traits data formatted for BCI; fixes issue #6

merge.data.BCI.R

@@ -51,8 +51,26 @@ length(unique(data.bci$sp))
 data.trait <- read.csv("./data/raw/DataBCI/BCITRAITS_20101220.csv", stringsAsFactors = FALSE, 
     header = T)
 data.trait$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.trait <- data.trait[,c("GENUS.","SP.","Latin","SEED_DRY","LMALAM_AVD","LMALAM_SED","LMALAM_ND","SG100C_AVG","SG100C_SEM","SG100C_N","HEIGHT_AVG","HEIGHT_SEM","HEIGHT_N")]
+data.trait$sp <- data.trait[["SP."]]; data.trait[["SP."]] <- NULL
+data.trait$Leaf.N.mean <- NA;
+data.trait$Leaf.N.sd <- NA;
+data.trait$Seed.mass.mean <- data.trait$SEED_DRY*1000; data.trait$SEED_DRY <- NULL
+data.trait$Seed.mass.sd <- NA; 
+data.trait$SLA.mean <- 1/data.trait$LMALAM_AVD; data.trait$SLA.mean <- data.trait$SLA.mean*1000 ## Conversion from g m^-2 to mm2 mg^-1
+data.trait$SLA.sd <- 1/data.trait$LMALAM_SED; data.trait$SLA.sd <- data.trait$SLA.sd*1000 ## Conversion from g m^-2 to mm2 mg^-1
+data.trait$SLA.sd <- data.trait$SLA.sd*sqrt(data.trait$LMALAM_ND)
+data.trait$LMALAM_AVD <- data.trait$LMALAM_SED <- data.trait$LMALAM_ND <- NULL
+data.trait$Wood.density.mean <- data.trait$SG100C_AVG; 
+data.trait$Wood.density.sd <- data.trait$SG100C_SEM*sqrt(data.trait$SG100C_N)
+data.trait$SG100C_AVG <- data.trait$SG100C_N <- data.trait$SG100C_SEM <- NULL
+data.trait$Max.height.mean <- log10(data.trait$HEIGHT_AVG)
+data.trait$Max.height.sd <-  log10(data.trait$HEIGHT_SEM*sqrt(data.trait$HEIGHT_N))
+data.trait$HEIGHT_SEM <- data.trait$HEIGHT_N <- data.trait$HEIGHT_AVG <- NULL
+
+#data.bci <- merge(data.bci, data.trait[, c(ncol(data.trait), 3, 7:10, 13, 15, 18, 
+#    20:21)], by = "Latin", all.x = T)
+
 
 ########################################## FORMAT INDIVIDUAL TREE DATA
 data.bci <- data.bci[order(data.bci[["TreeID"]]),]
@@ -67,7 +85,7 @@ data.bci$obs.id <- apply(data.bci[,c("TreeID","Census")],1,paste,collapse="_")
 data.bci$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$HEIGHT_AVG
+data.bci$htot <- NA
 data.bci$sp.name <- data.bci$Latin
 data.bci$weights <- 1/(pi*(0.5*data.bci$D/100)^2)
 ###################### ECOREGION bci has only 1 eco-region