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READ.DATA.NFI.FRANCE.R 25.74 KiB
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############################################################
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############################################################
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########## READ, MERGE AND CLEAN ALL NFI DATA NEW METHODS
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### read TREE table downloaded from the web
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arbre2005 <- read.csv("./data/raw/DataFrance/2005/arbres_foret_2005.csv",sep=";", stringsAsFactors=FALSE)
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summary(arbre2005)
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arbre2006 <- read.csv("./data/raw/DataFrance/2006/arbres_foret_2006.csv",sep=";", stringsAsFactors=FALSE)
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summary(arbre2006)
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arbre2007 <- read.csv("./data/raw/DataFrance/2007/arbres_foret_2007.csv",sep=";", stringsAsFactors=FALSE)
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summary(arbre2007)
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arbre2008 <- read.csv("./data/raw/DataFrance/2008/arbres_foret_2008.csv",sep=";", stringsAsFactors=FALSE)
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summary(arbre2005)
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arbre2009 <- read.csv("./data/raw/DataFrance/2009/arbres_foret_2009.csv",sep=";", stringsAsFactors=FALSE)
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summary(arbre2009)
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arbre2010 <- read.csv("./data/raw/DataFrance/2010/arbres_foret_2010.csv",sep=";", stringsAsFactors=FALSE)
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summary(arbre2010)
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arbre2011 <- read.csv("./data/raw/DataFrance/2011/arbres_foret_2011.csv",sep=";", stringsAsFactors=FALSE)
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#### 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 ...)
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### NEED TO UPDATE VEGET FROM ACCI
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arbre2007$veget[arbre2007$acci>0] <- 1
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arbre2008$veget[arbre2008$acci>0] <- 1
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arbre2009$veget[arbre2009$acci>0] <- 1
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arbre2010$veget[arbre2010$acci>0] <- 1
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arbre2011$veget[arbre2011$acci>0] <- 1
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##
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arbre2005$veget <- unclass(arbre2005$veget)-1
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arbre2006$veget <- unclass(arbre2006$veget)-1
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######
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## ORI NEED TO BE DEGRADED SINCE 2007 to two level from resprout or from seed
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arbre2007$ori[arbre2007$ori==2] <- 0
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arbre2008$ori[arbre2008$ori==2] <- 0
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arbre2009$ori[arbre2009$ori==2] <- 0
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arbre2010$ori[arbre2010$ori==2] <- 0
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arbre2011$ori[arbre2011$ori==2] <- 0
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##############################
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### merge all table adding NA when no variable for that year
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arbre.tot <- data.frame(idp=c(arbre2005$idp,arbre2006$idp,arbre2007$idp,arbre2008$idp,arbre2009$idp,arbre2010$idp,arbre2011$idp),
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                        a=c(arbre2005$a,arbre2006$a,arbre2007$a,arbre2008$a,arbre2009$a,arbre2010$a,arbre2011$a),
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                        veget=c(arbre2005$veget,arbre2006$veget,arbre2007$veget,arbre2008$veget,arbre2009$veget,arbre2010$veget,arbre2011$veget),
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                        simplif=c(rep(NA,length(arbre2005$idp)),rep(NA,length(arbre2006$idp)),rep(NA,length(arbre2007$idp)),
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                            rep(NA,length(arbre2008$idp)),arbre2009$simplif,arbre2010$simplif,arbre2011$simplif),
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                        acci=c(rep(NA,length(arbre2005$idp)),rep(NA,length(arbre2006$idp)),arbre2007$acci,arbre2008$acci,arbre2009$acci,
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                            arbre2010$acci,arbre2011$acci),
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                        espar=c(as.character(arbre2005$espar),as.character(arbre2006$espar),as.character(arbre2007$espar),
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                            as.character(arbre2008$espar),as.character(arbre2009$espar),as.character(arbre2010$espar),as.character(arbre2011$espar)),
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                        ori=c(arbre2005$ori,arbre2006$ori,arbre2007$ori,arbre2008$ori,arbre2009$ori,arbre2010$ori,arbre2011$ori),
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                        lib=c(arbre2005$lib,arbre2006$lib,arbre2007$lib,arbre2008$lib,arbre2009$lib,arbre2010$lib,arbre2011$lib),
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                        forme=c(arbre2005$forme,arbre2006$forme,arbre2007$forme,arbre2008$forme,arbre2009$forme,arbre2010$forme,arbre2011$forme),
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                        tige=c(arbre2005$tige,arbre2006$tige,arbre2007$tige,arbre2008$tige,arbre2009$tige,arbre2010$tige,arbre2011$tige),
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                        mortb=c(rep(NA,length(arbre2005$idp)),arbre2006$mortb,arbre2007$mortb,arbre2008$mortb,arbre2009$mortb,arbre2010$mortb,
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                            arbre2011$mortb),
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                        sfgui=c(rep(NA,length(arbre2005$idp)),rep(NA,length(arbre2006$idp)),rep(NA,length(arbre2007$idp)),arbre2008$sfgui,
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                            arbre2009$sfgui,arbre2010$sfgui,arbre2011$sfgui),
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                        sfgeliv=c(rep(NA,length(arbre2005$idp)),rep(NA,length(arbre2006$idp)),rep(NA,length(arbre2007$idp)),arbre2008$sfgeliv,
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                            arbre2009$sfgeliv,arbre2010$sfgeliv,arbre2011$sfgeliv),
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                        sfpied=c(rep(NA,length(arbre2005$idp)),rep(NA,length(arbre2006$idp)),rep(NA,length(arbre2007$idp)),arbre2008$sfpied,
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                            arbre2009$sfpied,arbre2010$sfpied,arbre2011$sfpied),
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                        sfdorge=c(rep(NA,length(arbre2005$idp)),rep(NA,length(arbre2006$idp)),rep(NA,length(arbre2007$idp)),arbre2008$sfdorge,
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                            arbre2009$sfdorge,arbre2010$sfdorge,arbre2011$sfdorge),
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                        sfcoeur=c(rep(NA,length(arbre2005$idp)),rep(NA,length(arbre2006$idp)),rep(NA,length(arbre2007$idp)),
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                            rep(NA,length(arbre2008$idp)),arbre2009$sfcoeur,arbre2010$sfcoeur,arbre2011$sfcoeur),
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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)
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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$espar2)],na.rm=T)) } else { lmodel2.res <- lmodel2(C13~C0 ,data=arbre.cycle3,range.x="relative",range.y="relative")
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arbre_mort05_07$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),
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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))),## assume that all dead tree are sampled on the whole plot as explained in the method 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))))## 1 = dead ## 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