solved issue with test in traits data

R/FUN.TRY.R

-############################################ FUNCTION TO EXTRACT DECTED OUTLIER AND FORMAT TRY DATA Georges Kunstler
+################# FUNCTION TO EXTRACT DECTED OUTLIER AND FORMAT TRY DATA Georges Kunstler
 ############################################ 14/06/2013
 
 library(MASS)
@@ -258,8 +258,9 @@ fun.extract.format.sp.traits.TRY <- function(sp, sp.syno.table, data) {
     extract.species.try <- fun.turn.list.in.DF(sp, res.list)
 
     ##### TODO ADD A TEST OF GOOD EXTRACTION OF TRAITS
-    test.num <- sample(1:length(sp),1)
-   if( extract.species.try[test.num,"SLA.mean"] !=  fun.species.traits(sp[test.num], species.table = sp.syno.table, 
+    test.num <- sample((1:length(sp))[!is.na(extract.species.try[["SLA.mean"]])],1)
+
+    if( extract.species.try[test.num,"SLA.mean"] !=  fun.species.traits(sp[test.num], species.table = sp.syno.table, 
         traits = traits, data = data)$mean[grep("SLA",traits)]) stop('traits value not good for the  species in extraction from TRY')
     ############### add mean sd of species or genus if we want to use that
     sd.vec.sp <- readRDS(file = "./data/process/sd.vec.sp.rds")
@@ -286,3 +287,4 @@ fun.extract.format.sp.traits.TRY <- function(sp, sp.syno.table, data) {
     return(data.frame.TRY)
 }
 
+

R/format.function.R

@@ -302,7 +302,7 @@ if(sum(!data.BA.sp[["obs.id"]] == data[["obs.id"]]) >0) stop("competition index
 if(is.data.frame(data.TRY)){
    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)
-   ### TO DO ADD OPTION TO INCLUE OTHER DATA on MAX HEIGHT
+   ### TODO ADD OPTION TO INCLUE OTHER DATA on MAX HEIGHT
    ## save everything as a list
    print(dim(data.traits))
    list.temp <- list(data.tree=data,data.BA.SP=data.BA.sp,data.traits=data.traits)

merge.data.US.R

@@ -104,6 +104,8 @@ ecoregion.unique <- unique(data.tree[["ecocode"]])
 
 
 #### lapply function
-system.time(lapply(ecoregion.unique[3], FUN = fun.data.per.ecoregion, data.tot = data.tree, 
+
+
+system.time(lapply(ecoregion.unique, FUN = fun.data.per.ecoregion, data.tot = data.tree, 
     plot.name = "subplot", weight.full.plot = NA, name.country = "US", data.TRY = TRY.DATA.FORMATED, 
     species.lookup = species.clean))