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Georges Kunstler authored4ee603d5
### MERGE paracou DATA### Edited by FHrm(list = ls()); source("./R/format.function.R"); library(reshape)########################### READ DATA####################### read individuals tree datadata.paracou <- read.table("./data/raw/DataParacou/20130717_paracou_1984_2012.csv",header=TRUE,stringsAsFactors=FALSE,sep = ";", na.strings = "NULL")#barplot(apply(!is.na(data.paracou[,paste("circ_",1984:2012,sep="")]),MARGIN=2,FUN=sum),las=3)# select good columnsdata.paracou <- data.paracou[,c("foret","parcelle","carre","arbre","vernaculaire","idtaxon", "x","y","circ_2001","code_2001","circ_2005","code_2005", "circ_2009","code_2009","campagne_mort","type_mort")]colnames(data.paracou) <- c("forest","plot","subplot","tree","vernacular","taxonid","x","y","circum2001","code2001","circum2005","code2005","circum2009","code2009","yeardied","typedeath")for(k in 7:14) { data.paracou[,k] <- gsub(",",".",data.paracou[,k]); data.paracou[,k] <- as.numeric(data.paracou[,k]) } ## Replace all , in decimals with .data.paracou$treeid <- apply(data.paracou[,1:4],1,paste,collapse="."); ## Create a tree iddata.paracou <- data.paracou[,c(ncol(data.paracou),1:(ncol(data.paracou)-1))] ## REMOVE ALL TREES WITH X OR Y >250 m or NA ASK GHISLAIN!!!data.paracou <- subset(data.paracou,subset=(!is.na(data.paracou[["x"]])) & data.paracou[["x"]]<251 & data.paracou[["y"]]<251)## plot each pdf("./figs/plots.paracou.pdf")lapply(unique(data.paracou[["plot"]]),FUN=fun.circles.plot,data.paracou[['x']],data.paracou[['y']],data.paracou[["plot"]],data.paracou[["circum2009"]],inches=0.2)dev.off()pdf("./figs/plots.paracou.pdf")by(data.paracou[["circum2009"]],INDICES=data.paracou[["plot"]],FUN=function(x) hist(x,breaks=50))dev.off()######################## PLOT 16 17 18 ARE STRANGE ASK GHSILAIN#####################data.paracou <- subset(data.paracou,subset=! data.paracou[["plot"]] %in% 16:18)## keep only tree alive in 2001data.paracou <- subset(data.paracou,subset=!(as.numeric(data.paracou[["yeardied"]])<=2001 & !is.na(data.paracou[["yeardied"]])))### read species namesspecies.clean <- read.csv("./data/raw/DataParacou/20130717_paracou_taxonomie.csv",stringsAsFactors=FALSE, header = T, sep = ";")## SPECIES CODE COME FROM idTaxon in paracou_taxonomie and taxonid in paracou_1984_2012 to match the traits data we need to use the "Genus species"## we better work not work with vernacular because this doesn't match necesseraly the Genus species taxonomiespecies.clean$sp <- species.clean[["idTaxon"]]## data.paracou <- merge(data.paracou, as.data.frame(species.clean[!duplicated(species.clean[["sp"]]),c("Genre","Espece","sp")]), by = "sp", sort = FALSE)######################################## MASSAGE TRAIT DATA######################################################################## FORMAT INDIVIDUAL TREE DATA#############data.paracou2 <- data.paracou[rep(1:nrow(data.paracou),each=2),c(1:10,(ncol(data.paracou)-2):ncol(data.paracou))]rownames(data.paracou2) <- 1:nrow(data.paracou2); data.paracou2 <- as.data.frame(data.paracou2)data.paracou2$yr1 <- rep(c(2001,2001+4),nrow(data.paracou)); data.paracou2$yr2 <- rep(c(2005,2005+4),nrow(data.paracou))data.paracou2$year <- rep(c(4,4),nrow(data.paracou))data.paracou2$dbh1 <- c(rbind(data.paracou$circum2001/pi,data.paracou$circum2005/pi))data.paracou2$dbh2 <- c(rbind(data.paracou$circum2005/pi,data.paracou$circum2009/pi))data.paracou2$code1 <- c(as.numeric(rbind(data.paracou$code2001,data.paracou$code2005)))data.paracou2$code2 <- c(as.numeric(rbind(data.paracou$code2005,data.paracou$code2009)))data.paracou2$dead <- rep(0,nrow(data.paracou)*2)data.paracou2$dead[c(as.numeric(data.paracou[["yeardied"]]) %in% 2002:2005 & (!is.na(data.paracou[["yeardied"]])), as.numeric(data.paracou[["yeardied"]]) %in% 2006:2009 & (!is.na(data.paracou[["yeardied"]])))] <- 17172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140
data.paracou2$sp <- data.paracou[["taxonid"]]
## remove tree dead in 2005 in second census (2005-2009)
data.paracou <- subset(data.paracou2,subset=!(data.paracou2[['yr1']] ==2005 & (as.numeric(data.paracou[["yeardied"]]) %in% 2002:2005 & (!is.na(data.paracou[["yeardied"]])))))
## change unit and names of variables to be the same in all data for the tree
data.paracou$G <- 10*(data.paracou$dbh2-data.paracou$dbh1)/data.paracou$year ## diameter growth in mm per year
data.paracou$G[data.paracou$code1>0] <- NA ## indivs with code indicating problem in dbh measurment at dbh1
data.paracou$G[data.paracou$code2>0] <- NA ## indivs with code indicating problem in dbh measurment at dbh2
data.paracou[which(data.paracou$G < -50),] ## THERE SEEMS TO BE SOME PROBLEMS WITH THE DBH DATA ## much less issue
data.paracou$D <- data.paracou[["dbh1"]]; data.paracou$D[data.paracou$D == 0] <- NA ;## diameter in cm
data.paracou$plot <- data.paracou$plot#apply(data.paracou[,c("forest","plot","subplot")],1,paste,collapse=".") ## plot code
data.paracou$htot <- rep(NA,length(data.paracou[["G"]])) ## height of tree in m - MISSING
data.paracou$obs.id <- 1:nrow(data.paracou)
### delete recruit in 2001 or 2005 for first census
data.paracou <- subset(data.paracou,subset=!is.na(data.paracou$D))
## minimum circumfer 30 delete all tree with a dbh <30/pi,
data.paracou <- subset(data.paracou,subset= data.paracou[["D"]]>(30/pi))
######################
## ECOREGION
###################
## paracou has only 1 eco-region YES NO ECOREGION
######################
## PERCENT DEAD
###################
## variable percent dead
## compute numer of dead per plot to remove plot with disturbance
## THERE ARE LOTS OF NAs - DID YOU WANT TO REMOVE THEM OR TREAT THEM AS ALIVE
perc.dead <- tapply(data.paracou[["dead"]],INDEX=data.paracou[["plot"]],FUN=function.perc.dead2)
data.paracou <- merge(data.paracou,data.frame(plot=names(perc.dead),perc.dead=perc.dead), by = "plot", sort=FALSE)
###########################################################
### PLOT SELECTION FOR THE ANALYSIS
###################
## Nothing to remove
#vec.abio.var.names <- c("MAT","MAP") ## MISSING NEED OTHER BASED ON TOPOGRAPHY ASK BRUNO
vec.basic.var <- c("obs.id","treeid","sp","plot","D","G","dead","year","htot","x","y","perc.dead")
data.tree <- subset(data.paracou,select=c(vec.basic.var))
##############################################
## COMPUTE MATRIX OF COMPETITION INDEX WITH SUM OF BA PER SPECIES IN EACH PLOT in m^2/ha without the target species
###########################
## NEED TO COMPUTE BASED ON RADIUS AROUND TARGET TREE
## TODO NEED TO ADD BUFFER ZONE
data.tree.s <- subset(data.tree,subset=data.tree[["plot"]] ==1)
BA.SP.FUN.XY(obs.id,xy.table,diam,sp,Rlim){
data.BA.SP <- BA.SP.FUN(id.tree=as.vector(data.paracou[["treeid"]]), diam=as.vector(data.paracou[["D"]]),
sp=as.vector(data.paracou[["sp"]]), id.plot=as.vector(data.paracou[["plot"]]),
weights=1/(pi*(0.5*data.paracou$D/100)^2), weight.full.plot=NA)
## change NA and <0 data for 0
data.BA.SP[is.na(data.BA.SP)] <- 0; data.BA.SP[,-1][data.BA.SP[,-1]<0] <- 0
### CHECK IF sp and sp name for column are the same
if(sum(!(names(data.BA.SP)[-1] %in% unique(data.paracou[["sp"]]))) >0) stop("competition index sp name not the same as in data.tree")
#### compute BA tot for all competitors
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BATOT.COMPET <- apply(data.BA.SP[,-1],1,sum,na.rm=TRUE)
data.BA.SP$BATOT.COMPET <- BATOT.COMPET; rm(BATOT.COMPET)
### create data frame
names(data.BA.SP) <- c("tree.id",names(data.BA.SP)[-1])
data.BA.sp <- merge(data.frame(tree.id=data.paracou[["tree.id"]],ecocode=data.paracou[["ecocode"]]),data.BA.SP,by="tree.id",sort=FALSE)
## test
if(sum(!data.BA.sp[["tree.id"]] == data.tree[["tree.id"]]) >0) stop("competition index not in the same order than data.tree")
## save everything as a list
list.paracou <- list(data.tree=data.tree,data.BA.SP=data.BA.sp,data.traits=data.traits)
save(list.spain,file="./data/process/list.paracou.Rdata")