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Commit 87744325 authored by Georges Kunstler's avatar Georges Kunstler
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global format and functoin to remove growth outlier

parent 1d1c1227
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Makefile
View file @ 87744325
......@@ -27,7 +27,7 @@ $(D2)/TRY/data.TRY.std.rds:
BCI: $(D3)/BCI/Done.txt
$(D3)/BCI/Done.txt: R/process.data/process-fun.R $(D2)/BCI/traits.csv
Rscript -e "source('$<'); process_bigplot_dataset('BCI', Rlim=15,std.traits='local'); process_bigplot_dataset('BCI', Rlim=15,std.traits='no'); process_bigplot_dataset('BCI', Rlim=15,std.traits='global');"
Rscript -e "source('$<'); process_bigplot_dataset('BCI', Rlim=15,std.traits='local'); process_bigplot_dataset('BCI', Rlim=15,std.traits='global'); process_bigplot_dataset('BCI', Rlim=15,std.traits='no');"
$(D2)/BCI/traits.csv: R/find.trait/BCI.R R/find.trait/trait-fun.R $(D2)/BCI/tree.csv
Rscript $<
......@@ -40,7 +40,7 @@ $(D2)/BCI/tree.csv: R/format.data/BCI.R $(shell find $(D1)/BCI -type f)
Japan: $(D3)/Japan/Done.txt
$(D3)/Japan/Done.txt: R/process.data/process-fun.R $(D2)/Japan/traits.csv
Rscript -e "source('$<'); process_bigplot_dataset('Japan', Rlim=15,std.traits='local'); process_bigplot_dataset('Japan', Rlim=15,std.traits='no'); process_bigplot_dataset('Japan', Rlim=15,std.traits='global');"
Rscript -e "source('$<'); process_bigplot_dataset('Japan', Rlim=15,std.traits='local'); process_bigplot_dataset('Japan', Rlim=15,std.traits='global'); process_bigplot_dataset('Japan', Rlim=15,std.traits='no');"
$(D2)/Japan/traits.csv: R/find.trait/Japan.R R/find.trait/trait-fun.R $(D2)/Japan/tree.csv
Rscript $<
......@@ -65,7 +65,7 @@ $(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='local'); 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='local'); process_bigplot_dataset('Mbaiki', Rlim=15,std.traits='global'); process_bigplot_dataset('Mbaiki', Rlim=15,std.traits='no');"
$(D2)/Mbaiki/traits.csv: R/find.trait/Mbaiki.R R/find.trait/trait-fun.R $(D2)/Mbaiki/tree.csv
Rscript $<
......@@ -90,7 +90,7 @@ $(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='local'); process_inventory_dataset('France',std.traits='no');process_inventory_dataset('France',std.traits='global');"
Rscript -e "source('$<'); process_inventory_dataset('France',std.traits='local'); process_inventory_dataset('France',std.traits='global');process_inventory_dataset('France',std.traits='no');"
$(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 $<
......@@ -103,7 +103,7 @@ $(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='local'); 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='local'); process_bigplot_dataset('Fushan', Rlim=15,std.traits='global');process_bigplot_dataset('Fushan', Rlim=15,std.traits='no');"
$(D2)/Fushan/traits.csv: R/find.trait/Fushan.R R/find.trait/trait-fun.R $(D2)/Fushan/tree.csv
......@@ -117,7 +117,7 @@ $(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='local'); process_inventory_dataset('NSW',std.traits='no');process_inventory_dataset('NSW',std.traits='global');"
Rscript -e "source('$<'); process_inventory_dataset('NSW',std.traits='local'); process_inventory_dataset('NSW',std.traits='global');process_inventory_dataset('NSW',std.traits='no');"
$(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 $<
......@@ -130,7 +130,7 @@ $(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='local'); process_inventory_dataset('NVS',std.traits='no'); process_inventory_dataset('NVS',std.traits='global');"
Rscript -e "source('$<'); process_inventory_dataset('NVS',std.traits='local'); process_inventory_dataset('NVS',std.traits='global'); process_inventory_dataset('NVS',std.traits='no');"
$(D2)/NVS/traits.csv: R/find.trait/NVS.R R/find.trait/trait-fun.R $(D2)/NVS/tree.csv
Rscript $<
......@@ -143,7 +143,7 @@ $(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='local'); 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='local'); process_bigplot_dataset('Paracou', Rlim=15,std.traits='global'); process_bigplot_dataset('Paracou', Rlim=15,std.traits='no');"
$(D2)/Paracou/traits.csv: R/find.trait/Paracou.R R/find.trait/trait-fun.R $(D2)/Paracou/tree.csv
Rscript $<
......@@ -156,7 +156,7 @@ $(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='local'); process_inventory_dataset('Spain',std.traits='no'); process_inventory_dataset('Spain',std.traits='global');"
Rscript -e "source('$<'); process_inventory_dataset('Spain',std.traits='local'); process_inventory_dataset('Spain',std.traits='global'); process_inventory_dataset('Spain',std.traits='no');"
$(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 $<
......@@ -169,7 +169,7 @@ $(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='local'); process_inventory_dataset('Sweden',std.traits='no'); process_inventory_dataset('Sweden',std.traits='global');"
Rscript -e "source('$<'); process_inventory_dataset('Sweden',std.traits='local'); process_inventory_dataset('Sweden',std.traits='global'); process_inventory_dataset('Sweden',std.traits='no');"
$(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 $<
......@@ -182,7 +182,7 @@ $(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='local'); process_inventory_dataset('Swiss',std.traits='no'); process_inventory_dataset('Swiss',std.traits='global');"
Rscript -e "source('$<'); process_inventory_dataset('Swiss',std.traits='local'); process_inventory_dataset('Swiss',std.traits='global'); process_inventory_dataset('Swiss',std.traits='no');"
$(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 $<
......@@ -195,7 +195,7 @@ $(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='global'); process_inventory_dataset('US',std.traits='local'); process_inventory_dataset('US',std.traits='no');"
Rscript -e "source('$<'); process_inventory_dataset('US',std.traits='local'); process_inventory_dataset('US',std.traits='global'); process_inventory_dataset('US',std.traits='no');"
$(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 $<
......
R/format.data/BCI.R
View file @ 87744325
......@@ -97,10 +97,12 @@ data.bci$y <- data.bci$gy; data.bci$gy <- NULL
data.bci$G <- (data.bci$DBH2 - data.bci$DBH1)/data.bci$year ## diameter growth in mm per year - BASED ON UNROUNDED YEARS
data.bci$BA.G <- (pi*(data.bci$DBH2/20)^2 -pi*(data.bci$DBH1/20)^2)/data.bci$year ## BA growth in cm2/yr
data.bci$G[data.bci$Status1=="missing" | data.bci$Status2=="missing"] <- NA
data.bci$G[abs(data.bci$HOM2-data.bci$HOM1)>0.005 & !is.na(data.bci$HOM2-data.bci$HOM1)] <- NA
data.bci$G[abs(data.bci$HOM2-data.bci$HOM1)>0.005 &
!is.na(data.bci$HOM2-data.bci$HOM1)] <- NA
data.bci$G[data.bci$Codes2 %in% c('RF','RP','RT','R')] <- NA
data.bci$BA.G[data.bci$Status1=="missing" | data.bci$Status2=="missing"] <- NA
data.bci$BA.G[abs(data.bci$HOM2-data.bci$HOM1)>0.005 & !is.na(data.bci$HOM2-data.bci$HOM1)] <- NA
data.bci$BA.G[abs(data.bci$HOM2-data.bci$HOM1)>0.005 &
!is.na(data.bci$HOM2-data.bci$HOM1)] <- NA
data.bci$BA.G[data.bci$Codes2 %in% c('RF','RP','RT','R')] <- NA
data.bci$G[data.bci$Latin %in% sp.palm.fern] <- NA ## remove fern and palm
data.bci$BA.G[data.bci$Latin %in% sp.palm.fern] <- NA ## remove fern and palm
......@@ -113,10 +115,18 @@ data.bci$Latin <- NULL
data.bci$census <- data.bci$Census
data.bci$Census <- NULL
## LIMIT TO TREES > 10CM dbh
data.bci <- subset(data.bci,subset=data.bci[["D"]]>=10 & !is.na(data.bci[["D"]])) ### select only tree above 10cm of dbh at census 1
## data.bci <- subset(data.bci,subset=data.bci[["census"]] %in% c(6,5)) ### select only census 6
## remove plot sherman
data.bci <- subset(data.bci,subset=data.bci[["cluster"]] != 'sherman')
## remove bci census 1 because too much error
data.bci <- subset(data.bci,subset=!(data.bci[["cluster"]] == 'bci' & data.bci[["census"]] ==1))
# rename census from 1
data.bci[['census']][data.bci[['cluster']]=='bci'] <- data.bci[['census']][data.bci[['cluster']]=='bci'] -1
## read plots coordinates
coord <- read.csv('data/raw/BCI/Cndt_1ha_coordinates.csv', header = TRUE, stringsAsFactors = FALSE)
......@@ -155,7 +165,8 @@ data.bci$MAP <- clim$MAP
data.bci[["ecocode"]] <- "tropical"
###################### PLOT SELECTION FOR THE ANALYSIS
vec.basic.var <- c("obs.id","tree.id", "sp", "sp.name", "cluster","plot", "ecocode", "D", "G","BA.G", "dead",
vec.basic.var <- c("obs.id","tree.id", "sp", "sp.name",
"cluster","plot", "ecocode", "D", "G","BA.G", "dead",
'Lon','Lat',"x", "y", "census",'MAT','MAP')
data.tree <- subset(data.bci, select = c(vec.basic.var))
......@@ -165,7 +176,6 @@ data.tree <- fun.convert.type.B(data.tree)
write.csv(data.tree,file="output/formatted/BCI/tree.csv",row.names = FALSE)
### write data plot with variables only at the plot level. I should delete them from the tree table but so far I keep them to not distroy later code
vec.basic.var.p <- c("plot", "cluster", "Lon","Lat","ecocode","MAT","MAP")
data.plot <- subset(data.tree, subset=!duplicated(data.tree$cluster),select = c(vec.basic.var.p))
write.csv(data.plot,file="output/formatted/BCI/plot.csv",row.names = FALSE)
R/format.data/format-fun.R
View file @ 87744325
......@@ -122,3 +122,39 @@ symbols(x.t,y.t,circles=D.t ,main=plot.select,inches=inches,fg=fg,...)
}
##' .. remove too negative growth based on Condit R package with param fitted to BCI ..
##'
##' .. taken from trim.growth function in CTFS.R ..
##' @title trim.negative.growth
##' @param dbh1 in mm
##' @param dbh2 in mm
##' @param slope not to be changed
##' @param intercept
##' @param err.limit
##' @return a vector TRUE FALSE with FALSE outlier to be removed
##' @author Kunstler
trim.negative.growth <- function(dbh1,dbh2,slope=0.006214,
intercept=.9036,err.limit=5){
stdev.dbh1 <- slope*dbh1+intercept
bad.grow <- which(dbh2<=(dbh1-err.limit*stdev.dbh1))
accept <- rep(TRUE,length(dbh1))
accept[bad.grow] <- FALSE
accept[is.na(dbh1) | is.na(dbh2) | dbh2<=0 | dbh1<=0] <- FALSE
return(accept)
}
##' .. remove too high growth ..
##'
##' .. taken from trim.growth in Condit CTFS R package ..
##' @title trim.positive.growth
##' @param growth in mm
##' @param maxgrow in mm
##' @return TRUE FALSE vector with FALSE outlier
##' @author Kunstler
trim.positive.growth <- function(growth,maxgrow=75){
bad.grow <- which(growth>maxgrow)
accept <- rep(TRUE,length(growth))
accept[bad.grow] <- FALSE
accept[is.na(growth)] <- FALSE
return(accept)
}
R/process.data/test.tree.CWM-fun.R
View file @ 87744325
####
################################
## function for test.tree.CWM
source("R/utils/plot.R")
load.processed.data <- function(path,file.name="data.tree.tot.csv"){
fname <- file.path(path,file.name )
......@@ -228,37 +230,7 @@ fun.test.value.one.ecoregion.B <- function(data.CWM,set,ecocode.select,path.form
}
## plot CWM
fun.hist.var <- function(var,set,data){
hist(data[[var]],xlab=var,main=set)
}
fun.plot.plot.CWM <- function(data.CWM,set){
trait.name <- c("Leaf.N","Seed.mass","SLA","Wood.density","Max.height")
name.var <- c("focal",
"CWM.fill",
"abs.CWM.fill")
png(paste("figs/test.processed/fig",set,"BATOT.G.BA.B","png",sep="."))
par( mfrow=c(1,2))
plot(data.CWM[["BATOT"]],data.CWM[["G"]],xlab="BATOT",ylab="G")
plot(data.CWM[["BATOT"]],data.CWM[["BA.G"]],xlab="BATOT",ylab="BA.G")
dev.off()
pdf(paste("figs/test.processed/fig",set,"CWM","pdf",sep="."))
par(mfrow=c(5,3))
for (i in trait.name){
try(histt <- lapply(paste(i,name.var,sep="."),fun.hist.var,set,data.CWM))
}
dev.off()
pdf(paste("figs/test.processed/fig",set,"perc","pdf",sep="."))
par(mfrow=c(2,3))
try(histt <- lapply(paste(trait.name,"perc.species",sep="."),fun.hist.var,set,data.CWM))
dev.off()
}
#### compute description of each table
fun.perc.non.missing <- function(i,var.name,var.names.perc,data){
sel <- data[[var.names.perc[i]]]>0.9 & !is.na(data[[var.names.perc[i]]])
return( sum(!is.na((data[[var.name[i]]])[sel]))/length(data[[var.name[i]]][sel]))
......@@ -323,7 +295,6 @@ fun.test.set.tree.CWM.I <- function(set,filedir){
fun.test.set.ecocode.tree.CWM.I(data.temp,set,ecocode.select)
list.perc[[ecocode.select]] <- fun.compute.percentage.species.genus(data.temp)
fun.test.range.vars.q(data.temp,paste(set,ecocode.select))
## fun.plot.plot.CWM (data.temp,paste(set,ecocode.select))
}
mat.perc <- do.call("rbind",list.perc)
df.perc <- data.frame(set=rep(set,nrow(mat.perc)),ecocode=rownames(mat.perc),
......@@ -348,7 +319,6 @@ fun.test.set.tree.CWM.B <- function(set,filedir){
fun.test.set.ecocode.tree.CWM.B(data.temp,set,ecocode.select)
list.perc[[ecocode.select]] <- fun.compute.percentage.species.genus(data.temp)
fun.test.range.vars.q(data.temp,paste(set,ecocode.select))
## fun.plot.plot.CWM (data.temp,paste(set,ecocode.select))
}
mat.perc <- do.call("rbind",list.perc)
df.perc <- data.frame(set=rep(set,nrow(mat.perc)),ecocode=rownames(mat.perc),mat.perc)
......@@ -384,3 +354,99 @@ if (type=='I'){
}
return(data.all)
}
#### PLOT VAR PER SET
## plot hist of each var
fun.hist.var <- function(data,var,...){
tryCatch(hist(data[[var]],xlab=var,main=unique(data[['set']]),...),
warning=function(w) print('warnings'),
error=function(e){print(paste(unique(data[['set']]),'do not have value for',var));
plot(0,0,main=unique(data[['set']]))})
}
fun.hist.var.set <- function(data,var,...){
par(mfrow=c(5,3),mar=c(4.5,3.5,0.5,0.5),mgp=c(1.5,0.5,0))
by(data,INDICES=data[['set']],FUN=fun.hist.var,var=var,xlim=range(data[[var]],na.rm=TRUE),...)
}
fun.plot.xy <- function(data,var.x,var.y,...){
tryCatch(plot(data[[var.x]],data[[var.y]],xlab=var.x,ylab=var.y,main=unique(data[['set']]),...),
warning=function(w) print('warnings'),
error=function(e){print(paste(unique(data[['set']]),'do not have value for',var.x,'or',var.y));
plot(0,0,main=unique(data[['set']]))})
}
fun.plot.xy.set <- function(data,var.x,var.y,...){
par(mfrow=c(5,3),mar=c(4.5,3.5,0.5,0.5),mgp=c(1.5,0.5,0))
by(data,INDICES=data[['set']],FUN=fun.plot.xy,var.x=var.x,var.y=var.y,
xlim=range(data[[var.x]],na.rm=TRUE),
ylim=range(data[[var.y]],na.rm=TRUE),...)
}
fun.plot.hist.trait.per.set <- function(data){
trait.name <- c("Leaf.N","Seed.mass","SLA","Wood.density","Max.height")
name.var <- c("focal",
"CWM.fill",
"abs.CWM.fill")
for (i in name.var){
for (t in trait.name){
var.temp <- paste(t,i,sep=".")
to.pdf(fun.hist.var.set(data,var=var.temp),
paste("figs/test.processed/fig",t,i,"pdf",sep="."))
}
}
}
## remove growth outliers
##' .. remove too negative growth based on Condit R package with param fitted to BCI ..
##'
##' .. taken from trim.growth function in CTFS.R ..
##' @title trim.negative.growth
##' @param dbh1 in mm
##' @param dbh2 in mm
##' @param slope not to be changed
##' @param intercept
##' @param err.limit
##' @return a vector TRUE FALSE with FALSE outlier to be removed
##' @author Kunstler
trim.negative.growth <- function(dbh1,dbh2,slope=0.006214,
intercept=.9036,err.limit=5){
stdev.dbh1 <- slope*dbh1+intercept
bad.grow <- which(dbh2<=(dbh1-err.limit*stdev.dbh1))
accept <- rep(TRUE,length(dbh1))
accept[bad.grow] <- FALSE
accept[is.na(dbh1) | is.na(dbh2) | dbh2<=0 | dbh1<=0] <- FALSE
return(accept)
}
##' .. remove too high growth ..
##'
##' .. taken from trim.growth in Condit CTFS R package ..
##' @title trim.positive.growth
##' @param growth in mm
##' @param maxgrow in mm
##' @return TRUE FALSE vector with FALSE outlier
##' @author Kunstler
trim.positive.growth <- function(growth,maxgrow=75){
bad.grow <- which(growth>maxgrow)
accept <- rep(TRUE,length(growth))
accept[bad.grow] <- FALSE
accept[is.na(growth)] <- FALSE
return(accept)
}
#####
## function compute FD per plot
## TODO
fun.compute.sd.var.cluster <- function(data,var){
cluster.unique.id <- paste(data[['set'],data[['ecocode']],data[['cluster']])
tapply(data[[var]],INDEX=cluster.unique.id,FUN=sd,na.rm=TRUE)
}
R/process.data/test.tree.CWM.R
View file @ 87744325
......@@ -28,7 +28,7 @@ rm(data.all)
## test all set
library(doParallel)
registerDoParallel(cores=5)
lmat.perc.I <- lapply(sets.I, fun.test.set.tree.CWM.I,filedir=filedir)
lmat.perc.I <- mclapply(sets.I, fun.test.set.tree.CWM.I,filedir=filedir,mc.cores= getOption("mc.cores", 5))
mat.perc.I <- do.call("rbind", lmat.perc.I)
......@@ -37,23 +37,28 @@ mat.perc.B <- do.call("rbind",lmat.perc.B)
mat.perc <- data.frame(rbind(mat.perc.I,mat.perc.B),stringsAsFactors=FALSE)
mat.perc <- data.frame(lapply(mat.perc, function(x) (unlist(x))))
write.csv(mat.perc,file=file.path(filedir, "all.sites.perc.traits.csv"), row.names=FALSE)
write.csv(mat.perc,file=file.path(filedir, "all.sites.perc.traits.csv"),
row.names=FALSE)
## format table for report
mat.perc <- read.csv(file=file.path(filedir, "all.sites.perc.traits.csv"))
## genus perc
mat.num.g <- mat.perc[,c(1:3,9:13)]
mat.num.g[,4:8] <- mat.perc[,9:13]/mat.perc[,3]
names(mat.num.g) <- c('set','ecoregion','P obs total','P Leaf N','P Seed mass','P SLA','P Wood density','P Max height')
names(mat.num.g) <- c('set','ecoregion','P obs total','P Leaf N',
'P Seed mass','P SLA','P Wood density','P Max height')
library('pander')
pandoc.table(mat.num.g,caption="Number of tree radial growth observation per data sets and ecoregion.",split.tables='Inf')
pandoc.table(mat.num.g,
caption="Number of tree radial growth observation per data sets and ecoregion.",
split.tables='Inf')
## species perc
mat.num.sp <- mat.perc[,c(1:8)]
mat.num.sp[,4:8] <- mat.perc[,4:8]/mat.perc[,3]
pandoc.table(mat.num.sp,caption="Number of tree radial growth observation per data sets and ecoregion.",split.tables='Inf')
pandoc.table(mat.num.sp,
caption="Number of tree radial growth observation per data sets and ecoregion.",
split.tables='Inf')
### read all data
......@@ -61,6 +66,39 @@ data.all <- read.csv(file=file.path(filedir, "data.all.csv"))
if(dim(data.all)[1] != sum(mat.perc[['num.obs']])) stop('error not same dimension per ecoregion and total')
data.all[['G']][!(trim.positive.growth(data.all[['G']]) &
trim.negative.growth(dbh1=data.all[['D']]*10,
dbh2=data.all[['D']]*10 +data.all[['year']]*data.all[['G']]))] <- NA
data.all[['BA.G']][!(trim.positive.growth(data.all[['G']]) &
trim.negative.growth(data.all[['D']]*10,dbh2=data.all[['D']]*10 +data.all[['year']]*data.all[['G']]))] <- NA
## plot
fun.plot.hist.trait.per.set(data.all)
to.pdf(fun.hist.var.set(data.all,var='BATOT',cex=0.6),
filename="figs/test.processed/fig.BATOT.set.pdf")
to.pdf(fun.hist.var.set(data.all,var='G',cex=0.6),
filename="figs/test.processed/fig.G.set.pdf")
to.pdf(fun.hist.var.set(data.all,var='BA.G',cex=0.6),
filename="figs/test.processed/fig.BA.G.set.pdf")
to.pdf(fun.hist.var.set(data.all,var='D',cex=0.6),
filename="figs/test.processed/fig.D.set.pdf")
to.dev(fun.plot.xy.set(data.all,var.x='BATOT',var.y='BA.G',cex=0.6),dev=png,
filename="figs/test.processed/fig.xy.BATOT.BA.G.set.png")
to.dev(fun.plot.xy.set(data.all,var.x='D',var.y='BA.G',cex=0.6),dev=png,
filename="figs/test.processed/fig.xy.D.BA.G.set.png")
to.dev(fun.plot.xy.set(data.all,var.x='D',var.y='G',cex=0.6),dev=png,
filename="figs/test.processed/fig.xy.D.G.set.png")
fun.plot.xy.trait.per.set(data.all,var.x='BATOT',var.y='BA.G')
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