modified Paracou and Swiss

R/format.function.R

@@ -8,6 +8,19 @@
 ######
 ######
 ## FUNCTION TO PLOT MAP OF TREE
+##' .. 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 ... 
+##' @return 
+##' @author Kunstler
 fun.circles.plot <- function(plot.select,x,y,plot,D,inches,...){
 x.t <- x[plot==plot.select]
 y.t <- y[plot==plot.select]
@@ -108,8 +121,20 @@ print("columns removed")
 return( (data.merge))
 }
 
-#### function with X Y coordinates based on a neighborhood of radius R
-
+#### 
+##' .. function compute competition index with X Y coordinates based on a neighborhood of radius R ..
+##'
+##' .. content for \details{} ..
+##' @title 
+##' @param obs.id id of the observation (if one tree as multiple growth measurement one obs.id per measurment
+##' @param xy.table table with x.y of teh individual
+##' @param diam diam in cm
+##' @param sp species
+##' @param Rlim radius of neighborhood search
+##' @param parallel run in paralle or not ?
+##' @param rpuDist run with GPU distance computation
+##' @return a data frame with nrow = length of obs.id and ncol =unique(sp)
+##' @author Kunstler
 BA.SP.FUN.XY <-  function(obs.id,xy.table,diam,sp,Rlim,parallel=FALSE,rpuDist=FALSE){
 rownames(xy.table) <- obs.id
 if(rpuDist){

merge.data.PARACOU.R

 ### MERGE paracou DATA
 ### Edited by FH
-rm(list = ls()); source("./R/format.function.R"); library(reshape)
+rm(list = ls())
+source("./R/format.function.R")
+library(reshape)
 
 #########################
 ## READ DATA
 ####################
 ### read individuals tree data
-data.paracou <- read.table("./data/raw/DataParacou/20130717_paracou_1984_2012.csv",header=TRUE,stringsAsFactors=FALSE,sep = ";", na.strings = "NULL")
+data.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 columns
@@ -16,9 +19,12 @@ data.paracou <- data.paracou[,c("foret","parcelle","carre","arbre","vernaculaire
 colnames(data.paracou) <- c("forest","plot","subplot","tree","vernacular","taxonid","x","y","circum2001","code2001","circum2005","code2005","circum2009","code2009","yeardied","typedeath")
 
 ### change numeric separator
-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$treeid <- apply(data.paracou[,1:4],1,paste,collapse="."); ## Create a tree id
+numeric.col.name <-   c("x","y","circum2001","code2001","circum2005","code2005","circum2009","code2009")
+for(k in numeric.col.name){ 
+	data.paracou[,k] <- gsub(",",".",data.paracou[,k]); data.paracou[,k] <- as.numeric(data.paracou[,k])
+    } ## Replace all , in decimals with .
+
+data.paracou$treeid <- apply(data.paracou[,c("plot","subplot","tree")],1,paste,collapse="."); ## Create a tree id
 data.paracou <- data.paracou[,c(ncol(data.paracou),1:(ncol(data.paracou)-1))]	
 
 ## ## plot each plot

merge.data.SWISS.R

@@ -11,8 +11,12 @@ data.swiss2 <- read.csv("./data/raw/DataSwiss/LFI23.csv",header=TRUE,stringsAsFa
 data.swiss3 <- read.csv("./data/raw/DataSwiss/LFI34.csv",header=TRUE,stringsAsFactors =FALSE)
 data.swiss <- rbind(data.swiss1, data.swiss2, data.swiss3)
 rm(data.swiss1, data.swiss2, data.swiss3)
-data.swiss <- data.swiss[order(data.swiss$BANR),]; data.swiss <- data.swiss[,c(2:19)]
-colnames(data.swiss) <- c("Inventid","siteid","treeid","x","y","spcode","sp.name","year","dbh1","dbh2","ba1","ba2","ba_diff","dbh_diff","repfactor1","repfactor2","ht1","ht2")
+data.swiss <- data.swiss[order(data.swiss$BANR),]
+data.swiss <- data.swiss[,c("INVNR","CLNR","BANR","X","Y","BAUMART","TEXT","VEGPER",
+                            "BHD1","BHD2","BA1","BA2","BAI","BHD_DIFF","RPSTZ1","RPSTZ2","HOEHE1","HOEHE2")]
+
+colnames(data.swiss) <- c("Inventid","siteid","treeid","x","y","spcode","sp.name","year",
+                          "dbh1","dbh2","ba1","ba2","ba_diff","dbh_diff","repfactor1","repfactor2","ht1","ht2")
 
 ## Do not need to read in spp list as it is already available in data.swiss
 
@@ -42,7 +46,7 @@ data.swiss$htot <- data.swiss$ht1 ## height of tree in m
 ## ECOREGION
 ###################
 ## Ecoregion not available for swiss data 
-
+data.swiss$ecocode <- rep("A",nrow(data.swiss))
 ######################
 ## PERCENT DEAD
 ###################