merge.data.BCI.R

### MERGE BCI DATA Edited by FH
rm(list = ls())
source("./R/format.function.R")
library(reshape)

######################### READ DATA read individuals tree data Requires careful formatting of 7 census
######################### datasets The raw data is such that, once a tree dies in census X, then it no
######################### longer exists in census X+1, X+2 etc...
data.bci1 <- read.table("./data/raw/DataBCI/census1/PlotsDataReport.txt", header = TRUE, 
    stringsAsFactors = FALSE, sep = "\t")
big.bci <- NULL
for (k in 2:7) {
    new.directory <- paste("./data/raw/DataBCI/census", k, "/PlotsDataReport.txt", 
        sep = "")
    data.bci2 <- read.table(new.directory, header = TRUE, stringsAsFactors = FALSE, 
        sep = "\t")
    if (!is.null(big.bci)) {
        sub.bci <- merge(data.bci1[, c(2:7, 11, 13)], data.frame(TreeID = data.bci2[["TreeID"]], 
            DBH2 = data.bci2[["DBH"]], Date2 = data.bci2[["Date"]], dead = as.numeric(data.bci2[["Status"]] == 
                "dead")), sort = T, by = "TreeID")
        big.bci <- rbind(big.bci, sub.bci)
    }
    if (is.null(big.bci)) {
        big.bci <- merge(data.bci1[, c(2:7, 11, 13)], data.frame(TreeID = data.bci2[["TreeID"]], 
            DBH2 = data.bci2[["DBH"]], Date2 = data.bci2[["Date"]], dead = as.numeric(data.bci2[["Status"]] == 
                "dead")), sort = T, by = "TreeID")
    }
    data.bci1 <- data.bci2
    cat("Census", k, "now included\n")
}
rm(data.bci1, data.bci2, sub.bci)
big.bci <- big.bci[order(big.bci$TreeID), ]
colnames(big.bci)[c(7:8)] <- c("DBH1", "Date1")
data.bci <- big.bci
rm(big.bci)

### read species names
species.clean <- read.table("./data/raw/DataBCI/TaxonomyDataReport.txt", stringsAsFactors = FALSE, 
    header = T, sep = "\t")

## Try to relate SpeciesID in species.clean species names in data.bci
data.bci$sp2 = species.clean$SpeciesID[match(data.bci$Latin, paste(species.clean[["Genus"]], 
    species.clean[["species"]]))]
length(unique(data.bci$sp))

###################################### MASSAGE TRAIT DATA Use HEIGHT_AVG, LMALAM_AVD, SEED_DRY, BUT I DO NOT KNOW
###################################### WHICH WOOD DENSITY VARIABLE TO USE
data.trait <- read.csv("./data/raw/DataBCI/BCITRAITS_20101220.csv", stringsAsFactors = FALSE, 
    header = T)
data.trait$Latin <- apply(data.trait[, 1:2], 1, paste, collapse = " ")
data.bci <- merge(data.bci, data.trait[, c(ncol(data.trait), 3, 7:10, 13, 15, 18, 
    20:21)], by = "Latin", all.x = T)

data.bci <- data.bci[order(data.bci$TreeID), ]
########################################## FORMAT INDIVIDUAL TREE DATA
data.bci$Date1 <- as.Date(data.bci$Date1)
data.bci$Date2 <- as.Date(data.bci$Date2)
# data.bci$yr1 <- format(strptime(data.bci$Date1, format = '%Y-%m-%d'),'%Y')
# data.bci$yr2 <- format(strptime(data.bci$Date2, format = '%Y-%m-%d'),'%Y')
data.bci$year <- as.numeric(difftime(data.bci$Date2, data.bci$Date1, units = "weeks")/52)  ## Not rounded 

## change unit and names of variables to be the same in all data for the tree
data.bci$G <- 10 * (data.bci$DBH1 - data.bci$DBH1)/data.bci$year  ## diameter growth in mm per year - BASED ON UNROUNDED YEARS
data.bci$D <- data.bci[["DBH1"]]
data.bci$plot <- data.bci[["Quadrat"]]  ## plot code?
data.bci$htot <- data.bci$HEIGHT_AVG
data.bci$sp.name <- data.bci$Latin

###################### ECOREGION bci has only 1 eco-region