traits formatting for NSW

merge.data.NSW.R

-### MERGE NSW DATA Edited by FH
+### MERGE NSW DATA
 rm(list = ls())
 source("./R/format.function.R")
 library(reshape)
@@ -48,7 +48,19 @@ data.nswtnd$Date.of.measure <- as.vector(sapply(data.nswtnd$Date.of.measure, fun
 data.nsw <- rbind(data.nswbrc, data.nswbrt, data.nswbs1, data.nswbs2, data.nswtnd)
 
 ###################################### MASSAGE TRAIT DATA
-data.traits <- read.csv("./data/raw/DataNSW/NSW_traits.csv", header = TRUE, stringsAsFactors = FALSE)
+data.trait <- read.csv("./data/raw/DataNSW/NSW_traits.csv", header = TRUE, stringsAsFactors = FALSE)
+data.trait$sp <- data.trait[["Species.all"]]; data.trait[["Species.all"]] <- NULL ## There is not sp.code in data.nsw; using spp name as code
+data.trait$Latin_name <- data.trait$sp
+data.trait$Leaf.N.mean <- NA
+data.trait$Leaf.N.sd <- NA
+data.trait$Seed.mass.mean <- (10^data.trait$SDM_log10_g)*1000; data.trait$SDM_log10_g <- NULL ## conversion from log10 g to mg
+data.trait$Seed.mass.sd <- NA
+data.trait$SLA.mean <- NA
+data.trait$SLA.sd <- NA
+data.trait$Wood.density.mean <- data.trait[["WD_basic_kg.m3"]]/1000; data.trait[["WD_basic_kg.m3"]] <- NULL ## conversion from kg/m3 to mg/mm3
+data.trait$Wood.density.sd <- NA
+data.trait$Max.height.mean <- data.trait$Log10_Hmax_m; data.trait$Log10_Hmax_m <- NULL
+data.trait$Max.height.sd <- NA
 
 ########################################## FORMAT INDIVIDUAL TREE DATA Each tree has at most 3 observations (from prelim
 ########################################## checks of the data)
@@ -86,7 +98,7 @@ data.nsw$dead <- rep(NA, nrow(data.nsw))  ## dummy variable for dead tree 0 aliv
 data.nsw$sp <- as.numeric(factor(data.nsw[["species"]]))  ## species code - use the spp name as code
 data.nsw$sp.name <- data.nsw[["species"]]; data.nsw$species <- NULL
 data.nsw$plot <- as.character(data.nsw[["Plot"]])  ## plot code
-data.nsw$htot <- rep(NA, nrow(data.nsw))  ## height of tree in m - MISSING
+data.nsw$htot <- rep(NA, nrow(data.nsw))  ## height of tree in m
 ### add plot weights for computation of competition index (in 1/m^2) - from the
 ### original excel file
 data.nsw$weights <- rep(NA, nrow(data.nsw))
@@ -102,7 +114,7 @@ data.nsw$weights[grep("END", data.nsw$Plot)] <- 1/(40 * 50)
 data.nsw$weights[grep("TND", data.nsw$Plot)] <- 1/(40 * 50)
 
 data.nsw$obs.id <- 1:nrow(data.nsw) ## Should change this when census variable is created
-
+data.nsw$cenus <- data.nsw$year1 ## Census variable
 ###################### ECOREGION nsw has only 1 eco-region
 
 ###################### PERCENT DEAD NO DATA ON MORTALITY