formatting traits data for FUSHAN and NZ

merge.data.FUSHAN.R

@@ -4,18 +4,31 @@ source("./R/format.function.R")
 library(reshape)
 
 ######################### READ DATA read individuals tree data
-data.fushan <- load("./data/raw/DataFushan/fushan.RData")
+data.fushan <- load("./data/raw/DataFushan/fushan.rdata")
 data.fushan <- data.frame(fushan)
 rm(fushan)
-data.trait <- read.table("./data/raw/DataFushan/fs_trait_Kunstler.txt", header = T, 
-    sep = "\t")
-colnames(data.trait) <- c("sp", "sla", "wd", "seedmassmg", "meanN", "maxheightm")
 
 ### read species names
 species.clean <- read.csv("./data/raw/DataFushan/Splist_Fushan_En.csv", stringsAsFactors = FALSE)
 
 ###################################### MASSAGE TRAIT DATA Obtain maximum height per species from data.trait no sd
 ###################################### available as we have only one observation for species
+data.trait <- read.table("./data/raw/DataFushan/fs_trait_Kunstler.txt", header = T, 
+    sep = "\t")
+colnames(data.trait) <- c("sp", "sla", "wd", "seedmassmg", "meanN", "maxheightm")
+data.trait <- merge(data.trait, data.frame(sp = species.clean$sp, Latin = apply(species.clean[,c("genus","epithet")],1,paste,collapse="_"), 
+	stringsAsFactors = F), by = "sp")
+data.trait$Leaf.N.mean <- data.trait$meanN*10; data.trait$meanN <- NULL; ## conversion from percentage to mg/g
+data.trait$Leaf.N.sd <- NA
+data.trait$Seed.mass.mean <- data.trait$seedmassmg; data.trait$seedmassmg <- NULL
+data.trait$Seed.mass.sd <- NA
+data.trait$SLA.mean <- data.trait$sla/10; data.trait$sla <- NULL
+data.trait$SLA.sd <- NA
+data.trait$Wood.density.mean <- data.trait$wd; data.trait$wd <- NULL
+data.trait$Wood.density.sd <- NA
+data.trait$Max.height.mean <- log10(data.trait$maxheightm); data.trait$maxheightm <- NULL
+data.trait$Max.height.sd <- NA
+
 data.max.height <- data.frame(sp = data.trait$sp, Max.height = log10(data.trait$maxheightm))
 data.fushan <- merge(data.fushan, data.max.height, by = "sp")
 

merge.data.NZ.R

@@ -28,6 +28,17 @@ data.trait <- read.csv("./data/raw/DataNVS/nz_traits_130801.csv", , header = TRU
     stringsAsFactors = FALSE)
 data.trait <- data.trait[, -1]
 colnames(data.trait)[1] <- "sp"
+data.trait$Latin <- NULL
+data.trait$Leaf.N.mean <- data.trait$leafn*10; data.trait$leafn <- NULL ## conversion from % to mg/g
+data.trait$Leaf.N.sd <- NA ## conversion from % to mg/g
+data.trait$Seed.mass.mean <- data.trait$seed.mg; data.trait$seed.mg <- NULL
+data.trait$Seed.mass.sd <- NA
+data.trait$SLA.mean <- 1/data.trait$lma.gm2; data.trait$SLA.mean <- data.trait$SLA.mean*1000; data.trait$lma.gm2 <- NULL ## conversion of g/m2 to mm2/g1
+data.trait$SLA.sd <- NA
+data.trait$Wood.density.mean <- data.trait$wood; data.trait$wood <- NULL
+data.trait$Wood.density.sd <- NA
+data.trait$Max.height.mean <- log10(data.trait$height.m); data.trait$height.m <- NULL
+data.trait$Max.height.sd <- NA
 
 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)
@@ -118,4 +129,3 @@ system.time(lapply(ecoregion.unique, FUN = fun.data.per.ecoregion, data.tot = da
     species.lookup = species.clean)) 
 
 
-