From 6b375a52824d4a72617c040876ab858f3903f77c Mon Sep 17 00:00:00 2001
From: Georges Kunstler <Georges.Kunstler@gmail.com>
Date: Wed, 4 Sep 2013 09:35:30 +1000
Subject: [PATCH] metadataFRANCE and new unique file for France

---
 R/CLIMATE.FRANCE.R                            | 238 ----------
 R/READ.DATA.NFI.FRANCE.R                      | 432 ------------------
 merge.data.FRANCE.R                           |  24 +-
 ms/metadata/France/_file_index.csv            |  85 +---
 ms/metadata/France/_site_details.csv          |  24 +-
 .../France/files/2005_arbres_foret_2005.csv   |   2 -
 .../files/2005_arbres_morts_foret_2005.csv    |   2 -
 .../files/2005_arbres_peupleraie_2005.csv     |   2 -
 .../files/2005_documentation_2005-2.csv       |   2 -
 .../France/files/2005_documentation_flore.csv |   2 -
 .../France/files/2005_ecologie_2005.csv       |   2 -
 ms/metadata/France/files/2005_flore_2005.csv  |   2 -
 .../files/2005_placettes_foret_2005.csv       |   2 -
 .../files/2005_placettes_peupleraie_2005.csv  |   2 -
 .../France/files/2006_arbres_foret_2006.csv   |   2 -
 .../files/2006_arbres_morts_foret_2006.csv    |   2 -
 .../files/2006_arbres_peupleraie_2006.csv     |   2 -
 .../France/files/2006_couverts_foret_2006.csv |   2 -
 .../files/2006_documentation_2006-2.csv       |   2 -
 .../France/files/2006_documentation_flore.csv |   2 -
 .../France/files/2006_ecologie_2006.csv       |   2 -
 ms/metadata/France/files/2006_flore_2006.csv  |   2 -
 .../files/2006_placettes_foret_2006.csv       |   2 -
 .../files/2006_placettes_peupleraie_2006.csv  |   2 -
 .../France/files/2007_arbres_foret_2007.csv   |   2 -
 .../files/2007_arbres_morts_foret_2007.csv    |   2 -
 .../files/2007_arbres_peupleraie_2007.csv     |   2 -
 .../France/files/2007_couverts_foret_2007.csv |   2 -
 .../files/2007_documentation_2007-2.csv       |   2 -
 .../France/files/2007_documentation_flore.csv |   2 -
 .../France/files/2007_ecologie_2007.csv       |   2 -
 ms/metadata/France/files/2007_flore_2007.csv  |   2 -
 .../files/2007_placettes_foret_2007.csv       |   2 -
 .../files/2007_placettes_peupleraie_2007.csv  |   2 -
 .../France/files/2008_arbres_foret_2008.csv   |   2 -
 .../files/2008_arbres_morts_foret_2008.csv    |   2 -
 .../2008_arbres_morts_peupleraie_2008.csv     |   2 -
 .../files/2008_arbres_peupleraie_2008.csv     |   2 -
 .../France/files/2008_couverts_foret_2008.csv |   2 -
 .../files/2008_documentation_2008-2.csv       |   2 -
 .../France/files/2008_documentation_flore.csv |   2 -
 .../France/files/2008_ecologie_2008.csv       |   2 -
 ms/metadata/France/files/2008_flore_2008.csv  |   2 -
 .../files/2008_placettes_foret_2008.csv       |   2 -
 .../files/2008_placettes_peupleraie_2008.csv  |   2 -
 .../France/files/2009_arbres_foret_2009.csv   |   2 -
 .../files/2009_arbres_morts_foret_2009.csv    |   2 -
 .../2009_arbres_morts_peupleraie_2009.csv     |   2 -
 .../files/2009_arbres_peupleraie_2009.csv     |   2 -
 .../France/files/2009_couverts_foret_2009.csv |   2 -
 .../files/2009_documentation_2009-2.csv       |   2 -
 .../France/files/2009_documentation_flore.csv |   2 -
 .../France/files/2009_ecologie_2009.csv       |   2 -
 ms/metadata/France/files/2009_flore_2009.csv  |   2 -
 .../files/2009_placettes_foret_2009.csv       |   2 -
 .../files/2009_placettes_peupleraie_2009.csv  |   2 -
 .../France/files/2010_arbres_foret_2010.csv   |   2 -
 .../files/2010_arbres_morts_foret_2010.csv    |   2 -
 .../2010_arbres_morts_peupleraie_2010.csv     |   2 -
 .../files/2010_arbres_peupleraie_2010.csv     |   2 -
 .../France/files/2010_couverts_foret_2010.csv |   2 -
 .../France/files/2010_documentation_2010.csv  |   2 -
 .../France/files/2010_documentation_flore.csv |   2 -
 .../France/files/2010_ecologie_2010.csv       |   2 -
 ms/metadata/France/files/2010_flore_2010.csv  |   2 -
 .../files/2010_placettes_foret_2010.csv       |   2 -
 .../files/2010_placettes_peupleraie_2010.csv  |   2 -
 .../France/files/2011_arbres_foret_2011.csv   |   2 -
 .../files/2011_arbres_morts_foret_2011.csv    |   2 -
 .../2011_arbres_morts_peupleraie_2011.csv     |   2 -
 .../files/2011_arbres_peupleraie_2011.csv     |   2 -
 .../France/files/2011_couverts_foret_2011.csv |   2 -
 .../France/files/2011_documentation_2011.csv  |   2 -
 .../France/files/2011_documentation_flore.csv |   2 -
 .../France/files/2011_ecologie_2011.csv       |   2 -
 ms/metadata/France/files/2011_flore_2011.csv  |   2 -
 .../files/2011_placettes_foret_2011.csv       |   2 -
 .../files/2011_placettes_peupleraie_2011.csv  |   2 -
 .../France/files/altitude_SER_alti.csv        |   2 -
 .../France/files/altitude_SER_alti_2011.csv   |   2 -
 .../files/climate_piedallu_placettesGK2.csv   |  95 ----
 ...climate_piedallu_placettesGK_avec 2011.csv |  95 ----
 .../France/files/climate_piedallu_texture.csv |  10 -
 ms/metadata/France/files/cycle3_arbres2.csv   |   2 -
 .../France/files/cycle3_data.arbre.tot.csv    |   2 -
 .../France/files/cycle3_speciesnames.csv      |   2 -
 86 files changed, 18 insertions(+), 1141 deletions(-)
 delete mode 100644 R/CLIMATE.FRANCE.R
 delete mode 100644 R/READ.DATA.NFI.FRANCE.R
 delete mode 100644 ms/metadata/France/files/2005_arbres_foret_2005.csv
 delete mode 100644 ms/metadata/France/files/2005_arbres_morts_foret_2005.csv
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 delete mode 100644 ms/metadata/France/files/2005_documentation_flore.csv
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 delete mode 100644 ms/metadata/France/files/climate_piedallu_placettesGK_avec 2011.csv
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 delete mode 100644 ms/metadata/France/files/cycle3_data.arbre.tot.csv
 delete mode 100644 ms/metadata/France/files/cycle3_speciesnames.csv

diff --git a/R/CLIMATE.FRANCE.R b/R/CLIMATE.FRANCE.R
deleted file mode 100644
index 0bd3cca..0000000
--- a/R/CLIMATE.FRANCE.R
+++ /dev/null
@@ -1,238 +0,0 @@
-################################################ LOAD and PROCEED CLIMATIC DATA
-source("./R/FUN.climate.R")
-## Data extracted from C. Piedallu data base with Radition with cloud cover for
-## each plots Piedallu, C, and J Gegout. 2008. “Efficient Assessment of
-## Topographic Solar Radiation to Improve Plant Distribution Models.” Agricultural
-## and Forest Meteorology 148 (11) (October): 1696–1706.
-## doi:10.1016/j.agrformet.2008.06.001.  Temperature and precipitation with
-## temperature corrected by elevation based on Piedallu, C., J. C. Gégout, V.
-## Perez, F. Lebourgeois, and R. Field. 2012. “Soil Water Balance Performs Better
-## Than Climatic Water Variables in Tree Species Distribution Modelling.” Global
-## Ecology and Biogeography.
-## http://onlinelibrary.wiley.com/doi/10.1111/geb.12012/full.
-
-###### LOAD PIDEALLU DATA
-data.CLIM <- read.csv("./data/raw/DataFrance/climate_piedallu/placettesGK_avec_2011.csv", 
-    header = T, sep = "\t", stringsAsFactors = FALSE, dec = ",", na.strings = "")
-print(names(data.CLIM))
-
-data.CLIM$rumkg_500 <- as.numeric(gsub(",", ".", data.CLIM$rumkg_500))
-
-
-######################################### COMPUTE CLIMATIC VARIABLES !!!
-
-### NEED TO COMPUTE DDG5 NEED TO COMPUTE SOIL MAX WATER CONTENT NEED TO COMPUTE PET
-### NEED TO COMPUTE WATER BUDGET
-
-## remove NA lines
-data.CLIM.na <- is.na(data.CLIM[["tmoy6190_1_cor"]])
-data.CLIM2 <- data.CLIM[!data.CLIM.na, ]
-
-### apply function sgdd
-sgdd.vec <- apply(data.CLIM2[, 82:93], MARGIN = 1, FUN = fun.sgdd)
-MeanT.vec <- apply(data.CLIM2[, 82:93], MARGIN = 1, FUN = mean)
-plot(MeanT.vec, sgdd.vec)
-dim(data.CLIM)
-
-################################################# Max Soil Water Content compute based on Piedallu, C., J. C. Gégout, A. Bruand,
-################################################# and I. Seynave. 2011. “Mapping Soil Water Holding Capacity over Large Areas to
-################################################# Predict Potential Production of Forest Stands.” Geoderma 160 (3): 355–366.
-
-### read data texture as in Piedallu et al. 2011
-data.texture <- read.table("./data/raw/DataFrance/climate_piedallu/texture.txt", 
-    header = T)
-### load ecological data
-load(file = "./data/process/ecologie_tot.Rdata")
-head(ecologie_tot)
-
-codeprof <- c(2.5, 10, 20, 30, 40, 50, 60, 70, 80, 92.5)  # code prof en cm
-codecaillou <- c(2.5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 97.5)  ## code percentage en %
-
-# compute swhc
-swhc <- fun.swhc(affroc = ecologie_tot$affroc, cailloux = ecologie_tot$cailloux, 
-    text2 = ecologie_tot$text2, text1 = ecologie_tot$text1, prof2 = ecologie_tot$prof2, 
-    prof1 = ecologie_tot$prof1, codeprof, codecaillou, data.texture)
-swhc[is.na(ecologie_tot$prof2)] <- NA
-
-### add to ecological data based
-ecologie_tot$SWHC <- swhc
-
-
-################################## COMPUTE PET WITH TURC FORMULA unit to convert radneb61_ from J/cm2/month in
-################################## MJ/m2/day /100/30 then to convert in KJ/m2/day as in Nick formula *1000
-
-## RAD and Temperature of the 12 months
-radneb61_1to12 <- 66:77
-tmoy6190_1_cor.1to12 <- 82:93
-
-### apply in parallel
-library(doParallel)
-registerDoParallel(cores = 6)  ## affect automaticaly half of the core detected to the foreach
-getDoParWorkers()  ## here 8 core so 4 core if want to use more registerDoParallel(cores=6)
-
-PET.matrix <- foreach(i = 1:length(data.CLIM$idp), .combine = rbind) %dopar% {
-    fun.PET(i, rad = data.CLIM[, radneb61_1to12], temp = data.CLIM[, tmoy6190_1_cor.1to12])
-}
-
-PET.matrix <- PET.matrix[!data.CLIM.na, ]
-PET.matrix[PET.matrix < 0] <- 0  ## affect zero if negative PET
-
-## plot to check PET computed by me vs PET of Christian par(mfrow=c(3,4)) for (i
-## in 1:12) {plot(PET.matrix[,i],data.CLIM2[,i+48]) ; lines(0:100,0:100)}
-
-colnames(PET.matrix) <- paste("PET.cor.", 1:12, sep = "")
-############## MERGE CLIMATE and PET
-data.CLIM2 <- cbind(data.CLIM2, PET.matrix, sgdd = sgdd.vec)
-
-### MERGE WITH ECOLOGICAL DATA
-ecologie.clim <- merge(ecologie_tot, data.CLIM2, by = "idp", all.x = T)
-dim(ecologie_tot)
-dim(ecologie.clim)
-names(ecologie.clim)
-
-
-ecologie.clim2 <- ecologie.clim[!is.na(ecologie.clim$PET.cor.1) & !is.na(ecologie.clim$SWHC), 
-    ]
-
-########################################################################################### COMPUTE WATER BUDGET
-
-## ### test function
-## fun.WaterBudget(i=16,prcp.m=(ecologie.clim2[,paste('prec6190_',1:12,sep='')]),
-## PET.m=(ecologie.clim2[,paste('PET.cor.',1:12,sep='')]),
-## Ta.m=(ecologie.clim2[,c('tmoy6190_1_cor',paste('tmoy6190_1_cor.',1:11,sep=''))]),
-## SWHC.v=(ecologie.clim2[ ,'SWHC']),n=2)
-
-
-### apply function in parallel
-library(doParallel)
-registerDoParallel(cores = 6)  ## affect automaticaly half of the core detected to the foreach
-getDoParWorkers()  ## here 8 core so 4 core if want to use more registerDoParallel(cores=6)
-
-WBWS.matrix <- foreach(i = 1:length(ecologie.clim2$idp), .combine = rbind) %dopar% 
-    {
-        fun.WaterBudget(i, prcp.m = (ecologie.clim2[, paste("prec6190_", 1:12, sep = "")]), 
-            PET.m = (ecologie.clim2[, paste("PET.cor.", 1:12, sep = "")]), Ta.m = (ecologie.clim2[, 
-                c("tmoy6190_1_cor", paste("tmoy6190_1_cor.", 1:11, sep = ""))]), 
-            SWHC.v = (ecologie.clim2[, "SWHC"]), n = 2)
-    }
-
-### MERGE all and saved
-WBWS.matrix2 <- cbind(idp = ecologie.clim2$idp, WBWS.matrix)
-ecologie.clim.data <- merge(ecologie.clim, WBWS.matrix2, by = "idp", all.x = T)
-
-##### change tplant not good format
-load("./data/process/placette_tot.Rdata")
-ecologie.clim.data$tplant <- placette_tot$tplant
-
-### Compute mean T and annual sum of precip
-
-ecologie.clim.data$MAT <- apply(ecologie.clim.data[, 114:125], MARGIN = 1, FUN = mean)
-ecologie.clim.data$SAP <- apply(ecologie.clim.data[, 69:80], MARGIN = 1, FUN = sum)
-
-
-saveRDS(ecologie.clim.data, file = "./data/process/ecologie.clim.data.rds")
-
-
-
-
-
-
-######################################################### FIGURES OF CLIMATIC DATA
-ecologie.clim.data <- readRDS("./data/process/ecologie.clim.data.rds")
-names(ecologie.clim.data)
-
-### check climatic data
-
-pdf("./figs/sgdd.tmin.map.pdf")
-par(mfrow = c(2, 2))
-plot(ecologie.clim.data$xl93, ecologie.clim.data$yl93, col = rev(heat.colors(10))[cut(ecologie.clim.data$sgdd, 
-    quantile(ecologie.clim.data$sgdd, probs = (0:10)/10, na.rm = T), labels = F)], 
-    cex = 0.2, pty = "s", xlab = NA, ylab = NA, main = "SGDD")
-
-plot(ecologie.clim.data$xl93, ecologie.clim.data$yl93, col = rev(heat.colors(10))[cut(ecologie.clim.data$tmin6190_min_cor, 
-    quantile(ecologie.clim.data$tmin6190_min_cor, probs = (0:10)/10, na.rm = T), 
-    labels = F)], cex = 0.2, pty = "s", xlab = NA, ylab = NA, main = "Tmin")
-plot(ecologie.clim.data$tmin6190_min_cor, ecologie.clim.data$sgdd, cex = 0.2, xlab = "Tmin", 
-    ylab = "SGDD")
-dev.off()
-
-pdf("./figs/Water.map.pdf")
-par(mfrow = c(2, 2), mar = c(1, 1, 1, 1))
-plot(ecologie.clim.data$xl93, ecologie.clim.data$yl93, col = rev(colorRampPalette(c("blue", 
-    "red"))(10))[cut(ecologie.clim.data$WB.y, quantile(ecologie.clim.data$WB.y, probs = (0:10)/10, 
-    na.rm = T), labels = F)], cex = 0.2, pty = "s", xlab = NA, ylab = NA)
-plot(ecologie.clim.data$xl93, ecologie.clim.data$yl93, col = rev(colorRampPalette(c("blue", 
-    "red"))(10))[cut(ecologie.clim.data$WB.s, quantile(ecologie.clim.data$WB.s, probs = (0:10)/10, 
-    na.rm = T), labels = F)], cex = 0.2, pty = "s", xlab = NA, ylab = NA)
-plot(ecologie.clim.data$xl93, ecologie.clim.data$yl93, col = rev(colorRampPalette(c("blue", 
-    "red"))(10))[cut(ecologie.clim.data$WS.y, quantile(ecologie.clim.data$WS.y, probs = (0:10)/10, 
-    na.rm = T), labels = F)], cex = 0.2, pty = "s", xlab = NA, ylab = NA)
-plot(ecologie.clim.data$xl93, ecologie.clim.data$yl93, col = rev(colorRampPalette(c("blue", 
-    "red"))(10))[cut(ecologie.clim.data$WS.s, quantile(ecologie.clim.data$WS.s, probs = (0:10)/10, 
-    na.rm = T), labels = F)], cex = 0.2, pty = "s", xlab = NA, ylab = NA)
-dev.off()
-
-pdf("./figs/Water.var,cor.pdf")
-par(mfrow = c(2, 2))
-plot(ecologie.clim.data[["WB.y"]], ecologie.clim.data[["WS.y"]], xlab = "WB year", 
-    ylab = "ratio AET/D year", cex = 0.2)
-plot(ecologie.clim.data[["WB.s"]], ecologie.clim.data[["WS.s"]], xlab = "WB growing season", 
-    ylab = "ratio AET/D growing season", cex = 0.2)
-plot(ecologie.clim.data[["WB.s"]], ecologie.clim.data[["WB.y"]], xlab = "WB growing season", 
-    ylab = "WB growing year", cex = 0.2)
-plot(ecologie.clim.data[["WS.s"]], ecologie.clim.data[["WS.y"]], xlab = "ratio AET/D growing season", 
-    ylab = "ratio AET/D year", cex = 0.2)
-dev.off()
-pdf("./figs/sgdd.water.cor.pdf")
-plot(ecologie.clim.data[["sgdd"]], ecologie.clim.data[["WS.y"]], xlab = "SGDD", ylab = "ratio AET/D year", 
-    cex = 0.2)
-dev.off()
-
-### DO PCA OF CLIMATIC DATA
-
-data.prc <- prcomp(ecologie.clim.data[apply(is.na(ecologie.clim.data[, c("sgdd", 
-    "tmin6190_min_cor", "WB.s", "WS.s")]), MARGIN = 1, FUN = sum) < 1, c("sgdd", 
-    "tmin6190_min_cor", "WB.s", "WS.s")], na.action = na.omit, scale = T)
-summary(data.prc)
-scores <- data.prc$x
-pdf("./figs/climate.pca.pdf")
-biplot(data.prc, pch = 1, xlabs = rep(".", length(data.prc$x[, 1])), ylabs = c("SGDD", 
-    "Tmin", "WB", "WS"))
-text(150, 180, labels = paste("Var PC1 ", ((summary(data.prc)))$importance[2, 1], 
-    sep = ""))
-text(150, 165, labels = paste("Var PC2 ", ((summary(data.prc)))$importance[2, 2], 
-    sep = ""))
-dev.off()
-
-
-##### FIGS on elevation correction of temperature done by Christian map of diff
-##### between mean altitude of the 1x1km cell and actual elevation of the plots
-pdf("./figs/map.error.alti.pdf")
-plot(data.CLIM$xl2, data.CLIM$yl2, col = "grey", cex = 0.3, xlab = "X", ylab = "Y")
-data.temp <- data.CLIM[data.CLIM$diff..altIFN...mnt50 < (-100) | (data.CLIM$diff..altIFN...mnt50 > 
-    100), ]
-points(data.temp$xl2, data.temp$yl2, col = c("red", "coral3", "coral", "grey", "coral", 
-    "coral3", "red")[cut(data.temp$diff..altIFN...mnt50, breaks = c(-500, -300, -200, 
-    -100, 100, 200, 300, 500), labels = F)], cex = 0.5, pch = 1)
-dev.off()
-
-##### PLOT HIST OF ALL VARIABLES
-pdf("./figs/climatvar.hist.pdf")
-par(mfrow = c(3, 4))
-for (i in 37:48) hist(data.CLIM[, i], xlab = "Monthly Precip (mm)", main = names(data.CLIM)[i])
-
-par(mfrow = c(3, 4))
-for (i in 49:60) hist(data.CLIM[, i], xlab = "PET (mm)", main = names(data.CLIM)[i])
-
-par(mfrow = c(3, 4))
-for (i in 66:77) hist(data.CLIM[, i], xlab = "Radiation (?)", main = names(data.CLIM)[i])
-
-par(mfrow = c(3, 4))
-for (i in 82:93) hist(data.CLIM[, i], xlab = "temperature (C)", main = names(data.CLIM)[i])
-dev.off()
-
-pdf("./figs/xyplot.Tunco.Tcor.pdf")
-par(mfrow = c(3, 4))
-for (i in 1:12) plot(data.CLIM[, (23:34)[i]], data.CLIM[, (82:94)[i]], xlab = "temperature (C) uncorrected", 
-    ylab = "temperature (C) corrected", main = names(data.CLIM)[(23:34)[i]])
-dev.off() 
diff --git a/R/READ.DATA.NFI.FRANCE.R b/R/READ.DATA.NFI.FRANCE.R
deleted file mode 100644
index fe4f8c5..0000000
--- a/R/READ.DATA.NFI.FRANCE.R
+++ /dev/null
@@ -1,432 +0,0 @@
-############################################################ READ, MERGE AND CLEAN ALL NFI DATA NEW METHODS
-
-### read TREE table downloaded from the web
-arbre2005 <- read.csv("./data/raw/DataFrance/2005/arbres_foret_2005.csv", sep = ";", 
-    stringsAsFactors = FALSE)
-summary(arbre2005)
-arbre2006 <- read.csv("./data/raw/DataFrance/2006/arbres_foret_2006.csv", sep = ";", 
-    stringsAsFactors = FALSE)
-summary(arbre2006)
-arbre2007 <- read.csv("./data/raw/DataFrance/2007/arbres_foret_2007.csv", sep = ";", 
-    stringsAsFactors = FALSE)
-summary(arbre2007)
-arbre2008 <- read.csv("./data/raw/DataFrance/2008/arbres_foret_2008.csv", sep = ";", 
-    stringsAsFactors = FALSE)
-summary(arbre2005)
-arbre2009 <- read.csv("./data/raw/DataFrance/2009/arbres_foret_2009.csv", sep = ";", 
-    stringsAsFactors = FALSE)
-summary(arbre2009)
-arbre2010 <- read.csv("./data/raw/DataFrance/2010/arbres_foret_2010.csv", sep = ";", 
-    stringsAsFactors = FALSE)
-summary(arbre2010)
-arbre2011 <- read.csv("./data/raw/DataFrance/2011/arbres_foret_2011.csv", sep = ";", 
-    stringsAsFactors = FALSE)
-
-
-
-
-
-#### ALL TREE after 2007 don't have the veget value as in 2005 aned 2006 because new
-#### variable ACCI for tree with accident (trunk broken ...)  NEED TO UPDATE VEGET
-#### FROM ACCI
-arbre2007$veget[arbre2007$acci > 0] <- 1
-arbre2008$veget[arbre2008$acci > 0] <- 1
-arbre2009$veget[arbre2009$acci > 0] <- 1
-arbre2010$veget[arbre2010$acci > 0] <- 1
-arbre2011$veget[arbre2011$acci > 0] <- 1
-## 
-arbre2005$veget <- unclass(arbre2005$veget) - 1
-arbre2006$veget <- unclass(arbre2006$veget) - 1
-
-###### ORI NEED TO BE DEGRADED SINCE 2007 to two level from resprout or from seed
-arbre2007$ori[arbre2007$ori == 2] <- 0
-arbre2008$ori[arbre2008$ori == 2] <- 0
-arbre2009$ori[arbre2009$ori == 2] <- 0
-arbre2010$ori[arbre2010$ori == 2] <- 0
-arbre2011$ori[arbre2011$ori == 2] <- 0
-
-
-############################## merge all table adding NA when no variable for that year
-arbre.tot <- data.frame(idp = c(arbre2005$idp, arbre2006$idp, arbre2007$idp, arbre2008$idp, 
-    arbre2009$idp, arbre2010$idp, arbre2011$idp), a = c(arbre2005$a, arbre2006$a, 
-    arbre2007$a, arbre2008$a, arbre2009$a, arbre2010$a, arbre2011$a), veget = c(arbre2005$veget, 
-    arbre2006$veget, arbre2007$veget, arbre2008$veget, arbre2009$veget, arbre2010$veget, 
-    arbre2011$veget), simplif = c(rep(NA, length(arbre2005$idp)), rep(NA, length(arbre2006$idp)), 
-    rep(NA, length(arbre2007$idp)), rep(NA, length(arbre2008$idp)), arbre2009$simplif, 
-    arbre2010$simplif, arbre2011$simplif), acci = c(rep(NA, length(arbre2005$idp)), 
-    rep(NA, length(arbre2006$idp)), arbre2007$acci, arbre2008$acci, arbre2009$acci, 
-    arbre2010$acci, arbre2011$acci), espar = c(as.character(arbre2005$espar), as.character(arbre2006$espar), 
-    as.character(arbre2007$espar), as.character(arbre2008$espar), as.character(arbre2009$espar), 
-    as.character(arbre2010$espar), as.character(arbre2011$espar)), ori = c(arbre2005$ori, 
-    arbre2006$ori, arbre2007$ori, arbre2008$ori, arbre2009$ori, arbre2010$ori, arbre2011$ori), 
-    lib = c(arbre2005$lib, arbre2006$lib, arbre2007$lib, arbre2008$lib, arbre2009$lib, 
-        arbre2010$lib, arbre2011$lib), forme = c(arbre2005$forme, arbre2006$forme, 
-        arbre2007$forme, arbre2008$forme, arbre2009$forme, arbre2010$forme, arbre2011$forme), 
-    tige = c(arbre2005$tige, arbre2006$tige, arbre2007$tige, arbre2008$tige, arbre2009$tige, 
-        arbre2010$tige, arbre2011$tige), mortb = c(rep(NA, length(arbre2005$idp)), 
-        arbre2006$mortb, arbre2007$mortb, arbre2008$mortb, arbre2009$mortb, arbre2010$mortb, 
-        arbre2011$mortb), sfgui = c(rep(NA, length(arbre2005$idp)), rep(NA, length(arbre2006$idp)), 
-        rep(NA, length(arbre2007$idp)), arbre2008$sfgui, arbre2009$sfgui, arbre2010$sfgui, 
-        arbre2011$sfgui), sfgeliv = c(rep(NA, length(arbre2005$idp)), rep(NA, length(arbre2006$idp)), 
-        rep(NA, length(arbre2007$idp)), arbre2008$sfgeliv, arbre2009$sfgeliv, arbre2010$sfgeliv, 
-        arbre2011$sfgeliv), sfpied = c(rep(NA, length(arbre2005$idp)), rep(NA, length(arbre2006$idp)), 
-        rep(NA, length(arbre2007$idp)), arbre2008$sfpied, arbre2009$sfpied, arbre2010$sfpied, 
-        arbre2011$sfpied), sfdorge = c(rep(NA, length(arbre2005$idp)), rep(NA, length(arbre2006$idp)), 
-        rep(NA, length(arbre2007$idp)), arbre2008$sfdorge, arbre2009$sfdorge, arbre2010$sfdorge, 
-        arbre2011$sfdorge), sfcoeur = c(rep(NA, length(arbre2005$idp)), rep(NA, length(arbre2006$idp)), 
-        rep(NA, length(arbre2007$idp)), rep(NA, length(arbre2008$idp)), arbre2009$sfcoeur, 
-        arbre2010$sfcoeur, arbre2011$sfcoeur), c13 = c(arbre2005$c13, arbre2006$c13, 
-        arbre2007$c13, arbre2008$c13, arbre2009$c13, arbre2010$c13, arbre2011$c13), 
-    ir5 = c(arbre2005$ir5, arbre2006$ir5, arbre2007$ir5, arbre2008$ir5, arbre2009$ir5, 
-        arbre2010$ir5, arbre2011$ir5), htot = c(arbre2005$htot, arbre2006$htot, arbre2007$htot, 
-        arbre2008$htot, arbre2009$htot, arbre2010$htot, arbre2011$htot), hdec = c(rep(NA, 
-        length(arbre2005$idp)), rep(NA, length(arbre2006$idp)), rep(NA, length(arbre2007$idp)), 
-        arbre2008$hdec, arbre2009$hdec, arbre2010$hdec, arbre2011$hdec), decoupe = c(rep(NA, 
-        length(arbre2005$idp)), rep(NA, length(arbre2006$idp)), rep(NA, length(arbre2007$idp)), 
-        arbre2008$decoupe, arbre2009$decoupe, arbre2010$decoupe, arbre2011$decoupe), 
-    q1 = c(arbre2005$q1, arbre2006$q1, arbre2007$q1, arbre2008$q1, arbre2009$q1, 
-        arbre2010$q1, arbre2011$q1), q2 = c(arbre2005$q2, arbre2006$q2, arbre2007$q2, 
-        arbre2008$q2, arbre2009$q2, arbre2010$q2, arbre2011$q2), q3 = c(arbre2005$q3, 
-        arbre2006$q3, arbre2007$q3, arbre2008$q3, arbre2009$q3, arbre2010$q3, arbre2011$q3), 
-    r = c(arbre2005$r, arbre2006$r, arbre2007$r, arbre2008$r, arbre2009$r, arbre2010$r, 
-        arbre2011$r), lfsd = c(arbre2005$lfsd, arbre2006$lfsd, arbre2007$lfsd, arbre2008$lfsd, 
-        arbre2009$lfsd, arbre2010$lfsd, arbre2011$lfsd), age = c(rep(NA, length(arbre2005$idp)), 
-        rep(NA, length(arbre2006$idp)), rep(NA, length(arbre2007$idp)), arbre2008$age, 
-        arbre2009$age, arbre2010$age, arbre2011$age), v = c(arbre2005$v, arbre2006$v, 
-        arbre2007$v, arbre2008$v, arbre2009$v, arbre2010$v, arbre2011$v), w = c(arbre2005$w, 
-        arbre2006$w, arbre2007$w, arbre2008$w, arbre2009$w, arbre2010$w, arbre2011$w), 
-    YEAR = c(rep(2005, length(arbre2005$idp)), rep(2006, length(arbre2006$idp)), 
-        rep(2007, length(arbre2007$idp)), rep(2008, length(arbre2008$idp)), rep(2009, 
-            length(arbre2009$simplif)), rep(2010, length(arbre2010$simplif)), rep(2011, 
-            length(arbre2011$simplif))))
-
-rm(arbre2005, arbre2006, arbre2007, arbre2008, arbre2009, arbre2010, arbre2011)
-gc()
-######################################################## #### check problem of unit for c13 ir5 and htot by plotting the data
-######################################################## plot(arbre.tot$c13,arbre.tot$ir5,col=unclass(factor(arbre.tot$YEAR)),cex=0.1)
-######################################################## boxplot(arbre.tot$c13~arbre.tot$YEAR,ylab='c13')
-######################################################## boxplot(arbre.tot$ir5~arbre.tot$YEAR,ylab='ir5')
-######################################################## boxplot(arbre.tot$htot~arbre.tot$YEAR,ylab='htot')
-######################################################## boxplot(arbre.tot$age~arbre.tot$YEAR,ylab='age') ##### SOMETHING VERY STRANGE
-######################################################## FOR THE AGE WITH SEVERAL TREE OVER 1000 YEARS OLD
-######################################################## boxplot(arbre.tot$mortb~arbre.tot$YEAR,ylab='mortality branche')
-######################################################## boxplot(arbre.tot$veget~arbre.tot$YEAR,ylab='accident')
-######################################################## boxplot(arbre.tot$simplif~arbre.tot$YEAR,ylab='accident')
-######################################################## boxplot(arbre.tot$w~arbre.tot$YEAR,ylab='accident')
-######################################################## boxplot(arbre.tot$ori~arbre.tot$YEAR,ylab='accident')
-######################################################## boxplot(arbre.tot$lib~arbre.tot$YEAR,ylab='accident')
-######################################################## boxplot(arbre.tot$forme~arbre.tot$YEAR,ylab='accident')
-######################################################## boxplot(arbre.tot$tige~arbre.tot$YEAR,ylab='accident') ### NEED TO USE ONLY THE
-######################################################## TIGE == 1 in the ANALYSIS
-######################################################## boxplot(arbre.tot$sfgui~arbre.tot$YEAR,ylab='accident')
-######################################################## boxplot(arbre.tot$sfgeliv~arbre.tot$YEAR,ylab='accident')
-
-
-## ##### CHECK OTHER VARIABLE OK DONE ### USE BRANCH MORTALITY AS AN INDICATOR OF
-## MORTALITY ?? ABIOTIC STRESS ?
-
-## x11() plot(arbre.tot$c13,arbre.tot$htot,col=unclass(factor(arbre.tot$YEAR)))
-
-save(arbre.tot, file = "./data/process/arbre.tot.Rdata")
-
-
-
-######################################### DEAD
-
-
-############################################################## READ AND MERGE DEAD DATA MERGE WITH DEAD TREE and MERGE WITH PLOT DATA!!
-
-### read DEAD TREE table downloaded from the web
-arbre_mort2005 <- read.csv("./data/raw/DataFrance/2005/arbres_morts_foret_2005.csv", 
-    sep = ";", stringsAsFactors = FALSE)
-## summary(arbre_mort2005)
-arbre_mort2006 <- read.csv("./data/raw/DataFrance/2006/arbres_morts_foret_2006.csv", 
-    sep = ";", stringsAsFactors = FALSE)
-## summary(arbre_mort2006)
-arbre_mort2007 <- read.csv("./data/raw/DataFrance/2007/arbres_morts_foret_2007.csv", 
-    sep = ";", stringsAsFactors = FALSE)
-## summary(arbre_mort2007)
-arbre_mort2008 <- read.csv("./data/raw/DataFrance/2008/arbres_morts_foret_2008.csv", 
-    sep = ";", stringsAsFactors = FALSE)
-## summary(arbre_mort2005)
-arbre_mort2009 <- read.csv("./data/raw/DataFrance/2009/arbres_morts_foret_2009.csv", 
-    sep = ";", stringsAsFactors = FALSE)
-## summary(arbre_mort2009)
-arbre_mort2010 <- read.csv("./data/raw/DataFrance/2010/arbres_morts_foret_2010.csv", 
-    sep = ";", stringsAsFactors = FALSE)
-## summary(arbre_mort2010)
-arbre_mort2011 <- read.csv("./data/raw/DataFrance/2011/arbres_morts_foret_2011.csv", 
-    sep = ";", stringsAsFactors = FALSE)
-
-## names(arbre_mort2005) names(arbre_mort2006) names(arbre_mort2007)
-## names(arbre_mort2008) names(arbre_mort2009) names(arbre_mort2010)
-## names(arbre_mort2011)
-
-### merge 2005 2006 2007 to compute c13
-
-arbre_mort05_07 <- rbind(arbre_mort2005, arbre_mort2006, arbre_mort2007)
-arbre_mort05_07$c13 <- rep(NA, length(arbre_mort05_07$c0))
-arbre_mort05_07$espar2 <- as.numeric(substr(arbre_mort05_07$espar, 1, 2))
-arbre_mort05_07$year <- c(rep(2005, length = length(arbre_mort2005[, 1])), rep(2006, 
-    length = length(arbre_mort2006[, 1])), rep(2007, length = length(arbre_mort2007[, 
-    1])))
-
-#### NEED TO CONVERT c0 into c13 before 2008 before 2008 no date dead but all tree
-#### died less than 5 years ago.  need to do convertion between c0 and c13.  for
-#### that use the NFI data from previous inventory that were reporting both c0 and
-#### c13 for all species fit an allometric relationship and then use it to predict
-#### c13 in this data base
-
-### READ DATA CYCLE 3 ORGINAL /// NEED TO CONVERT C0 and C13 in cm *100
-arbre.cycle3 <- read.table("./data/raw/DataFrance/cycle3/data.arbre.tot.txt", sep = " ", 
-    stringsAsFactors = FALSE)
-### change the C from m to cm
-arbre.cycle3$C0 <- arbre.cycle3$C0 * 100
-arbre.cycle3$C13 <- arbre.cycle3$C13 * 100
-
-
-## LOAD library RMA regression
-library(lmodel2)
-
-
-## the regression between C13 and C0 vary between species, but not same species in
-## cycle 3 because less details (the classification is only based on number and no
-## letters remove the letters and apply the same model to all species that have
-## the same number code
-species.list <- c(as.numeric(names(table(substr(arbre_mort05_07$espar, 1, 2))))[-1])
-## length(table(arbre.cycle3$ESS))
-
-for (i in species.list) {
-    if (sum(arbre.cycle3$ESS == i) > 50) {
-        lmodel2.res <- lmodel2(C13 ~ C0, data = arbre.cycle3[arbre.cycle3$ESS == 
-            i, ], range.x = "relative", range.y = "relative")
-        arbre_mort05_07$c13[arbre_mort05_07$espar2 == i & !is.na(arbre_mort05_07$espar2)] <- lmodel2.res$regression.results[4, 
-            2] + arbre_mort05_07$c0[arbre_mort05_07$espar2 == i & !is.na(arbre_mort05_07$espar2)] * 
-            lmodel2.res$regression.results[4, 3]
-        print(i)
-        print(lmodel2.res$regression.results[4, 2:3])
-        print(range(arbre_mort05_07$c13[arbre_mort05_07$espar2 == i & !is.na(arbre_mort05_07$espar2)], 
-            na.rm = T))
-    } else {
-        lmodel2.res <- lmodel2(C13 ~ C0, data = arbre.cycle3, range.x = "relative", 
-            range.y = "relative")
-        arbre_mort05_07$c13[arbre_mort05_07$espar2 == i & !is.na(arbre_mort05_07$espar2)] <- lmodel2.res$regression.results[4, 
-            2] + arbre_mort05_07$c0[arbre_mort05_07$espar2 == i & !is.na(arbre_mort05_07$espar2)] * 
-            lmodel2.res$regression.results[4, 3]
-        print(i)
-        print(lmodel2.res$regression.results[4, 2:3])
-        print(range(arbre_mort05_07$c13[arbre_mort05_07$espar2 == i & !is.na(arbre_mort05_07$espar2)], 
-            na.rm = T))
-        
-    }
-}
-
-### for species with NO DATA in cycle 3 apply mean model over all species
-lmodel2.res <- lmodel2(C13 ~ C0, data = arbre.cycle3, range.x = "relative", range.y = "relative")
-arbre_mort05_07$c13[is.na(arbre_mort05_07$espar2)] <- lmodel2.res$regression.results[4, 
-    2] + arbre_mort05_07$c0[is.na(arbre_mort05_07$espar2)] * lmodel2.res$regression.results[4, 
-    3]
-
-## check predicted C13 from C0
-head(cbind(arbre_mort05_07$c13, arbre_mort05_07$c0, arbre_mort05_07$espar))
-
-### ok donne c13 added
-
-######################## MERGE WITH other dead data
-
-arbre_mort_tot <- data.frame(idp = c(arbre_mort05_07$idp, arbre_mort2008$idp, arbre_mort2009$idp, 
-    arbre_mort2010$idp, arbre_mort2011$idp), a = c(arbre_mort05_07$a, arbre_mort2008$a, 
-    arbre_mort2009$a, arbre_mort2010$a, arbre_mort2011$a), espar = c(as.character(arbre_mort05_07$espar), 
-    as.character(arbre_mort2008$espar), as.character(arbre_mort2009$espar), as.character(arbre_mort2010$espar), 
-    as.character(arbre_mort2011$espar)), ori = c(arbre_mort05_07$ori, arbre_mort2008$ori, 
-    arbre_mort2009$ori, arbre_mort2010$ori, arbre_mort2011$ori), veget = c(arbre_mort05_07$veget, 
-    arbre_mort2008$veget, arbre_mort2009$veget, arbre_mort2010$veget, arbre_mort2011$veget), 
-    datemort = c(rep(NA, length(arbre_mort05_07$ori)), arbre_mort2008$datemort, arbre_mort2009$datemort, 
-        arbre_mort2010$datemort, arbre_mort2011$datemort), c13 = c(arbre_mort05_07$c13, 
-        arbre_mort2008$c13, arbre_mort2009$c13, arbre_mort2010$c13, arbre_mort2011$c13), 
-    v = c(arbre_mort05_07$v, arbre_mort2008$v, arbre_mort2009$v, arbre_mort2010$v, 
-        arbre_mort2011$v), w = c(arbre_mort05_07$w, arbre_mort2008$w, arbre_mort2009$w, 
-        arbre_mort2010$w, arbre_mort2011$w), YEAR = c(rep(2005, length(arbre_mort2005$idp)), 
-        rep(2006, length(arbre_mort2006$idp)), rep(2007, length(arbre_mort2007$idp)), 
-        rep(2008, length(arbre_mort2008$idp)), rep(2009, length(arbre_mort2009$idp)), 
-        rep(2010, length(arbre_mort2010$idp)), rep(2011, length(arbre_mort2011$idp))))
-rm(arbre.cycle3, arbre_mort2005, arbre_mort2006, arbre_mort2007, arbre_mort2008, 
-    arbre_mort2009, arbre_mort2010, arbre_mort2011)
-gc()
-
-save(arbre_mort_tot, file = "./data/process/arbre_mort_tot.Rdata")
-
-
-
-################################################################################ MERGE DEAD AND ALIVE TREE
-
-
-head(arbre_mort_tot)
-head(arbre.tot)
-
-arbre.ALIVE.DEAD <- data.frame(idp = c(arbre.tot$idp, arbre_mort_tot$idp), a = c(arbre.tot$a, 
-    arbre_mort_tot$a), veget = c(arbre.tot$veget, arbre_mort_tot$veget), simplif = c(arbre.tot$simplif, 
-    rep(NA, length = length(arbre_mort_tot$idp))), acci = c(arbre.tot$acci, rep(NA, 
-    length = length(arbre_mort_tot$idp))), espar = c(as.character(arbre.tot$espar), 
-    as.character(arbre_mort_tot$espar)), ori = c(arbre.tot$ori, arbre_mort_tot$ori), 
-    lib = c(arbre.tot$lib, rep(NA, length = length(arbre_mort_tot$idp))), forme = c(arbre.tot$forme, 
-        rep(NA, length = length(arbre_mort_tot$idp))), tige = c(arbre.tot$tige, rep(NA, 
-        length = length(arbre_mort_tot$idp))), mortb = c(arbre.tot$mortb, rep(NA, 
-        length = length(arbre_mort_tot$idp))), sfgui = c(arbre.tot$sfgui, rep(NA, 
-        length = length(arbre_mort_tot$idp))), sfgeliv = c(arbre.tot$sfgeliv, rep(NA, 
-        length = length(arbre_mort_tot$idp))), sfpied = c(arbre.tot$sfpied, rep(NA, 
-        length = length(arbre_mort_tot$idp))), sfdorge = c(arbre.tot$sfdorge, rep(NA, 
-        length = length(arbre_mort_tot$idp))), sfcoeur = c(arbre.tot$sfcoeur, rep(NA, 
-        length = length(arbre_mort_tot$idp))), c13 = c(arbre.tot$c13, arbre_mort_tot$c13), 
-    ir5 = c(arbre.tot$ir5, rep(NA, length = length(arbre_mort_tot$idp))), htot = c(arbre.tot$htot, 
-        rep(NA, length = length(arbre_mort_tot$idp))), hdec = c(arbre.tot$hdec, rep(NA, 
-        length = length(arbre_mort_tot$idp))), decoupe = c(arbre.tot$decoupe, rep(NA, 
-        length = length(arbre_mort_tot$idp))), q1 = c(arbre.tot$q1, rep(NA, length = length(arbre_mort_tot$idp))), 
-    q2 = c(arbre.tot$q2, rep(NA, length = length(arbre_mort_tot$idp))), q3 = c(arbre.tot$q3, 
-        rep(NA, length = length(arbre_mort_tot$idp))), r = c(arbre.tot$r, rep(NA, 
-        length = length(arbre_mort_tot$idp))), lfsd = c(arbre.tot$lfsd, rep(NA, length = length(arbre_mort_tot$idp))), 
-    age = c(arbre.tot$age, rep(NA, length = length(arbre_mort_tot$idp))), v = c(arbre.tot$v, 
-        arbre_mort_tot$v), w = c(arbre.tot$w, rep(10000/(pi * (c(15))^2), length = length(arbre_mort_tot$w))), 
-    YEAR = c(arbre.tot$YEAR, arbre_mort_tot$YEAR), datemort = c(rep(NA, length = length(arbre.tot$YEAR)), 
-        arbre_mort_tot$datemort), dead = c(rep(0, length = length(arbre.tot$YEAR)), 
-        rep(1, length = length(arbre_mort_tot$idp))))
-## dead: 1 = dead w: assume that all dead tree are sampled on the whole plot as
-## explained in the method
-
-## delete plot with DEAD tree missing because of no C13 or no espar
-arbre.ALIVE.DEAD2 <- arbre.ALIVE.DEAD[!(arbre.ALIVE.DEAD$idp %in% unique(c(names(tapply(is.na(arbre.ALIVE.DEAD$c13), 
-    INDEX = arbre.ALIVE.DEAD$idp, FUN = sum))[tapply(is.na(arbre.ALIVE.DEAD$c13), 
-    INDEX = arbre.ALIVE.DEAD$idp, FUN = sum) > 0], names(tapply(is.na(arbre.ALIVE.DEAD$espar), 
-    INDEX = arbre.ALIVE.DEAD$idp, FUN = sum))[tapply(is.na(arbre.ALIVE.DEAD$espar), 
-    INDEX = arbre.ALIVE.DEAD$idp, FUN = sum) > 0]))), ]
-
-save(arbre.ALIVE.DEAD2, file = "./data/process/arbre.ALIVE.DEAD2.Rdata")
-
-
-######################################################################################## LOAD DATA FOR PLOT INFO read DEAD TREE table downloaded from the web
-placette2005 <- read.csv("./data/raw/DataFrance/2005/placettes_foret_2005.csv", sep = ";", 
-    stringsAsFactors = FALSE)
-## summary(placette2005)
-placette2006 <- read.csv("./data/raw/DataFrance/2006/placettes_foret_2006.csv", sep = ";", 
-    stringsAsFactors = FALSE)
-## summary(placette2006)
-placette2007 <- read.csv("./data/raw/DataFrance/2007/placettes_foret_2007.csv", sep = ";", 
-    stringsAsFactors = FALSE)
-## summary(placette2007)
-placette2008 <- read.csv("./data/raw/DataFrance/2008/placettes_foret_2008.csv", sep = ";", 
-    stringsAsFactors = FALSE)
-## summary(placette2005)
-placette2009 <- read.csv("./data/raw/DataFrance/2009/placettes_foret_2009.csv", sep = ";", 
-    stringsAsFactors = FALSE)
-## summary(placette2009)
-placette2010 <- read.csv("./data/raw/DataFrance/2010/placettes_foret_2010.csv", sep = ";", 
-    stringsAsFactors = FALSE)
-## summary(placette2010)
-placette2011 <- read.csv("./data/raw/DataFrance/2011/placettes_foret_2011.csv", sep = ";", 
-    stringsAsFactors = FALSE)
-
-## names(placette2005) ## uta -> uta1 ## sfo NA ## plisi NA names(placette2006) ##
-## plisi NA names(placette2007) ## dcespar1 dcespar2 tpespar1 tpespar2 iti pentexp
-## NA ## deleted acces names(placette2008) ## gest incid peupnr portance asperite
-## names(placette2009) names(placette2010) names(placette2011)
-
-placette2005$tplant <- as.character(placette2005$tplant)
-placette2005$tplant[placette2005$tplant == ""] <- 0
-placette2006$tplant[placette2006$tplant == ""] <- 0
-
-
-
-### for selection of plot use plisi=0 dc=0 tplant=0 incid indicateur d incident
-### récent utilisé ou pas ?? avec ou sans perturbatrion naturelle
-
-placette_tot <- data.frame(idp = c(placette2005$idp, placette2006$idp, placette2007$idp, 
-    placette2008$idp, placette2009$idp, placette2010$idp, placette2011$idp), xl93 = c(placette2005$xl93, 
-    placette2006$xl93, placette2007$xl93, placette2008$xl93, placette2009$xl93, placette2010$xl93, 
-    placette2011$xl93), yl93 = c(placette2005$yl93, placette2006$yl93, placette2007$yl93, 
-    placette2008$yl93, placette2009$yl93, placette2010$yl93, placette2011$yl93), 
-    dep = c(placette2005$dep, placette2006$dep, placette2007$dep, placette2008$dep, 
-        placette2009$dep, placette2010$dep, placette2011$dep), csa = c(placette2005$csa, 
-        placette2006$csa, placette2007$csa, placette2008$csa, placette2009$csa, placette2010$csa, 
-        placette2011$csa), plisi = c(rep(NA, length(placette2005$tm2)), rep(NA, length(placette2006$idp)), 
-        placette2007$plisi, placette2008$plisi, placette2009$plisi, placette2010$plisi, 
-        placette2011$plisi), uta1 = c(placette2005$uta, placette2006$uta1, placette2007$uta1, 
-        placette2008$uta1, placette2009$uta1, placette2010$uta1, placette2011$uta1), 
-    tm2 = c(placette2005$tm2, placette2006$tm2, placette2007$tm2, placette2008$tm2, 
-        placette2009$tm2, placette2010$tm2, placette2011$tm2), sfo = c(rep(NA, length(placette2005$tm2)), 
-        placette2006$sfo, placette2007$sfo, placette2008$sfo, placette2009$sfo, placette2010$sfo, 
-        placette2011$sfo), incid = c(rep(NA, length(placette2005$idp)), rep(NA, length(placette2006$idp)), 
-        rep(NA, length(placette2007$idp)), rep(NA, length(placette2008$idp)), placette2009$incid, 
-        placette2010$incid, placette2011$incid), dc = c(placette2005$dc, placette2006$dc, 
-        placette2007$dc, placette2008$dc, placette2009$dc, placette2010$dc, placette2011$dc), 
-    tplant = c(placette2005$tplant, placette2006$tplant, placette2007$tplant, placette2008$tplant, 
-        placette2009$tplant, placette2010$tplant, placette2011$tplant), esspre = c(placette2005$esspre, 
-        placette2006$esspre, placette2007$esspre, placette2008$esspre, placette2009$esspre, 
-        placette2010$esspre, placette2011$esspre), cac = c(placette2005$cac, placette2006$cac, 
-        placette2007$cac, placette2008$cac, placette2009$cac, placette2010$cac, placette2011$cac), 
-    ess_age_1 = c(placette2005$ess_age_1, placette2006$ess_age_1, placette2007$ess_age_1, 
-        placette2008$ess_age_1, placette2009$ess_age_1, placette2010$ess_age_1, placette2011$ess_age_1), 
-    YEAR = c(rep(2005, length(placette2005$idp)), rep(2006, length(placette2006$idp)), 
-        rep(2007, length(placette2007$idp)), rep(2008, length(placette2008$idp)), 
-        rep(2009, length(placette2009$idp)), rep(2010, length(placette2010$idp)), 
-        rep(2011, length(placette2011$idp))))
-
-rm(placette2005, placette2006, placette2007, placette2008, placette2009, placette2010, 
-    placette2011)
-
-
-save(placette_tot, file = "./data/process/placette_tot.Rdata")
-
-##################################### LOAD elevation data LOAD ALTITUDE DATA
-##################################### load('./data/process/placette_tot.Rdata')
-alti <- read.csv("./data/raw/DataFrance/altitude/SER_alti.csv", header = T, sep = ";", 
-    stringsAsFactors = FALSE)
-alti2011 <- read.csv("./data/raw/DataFrance/altitude/SER_alti_2011.csv", header = T, 
-    sep = ";", stringsAsFactors = FALSE)
-names(alti2011) <- names(alti)
-alti.tot <- rbind(alti, alti2011)
-
-## sum( placette_tot$idp %in% alti.tot$IDP)/length(placette_tot$idp)
-## table(placette_tot$YEAR[! placette_tot$idp %in% alti.tot$IDP])
-
-placette_tot.alti <- merge(placette_tot, alti.tot, by.x = "idp", by.y = "IDP")
-
-### write csv file for Piedallu
-write.csv(placette_tot.alti, "./data/process/placette_tot.alti.csv")
-
-### write new fiel for 2011
-write.csv(placette_tot.alti[placette_tot.alti$YEAR == 2011, ], "./data/process/placette_tot.alti.2011.csv")
-
-
-######################################### LOAD DATA ECOLOGIE read DEAD TREE table downloaded from the web
-ecologie2005 <- read.csv("./data/raw/DataFrance/2005/ecologie_2005.csv", sep = ";", 
-    stringsAsFactors = FALSE)
-## summary(ecologie2005)
-ecologie2006 <- read.csv("./data/raw/DataFrance/2006/ecologie_2006.csv", sep = ";", 
-    stringsAsFactors = FALSE)
-## summary(ecologie2006)
-ecologie2007 <- read.csv("./data/raw/DataFrance/2007/ecologie_2007.csv", sep = ";", 
-    stringsAsFactors = FALSE)
-## summary(ecologie2007)
-ecologie2008 <- read.csv("./data/raw/DataFrance/2008/ecologie_2008.csv", sep = ";", 
-    stringsAsFactors = FALSE)
-## summary(ecologie2005)
-ecologie2009 <- read.csv("./data/raw/DataFrance/2009/ecologie_2009.csv", sep = ";", 
-    stringsAsFactors = FALSE)
-## summary(ecologie2009)
-ecologie2010 <- read.csv("./data/raw/DataFrance/2010/ecologie_2010.csv", sep = ";", 
-    stringsAsFactors = FALSE)
-## summary(ecologie2010)
-ecologie2011 <- read.csv("./data/raw/DataFrance/2011/ecologie_2011.csv", sep = ";", 
-    stringsAsFactors = FALSE)
-
-
-ecologie_tot <- rbind(ecologie2005, ecologie2006, ecologie2007, ecologie2008, ecologie2009, 
-    ecologie2010, ecologie2011)
-head(ecologie_tot)
-rm(ecologie2005, ecologie2006, ecologie2007, ecologie2008, ecologie2009, ecologie2010, 
-    ecologie2011)
-
-save(ecologie_tot, file = "./data/process/ecologie_tot.Rdata")
-
-
- 
diff --git a/merge.data.FRANCE.R b/merge.data.FRANCE.R
index 36aec35..277893a 100644
--- a/merge.data.FRANCE.R
+++ b/merge.data.FRANCE.R
@@ -1,28 +1,10 @@
 ############################################# MERGE FRENCH DATA
 source("./R/format.function.R")
-## source('./R/READ.DATA.NFI.FRANCE.R') need to be run if no already doen (long
-## ...)  source('./R/CLIMATE.FRANCE.R')
-
-########################################################################### READ DATA (test)
-
-### read individuals tree data
-load("./data/process/arbre.ALIVE.DEAD2.Rdata")
-
-### read climate
-ecologie.clim.data <- readRDS("./data/process/ecologie.clim.data.rds")
-#### merge
-dataIFN.FRANCE.t <- merge(arbre.ALIVE.DEAD2, subset(ecologie.clim.data, select = c("idp", 
-    "SER", "sgdd", "WB.y", "WB.s", "WS.y", "WS.s", "MAT", "SAP")), by = "idp")
-rm(arbre.ALIVE.DEAD2, ecologie.clim.data)
-
-#### load plot data and merge
-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)
 
+################################ READ DATA (test)
+dataIFN.FRANCE <- read.csv("./data/raw/DataFrance/dataIFN.FRANCE.csv", stringsAsFactors = FALSE)
 ### read IFN species names and clean
-species.clean <- fun.clean.species.tab(read.csv("./data/species.list/species.csv", 
+species.clean <- fun.clean.species.tab(read.csv("./data/raw/DataFrance/species.csv", 
     sep = "\t", stringsAsFactors = FALSE))
 
 ### read TRY data
diff --git a/ms/metadata/France/_file_index.csv b/ms/metadata/France/_file_index.csv
index 20a2ba1..d40b80c 100644
--- a/ms/metadata/France/_file_index.csv
+++ b/ms/metadata/France/_file_index.csv
@@ -1,82 +1,3 @@
-filename,sep,skip,contents
-2005/arbres_foret_2005.csv,c,0, 
-2005/arbres_morts_foret_2005.csv,c,0, 
-2005/arbres_peupleraie_2005.csv,c,0, 
-2005/documentation_2005-2.csv,c,0, 
-2005/documentation_flore.csv,c,0, 
-2005/ecologie_2005.csv,c,0, 
-2005/flore_2005.csv,c,0, 
-2005/placettes_foret_2005.csv,c,0, 
-2005/placettes_peupleraie_2005.csv,c,0, 
-2006/arbres_foret_2006.csv,c,0, 
-2006/arbres_morts_foret_2006.csv,c,0, 
-2006/arbres_peupleraie_2006.csv,c,0, 
-2006/couverts_foret_2006.csv,c,0, 
-2006/documentation_2006-2.csv,c,0, 
-2006/documentation_flore.csv,c,0, 
-2006/ecologie_2006.csv,c,0, 
-2006/flore_2006.csv,c,0, 
-2006/placettes_foret_2006.csv,c,0, 
-2006/placettes_peupleraie_2006.csv,c,0, 
-2007/arbres_foret_2007.csv,c,0, 
-2007/arbres_morts_foret_2007.csv,c,0, 
-2007/arbres_peupleraie_2007.csv,c,0, 
-2007/couverts_foret_2007.csv,c,0, 
-2007/documentation_2007-2.csv,c,0, 
-2007/documentation_flore.csv,c,0, 
-2007/ecologie_2007.csv,c,0, 
-2007/flore_2007.csv,c,0, 
-2007/placettes_foret_2007.csv,c,0, 
-2007/placettes_peupleraie_2007.csv,c,0, 
-2008/arbres_foret_2008.csv,c,0, 
-2008/arbres_morts_foret_2008.csv,c,0, 
-2008/arbres_morts_peupleraie_2008.csv,c,0, 
-2008/arbres_peupleraie_2008.csv,c,0, 
-2008/couverts_foret_2008.csv,c,0, 
-2008/documentation_2008-2.csv,c,0, 
-2008/documentation_flore.csv,c,0, 
-2008/ecologie_2008.csv,c,0, 
-2008/flore_2008.csv,c,0, 
-2008/placettes_foret_2008.csv,c,0, 
-2008/placettes_peupleraie_2008.csv,c,0, 
-2009/arbres_foret_2009.csv,c,0, 
-2009/arbres_morts_foret_2009.csv,c,0, 
-2009/arbres_morts_peupleraie_2009.csv,c,0, 
-2009/arbres_peupleraie_2009.csv,c,0, 
-2009/couverts_foret_2009.csv,c,0, 
-2009/documentation_2009-2.csv,c,0, 
-2009/documentation_flore.csv,c,0, 
-2009/ecologie_2009.csv,c,0, 
-2009/flore_2009.csv,c,0, 
-2009/placettes_foret_2009.csv,c,0, 
-2009/placettes_peupleraie_2009.csv,c,0, 
-2010/arbres_foret_2010.csv,c,0, 
-2010/arbres_morts_foret_2010.csv,c,0, 
-2010/arbres_morts_peupleraie_2010.csv,c,0, 
-2010/arbres_peupleraie_2010.csv,c,0, 
-2010/couverts_foret_2010.csv,c,0, 
-2010/documentation_2010.csv,c,0, 
-2010/documentation_flore.csv,c,0, 
-2010/ecologie_2010.csv,c,0, 
-2010/flore_2010.csv,c,0, 
-2010/placettes_foret_2010.csv,c,0, 
-2010/placettes_peupleraie_2010.csv,c,0, 
-2011/arbres_foret_2011.csv,c,0, 
-2011/arbres_morts_foret_2011.csv,c,0, 
-2011/arbres_morts_peupleraie_2011.csv,c,0, 
-2011/arbres_peupleraie_2011.csv,c,0, 
-2011/couverts_foret_2011.csv,c,0, 
-2011/documentation_2011.csv,c,0, 
-2011/documentation_flore.csv,c,0, 
-2011/ecologie_2011.csv,c,0, 
-2011/flore_2011.csv,c,0, 
-2011/placettes_foret_2011.csv,c,0, 
-2011/placettes_peupleraie_2011.csv,c,0, 
-altitude/SER_alti_2011.csv,c,0, 
-altitude/SER_alti.csv,c,0, 
-climate_piedallu/placettesGK_avec 2011.csv,c,0, 
-climate_piedallu/placettesGK2.csv,c,0, 
-climate_piedallu/texture.txt,t,0, 
-cycle3/arbres2.txt,t,0, 
-cycle3/data.arbre.tot.txt,t,0, 
-cycle3/speciesnames.txt,t,0, 
+filename	sep	skip	contents
+dataIFN.FRANCE.csv	t	0	data for IFN France with climatic variables
+species.csv	t	0	species code and species Latin name
diff --git a/ms/metadata/France/_site_details.csv b/ms/metadata/France/_site_details.csv
index 7be6de1..e062cfe 100644
--- a/ms/metadata/France/_site_details.csv
+++ b/ms/metadata/France/_site_details.csv
@@ -1,12 +1,12 @@
-Item,Details
-contact name,
-contact email,
-contact affiliation,
-dataset name,
-country,
-climate,
-vegetation type,
-minimum tree size,
-field methodology,
-trait information,
-key references,
+Item	Details
+contact name	Georges Kunstler
+contact email	georges.kunstler@gmail.com
+contact affiliation	Irstea, UR Mountain Ecosystems, St-Martin-d'H?res, France & Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
+dataset name	French National Forest Inventory
+country	France
+climate	The climate of the lowlands varies from Mediterranean through oceanic to continental
+vegetation type	Mediterranean, temperate and mountain forests
+minimum tree size	7.5 cm
+field methodology	Data extracted from http://inventaire-forestier.ign.fr/spip/ . The French National Forest Inventory (http://inventaire-forestier.ign.fr) comprises a network of temporary plots established on a a sample of grid of approximately 1000 x 1000 m (plot randomly located in a square of 450m around the centre of the cell) covering the French national territory with contrasting climatic (collected between 2005 and 2011). The climate of the lowlands varies from Mediterranean through oceanic to continental, but the climate is also strongly affected by the elevation in mountain areas. For each measured tree, stem circumference, species, status (alive or died in the last 5 years), and radial growth over five years were recorded.  The radial growth was determined from two short cores taken at breast height.
+trait information	extracted from TRY
+key references	http://inventaire-forestier.ign.fr/spip/
diff --git a/ms/metadata/France/files/2005_arbres_foret_2005.csv b/ms/metadata/France/files/2005_arbres_foret_2005.csv
deleted file mode 100644
index c0ff2cd..0000000
--- a/ms/metadata/France/files/2005_arbres_foret_2005.csv
+++ /dev/null
@@ -1,2 +0,0 @@
-use,var,units,description
-0,idp.a.veget.espar.ori.lib.forme.tige.c13.ir5.htot.q1.q2.q3.r.lfsd.v.w,,
diff --git a/ms/metadata/France/files/2005_arbres_morts_foret_2005.csv b/ms/metadata/France/files/2005_arbres_morts_foret_2005.csv
deleted file mode 100644
index ecaac75..0000000
--- a/ms/metadata/France/files/2005_arbres_morts_foret_2005.csv
+++ /dev/null
@@ -1,2 +0,0 @@
-use,var,units,description
-0,idp.a.espar.ori.veget.c0.v.w,,
diff --git a/ms/metadata/France/files/2005_arbres_peupleraie_2005.csv b/ms/metadata/France/files/2005_arbres_peupleraie_2005.csv
deleted file mode 100644
index 8c4d932..0000000
--- a/ms/metadata/France/files/2005_arbres_peupleraie_2005.csv
+++ /dev/null
@@ -1,2 +0,0 @@
-use,var,units,description
-0,idp.a.veget.espar.clon.ori.c13.htot.q1.q2.q3.r.lfsd.v.w,,
diff --git a/ms/metadata/France/files/2005_documentation_2005-2.csv b/ms/metadata/France/files/2005_documentation_2005-2.csv
deleted file mode 100644
index 17ae6ba..0000000
--- a/ms/metadata/France/files/2005_documentation_2005-2.csv
+++ /dev/null
@@ -1,2 +0,0 @@
-use,var,units,description
-0,donnee.code.libelle,,
diff --git a/ms/metadata/France/files/2005_documentation_flore.csv b/ms/metadata/France/files/2005_documentation_flore.csv
deleted file mode 100644
index e124094..0000000
--- a/ms/metadata/France/files/2005_documentation_flore.csv
+++ /dev/null
@@ -1,2 +0,0 @@
-use,var,units,description
-0,codtax.nomlatin.lib_ref.numnomen,,
diff --git a/ms/metadata/France/files/2005_ecologie_2005.csv b/ms/metadata/France/files/2005_ecologie_2005.csv
deleted file mode 100644
index b88b60a..0000000
--- a/ms/metadata/France/files/2005_ecologie_2005.csv
+++ /dev/null
@@ -1,2 +0,0 @@
-use,var,units,description
-0,idp.dateeco.obsdate.topo.obstopo.pent2.expo.masque.humus.obspedo.roche.obsroc.affroc.afpla.cailloux.cai40.text2.text1.prof2.prof1.obsprof.pcalc.pcalf.pox.ppseudo.pgley.obshydr.tsol.lign1.lign2.herb.obsveget,,
diff --git a/ms/metadata/France/files/2005_flore_2005.csv b/ms/metadata/France/files/2005_flore_2005.csv
deleted file mode 100644
index 8b39b98..0000000
--- a/ms/metadata/France/files/2005_flore_2005.csv
+++ /dev/null
@@ -1,2 +0,0 @@
-use,var,units,description
-0,idp.codtax.abond,,
diff --git a/ms/metadata/France/files/2005_placettes_foret_2005.csv b/ms/metadata/France/files/2005_placettes_foret_2005.csv
deleted file mode 100644
index 837cd81..0000000
--- a/ms/metadata/France/files/2005_placettes_foret_2005.csv
+++ /dev/null
@@ -1,2 +0,0 @@
-use,var,units,description
-0,idp.xl93.yl93.dep.csa.uta.tm2.dc.tplant.dist.acces.pentn.portn.esspre.cac.ess_age_1,,
diff --git a/ms/metadata/France/files/2005_placettes_peupleraie_2005.csv b/ms/metadata/France/files/2005_placettes_peupleraie_2005.csv
deleted file mode 100644
index e074303..0000000
--- a/ms/metadata/France/files/2005_placettes_peupleraie_2005.csv
+++ /dev/null
@@ -1,2 +0,0 @@
-use,var,units,description
-0,idp.xl93.yl93.dep.csa.uta.dc.dist.portn.cac,,
diff --git a/ms/metadata/France/files/2006_arbres_foret_2006.csv b/ms/metadata/France/files/2006_arbres_foret_2006.csv
deleted file mode 100644
index 1470c28..0000000
--- a/ms/metadata/France/files/2006_arbres_foret_2006.csv
+++ /dev/null
@@ -1,2 +0,0 @@
-use,var,units,description
-0,idp.a.veget.espar.ori.lib.forme.tige.mortb.c13.ir5.htot.q1.q2.q3.r.lfsd.v.w,,
diff --git a/ms/metadata/France/files/2006_arbres_morts_foret_2006.csv b/ms/metadata/France/files/2006_arbres_morts_foret_2006.csv
deleted file mode 100644
index ecaac75..0000000
--- a/ms/metadata/France/files/2006_arbres_morts_foret_2006.csv
+++ /dev/null
@@ -1,2 +0,0 @@
-use,var,units,description
-0,idp.a.espar.ori.veget.c0.v.w,,
diff --git a/ms/metadata/France/files/2006_arbres_peupleraie_2006.csv b/ms/metadata/France/files/2006_arbres_peupleraie_2006.csv
deleted file mode 100644
index 8c4d932..0000000
--- a/ms/metadata/France/files/2006_arbres_peupleraie_2006.csv
+++ /dev/null
@@ -1,2 +0,0 @@
-use,var,units,description
-0,idp.a.veget.espar.clon.ori.c13.htot.q1.q2.q3.r.lfsd.v.w,,
diff --git a/ms/metadata/France/files/2006_couverts_foret_2006.csv b/ms/metadata/France/files/2006_couverts_foret_2006.csv
deleted file mode 100644
index 9dbcf38..0000000
--- a/ms/metadata/France/files/2006_couverts_foret_2006.csv
+++ /dev/null
@@ -1,2 +0,0 @@
-use,var,units,description
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index 17ae6ba..0000000
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-- 
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