds
Rscript $< ; rm -f $(D5)/Done.txt
......@@ -201,7 +201,7 @@ $(D2)/Swiss/tree.csv: R/format.data/Swiss.R $(shell find $(D1)/Swiss -type f)
US: $(D3)/US/Done.txt
$(D3)/US/Done.txt: R/process.data/process-fun.R $(D2)/US/traits.csv
Rscript -e "source('$<'); process_inventory_dataset('US',std.traits='no'); process_inventory_dataset('US',std.traits='global');"
Rscript -e "source('$<'); process_inventory_dataset('US',std.traits='global');"
$(D2)/US/traits.csv: R/find.trait/US.R R/find.trait/trait-fun.R $(D2)/US/tree.csv $(D2)/TRY/data.TRY.std.rds
Rscript $< ; rm -f $(D5)/Done.txt
......@@ -218,13 +218,13 @@ $(D4)/Done.txt: R/format.data/test.tree.R $(D3tree)
#-------------------------------------------------------
TEST.TRAITS: $(D5)/Done.txt
$(D5)/Done.txt: R/find.trait/test.traits.R $(D4)/Done.txt $(D3traits)
$(D5)/Done.txt: R/find.trait/test.traits.R $(D3traits)
Rscript $<
#-------------------------------------------------------
TEST.CWM: $(D6)/Done.txt
$(D6)/Done.txt: R/process.data/test.tree.CWM.R $(D5)/Done.txt $(D3Done)
$(D6)/Done.txt: R/process.data/test.tree.CWM.R $(D3Done)
Rscript $<
#-------------------------------------------------------
......
R/analysis/glmer.run.all.R
View file @ 6fd5b3c4
......@@ -58,7 +58,8 @@ model.files.glmer.Tf.4 <-
fun.call.glmer.and.save <- function(formula,df.lmer,path.out){
Start <- Sys.time()
glmer.output <- glmer(formula=formula,data=df.lmer,family=binomial)
glmer.output <- glmer(formula=formula,data=df.lmer,
family=binomial(link = 'cloglog'))
end <- Sys.time()
print(end - Start)
print(summary(glmer.output))
......@@ -67,12 +68,14 @@ fun.call.glmer.and.save <- function(formula,df.lmer,path.out){
run.glmer <- function (model.file, trait,
min.obs=5, sample.size=NA,
type.filling) {
type.filling, fname = 'data.all.no.std.csv') {
require(lme4)
source(model.file, local = TRUE)
model <- load.model()
#= Path for output
path.out <- output.dir.glmer(model$name, trait,
if(fname == 'data.all.no.std.csv') dir <- 'all.no.log'
if(fname == 'data.all.csv') dir <- 'all.log'
path.out <- output.dir.glmer(dir, model$name, trait,
type.filling=type.filling)
print(path.out)
dir.create(path.out, recursive=TRUE, showWarnings=FALSE)
......@@ -81,7 +84,8 @@ run.glmer <- function (model.file, trait,
trait,"\n")
df.glmer <- load.and.prepare.data.for.glmer(trait,
min.obs, sample.size,
type.filling=type.filling) # return a DF
type.filling=type.filling,
fname = fname) # return a DF
cat("Ok data with Nobs",nrow(df.glmer),"\n")
#= Run model
fun.call.glmer.and.save(formula=model$glmer.formula,df.glmer,path.out)
......@@ -89,8 +93,25 @@ run.glmer <- function (model.file, trait,
#========================================================================
output.dir.glmer <- function (model, trait, type.filling) {
file.path("output/glmer", 'all',trait,type.filling,model)
output.dir.glmer <- function (dir, model, trait, type.filling) {
file.path("output/glmer", dir,trait,type.filling,model)
}
fun.load.data.all <- function(base.dir,fname){
data.all.sample <- read.csv(file = file.path(base.dir, fname),
stringsAsFactors = FALSE, nrows = 1000)
classes <- sapply(data.all.sample, class)
classes[classes=='integer'] <- "numeric"
nrows <- as.numeric(system(paste('wc -l < ',file.path(base.dir, fname)),
intern = TRUE))
data.tree.tot <- read.csv(file = file.path(base.dir, fname),
stringsAsFactors = FALSE,
nrows = nrows,
colClasses = classes)
return(data.tree.tot)
}
......@@ -99,37 +120,37 @@ output.dir.glmer <- function (model, trait, type.filling) {
#============================================================
load.and.prepare.data.for.glmer <- function(trait,
min.obs, sample.size, type.filling,
fname = 'data.all.no.std.csv',
base.dir = "output/processed/"){
### load data
data.all.sample <- read.csv(file=file.path(base.dir, "data.all.csv"),
stringsAsFactors=FALSE,nrows=1000)
classes <- sapply(data.all.sample,class)
classes[classes=='integer'] <- "numeric"
nrows <- as.numeric(system('wc -l < output/processed/data.all.csv',
intern=TRUE))
data.tree.tot <- read.csv(file=file.path(base.dir, "data.all.csv"),
stringsAsFactors=FALSE,
nrows=nrows,
colClasses=classes)
data.tree.tot <- fun.load.data.all(base.dir,fname)
fun.data.for.glmer(data.tree.tot,trait,type.filling=type.filling)
}
fun.select.data.for.analysis <- function(data.tree,abs.CWM.tntf,perc.neigh,
fun.select.data.for.analysis <- function(data.tree,abs.CWM.tntf,
perc.neigh.sp,
perc.neigh.gs,
BATOT,min.obs,
min.perc.neigh=0.80){
min.perc.neigh.sp = 0.90,
min.perc.neigh.gs = 0.95){
## remove tree with NA
data.tree <- subset(data.tree,subset=(!is.na(data.tree[["dead"]])) &
(!is.na(data.tree[["D"]])) )
(!is.na(data.tree[["D"]])) &
(!is.na(data.tree[['year']])))
## remove tree with zero
data.tree <- subset(data.tree,subset=data.tree[["D"]]>9.9)
## select species with missing traits
data.tree <- data.tree[(!is.na(data.tree[[abs.CWM.tntf]]) &
!is.na(data.tree[[BATOT]])),]
# select obs abov min perc.neigh
data.tree <- subset(data.tree,subset=data.tree[[perc.neigh]] > min.perc.neigh &
!is.na(data.tree[[perc.neigh]]))
# select obs abov min perc.neigh species
data.tree <- subset(data.tree, subset = data.tree[[perc.neigh.sp]] >
min.perc.neigh.sp &
!is.na(data.tree[[perc.neigh.sp]]))
# select obs abov min perc.neigh genus
data.tree <- subset(data.tree, subset = data.tree[[perc.neigh.gs]] >
min.perc.neigh.gs & !is.na(data.tree[[perc.neigh.gs]]))
# select species with minimum obs
data.tree <- subset(data.tree,subset=data.tree[["sp"]] %in%
names(table(factor(data.tree[["sp"]])))[table(factor(
......@@ -146,6 +167,7 @@ fun.get.the.variables.for.glmer.no.tree.id <- function(data.tree,BATOT,CWM.tn,
abs.CWM.tntf,tf,min.BA.G=50){
dead <- data.tree[["dead"]]
logD <- fun.center.and.standardized.var(log(data.tree[["D"]]))
logyear <- log(data.tree[["year"]])
MAT <- fun.center.and.standardized.var(data.tree[["MAT"]])
MAP <- fun.center.and.standardized.var(data.tree[["MAP"]])
species.id <- factor(data.tree[["sp"]])
......@@ -161,6 +183,7 @@ sumTnTfBn.diff <- sumTnBn-sumTfBn
sumBn <- data.tree[[BATOT]]
return(data.frame(dead=dead,
logD=logD,
logyear=logyear,
MAT = MAT,
MAP = MAP,
species.id=species.id,
......@@ -192,9 +215,13 @@ CWM.tn <- paste(trait,"CWM",'fill',sep=".")
abs.CWM.tntf <- paste(trait,"abs.CWM",'fill',sep=".")
tf <- paste(trait,"focal",sep=".")
BATOT <- "BATOT"
perc.neigh <- paste(trait,"perc",type.filling,sep=".")
data.tree <- fun.select.data.for.analysis(data.tree,abs.CWM.tntf,
perc.neigh,BATOT,min.obs)
perc.neigh.sp <- paste(trait, "perc", 'species', sep = ".")
perc.neigh.gs <- paste(trait, "perc", 'genus', sep = ".")
data.tree <- fun.select.data.for.analysis(data.tree,
abs.CWM.tntf,
perc.neigh.sp,
perc.neigh.gs,
BATOT,min.obs)
#= DATA LIST FOR JAGS
glmer.data <- fun.get.the.variables.for.glmer.no.tree.id(data.tree,BATOT,CWM.tn,abs.CWM.tntf,tf)
return(glmer.data)
......
R/analysis/lmer.output-fun.R
View file @ 6fd5b3c4
This diff is collapsed.
R/analysis/lmer.run.nolog.all.R
View file @ 6fd5b3c4
......@@ -12,17 +12,17 @@ run.models.for.set.all.traits <- function(model.file, fun.model, traits =
}
run.multiple.model.for.set.one.trait <- function(model.files, fun.model, trait,
type.filling, ...){
type.filling, cat.TF, ...){
for (m in model.files)
(run.model.for.set.one.trait (m, fun.model, trait,
type.filling = type.filling, ...))
type.filling = type.filling, cat.TF = cat.TF, ...))
}
run.model.for.set.one.trait <- function(model.file, fun.model, trait,
type.filling, ...){
type.filling, cat.TF, ...){
fun.model <- match.fun(fun.model)
try(fun.model(model.file, trait, type.filling = type.filling, ...))
try(fun.model(model.file, trait, type.filling = type.filling,cat.TF = cat.TF, ...))
}
......@@ -62,26 +62,31 @@ fun.call.lmer.and.save <- function(formula, df.lmer, path.out){
run.lmer <- function (model.file, trait,
min.obs = 10, sample.size = NA,
type.filling) {
type.filling, cat.TF, fname = 'data.all.no.std.csv') {
require(lme4)
source(model.file, local = TRUE)
model <- load.model()
#= Path for output
path.out <- output.dir.lmer(model$name, trait, 'all',
if(fname == 'data.all.no.std.csv') dir <- 'all.no.log'
if(fname == 'data.all.csv') dir <- 'all.log'
path.out <- output.dir.lmer(model$name, trait, dir,
type.filling = type.filling)
print(path.out)
dir.create(path.out, recursive = TRUE, showWarnings = FALSE)
cat("run lmer for model", model.file, " for trait",
cat("run lmer for model", model.file, " for trait",
trait, "\n")
df.lmer <- load.and.prepare.data.for.lmer(trait,
df.lmer <- load.and.prepare.data.for.lmer(trait,
min.obs, sample.size,
type.filling = type.filling)
type.filling = type.filling,
fname = fname, cat.TF = cat.TF)
# return a DF
cat("Ok data with Nobs", nrow(df.lmer),
"\n")
#= Run model
fun.call.lmer.and.save(formula = model$lmer.formula.tree.id,
df.lmer, path.out)
rm(df.lmer)
gc()
}
......@@ -91,36 +96,38 @@ output.dir.lmer <- function (model, trait, set, type.filling) {
file.path("output/lmer", set, trait, type.filling, model)
}
#============================================================
# Function to prepare data for lmer
#============================================================
load.and.prepare.data.for.lmer <- function(trait,
min.obs, sample.size, type.filling,
base.dir = "output/processed/"){
### load data
## library(data.table)
## data.tree.tot <- fread(file.path(base.dir, "data.all.csv"),
## stringsAsFactors = FALSE)
data.all.sample <- read.csv(file = file.path(base.dir, "data.all.csv"),
fun.load.data.all <- function(base.dir,fname){
data.all.sample <- read.csv(file = file.path(base.dir, fname),
stringsAsFactors = FALSE, nrows = 1000)
classes <- sapply(data.all.sample, class)
classes[classes=='integer'] <- "numeric"
nrows <- as.numeric(system('wc -l < output/processed/data.all.csv',
nrows <- as.numeric(system(paste('wc -l < ',file.path(base.dir, fname)),
intern = TRUE))
data.tree.tot <- read.csv(file = file.path(base.dir, "data.all.csv"),
data.tree.tot <- read.csv(file = file.path(base.dir, fname),
stringsAsFactors = FALSE,
nrows = nrows,
colClasses = classes)
return(data.tree.tot)
}
fun.data.for.lmer(data.tree.tot, trait, type.filling = type.filling)
#============================================================
# Function to prepare data for lmer
#============================================================
load.and.prepare.data.for.lmer <- function(trait,
min.obs, sample.size, type.filling,
cat.TF,
fname = 'data.all.no.std.csv',
base.dir = "output/processed"){
data.tree.tot <- fun.load.data.all(base.dir,fname)
fun.data.for.lmer(data.tree.tot, trait, type.filling = type.filling, cat.TF = cat.TF)
}
fun.select.data.for.analysis <- function(data.tree, abs.CWM.tntf, perc.neigh.sp,
perc.neigh.gs, BATOT, min.obs,
min.perc.neigh.sp = 0.90, min.perc.neigh.gs = 0.98, min.BA.G = -60,
min.perc.neigh.sp = 0.90,
min.perc.neigh.gs = 0.95,
min.BA.G = -60,
max.BA.G = 500){
## remove tree with NA
data.tree <- subset(data.tree, subset = (!is.na(data.tree[["BA.G"]])) &
......@@ -134,10 +141,12 @@ select.temp <- (!is.na(data.tree[[abs.CWM.tntf]]) &
!is.na(data.tree[[BATOT]]))
data.tree <- data.tree[select.temp, ]
# select obs abov min perc.neigh species
data.tree <- subset(data.tree, subset = data.tree[[perc.neigh.sp]] > min.perc.neigh.sp &
data.tree <- subset(data.tree, subset = data.tree[[perc.neigh.sp]] >
min.perc.neigh.sp &
!is.na(data.tree[[perc.neigh.sp]]))
# select obs abov min perc.neigh genus
data.tree <- subset(data.tree, subset = data.tree[[perc.neigh.gs]] > min.perc.neigh.gs &
data.tree <- subset(data.tree, subset = data.tree[[perc.neigh.gs]] >
min.perc.neigh.gs &
!is.na(data.tree[[perc.neigh.gs]]))
# select species with minimum obs
data.tree <- subset(data.tree, subset = data.tree[["sp"]] %in%
......@@ -154,7 +163,7 @@ return((x-mean(x))/sd(x))
fun.get.the.variables.for.lmer.tree.id <- function(data.tree, BATOT, CWM.tn,
abs.CWM.tntf, tf,
min.BA.G = 60){
logG <- fun.center.and.standardized.var(log(data.tree[["BA.G"]]+min.BA.G))
logG <- fun.center.and.standardized.var(log(data.tree[["BA.G"]] + min.BA.G))
logD <- fun.center.and.standardized.var(log(data.tree[["D"]]))
MAT <- fun.center.and.standardized.var(data.tree[["MAT"]])
MAP <- fun.center.and.standardized.var(data.tree[["MAP"]])
......@@ -189,13 +198,75 @@ return(data.frame(logG = logG,
sumBn = fun.center.and.standardized.var(sumBn)))
}
fun.get.the.variables.for.lmer.tree.id.cat <- function(data.tree, BATOT, CWM.tn,
abs.CWM.tntf, tf,
min.BA.G = 60){
logG <- fun.center.and.standardized.var(log(data.tree[["BA.G"]]+min.BA.G))
logD <- fun.center.and.standardized.var(log(data.tree[["D"]]))
MAT <- fun.center.and.standardized.var(data.tree[["MAT"]])
MAP <- fun.center.and.standardized.var(data.tree[["MAP"]])
species.id <- factor(data.tree[["sp"]])
tree.id <- factor(data.tree[["tree.id"]])
plot.id <- factor(data.tree[["plot"]])
set.id <- factor(data.tree[["set"]])
ecocode.id <- factor(data.tree[['ecocode']])
#get the three cwm per cat
vec.CWM.tn <- paste(CWM.tn, c('A_EV', 'A_D', 'C'), sep = '.')
vec.abs.CWM.tntf <- paste(abs.CWM.tntf, c('A_EV', 'A_D', 'C'), sep = '.')
sumTnTfBn.abs.A_EV<- data.tree[[vec.abs.CWM.tntf[1]]]
sumTnTfBn.abs.A_D <- data.tree[[vec.abs.CWM.tntf[2]]]
sumTnTfBn.abs.C <- data.tree[[vec.abs.CWM.tntf[3]]]
sumTnBn.A_EV<- data.tree[[vec.CWM.tn[1]]]
sumTnBn.A_D <- data.tree[[vec.CWM.tn[2]]]
sumTnBn.C <- data.tree[[vec.CWM.tn[3]]]
sumTfBn <- data.tree[[tf]]*data.tree[[BATOT]]
sumTfBn.A_EV <- as.numeric(data.tree[['SLA.cat']] == 1) *sumTfBn
sumTfBn.A_D <- as.numeric(data.tree[['SLA.cat']] == 2) *sumTfBn
sumTfBn.C <- as.numeric(data.tree[['SLA.cat']] == 3) *sumTfBn
sumBn <- data.tree[[BATOT]]
return(
data.frame(logG = logG,
logD = logD,
MAT = MAT,
MAP = MAP,
species.id = species.id,
tree.id = tree.id,
set.id = set.id,
ecocode.id = ecocode.id,
plot.id = plot.id,
sumTnTfBn.abs.A_EV =
fun.center.and.standardized.var(sumTnTfBn.abs.A_EV),
sumTnTfBn.abs.A_D =
fun.center.and.standardized.var(sumTnTfBn.abs.A_D),
sumTnTfBn.abs.C =
fun.center.and.standardized.var(sumTnTfBn.abs.C),
Tf.A_EV= fun.center.and.standardized.var(data.tree[[tf]] *
as.numeric(data.tree[['SLA.cat']] == 1)),
Tf.A_D= fun.center.and.standardized.var(data.tree[[tf]] *
as.numeric(data.tree[['SLA.cat']] == 2)),
Tf.C = fun.center.and.standardized.var(data.tree[[tf]] *
as.numeric(data.tree[['SLA.cat']] == 3)),
sumTnBn.A_EV= fun.center.and.standardized.var(sumTnBn.A_EV),
sumTnBn.A_D= fun.center.and.standardized.var(sumTnBn.A_D),
sumTnBn.C = fun.center.and.standardized.var(sumTnBn.C),
sumTfBn.A_EV= fun.center.and.standardized.var(sumTfBn.A_EV),
sumTfBn.A_D= fun.center.and.standardized.var(sumTfBn.A_D),
sumTfBn.C = fun.center.and.standardized.var(sumTfBn.C),
sumBn = fun.center.and.standardized.var(sumBn)))
}
#============================================================
# Function to prepare data for lmer with new CWM data
# that will be used in a simple linear model
#============================================================
fun.data.for.lmer <- function(data.tree, trait, min.obs = 10,
type.filling = 'species') {
type.filling = 'species', cat.TF) {
if(! trait %in% c("SLA", "Leaf.N", "Seed.mass",
"SLA", "Wood.density", "Max.height"))
stop("need trait to be in SLA Leaf.N Seed.mass
......@@ -209,12 +280,17 @@ perc.neigh.sp <- paste(trait, "perc", 'species', sep = ".")
perc.neigh.gs <- paste(trait, "perc", 'genus', sep = ".")
data.tree <- fun.select.data.for.analysis(data.tree,
abs.CWM.tntf,
perc.neigh,sp,
perc.neigh.sp,
perc.neigh.gs,
BATOT,
min.obs)
#= DATA LIST FOR LMER
lmer.data <- fun.get.the.variables.for.lmer.tree.id(data.tree,
if(!cat.TF) lmer.data <- fun.get.the.variables.for.lmer.tree.id(data.tree,
BATOT,
CWM.tn,
abs.CWM.tntf,
tf)
if(cat.TF) lmer.data <- fun.get.the.variables.for.lmer.tree.id.cat(data.tree,
BATOT,
CWM.tn,
abs.CWM.tntf,
......
R/analysis/model.glmer.all/model.glmer.LOGLIN.AD.Tf.MAT.MAP.R
View file @ 6fd5b3c4
load.model <- function () {
list(name="glmer.LOGLIN.AD.Tf.MAT.MAP",
glmer.formula=formula("dead~1+Tf+Tf:MAT+Tf:MAP+log+MAT+MAP+(1+logD|species.id)+(1|plot.id)+sumBn+sumBn:MAT+sumBn:MAP+sumTnTfBn.abs+sumTnTfBn.abs:MAT+sumTnTfBn.abs:MAP+(Tf-1|set.id)+(sumBn-1|set.id)+(sumTnTfBn.abs-1|set.id)"))
}
glmer.formula=formula("dead~1+offset(logyear)+Tf+Tf:MAT+Tf:MAP+log+MAT+MAP+(1+logD|species.id)+(1|plot.id)+sumBn+sumBn:MAT+sumBn:MAP+sumTnTfBn.abs+sumTnTfBn.abs:MAT+sumTnTfBn.abs:MAP+(Tf-1|set.id)+(sumBn-1|set.id)+(sumTnTfBn.abs-1|set.id)"))
}
R/analysis/model.glmer.all/model.glmer.LOGLIN.AD.Tf.R
View file @ 6fd5b3c4
load.model <- function () {
list(name="glmer.LOGLIN.AD.Tf",
glmer.formula=formula("dead~1+Tf+logD+(1+logD|species.id)+(1|plot.id)+sumBn+sumTnTfBn.abs+(Tf-1|set.id)+(sumBn-1|set.id)+(sumTnTfBn.abs-1|set.id)"))
}
glmer.formula=formula("dead~1+offset(logyear)+Tf+logD+(1+logD|species.id)+(1|plot.id)+sumBn+sumTnTfBn.abs+(Tf-1|set.id)+(sumBn-1|set.id)+(sumTnTfBn.abs-1|set.id)"))
}
R/analysis/model.glmer.all/model.glmer.LOGLIN.E.Tf.MAT.MAP.R
View file @ 6fd5b3c4
load.model <- function () {
list(name="glmer.LOGLIN.E.Tf.MAT.MAP",
glmer.formula=formula("dead~1+Tf+Tf:MAT+Tf:MAP+logD+MAT+MAP+sumBn+sumBn:MAT+sumBn:MAP+sumTnBn+sumTnBn:MAT+sumTnBn:MAP+(1+logD|species.id)+(1|plot.id)+(1|set.id)+(Tf-1|set.id)+(sumBn-1|set.id)+(sumTnBn-1|set.id)"))
}
glmer.formula=formula("dead~1+Tf+offset(logyear)+Tf:MAT+Tf:MAP+logD+MAT+MAP+sumBn+sumBn:MAT+sumBn:MAP+sumTnBn+sumTnBn:MAT+sumTnBn:MAP+(1+logD|species.id)+(1|plot.id)+(1|set.id)+(Tf-1|set.id)+(sumBn-1|set.id)+(sumTnBn-1|set.id)"))
}
R/analysis/model.glmer.all/model.glmer.LOGLIN.E.Tf.R
View file @ 6fd5b3c4
load.model <- function () {
list(name="glmer.LOGLIN.E.Tf",
glmer.formula=formula("dead~1+Tf+logD+sumBn+sumTnBn+(1+logD|species.id)+(1|plot.id)+(1|set.id)+(Tf-1|set.id)+(sumBn-1|set.id)+(sumTnBn-1|set.id)"))
}
glmer.formula=formula("dead~1+offset(logyear)+Tf+logD+sumBn+sumTnBn+(1+logD|species.id)+(1|plot.id)+(1|set.id)+(Tf-1|set.id)+(sumBn-1|set.id)+(sumTnBn-1|set.id)"))
}
R/analysis/model.glmer.all/model.glmer.LOGLIN.ER.AD.Tf.MAT.MAP.R
View file @ 6fd5b3c4
load.model <- function () {
list(name="glmer.LOGLIN.ER.AD.Tf.MAT.MAP",
glmer.formula=formula("dead~1+Tf+Tf:MAT+Tf:MAP+logD+MAT+MAP+(1-logD|species.id)+(1|plot.id)+(1|set.id)+sumBn+sumBn:MAT+sumBn:MAP+sumTfBn+sumTfBn:MAT+sumTfBn:MAP+sumTnBn+sumTnBn:MAT+sumTnBn:MAP+sumTnTfBn.abs+sumTnTfBn.abs:MAT+sumTnTfBn.abs:MAP+(Tf-1|set.id)+(sumTfBn-1|set.id)+(sumBn-1|set.id)+(sumTnBn-1|set.id)+(sumTnTfBn.abs-1|set.id)"))
glmer.formula=formula("dead~1+offset(logyear)+Tf+Tf:MAT+Tf:MAP+logD+MAT+MAP+(1-logD|species.id)+(1|plot.id)+(1|set.id)+sumBn+sumBn:MAT+sumBn:MAP+sumTfBn+sumTfBn:MAT+sumTfBn:MAP+sumTnBn+sumTnBn:MAT+sumTnBn:MAP+sumTnTfBn.abs+sumTnTfBn.abs:MAT+sumTnTfBn.abs:MAP+(Tf-1|set.id)+(sumTfBn-1|set.id)+(sumBn-1|set.id)+(sumTnBn-1|set.id)+(sumTnTfBn.abs-1|set.id)"))
}
R/analysis/model.glmer.all/model.glmer.LOGLIN.ER.AD.Tf.R
View file @ 6fd5b3c4
load.model <- function () {
list(name="glmer.LOGLIN.ER.AD.Tf",
glmer.formula=formula("dead~1+Tf+logD+(1+logD|species.id)+(1|plot.id)+(1|set.id)+sumBn+sumTfBn+sumTnBn+sumTnTfBn.abs+(Tf-1|set.id)+(sumTfBn-1|set.id)+(sumBn-1|set.id)+(sumTnBn-1|set.id)+(sumTnTfBn.abs-1|set.id)"))
glmer.formula=formula("dead~1+offset(logyear)+Tf+logD+(1+logD|species.id)+(1|plot.id)+(1|set.id)+sumBn+sumTfBn+sumTnBn+sumTnTfBn.abs+(Tf-1|set.id)+(sumTfBn-1|set.id)+(sumBn-1|set.id)+(sumTnBn-1|set.id)+(sumTnTfBn.abs-1|set.id)"))
}
R/analysis/model.glmer.all/model.glmer.LOGLIN.ER.Tf.MAT.MAP.R
View file @ 6fd5b3c4
load.model <- function () {
list(name="glmer.LOGLIN.ER.Tf.MAT.MAP",
glmer.formula=formula("dead~1+Tf+Tf:MAT+Tf:MAP+logD+MAT+MAP+(1+logD|species.id)+(1|plot.id)+(1|set.id)+sumBn+sumBn:MAT+sumBn:MAP+sumTfBn+sumTfBn:MAT+sumTfBn:MAP+sumTnBn+sumTnBn:MAT+sumTnBn:MAP+(Tf-1|set.id)+(sumTfBn-1|set.id)+(sumBn-1|set.id)+(sumTnBn-1|set.id)"))
glmer.formula=formula("dead~1+offset(logyear)+Tf+Tf:MAT+Tf:MAP+logD+MAT+MAP+(1+logD|species.id)+(1|plot.id)+(1|set.id)+sumBn+sumBn:MAT+sumBn:MAP+sumTfBn+sumTfBn:MAT+sumTfBn:MAP+sumTnBn+sumTnBn:MAT+sumTnBn:MAP+(Tf-1|set.id)+(sumTfBn-1|set.id)+(sumBn-1|set.id)+(sumTnBn-1|set.id)"))
}
R/analysis/model.glmer.all/model.glmer.LOGLIN.ER.Tf.R
View file @ 6fd5b3c4
load.model <- function () {
list(name="glmer.LOGLIN.ER.Tf",
glmer.formula=formula("dead~1+Tf+logD+(1+logD|species.id)+(1|plot.id)+(1|set.id)+sumBn+sumTfBn+sumTnBn+(Tf-1|set.id)+(sumTfBn-1|set.id)+(sumBn-1|set.id)+(sumTnBn-1|set.id)"))
glmer.formula=formula("dead~1+offset(logyear)+Tf+logD+(1+logD|species.id)+(1|plot.id)+(1|set.id)+sumBn+sumTfBn+sumTnBn+(Tf-1|set.id)+(sumTfBn-1|set.id)+(sumBn-1|set.id)+(sumTnBn-1|set.id)"))
}
R/analysis/model.glmer.all/model.glmer.LOGLIN.HD.Tf.MAT.MAP.R
View file @ 6fd5b3c4
load.model <- function () {
list(name="glmer.LOGLIN.HD.Tf.MAT.MAP",
glmer.formula=formula("dead~1+Tf+Tf:MAT+Tf:MAP+logD+MAT+MAP+(1+logD|species.id)+(1|plot.id)+(1|set.id)+sumBn+sumBn:MAT+sumBn:MAP+sumTnTfBn.diff+sumTnTfBn.diff:MAT+sumTnTfBn.diff:MAP+(Tf-1|set.id)+(sumBn-1|set.id)+(sumTnTfBn.diff-1|set.id)"))
}
glmer.formula=formula("dead~1+offset(logyear)+Tf+Tf:MAT+Tf:MAP+logD+MAT+MAP+(1+logD|species.id)+(1|plot.id)+(1|set.id)+sumBn+sumBn:MAT+sumBn:MAP+sumTnTfBn.diff+sumTnTfBn.diff:MAT+sumTnTfBn.diff:MAP+(Tf-1|set.id)+(sumBn-1|set.id)+(sumTnTfBn.diff-1|set.id)"))
}
R/analysis/model.glmer.all/model.glmer.LOGLIN.HD.Tf.R
View file @ 6fd5b3c4
load.model <- function () {
list(name="glmer.LOGLIN.HD.Tf",
glmer.formula=formula("dead~1+Tf+logD+(1+logD|species.id)+(1|plot.id)+(1|set.id)+sumBn+sumTnTfBn.diff+(Tf-1|set.id)+(sumBn-1|set.id)+(sumTnTfBn.diff-1|set.id)"))
}
glmer.formula=formula("dead~1+offset(logyear)+Tf+logD+(1+logD|species.id)+(1|plot.id)+(1|set.id)+sumBn+sumTnTfBn.diff+(Tf-1|set.id)+(sumBn-1|set.id)+(sumTnTfBn.diff-1|set.id)"))
}
R/analysis/model.glmer.all/model.glmer.LOGLIN.R.Tf.MAT.MAP.R
View file @ 6fd5b3c4
load.model <- function () {
list(name="glmer.LOGLIN.R.Tf.MAT.MAP",
glmer.formula=formula("dead~1+Tf+Tf:MAT+Tf:MAP+logD+MAT+MAP+sumBn+sumBn:MAT+sumBn:MAP+sumTfBn+sumTfBn:MAT+sumTfBn:MAP+(1+logD|species.id)+(1|plot.id)+(1|set.id)+(Tf-1|set.id)+(sumBn-1|set.id)+(sumTfBn-1|set.id)"))
}
glmer.formula=formula("dead~1+offset(logyear)+Tf+Tf:MAT+Tf:MAP+logD+MAT+MAP+sumBn+sumBn:MAT+sumBn:MAP+sumTfBn+sumTfBn:MAT+sumTfBn:MAP+(1+logD|species.id)+(1|plot.id)+(1|set.id)+(Tf-1|set.id)+(sumBn-1|set.id)+(sumTfBn-1|set.id)"))
}
R/analysis/model.glmer.all/model.glmer.LOGLIN.R.Tf.R
View file @ 6fd5b3c4
load.model <- function () {
list(name="glmer.LOGLIN.R.Tf",
glmer.formula=formula("dead~1+Tf+logD+sumBn+sumTfBn+(1+logD|species.id)+(1|plot.id)+(1|set.id)+(Tf-1|set.id)+(sumBn-1|set.id)+(sumTfBn-1|set.id)"))