new makefile for global

Makefile

@@ -26,7 +26,7 @@ $(D2)/TRY/data.TRY.std.rds:
 GLOBAL: $(D3)/Done.txt
 
 $(D3)/Done.txt: R/process.data/global.R R/process.data/process-fun.R $(D2)/traits.std.global.csv $(D5)/Done.txt
-	Rscript $<
+	Rscript $< ; Rscript R/process.data/merge.all.processed.data.R
 
 #-------------------------------------------------------
 

R/find.trait/Mbaiki.R

@@ -142,40 +142,6 @@ countsup.LeafN # 34
 countsup.SLA # 34
 countsup.WSG # 0
 
-## #=============================================================
-## # Phenology
-## d.pheno <- read.csv2(file="data/raw/Mbaiki/getpheno_cofortraits_20140212.csv",header=TRUE)
-## dim(d.pheno)
-## names(d.pheno)[8] <- "pheno"
-## head(d.pheno)
-## head(data.species.3)
-## Species.Name.From.List <- function (x) {
-##     genus <- x[1]
-##     sp <- x[2]
-##     lb <- paste(genus,sp,sep=" ")
-##     return(lb)
-## }
-## d.pheno$latin.binomial <- c(unlist(lapply(strsplit(as.character(d.pheno$species),split=" "),Species.Name.From.List)))
-## Unique.Paste <- function (x) {
-##     r <- paste(unique(x),collapse=" ")
-##     return(r)
-## }
-## Mat.Pheno <- as.data.frame(tapply(as.character(d.pheno$pheno),d.pheno$latin.binomial,Unique.Paste))
-## Mat.Pheno$latin.binomial <- row.names(Mat.Pheno)
-## row.names(Mat.Pheno) <- NULL
-## names(Mat.Pheno) <- c("D_EV","latin.binomial")
-## Mat.Pheno$D_EV <- as.character(Mat.Pheno$D_EV)
-## str(Mat.Pheno)
-## # Set leaf-exchanger to evergreen
-## w <- grep("leaf-exchanger",Mat.Pheno$D_EV)
-## Mat.Pheno$D_EV[w] <- "EV"
-## Mat.Pheno$D_EV[Mat.Pheno$D_EV=="decidue"] <- "D"
-## Mat.Pheno$D_EV[Mat.Pheno$D_EV=="sempervirente"] <- "EV"
-## Mat.Pheno$D_EV[!(Mat.Pheno$D_EV %in% c("D","EV"))] <- NA
-
-## # Merge
-## data.species.4 <- merge(data.species.3,Mat.Pheno,
-##                         by.x="Species",by.y="latin.binomial",all.x=TRUE)
 data.species.4 <- data.species.3
 #=============================================================
 # WSG with Dryad
@@ -291,6 +257,46 @@ data.traits <- merge(data.traits,
                      data.cat.extract[,c("sp","Phylo.group","Pheno.T")],
                      by="sp")
 
+#=============================================================
+# Phenology
+d.pheno <- read.csv2(file="data/raw/Mbaiki/getpheno_cofortraits_20140212.csv",header=TRUE)
+dim(d.pheno)
+names(d.pheno)[8] <- "pheno"
+head(d.pheno)
+head(data.species.3)
+Species.Name.From.List <- function (x) {
+    genus <- x[1]
+    sp <- x[2]
+    lb <- paste(genus,sp,sep=" ")
+    return(lb)
+}
+d.pheno$latin.binomial <- c(unlist(lapply(strsplit(as.character(d.pheno$species),split=" "),Species.Name.From.List)))
+Unique.Paste <- function (x) {
+    r <- paste(unique(x),collapse=" ")
+    return(r)
+}
+Mat.Pheno <- as.data.frame(tapply(as.character(d.pheno$pheno),d.pheno$latin.binomial,Unique.Paste))
+Mat.Pheno$latin.binomial <- row.names(Mat.Pheno)
+row.names(Mat.Pheno) <- NULL
+names(Mat.Pheno) <- c("D_EV","latin.binomial")
+Mat.Pheno$D_EV <- as.character(Mat.Pheno$D_EV)
+str(Mat.Pheno)
+# Set leaf-exchanger to evergreen
+w <- grep("leaf-exchanger",Mat.Pheno$D_EV)
+Mat.Pheno$D_EV[w] <- "EV"
+Mat.Pheno$D_EV[Mat.Pheno$D_EV=="decidue"] <- "D"
+Mat.Pheno$D_EV[Mat.Pheno$D_EV=="sempervirente"] <- "EV"
+Mat.Pheno$D_EV[!(Mat.Pheno$D_EV %in% c("D","EV"))] <- NA
+
+names(Mat.Pheno) <- c('D_EV','Latin_name')
+# Merge
+data.traits <- merge(data.traits,Mat.Pheno,
+                        by = "Latin_name",all.x=TRUE,all.y=FALSE)
+
+#
+data.traits$Pheno.T[!is.na(data.traits$D_EV)] <- data.traits$D_EV[!is.na(data.traits$D_EV)]
+data.traits$D_EV <-  NULL
+
 ## compute perc of traits cover per species
 print(sapply(c('Leaf.N','SLA','Seed.mass','Wood.density','Max.height'),
              fun.compute.perc.cover.one.trait,data.traits))

R/process.data/explore.processed.data.R

@@ -20,31 +20,6 @@ system.time(data.all <-  fread(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')
 
-## plots
-
-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, col = col.vec[data.all$set]), dev = png,
-       filename = "figs/test.processed/fig.xy.D.G.set.png") 
-to.dev(fun.plot.xy.set(data.all, var.x = 'BATOT', var.y = 'G', cex = 0.6),
-       dev = png,
-       filename = "figs/test.processed/fig.xy.BATOT.G.set.png") 
-
 
 ########
 ### TODO
@@ -68,7 +43,7 @@ boxplot(data.all$BATOT ~ data.all$set, las = 3)
 
 system.time(data.summarise <- fun.compute.all.var.cluster(data.all))
 
-### NEED TO CHECK WHY JAPAN REACH 300 of BATOT 
+### NEED TO CHECK WHY JAPAN REACH 300 of BATOT
 par(mfrow=c(1,2))
 plot(data.summarise$MAP,data.summarise$BATOT,
      ,col=col.vec[data.summarise$set],cex=0.1)

R/process.data/global.R

@@ -5,5 +5,5 @@ source('R/process.data/process-fun.R')
 set.big <- c('Fushan', 'Paracou', 'BCI', 'Mbaiki', 'Luquillo', 'Japan')
 set.inv <- c('Spain', 'Sweden', 'Canada', 'France', 'Swiss', 'NSW', 'NVS', 'US')
 
-for (i in set.bi) process_bigplot_dataset(i, Rlim=15, std.traits = 'global')
-for (i in set.in) process_inventory_dataset(i, std.traits = 'global')
+for (i in set.big) process_bigplot_dataset(i, Rlim=15, std.traits = 'global')
+for (i in set.inv) process_inventory_dataset(i, std.traits = 'global')

R/process.data/merge.all.processed.data.R

@@ -44,3 +44,49 @@ data.all$obs.id <- paste(data.all$ecocode,data.all$obs.id)
 
 write.csv(data.all,file=file.path(filedir, "data.all.csv"), row.names=FALSE)
 
+cat("finished", file = file.path(filedir, "Done.txt"))
+
+
+#######################################
+#######################################
+## plots
+
+fun.plot.hist.trait.per.set(data.all)
+pdf("figs/test.processed/boxplot.pdf")
+boxplot(BATOT~set,data=data.all,las=3)
+boxplot(D~set,data=data.all,las=3)
+boxplot(D~set,data=data.all,las=3)
+boxplot(BA.G~set,data=data.all,las=3)
+par(mar=c(10,4,4,4))
+barplot(tapply((data.all$Pheno.T=='D'),data.all$ecocode,
+              function(x) sum(x,na.rm=TRUE)/length(x)),
+       las=3,yaln='perc d')
+
+par(mar=c(10,4,4,4))
+barplot(tapply((data.all$Phylo.group=='Gymnosperm'),data.all$ecocode,
+              function(x) sum(x,na.rm=TRUE)/length(x)),
+       las=3,yaln='perc gym')
+dev.off()
+
+
+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, col = col.vec[data.all$set]), dev = png,
+       filename = "figs/test.processed/fig.xy.D.G.set.png")
+to.dev(fun.plot.xy.set(data.all, var.x = 'BATOT', var.y = 'G', cex = 0.6),
+       dev = png,
+       filename = "figs/test.processed/fig.xy.BATOT.G.set.png")
+