quiet library loading, optional output dir for ecorgeion

R/FUN.TRY.R

 ############################################ FUNCTION TO EXTRACT DECTED OUTLIER AND FORMAT TRY DATA Georges Kunstler
 ############################################ 14/06/2013
 
-library(MASS)
-library(doParallel)
-library(mvoutlier)
+library(MASS, quietly=TRUE)
+library(doParallel, quietly=TRUE)
+library(mvoutlier, quietly=TRUE)
 
 
 ######################################################## Build a function that extract the variables
@@ -133,7 +133,7 @@ f.quantile <- function(x, ind, probs) {
 }
 
 f.quantile.boot2 <- function(x, R, probs = 0.99) {
-    require(boot)
+    require(boot, quietly=TRUE)
     if (length(na.exclude(x)) > 0) {
         quant.boot <- boot(x, f.quantile, R = R, probs = probs)
         return(c(mean = mean(quant.boot$t), sd = sd(quant.boot$t), nobs = length(na.exclude(x))))

R/format.function.R

@@ -56,7 +56,7 @@ BA.fun <- function(diam, weights) {
 ##' @return data frame with tree.id and one column per species with basal area of the species (without the target tree)
 ##' @author Kunstler
 BA.SP.FUN <- function(obs.id, diam, sp, id.plot, weights, weight.full.plot) {
-    require(data.table)
+    require(data.table, quietly=TRUE)
     id.plot <- as.character(id.plot)
     obs.id <- as.character(obs.id)
     
@@ -133,7 +133,7 @@ BA.SP.FUN <- function(obs.id, diam, sp, id.plot, weights, weight.full.plot) {
 BA.SP.FUN.XY <- function(obs.id, xy.table, diam, sp, Rlim, parallel = FALSE, rpuDist = FALSE) {
     rownames(xy.table) <- obs.id
     if (rpuDist) {
-        require(rpud)
+        require(rpud, quietly=TRUE)
         dist.mat <- rpuDist(xy.table, upper = TRUE, diag = TRUE)
     } else {
         dist.mat <- as.matrix(dist(xy.table, upper = TRUE, diag = TRUE))
@@ -149,7 +149,7 @@ BA.SP.FUN.XY <- function(obs.id, xy.table, diam, sp, Rlim, parallel = FALSE, rpu
     fun.sum.sp <- function(x, sp) tapply(x, INDEX = sp, FUN = sum, na.rm = TRUE)
     if (parallel) {
         ## parallel version
-        require(doParallel)
+        require(doParallel, quietly=TRUE)
         registerDoParallel(cores = 4)
         mat <- dist.mat * BA.mat
         res.temp <- foreach(i = 1:nrow(mat), .combine = rbind) %dopar% {
@@ -185,14 +185,14 @@ fun.clean.species.tab <- function(species.tab) {
 
 ### compute quantile 99% and sd with a bootstrap
 
-library(boot)
+library(boot, quietly=TRUE)
 
 f.quantile <- function(x, ind, probs) {
     quantile(x[ind], probs = probs, na.rm = TRUE)
 }
 
 f.quantile.boot <- function(i, x, fac, R, probs = 0.99) {
-    require(boot)
+    require(boot, quietly=TRUE)
     if (length(na.exclude(x[fac == i])) > 0) {
         quant.boot <- boot(x[fac == i], f.quantile, R = R, probs = probs)
         return(as.matrix(c(mean = mean(quant.boot$t), sd = sd(quant.boot$t), nobs = length(na.exclude(x[fac == 
@@ -231,11 +231,11 @@ function.replace.NA.negative <- function(data.BA.SP) {
 
 ############################################################## function to generate data in good format per ecoregion
 fun.data.per.ecoregion <- function(ecoregion, data.tot, plot.name, weight.full.plot, 
-    name.country, data.TRY = NA, species.lookup = NA) {
-    require(data.table)
-    data.tot <- data.table(data.tot)
-    data <- data.tot[ecocode == ecoregion, ]
-    rm(data.tot)
+    name.country, data.TRY = NA, species.lookup = NA, output.dir = "./data/process") {
+    require(data.table, quietly=TRUE)
+    
+    print(paste("Working on Ecoregion %s", ecoregion))
+    data <- data.table(data.tot)[ecocode == ecoregion, ]
     data.BA.SP <- BA.SP.FUN(obs.id = as.vector(data[["obs.id"]]), diam = as.vector(data[["D"]]), 
         sp = as.vector(data[["sp"]]), id.plot = as.vector(data[[plot.name]]), weights = data[["weights"]], 
         weight.full.plot = weight.full.plot)
@@ -264,20 +264,17 @@ fun.data.per.ecoregion <- function(ecoregion, data.tot, plot.name, weight.full.p
     if (sum(!data.BA.sp[["obs.id"]] == data[["obs.id"]]) > 0) 
         stop("competition index not in the same order than data")
     ##### ADD TRY DATA OR TRAITS IF NEEDED
+    data.traits = NA
     if (!is.na(data.TRY)) {
-        sp.extract <- species.lookup[species.lookup[["sp"]] %in% unique(data[["sp"]]), 
-            ]
+        sp.extract <- species.lookup[species.lookup[["sp"]] %in% unique(data[["sp"]]), ]
         data.traits <- fun.extract.format.sp.traits.TRY(sp = sp.extract[["sp"]], 
             sp.syno.table = sp.extract, data.TRY)
-        ## save everything as a list
-        list.temp <- list(data.tree = data, data.BA.SP = data.BA.sp, data.traits = data.traits)
-        save(list.temp, file = paste("./data/process/list", name.country, ecoregion, 
-            "Rdata", sep = "."))
-    } else {
-        list.temp <- list(data.tree = data, data.BA.SP = data.BA.sp, data.traits = NA)
-        save(list.temp, file = paste("./data/process/list", name.country, ecoregion, 
-            "Rdata", sep = "."))
-    }
+    } 
+    
+    ## save everything as a list
+    list.temp <- list(data.tree = data, data.BA.SP = data.BA.sp, data.traits = data.traits)
+    save(list.temp, file = file.path(output.dir,paste("list", name.country, ecoregion, 
+        "Rdata", sep = ".")))
 }