traits BCI Fushan

R/find.trait/BCI.R

-##### FORMAT TRAIT FOR Canada
+##### FORMAT TRAIT FOR NCI
 source("trait.fun.R")
 
 ### read species names
@@ -52,18 +52,3 @@ write.csv(data.traits,file="../../output/formatted/BCI/traits.csv")
 
 
 
-## delete the sp code with no species
-species.clean <- subset(species.clean,subset=!is.na(species.clean$Latin_name))
-
-## read in data
-data.TRY.std <- readRDS("../../output/formatted/TRY/data.TRY.std.rds")
-## read us max height
-max.height <- read.csv(file="../../output/formatted/US/max.height.csv", stringsAsFactors = FALSE)
-max.height$sp <- paste("sp",max.height$sp,sep=".")
-
-data.traits <- fun.extract.format.sp.traits.TRY(sp=species.clean[["sp"]],sp.syno.table=species.clean,data=data.TRY.std)
-
-data.traits <- merge(data.traits,subset(max.height,select=c("sp","Max.height.mean","Max.height.sd")),by="sp",all.x=TRUE,all.y=FALSE)
-### TODO ADD GENUS MEAN FOR HEIGHT IF SPECIES IS MISSING
-write.csv(data.traits,file="../../output/formatted/Canada/traits.csv")
-

R/find.trait/Fushan.R

+##### FORMAT TRAIT FOR FUSHAN
+source("trait.fun.R")
+
+### read species names
+data.tree <- read.csv("../../output/formatted/Fushan/tree.csv", stringsAsFactors = FALSE)
+species.clean <- data.frame(sp=data.tree[!duplicated(data.tree[["sp"]]),"sp"],
+                             Latin_name=data.tree[!duplicated(data.tree[["sp"]]),"sp.name"],
+                             Latin_name_syn=data.tree[!duplicated(data.tree[["sp"]]),"sp.name"],
+                             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/Fushan/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$sp, Latin_name= species.clean$Latin_name, 
+	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$Max.height.sd <- NA
+data.trait$maxheightm <- NULL
+
+
+data.TRAITS.std <- data.trait
+rm(data.trait)
+
+## extract
+data.traits <- fun.extract.format.sp.traits.NOT.TRY(sp=species.clean$sp, Latin_name=species.clean$sp, data=data.TRAITS.std,name.match.traits="sp")
+
+### TODO ADD GENUS MEAN FOR HEIGHT IF SPECIES IS MISSING
+write.csv(data.traits,file="../../output/formatted/Fushan/traits.csv")
+
+
+

R/format.data/Fushan.R

@@ -24,7 +24,7 @@ data.fushan$sp.name <- rep(NA,nrow(data.fushan))
 v <- species.clean$sp
 for (i in 1:length(unique(data.fushan$sp))) {
     sel.spp <- which(data.fushan$sp == unique(data.fushan$sp)[i])
-    data.fushan$sp.name[sel.spp] <- paste(species.clean$family[sel.spp], species.clean$genus[sel.spp], 
+    data.fushan$sp.name[sel.spp] <- paste(species.clean$genus[sel.spp], 
         species.clean$epithet[sel.spp], sep = " ")
 }
 data.fushan$weights <- 1/(pi*(0.5*data.fushan$D/100)^2)
@@ -47,28 +47,3 @@ write.csv(data.tree,file="../../output/formatted/Fushan/tree.csv")
 
 
 
-################ 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/Fushan/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$maxheightm); 
-data.trait$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")
-data.trait$maxheightm <- NULL
-
-
-###### SAVE TRAITS IN STD FORMAT
-write.csv(data.trait,file='../../output/formatted/Fushan/trait.csv')
-