merge.data.NZ.R

### MERGE NZ DATA
rm(list = ls())
source("./R/format.function.R")
source("./R/FUN.TRY.R")
library(reshape)

######################### READ DATA read individuals tree and environmental data
data.nz <- read.csv("./data/raw/DataNVS/nz_treedata_growth_130801.csv", header = TRUE, 
    stringsAsFactors = FALSE, skip = 9)
data.nz <- data.nz[, -1]
data.nz$plid <- gsub("__", "_", data.nz$plid)
data.nz$plid <- gsub("_", ".", data.nz$plid)  ## Replace all underscores with a single dot

data.plot <- read.csv("./data/raw/DataNVS/nz_plotinfo_130801.csv", , header = TRUE, 
    stringsAsFactors = FALSE)
data.plot <- data.plot[, -1]
data.plot$plid <- gsub("__", "_", data.plot$plid)
data.plot$plid <- gsub("_", ".", data.plot$plid)  ## Replace all underscores with a single dot

data.nz <- merge(data.nz, data.frame(plid = data.plot$plid, Easting = data.plot$Easting, 
	Northing = data.plot$Northing, Locality = data.plot$Locality, MAP = data.plot$map, MAT = data.plot$mat, Broadclass = data.plot$BroadClass, 
	Specificclass = data.plot$SpecificClass, stringsAsFactors = F), sort = T, by = "plid")
rm(data.plot)
	
###################################### MASSAGE TRAIT DATA Maximum height per species is already available from
###################################### data.trait (in m); so no sd's and only obs per spp
data.trait <- read.csv("./data/raw/DataNVS/nz_traits_130801.csv", , header = TRUE, 
    stringsAsFactors = FALSE)
data.trait <- data.trait[, -1]
colnames(data.trait)[1] <- "sp"

data.max.height <- data.frame(code = data.trait[["sp"]], Max.height.mean = log10(data.trait[["height.m"]]), 
    Max.height.sd = NA, Max.height.nobs = 1)
# write.csv(data.max.height,file='./data/process/data.max.height.nz.csv') 

################################################################ FORMAT INDIVIDUAL TREE DATA

## change unit and names of variables to be the same in all data for the tree
data.nz$G <- 10 * (data.nz[["D1"]] - data.nz[["D0"]])/(data.nz[["t1"]] - data.nz[["t0"]])  ## diameter growth in mm per year
data.nz$year <- (data.nz[["t1"]] - data.nz[["t0"]])  ## number of year between measurement
data.nz$D <- data.nz[["D0"]]  ## diameter in cm
data.nz$dead <- as.numeric(is.na(data.nz[["D1"]]))  ## dummy variable for dead tree 0 alive 1 dead
data.nz$plot <- data.nz$plid; data.nz$plid <- NULL
data.nz$htot <- rep(NA, nrow(data.nz))  ## Max height is already available so have as missing
data.nz$tree.id <- data.nz$tag
head(subset(data.nz,subset=data.nz$tag %in% names(table(data.nz$tag))[table(data.nz$tag)==2])) ### 3 individuals with two observation with strange value check with Daniel and David add an issue
data.nz$obs.id <- as.character(1:nrow(data.nz))
data.nz$census <- rep(1,nrow(data.nz)) # only one census NEED TO CHECK WITH DANIEL AND DAVID add issue
data.nz$weights <- 1/(20*20) ## need to check with david

########################################## CHANGE COORDINATE SYSTEM 
########################################## system of Easting Northing to be in lat long WGS84
library(sp)
library(dismo)
library(rgdal)
data.sp <- data.nz[, c("tree.id", "Easting", "Northing")]
coordinates(data.sp) <- c("Easting", "Northing")  # define x y
proj4string(data.sp) <- CRS("+init=epsg:27200")  # define projection system of our data ## EPSG CODE 27200  NZGD49 / New Zealand Map Grid
summary(data.sp)

detach(package:rgdal)
data.sp2 <- spTransform(data.sp, CRS("+init=epsg:4326"))  ## change projection in WGS84 lat lon
data.nz$Lon <- coordinates(data.sp2)[, "Easting"]
data.nz$Lat <- coordinates(data.sp2)[, "Northing"]
## ## plot on world map
pdf("./figs/map.NZ.pdf")
library(rworldmap)
newmap <- getMap(resolution = 'coarse')
## # different resolutions available
plot(newmap,xlim=c(166,177),ylim=c(-34,-47))