merge.data.NZ.R

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

######################### READ DATA read individuals tree 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.trait <- read.csv("./data/raw/DataNVS/nz_traits_130801.csv", , header = TRUE, 
    stringsAsFactors = FALSE)
data.trait <- data.trait[, -1]
data.plot <- read.csv("./data/raw/DataNVS/nz_plotinfo_130801.csv", , header = TRUE, 
    stringsAsFactors = FALSE)
data.plot <- data.plot[, -1]
colnames(data.trait)[1] <- "sp"
data.plot$plid <- gsub("__", "_", data.plot$plid)
data.plot$plid <- gsub("_", ".", data.plot$plid)  ## Replace all underscores with a single dot
data.nz$plid <- gsub("__", "_", data.nz$plid)
data.nz$plid <- gsub("_", ".", data.nz$plid)  ## Replace all underscores with a single dot

###################################### 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.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') ## I
# was planning to save processed data in that folder

################################################################ 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$D <- data.nz[["D0"]]  ## diameter in mm convert to cm
data.nz$dead <- as.numeric(is.na(data.nz[["D1"]]))  ## dummy variable for dead tree 0 alive 1 dead
data.nz$sp <- data.nz$sp
data.nz$plot <- data.nz$plid
data.nz$htot <- rep(NA, length(data.nz[["sp"]]))  ## Max height is already available so have as missing
data.nz$tree.id <- data.nz[["tag"]]
data.nz$tree.id <- gsub("__", "_", data.nz$tree.id)
data.nz$tree.id <- gsub("_", ".", data.nz$tree.id)  ## tree unique id

########################################## CHANGE COORDINATE SYSTEM DON'T KNOW THE EPSG CODE HERE change coordinates
########################################## system of Easting Northing to be in lat long WGS84
data.nz <- merge(data.plot[, c(1, 3, 4)], data.nz, by = "plid")
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:23030")  # define projection system of our data ## EPSG CODE 23030 ED50 / UTM zone 30N
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 library(rworldmap) newmap <- getMap(resolution = 'coarse')
## # different resolutions available plot(newmap)
## points(data.sp2,cex=0.2,col='red')
rm(data.sp, data.sp2)

###################### ECOREGION merge greco to have no ecoregion with low number of observation
data.nz <- merge(data.nz, data.frame(plot = data.plot$plid, data.plot[, 11:12]), 
    by = "plot")
table(data.nz$Broad)

###################### PERCENT DEAD
perc.dead <- tapply(data.nz[["dead"]], INDEX = data.nz[["plot"]], FUN = function.perc.dead)
# ## VARIABLE TO SELECT PLOT WITH NOT BIG DISTURBANCE KEEP OFTHER VARIABLES IF
# AVAILABLE (disturbance record)