some progress on truning in a package but not finish

Makefile

@@ -12,8 +12,17 @@ D2tree :=  $(addsuffix /tree.csv,$(addprefix $(D2)/, $(sites) ))
 
 all: TRY sites
 
+data:
+	make -C R/format.data
+
+process: data
+	make -C R/process.data
+
 sites: $(sites)
 
+# clean:
+# 	make -C R/format.data clean
+
 #-------------------------------------------------------
 include mk/process_BCI.mk
 include mk/process_Fushan.mk

R/format.data/#format-fun.R#

+
+###################################################
+###################################################
+###################################################
+##### FUNCTION TO FORMAT DATA FOR THE WORKSHOP
+#### G. Kunstler 11/09/2013
+source("R/packages.R")
+check_packages(c("reshape", "boot", "RColorBrewer", "sp", "dismo",
+                 "rgdal", "foreign", "rworldmap"))
+
+############################
+## FUNCTION remove trailing white space
+trim.trailing <- function (x) sub("\\s+$", "", x)
+
+
+#############################################
+## FUN to clean species name for FRENCH NFI
+fun.clean.species.tab <- function(species.tab){
+species.tab2 <- species.tab[!is.na(species.tab$Latin_name), ]
+### species IFN reformat names
+## clean species names and synonyme names
+species.tab2$Latin_name <- (gsub("_", " ", species.tab2$Latin_name))
+species.tab2$Latin_name_syn<- (gsub("_", " ", species.tab2$Latin_name_syn))
+## remove trailing white space
+species.tab2$Latin_name_syn<- trim.trailing(species.tab2$Latin_name_syn)
+species.clean <- species.tab2[!duplicated(species.tab2$Latin_name), 
+                              c("code", "Latin_name",
+                                "Exotic_Native_cultivated")]
+names(species.clean) <- c("sp", "Latin_name", "Exotic_Native_cultivated")
+return(species.clean)
+}
+
+
+
+#####################################################
+### compute quantile 99% and sd with a bootstrap
+##' ..  compute quantile 99% and sd with a bootstra..
+##'
+##' @title f.quantile.boot
+##' @param i subset (species) for which to compute quantile
+##' @param x vector of height
+##' @param fac vector of subset
+##' @param R number of resampling
+##' @param probs probability of quantile to compute
+##' @return a matrix with # col and 1 row with mean sd adn nobs
+##' @author Kunstler
+f.quantile.boot <-  function(i, x, fac, R, probs = 0.99){
+require(boot,quietly = TRUE)
+ if(length( na.exclude(x[fac == i])) > 0 ){
+     quant.boot <- boot(x[fac == i], f.quantile, R = R, probs = probs)
+     return(as.matrix(c(mean = mean(quant.boot$t), sd = sd(quant.boot$t), 
+                        nobs = length(na.exclude(x[fac == i]))),
+                      ncol = 3, nrow = 1))
+ }else{
+     return(as.matrix(c(mean = NA, sd = NA, nobs = NA), ncol = 3, nrow = 1))
+ }
+}
+
+f.quantile <- function (x, ind, probs){
+    require(boot, quietly = TRUE)
+    quantile(x[ind], probs = probs, na.rm = TRUE)
+}
+
+#######################
+### function to compute number of dead per plot
+function.perc.dead <-  function(dead){
+ sum(dead)/length(dead)}
+
+## function to deal with missing value
+function.perc.dead2 <- function(dead) {
+    out <- sum(dead, na.rm = T)/length(dead[!is.na(dead)])
+    if(!is.finite(out)) out <- NA
+    return(out)
+}
+
+## function to convert var factor in character or numeric
+fun.convert.type.I <- function(data.tree){
+character.var <- c("sp", "sp.name", "ecocode")
+numeric.var <- c("D",  "G", "BA.G",  "dead", 
+      "Lon",  "Lat", "weights", "MAT", "MAP")
+factor.to.convert.var <- c("obs.id", "tree.id", "cluster",  "plot", "census")
+for (i in factor.to.convert.var)
+    data.tree[[i]] <- as.integer(factor(data.tree[[i]]))
+for (i in character.var)
+    data.tree[[i]] <- as.character(data.tree[[i]])
+for (i in numeric.var)
+    data.tree[[i]] <- as.numeric(data.tree[[i]])
+return(data.tree)
+}
+
+fun.convert.type.B <- function(data.tree){
+character.var <- c("sp", "sp.name", "ecocode")
+numeric.var <- c("D",  "G", "BA.G", "dead", 
+      "x", "y")
+factor.to.convert.var <- c("obs.id", "tree.id", "cluster",  "plot", "census")
+for (i in factor.to.convert.var) data.tree[[i]] <- as.integer(factor(data.tree[[i]]))
+for (i in character.var) data.tree[[i]] <- as.character(data.tree[[i]])
+for (i in numeric.var) data.tree[[i]] <- as.numeric(data.tree[[i]])
+return(data.tree)
+}
+
+
+
+######
+######
+## FUNCTION TO PLOT MAP OF TREE with function of DBH
+##' .. Function to plot map of tree with circle function of their dbh..
+##'
+##' .. content for \details{} ..
+##' @title
+##' @param plot.select the plot for which draw the map
+##' @param x
+##' @param y
+##' @param plot vectore of plot id for each tree
+##' @param D diameter in cm
+##' @param inches controling the circle size
+##' @param fg.l color circle
+##' @param ...
+##' @return
+##' @author Kunstler
+fun.circles.plot <- function(plot.select, x, y, plot, D, inches, fg.l, ...){
+x.t <- x[plot == plot.select]
+y.t <- y[plot == plot.select]
+D.t <- D[plot == plot.select]
+fg <- fg.l[plot == plot.select]
+D.t[is.na(D.t)] <-  0
+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)
+}    
+
+
+##################### CREATE PLOT BASED ON square.sxsquare.s m cell from X Y
+fun.quadrat <- function(x, y, square.s) {
+
+    if(sum(!is.na(x))>10){
+	vec.x <- seq(0, max(x, na.rm = T) + 20, by = square.s)
+	vec.y <- seq(0, max(y, na.rm = T) + 20, by = square.s)
+	x.cut <- cut(x, breaks = vec.x, include.lowest = TRUE)
+	y.cut <- cut(y, breaks = vec.y, include.lowest = TRUE)
+	out <- apply(cbind(x.cut, y.cut), 1, paste, collapse = ".")
+	out[is.na(x.cut)] <- NA
+	out[is.na(y.cut)] <- NA
+	
+	return(unclass(out))
+    }else{
+         return(rep(NA, length(x)))
+         }
+    }
+
+## function to apply per cluster
+fun.quadrat.cluster <- function(cluster.id, cluster, tree.id, x, y, square.s){
+temp <- fun.quadrat(x[cluster == cluster.id],  y[cluster == cluster.id],
+                    square.s = square.s)
+temp2 <- paste((cluster[cluster == cluster.id]), temp, sep = ".")
+temp2[is.na(temp)] <- NA
+return(data.frame(make.quad = temp2, tree.id = tree.id[cluster == cluster.id]))
+}
+
+
+fun_div <- function(sp){
+p_i <- table(factor(sp))/sum(table(factor(sp)))
+shannon <- -sum(p_i*log(p_i))
+simpson <- 1-sum(p_i^2)
+return(data.frame(shannon=shannon,simpson=simpson))
+}
+
+
+fun.sp.in.ecoregion <-  function(data,  thres.prop=0.05){
+    names(table(data[["sp"]]))[table(data[["sp"]])/length(data[["sp"]]) > thres.prop]
+}

R/format.data/Japan.R

 #!/usr/bin/env Rscript
 
 ### MERGE japan DATA
-rm(list = ls())
-source("R/format.data/format-fun.R")
-source("R/utils/plot.R")
+library(traitcompetition)
 library(reshape, quietly = TRUE)
 
-dir.create("output/formatted/Japan", recursive = TRUE, showWarnings = FALSE)
+path.root <- git.root()
+
+dir.create(file.path(path.root, "output/formatted/Japan"),
+           recursive = TRUE, showWarnings = FALSE)
 
 ######################### READ DATA read individuals tree data 
-filedir <- "data/raw/Japan/TreeData/"
+filedir <- file.path(path.root, "data/raw/Japan/TreeData/")
 filenames <- c("AI-BC1", "AU-DB1", "GR-DB1", "KK-DB1", "OG-DB1", 
                "SD-EB1", "TM-DB4", "AM-EB1", "AU-EC1", 
 	"HY-EC1", "KM-DB1", "OS-EC1", "SI-DB1", "TN-EB1", "AO-BC1", 
@@ -24,7 +25,7 @@ data.japan <- data.frame(x = 1, y = 1, id = 1, plot = 1, sp = 1, sp.name = 1,
                          dbh1 = 1, dbh2 = 1,
                          date1 = 1, date2 = 1, status1 = 1,
                          status2 = 1, er1 = NA, er2 = NA)
-for(i in 1:length(filenames)) {
+for(i in seq_along(filenames)) {
 	make.filename <- paste(filenames[i], "-tree-ver1.csv", sep = "")
 	cat("Working on dataset", make.filename, "\n")
 
@@ -32,9 +33,9 @@ for(i in 1:length(filenames)) {
         if(filenames[i] %in% c('CC-DB1', 'CC-DB2', 'CC-DB3', 'OG-DB1',
                                'OY-DB1', 'SD-EB1', 'TM-DB4')) next;
         
-	tmp.dat <- read.csv(paste(filedir, make.filename, sep = ""),
-                            header = T, 
-                            stringsAsFactors = FALSE,  fill = T)
+	tmp.dat <- read.csv(file.path(filedir, make.filename),
+                            header = TRUE, 
+                            stringsAsFactors = FALSE,  fill = TRUE)
 	how.many.measures <- length(grep("gbh", colnames(tmp.dat)))
 	if(how.many.measures == 1) next; 
 	
@@ -99,8 +100,8 @@ data.japan <- data.japan[-1, ]
 data.japan$date1 <- as.Date(as.character(data.japan$date1), format = "%Y%m%d")
 data.japan$date2 <- as.Date(as.character(data.japan$date2), format = "%Y%m%d")
 	
-site.data <- read.csv(file = "data/raw/Japan/ERDP_2011_01.5.1-SiteList.csv",
-                      header = T)
+site.data <- read.csv(file = file.path(path.root, "data/raw/Japan/ERDP_2011_01.5.1-SiteList.csv"),
+                      header = TRUE)
 data.japan <- merge(data.japan, data.frame(plot = site.data$PlotID,
                                            Lat = site.data$Latitude, 
 	                                   Lon = site.data$Longitude,
@@ -183,7 +184,6 @@ data.japan$plot <- data.japan$make.quad
 
 ## LOAD WORLDCLIM
 #### get wc climate 
-source("R/utils/climate.R")
 clim <- GetClimate(data.japan$Lat, data.japan$Lon)
 data.japan$MAT <- clim$MAT
 data.japan$MAP <- clim$MAP
@@ -223,10 +223,12 @@ data.japan <- merge(data.japan, data.biomes, by = 'cluster')
 table(data.japan$ecocode)
 
 
-## ### biomes from Whittaker
+## ### biomes from Whittake
+obj <- prepare.plotting.info()
 biomes <- fun.overly.plot.on.biomes(MAP = data.japan$MAP/10,
                                         MAT = data.japan$MAT,
-                          names.vec = 1:nrow(data.japan))
+                                    names.vec = 1:nrow(data.japan),
+                                    poly=obj$poly.DF)
 # plot
  plot.biome.map()
  points(data.japan$MAP/10,data.japan$MAT)
@@ -275,7 +277,7 @@ vec.basic.var <- c("obs.id", "tree.id",  "sp",  "sp.name",  "cluster", "plot",
 data.tree <- subset(data.japan,  select = c(vec.basic.var))
 
 data.tree <- fun.convert.type.B(data.tree)
-write.csv(data.tree, file = "output/formatted/Japan/tree.csv",
+write.csv(data.tree, file = file.path(path.root, "output/formatted/Japan/tree.csv"),
           row.names = FALSE)
 
 ### write data plot with variables only at the plot level.
@@ -283,6 +285,6 @@ write.csv(data.tree, file = "output/formatted/Japan/tree.csv",
 vec.basic.var.p <- c("plot", "cluster", "Lon","Lat","ecocode")
 data.plot <- subset(data.tree, subset=!duplicated(data.tree$cluster),
                     select = c(vec.basic.var.p))
-write.csv(data.plot, file = "output/formatted/Japan/plot.csv",
+write.csv(data.plot, file = file.path(path.root, "output/formatted/Japan/plot.csv"),
           row.names = FALSE)
 

R/format.data/Makefile

+include mk/process_BCI.mk
+include mk/process_Fushan.mk
+include mk/process_Paracou.mk
+include mk/process_Mbaiki.mk
+include mk/process_Luquillo.mk
+include mk/process_Japan.mk
+include mk/process_Canada.mk
+include mk/process_Spain.mk
+include mk/process_Sweden.mk
+include mk/process_France.mk
+include mk/process_Swiss.mk
+include mk/process_NSW.mk
+include mk/process_NVS.mk
+include mk/process_US.mk
+
+include mk/cible.tree.traits.mk
+
+SITES:= US Fushan Paracou BCI Mbaiki Luquillo Japan Spain Sweden Canada France Swiss NSW NVS 
+
+all: $(SITES)

R/format.data/mk/cible.tree.traits.mk

+tree.all.sites: $(D2)/BCI/tree.csv $(D2)/Fushan/tree.csv $(D2)/Paracou/tree.csv $(D2)/Mbaiki/tree.csv $(D2)/Luquillo/tree.csv $(D2)/Japan/tree.csv $(D2)/US/tree.csv $(D2)/Canada/tree.csv $(D2)/Spain/tree.csv $(D2)/Sweden/tree.csv $(D2)/France/tree.csv $(D2)/Swiss/tree.csv $(D2)/NSW/tree.csv $(D2)/NVS/tree.csv 
+ 
+traits.all.sites: $(D2)/BCI/traits.csv $(D2)/Fushan/traits.csv $(D2)/Paracou/traits.csv $(D2)/Mbaiki/traits.csv $(D2)/Luquillo/traits.csv $(D2)/Japan/traits.csv $(D2)/US/traits.csv $(D2)/Canada/traits.csv $(D2)/Spain/traits.csv $(D2)/Sweden/traits.csv $(D2)/France/traits.csv $(D2)/Swiss/traits.csv $(D2)/NSW/traits.csv $(D2)/NVS/traits.csv 

R/format.data/mk/process_BCI.mk

+BCI:  $(D3)/BCI/Done.no.txt $(D3)/BCI/Done.log.txt
+
+$(D3)/BCI/Done.no.txt: R/process.data/process-fun.R $(D2)/BCI/traits.csv 
+	Rscript -e "source('$<'); process_bigplot_dataset('BCI', Rlim=15,std.traits='no');"
+
+$(D3)/BCI/Done.log.txt: R/process.data/process-fun.R $(D2)/BCI/traits.csv 
+	Rscript -e "source('$<'); process_bigplot_dataset('BCI', Rlim=15,std.traits='log');"
+
+$(D2)/BCI/traits.csv: R/find.trait/BCI.R R/find.trait/trait-fun.R $(D2)/BCI/tree.csv 
+	Rscript $< 
+
+$(D2)/BCI/tree.csv: R/format.data/BCI.R $(shell find $(D1)/BCI -type f)
+	Rscript $<

R/format.data/mk/process_Canada.mk

+
+Canada:  $(D3)/Canada/Done.no.txt $(D3)/Canada/Done.log.txt
+
+$(D3)/Canada/Done.no.txt: R/process.data/process-fun.R  $(D2)/Canada/traits.csv 
+	Rscript -e "source('$<'); process_inventory_dataset('Canada',std.traits='no');"
+
+$(D3)/Canada/Done.log.txt: R/process.data/process-fun.R  $(D2)/Canada/traits.csv 
+	Rscript -e "source('$<'); process_inventory_dataset('Canada',std.traits='log');"
+
+$(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 $< 
+
+$(D2)/Canada/tree.csv: R/format.data/Canada.R $(shell find $(D1)/Canada -type f)
+	Rscript $< 
+

R/format.data/mk/process_France.mk

+
+France:  $(D3)/France/Done.no.txt $(D3)/France/Done.log.txt
+
+$(D3)/France/Done.no.txt: R/process.data/process-fun.R  $(D2)/France/traits.csv 
+	Rscript -e "source('$<'); process_inventory_dataset('France',std.traits='no');"
+
+$(D3)/France/Done.log.txt: R/process.data/process-fun.R  $(D2)/France/traits.csv 
+	Rscript -e "source('$<'); process_inventory_dataset('France',std.traits='log');"
+
+$(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 $< 
+
+$(D2)/France/tree.csv: R/format.data/France.R $(shell find $(D1)/France -type f)
+	Rscript $< 
+

R/format.data/mk/process_Fushan.mk

+Fushan:  $(D3)/Fushan/Done.no.txt $(D3)/Fushan/Done.log.txt
+
+$(D3)/Fushan/Done.no.txt: R/process.data/process-fun.R $(D2)/Fushan/traits.csv 
+	Rscript -e "source('$<'); process_bigplot_dataset('Fushan', Rlim=15,std.traits='no');"
+
+$(D3)/Fushan/Done.log.txt: R/process.data/process-fun.R $(D2)/Fushan/traits.csv 
+	Rscript -e "source('$<'); process_bigplot_dataset('Fushan', Rlim=15,std.traits='log');"
+
+$(D2)/Fushan/traits.csv: R/find.trait/Fushan.R R/find.trait/trait-fun.R $(D2)/Fushan/tree.csv 
+	Rscript $< 
+
+$(D2)/Fushan/tree.csv: R/format.data/Fushan.R $(shell find $(D1)/Fushan -type f)
+	Rscript $<

R/format.data/mk/process_Japan.mk

+Japan:  $(D3)/Japan/Done.no.txt $(D3)/Japan/Done.log.txt
+
+$(D3)/Japan/Done.no.txt: R/process.data/process-fun.R $(D2)/Japan/traits.csv 
+	Rscript -e "source('$<'); process_bigplot_dataset('Japan', Rlim=15,std.traits='no');"
+
+$(D3)/Japan/Done.log.txt: R/process.data/process-fun.R $(D2)/Japan/traits.csv 
+	Rscript -e "source('$<'); process_bigplot_dataset('Japan', Rlim=15,std.traits='log');"
+
+$(D2)/Japan/traits.csv: R/find.trait/Japan.R R/find.trait/trait-fun.R $(D2)/Japan/tree.csv 
+	Rscript $< 
+
+$(D2)/Japan/tree.csv: R/format.data/Japan.R $(shell find $(D1)/Japan -type f)
+	Rscript $<

R/format.data/mk/process_Luquillo.mk

+Luquillo:  $(D3)/Luquillo/Done.no.txt $(D3)/Luquillo/Done.log.txt
+
+$(D3)/Luquillo/Done.no.txt: R/process.data/process-fun.R $(D2)/Luquillo/traits.csv 
+	Rscript -e "source('$<'); process_bigplot_dataset('Luquillo', Rlim=15,std.traits='no');"
+
+$(D3)/Luquillo/Done.log.txt: R/process.data/process-fun.R $(D2)/Luquillo/traits.csv 
+	Rscript -e "source('$<'); process_bigplot_dataset('Luquillo', Rlim=15,std.traits='log');"
+
+$(D2)/Luquillo/traits.csv: R/find.trait/Luquillo.R R/find.trait/trait-fun.R $(D2)/Luquillo/tree.csv 
+	Rscript $< 
+
+$(D2)/Luquillo/tree.csv: R/format.data/Luquillo.R $(shell find $(D1)/Luquillo -type f)
+	Rscript $<

R/format.data/mk/process_Mbaiki.mk

+Mbaiki:  $(D3)/Mbaiki/Done.no.txt $(D3)/Mbaiki/Done.log.txt
+
+$(D3)/Mbaiki/Done.no.txt: R/process.data/process-fun.R $(D2)/Mbaiki/traits.csv 
+	Rscript -e "source('$<'); process_bigplot_dataset('Mbaiki', Rlim=15,std.traits='no');"
+
+$(D3)/Mbaiki/Done.log.txt: R/process.data/process-fun.R $(D2)/Mbaiki/traits.csv 
+	Rscript -e "source('$<'); process_bigplot_dataset('Mbaiki', Rlim=15,std.traits='log');"
+
+$(D2)/Mbaiki/traits.csv: R/find.trait/Mbaiki.R R/find.trait/trait-fun.R $(D2)/Mbaiki/tree.csv 
+	Rscript $< 
+
+$(D2)/Mbaiki/tree.csv: R/format.data/Mbaiki.R $(shell find $(D1)/Mbaiki -type f)
+	Rscript $<

R/format.data/mk/process_NSW.mk

+
+NSW:  $(D3)/NSW/Done.no.txt $(D3)/NSW/Done.log.txt
+
+$(D3)/NSW/Done.no.txt: R/process.data/process-fun.R  $(D2)/NSW/traits.csv 
+	Rscript -e "source('$<'); process_inventory_dataset('NSW',std.traits='no');"
+
+$(D3)/NSW/Done.log.txt: R/process.data/process-fun.R  $(D2)/NSW/traits.csv 
+	Rscript -e "source('$<'); process_inventory_dataset('NSW',std.traits='log');"
+
+$(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 $< 
+
+$(D2)/NSW/tree.csv: R/format.data/NSW.R $(shell find $(D1)/NSW -type f)
+	Rscript $< 
+

R/format.data/mk/process_NVS.mk

+
+NVS:  $(D3)/NVS/Done.no.txt $(D3)/NVS/Done.log.txt
+
+$(D3)/NVS/Done.no.txt: R/process.data/process-fun.R  $(D2)/NVS/traits.csv 
+	Rscript -e "source('$<'); process_inventory_dataset('NVS',std.traits='no');"
+
+$(D3)/NVS/Done.log.txt: R/process.data/process-fun.R  $(D2)/NVS/traits.csv 
+	Rscript -e "source('$<'); process_inventory_dataset('NVS',std.traits='log');"
+
+$(D2)/NVS/traits.csv: R/find.trait/NVS.R R/find.trait/trait-fun.R $(D2)/NVS/tree.csv $(D2)/TRY/data.TRY.std.rds
+	Rscript $< 
+
+$(D2)/NVS/tree.csv: R/format.data/NVS.R $(shell find $(D1)/NVS -type f)
+	Rscript $< 
+

R/format.data/mk/process_Paracou.mk

+Paracou:  $(D3)/Paracou/Done.no.txt $(D3)/Paracou/Done.log.txt
+
+$(D3)/Paracou/Done.no.txt: R/process.data/process-fun.R $(D2)/Paracou/traits.csv 
+	Rscript -e "source('$<'); process_bigplot_dataset('Paracou', Rlim=15,std.traits='no');"
+
+$(D3)/Paracou/Done.log.txt: R/process.data/process-fun.R $(D2)/Paracou/traits.csv 
+	Rscript -e "source('$<'); process_bigplot_dataset('Paracou', Rlim=15,std.traits='log');"
+
+$(D2)/Paracou/traits.csv: R/find.trait/Paracou.R R/find.trait/trait-fun.R $(D2)/Paracou/tree.csv 
+	Rscript $< 
+
+$(D2)/Paracou/tree.csv: R/format.data/Paracou.R $(shell find $(D1)/Paracou -type f)
+	Rscript $<

R/format.data/mk/process_Spain.mk

+
+Spain:  $(D3)/Spain/Done.no.txt $(D3)/Spain/Done.log.txt
+
+$(D3)/Spain/Done.no.txt: R/process.data/process-fun.R  $(D2)/Spain/traits.csv 
+	Rscript -e "source('$<'); process_inventory_dataset('Spain',std.traits='no');"
+
+$(D3)/Spain/Done.log.txt: R/process.data/process-fun.R  $(D2)/Spain/traits.csv 
+	Rscript -e "source('$<'); process_inventory_dataset('Spain',std.traits='log');"
+
+$(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 $< 
+
+$(D2)/Spain/tree.csv: R/format.data/Spain.R $(shell find $(D1)/Spain -type f)
+	Rscript $< 
+

R/format.data/mk/process_Sweden.mk

+
+Sweden:  $(D3)/Sweden/Done.no.txt $(D3)/Sweden/Done.log.txt
+
+$(D3)/Sweden/Done.no.txt: R/process.data/process-fun.R  $(D2)/Sweden/traits.csv 
+	Rscript -e "source('$<'); process_inventory_dataset('Sweden',std.traits='no');"
+
+$(D3)/Sweden/Done.log.txt: R/process.data/process-fun.R  $(D2)/Sweden/traits.csv 
+	Rscript -e "source('$<'); process_inventory_dataset('Sweden',std.traits='log');"
+
+$(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 $< 
+
+$(D2)/Sweden/tree.csv: R/format.data/Sweden.R $(shell find $(D1)/Sweden -type f)
+	Rscript $< 
+

R/format.data/mk/process_Swiss.mk

+
+Swiss:  $(D3)/Swiss/Done.no.txt $(D3)/Swiss/Done.log.txt
+
+$(D3)/Swiss/Done.no.txt: R/process.data/process-fun.R  $(D2)/Swiss/traits.csv 
+	Rscript -e "source('$<'); process_inventory_dataset('Swiss',std.traits='no');"
+
+$(D3)/Swiss/Done.log.txt: R/process.data/process-fun.R  $(D2)/Swiss/traits.csv 
+	Rscript -e "source('$<'); process_inventory_dataset('Swiss',std.traits='log');"
+
+$(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 $< 
+
+$(D2)/Swiss/tree.csv: R/format.data/Swiss.R $(shell find $(D1)/Swiss -type f)
+	Rscript $< 
+

R/format.data/mk/process_US.mk

+
+US:  $(D3)/US/Done.no.txt $(D3)/US/Done.log.txt
+
+$(D3)/US/Done.no.txt: R/process.data/process-fun.R  $(D2)/US/traits.csv 
+	Rscript -e "source('$<'); process_inventory_dataset('US',std.traits='no');"
+
+$(D3)/US/Done.log.txt: R/process.data/process-fun.R  $(D2)/US/traits.csv 
+	Rscript -e "source('$<'); process_inventory_dataset('US',std.traits='log');"
+
+$(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 $< 
+
+$(D2)/US/tree.csv: R/format.data/US.R $(shell find $(D1)/US -type f)
+	Rscript $< 
+

R/format.data/wc0.5

+../../wc0.5/
\ No newline at end of file