diff --git a/merge.data.BCI.R b/merge.data.BCI.R index f6c2a47c1a05a62071a599b251acf4b4c8dbbbe1..87d3b7787d51edfb7de6b4a0727a3aed44c7ac34 100644 --- a/merge.data.BCI.R +++ b/merge.data.BCI.R @@ -21,7 +21,7 @@ for(k in 2:7) { sort = T, by = "TreeID") } data.bci1 <- data.bci2 cat("Census", k, "now included\n") } -rm(data.bci1, data.bci2, data.bci3, sub.bci) +rm(data.bci1, data.bci2, sub.bci) big.bci <- big.bci[order(big.bci$TreeID),]; colnames(big.bci)[c(7:8)] <- c("DBH1","Date1") data.bci <- big.bci; rm(big.bci) @@ -39,8 +39,12 @@ length(unique(data.bci$sp)) ###################################### ## MASSAGE TRAIT DATA ############################ -## THERE ARE HEIGHT VARAIBLES IN THE TRAITS DATA, BUT WE WILL NEED TO DISCUSS WHICH ONES TO USE +## Use HEIGHT_AVG, LMALAM_AVD, SEED_DRY, BUT I DO NOT KNOW WHICH WOOD DENSITY VARIABLE TO USE +data.trait <- read.csv("./data/raw/DataBCI/BCITRAITS_20101220.csv",stringsAsFactors=FALSE, header = T) +data.trait$Latin <- apply(data.trait[,1:2], 1, paste, collapse = " ") +data.bci <- merge(data.bci, data.trait[,c(ncol(data.trait),3,7:10,13,15,18,20:21)], by = "Latin", all.x = T) +data.bci <- data.bci[order(data.bci$TreeID),] ########################################## ## FORMAT INDIVIDUAL TREE DATA ############# @@ -53,13 +57,13 @@ data.bci$year <- as.numeric(difftime(data.bci$Date2, data.bci$Date1, units = "we data.bci$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 <- rep(NA,length(data.bci[["G"]])) ## DOES IT COME FROM THE TRAITS DATA? +data.bci$htot <- data.bci$HEIGHT_AVG data.bci$sp.name <- data.bci$Latin ###################### ## ECOREGION ################### -## bci has only 1 eco-region? +## bci has only 1 eco-region ###################### ## PERCENT DEAD @@ -76,7 +80,6 @@ data.bci <- merge(data.bci,data.frame(plot=names(perc.dead),perc.dead=perc.dead) ################### ## Remove data with dead == 1 table(data.bci$dead) -## Nothing to remove vec.abio.var.names <- c("MAT","MAP") ## MISSING vec.basic.var <- c("treeid","sp","sp.name","plot","D","G","dead","year","htot","x","y","perc.dead")