read CANADA data

TRY.R

@@ -56,11 +56,11 @@ getDoParWorkers() ## here 8 core so 4 core if want to use more registerDoParalle
 ## head(TRY.DATA.FORMATED) 
 ## dim(TRY.DATA.FORMATED) 
 
-saveRDS(TRY.DATA.FORMATED,file="./data/TRY.DATA.FORMATED.rds")
+saveRDS(TRY.DATA.FORMATED,file="./data/process/TRY.DATA.FORMATED.rds")
 
 ########################
 ########## READ RDS
-TRY.DATA.FORMATED <- readRDS("./data/TRY.DATA.FORMATED.rds")
+TRY.DATA.FORMATED <- readRDS("./data/process/TRY.DATA.FORMATED.rds")
 ## TRY.DATA.FORMATED[TRY.DATA.FORMATED$ObservationID==1034196,"StdValue.Seed.mass"] <- NA
 ## head(TRY.DATA.FORMATED)
 
@@ -230,10 +230,10 @@ names(data.ifn.species.try.noout) <-  c(paste(c("Leaf.N","Seed.mass","SLA","Wood
 
 ## data.ifn.species.try.noout[data.ifn.species.try.noout$SLA.genus |data.ifn.species.try.noout$Wood.Density.genus  |data.ifn.species.try.noout$Seed.mass.genus ,]
 
-saveRDS(data.ifn.species.try.noout ,file="./data/data.ifn.species.try.noout.rds")
+saveRDS(data.ifn.species.try.noout ,file="./data/process/data.ifn.species.try.noout.rds")
 
 ####
-data.ifn.species.try.noout <- readRDS("./data/data.ifn.species.try.noout.rds")
+data.ifn.species.try.noout <- readRDS("./data/process/data.ifn.species.try.noout.rds")
 
 #####################################################################
 #### assume that the SD is equal mean species if less than 10 obs same for genus
@@ -313,7 +313,7 @@ print(fun.select.sd.with.to.few.obs.genus(data=data.TRY.sd.update,sd.names,nobs.
     sd.vec.genus[i]
 }
 
-saveRDS(data.TRY.sd.update,file="./data/data.TRY.sd.update.rds")
+saveRDS(data.TRY.sd.update,file="./data/process/data.TRY.sd.update.rds")
 
 ###
 # plot sd to show mark

merge.data.FRANCE.R

+#############################################
+#############################################
+#############################################
+### MERGE FRENCH DATA
+
+#########################
+### read individuals tree data
+load("./data/process/arbre.tot.merge.Rdata")
+head(arbre.tot.merge)
+### read climate
+ecologie.clim.data <- readRDS("./data/process/ecologie.clim.data.rds")
+head(ecologie.clim.data)
+
+#### merge
+dataIFN.FRANCE.t <- merge(arbre.tot.merge,ecologie.clim.data[,c("idp","SER","sgdd","WB.s","WB.y","WS.s","WS.y")],by="idp")
+rm(arbre.tot.merge,ecologie.clim.data)
+
+#### load plot data
+load("./data/process/placette_tot.Rdata")
+dataIFN.FRANCE <- merge(dataIFN.FRANCE.t,placette_tot[,names(placette_tot) != "YEAR"],by="idp")
+rm(placette_tot,dataIFN.FRANCE.t)
+save(dataIFN.FRANCE,file="./data/process/dataIFN.FRANCE.Rdata")

read.data.Canada.R

+##########################
+##########################
+### READ the funny format of the data
+
+##  read fiel per lines and remove "------" and leading and trailling "|  " "   |"
+texts <- grep("^[^-]",readLines("./data/raw/DataCanada/Canada_data2George.csv"),value=TRUE)
+texts <- sub("^[|] +","",texts)
+texts <- sub(" +[|]$","",texts)
+writeLines(texts,con="./data/raw/DataCanada/Canada_data2George_cleaned.txt")
+
+## read data cleaned
+data.Canada <- read.table("./data/raw/DataCanada/Canada_data2George_cleaned.txt",sep="|",header=TRUE,stringsAsFactors =FALSE)
+head(data.Canada)
+plot(data.Canada[["Lon"]],data.Canada[["Lat"]],cex=0.3)
+
+## plots
+length(table(data.Canada[["All_Trees_PlotID"]]))
+## plots and subplots
+length(table(paste( data.Canada[["All_Trees_PlotID"]],data.Canada[["SubPlotID"]])))

readme.txt

+###############################
+###############################
+## README 15/06/2013 G. Kunstler
+
+Code to format data
+ for the working group on traits and competition
+Sydney Maquarie University September 2013