update function for processing big plots to output csv

R/process.data/process.fun.R

@@ -344,14 +344,10 @@ fun.data.per.ecoregion <- function(ecoregion, data.tot, weight.full.plot, site.n
     if (sum(!data.BA.sp[["obs.id"]] == data[["obs.id"]]) > 0) 
         stop("competition index not in the same order than data")
     
-    ##### 
-    data.traits = NA
-    
     ## ADD TRY DATA IF NEEDED
+    data.TRAITS.s <- NA
     if (is.data.frame(data.TRAITS)) 
-        data.TRAITS.s <- subset(data.TRAITS, subset = data.TRAITS[[sp.code]] %in% 
-            data[[sp.code2]]) else data.TRAITS.s <- NA
-    
+        data.TRAITS.s <- subset(data.TRAITS, subset = data.TRAITS[[sp.code]] %in% data[[sp.code2]]) 
     
     write.csv(data, file = file.path(path, "data.tree.csv"), quote = FALSE, row.names = FALSE)
     write.csv(data.BA.sp, file = file.path(path, "data.BA.SP.csv"), quote = FALSE, 
@@ -363,10 +359,12 @@ fun.data.per.ecoregion <- function(ecoregion, data.tot, weight.full.plot, site.n
 ####### FUNCTION TO FORMAT DATA FOR BIG TROPICAL PLOT
 
 fun.data.per.bigplot <- function(data, site.name, data.TRAITS = NA, Rlim = 15, xy.name, 
-    parallel = FALSE, rpuDist = FALSE, sp.code = "sp", sp.code2 = "sp") {
+    parallel = FALSE, rpuDist = FALSE, sp.code = "sp", sp.code2 = "sp", out.dir = "output/processed/") {
     require(data.table)
-    dir.create(paste("output/processed/", site.name, sep = ""), recursive = TRUE, 
-        showWarnings = FALSE)
+    
+    path <- file.path(out.dir, site.name)
+    dir.create(path, recursive = TRUE, showWarnings = FALSE)
+   
     data$sp <- factor(data$sp)
     data.TRAITS$sp <- factor(data.TRAITS$sp)
     print(paste("plots :", unique(data[["plot"]])))
@@ -399,18 +397,19 @@ fun.data.per.bigplot <- function(data, site.name, data.TRAITS = NA, Rlim = 15, x
     if (sum(!as.character(data.BA.SP[["obs.id"]]) == as.character(data[["obs.id"]])) > 
         0) 
         stop("competition index not in the same order than data")
-    ##### ADD TRY DATA OR TRAITS IF NEEDED
-    if (is.data.frame(data.TRAITS)) {
-        data.TRAITS.s <- subset(data.TRAITS, subset = data.TRAITS[[sp.code]] %in% 
-            data[[sp.code2]])
-        list.temp <- list(data.tree = data, data.BA.SP = data.BA.SP, data.traits = data.TRAITS.s)
-        saveRDS(list.temp, file = paste("output/processed/", site.name, "/list.rds", 
-            sep = ""))
-    } else {
-        list.temp <- list(data.tree = data, data.BA.SP = data.BA.sp, data.traits = NA)
-        saveRDS(list.temp, file = paste("output/processed/", site.name, "/list.rds", 
-            sep = ""))
-    }
+
+    browser()
+    ## ADD TRY DATA IF NEEDED
+    data.TRAITS.s <- NA
+    if (is.data.frame(data.TRAITS)) 
+        data.TRAITS.s <- subset(data.TRAITS, subset = data.TRAITS[[sp.code]] %in% data[[sp.code2]]) 
+    
+    write.csv(data, file = file.path(path, "data.tree.csv"), quote = FALSE, row.names = FALSE)
+    write.csv(data.BA.sp, file = file.path(path, "data.BA.SP.csv"), quote = FALSE, 
+        row.names = FALSE)
+    write.csv(data.TRAITS.s, file = file.path(path, "data.traits.csv"), quote = FALSE, 
+        row.names = FALSE)
+
 }
 
 process_inventory_dataset <- function(set, path.formatted = "output/formatted", path.processed = "output/processed"){