From 88dfcafbf9d78ae10907f0e7f7f13eb937f0f91f Mon Sep 17 00:00:00 2001 From: fhui28 <fhui28@gmail.com> Date: Mon, 9 Sep 2013 14:08:11 +1000 Subject: [PATCH] traits data formatted for BCI; fixes issue #6 --- merge.data.BCI.R | 24 +++++++++++++++++++++--- 1 file changed, 21 insertions(+), 3 deletions(-) diff --git a/merge.data.BCI.R b/merge.data.BCI.R index 62f936e..f23adfc 100644 --- a/merge.data.BCI.R +++ b/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 -- GitLab