Fix TRY make, remove libs file

.gitignore

 output
 output_cluster
 ignore
-data/raw
+data/raw*
 figs
 *.xls
 *.xlsx

R/format.data/Makefile

@@ -5,7 +5,9 @@ D2 := $(ROOT)/output/formatted
 all: TRY Canada France NVS Spain Sweden Swiss US 
   # BCI Fushan NSW Paracou
 
-TRY: $(D2)/TRY/data.TRY.std.rds TRY.R
+TRY: $(D2)/TRY/data.TRY.std.rds
+
+$(D2)/TRY/data.TRY.std.rds: TRY.R
 	Rscript TRY.R
 	
 BCI: $(D2)/BCI/traits.csv

R/format.data/TRY.R

@@ -153,14 +153,14 @@ saveRDS(sd.vec.sp, file =  file.path(out.dir, "sd.vec.sp.rds"))
 saveRDS(sd.vec.genus, file =  file.path(out.dir, "sd.vec.genus.rds"))
 
 
-### plot sd to show mark
-pdf(file.path(out.dir, "sd.traits.pdf"))
-r <- barplot(sd.vec.sp, names.arg = c("Leaf.N", "SM", "SLA", "WD", "Vessel", "LL"), 
-    las = 2, ylim = c(0, 0.9), ylab = "sd log10")
-points(r[, 1], sd.vec.genus, col = "red", pch = 16, cex = 2)
-## for (i in 1:length(nobs.names)){ ## sd.obs <-
-## data.TRY.sd.update[[sd.names[i]]][!data.TRY.sd.update[[genus.names[i]]]] ##
-## points(rep(r[i,1],length(sd.obs)),sd.obs) ## sd.obs <-
-## data.TRY.sd.update[[sd.names[i]]][data.TRY.sd.update[[genus.names[i]]]] ##
-## points(rep(r[i,1],length(sd.obs)),sd.obs,col='red',pch=4) print(sd.obs) }
-dev.off() 
+# ### plot sd to show mark
+# pdf(file.path(out.dir, "sd.traits.pdf"))
+# r <- barplot(sd.vec.sp, names.arg = c("Leaf.N", "SM", "SLA", "WD", "Vessel", "LL"), 
+#     las = 2, ylim = c(0, 0.9), ylab = "sd log10")
+# points(r[, 1], sd.vec.genus, col = "red", pch = 16, cex = 2)
+# ## for (i in 1:length(nobs.names)){ ## sd.obs <-
+# ## data.TRY.sd.update[[sd.names[i]]][!data.TRY.sd.update[[genus.names[i]]]] ##
+# ## points(rep(r[i,1],length(sd.obs)),sd.obs) ## sd.obs <-
+# ## data.TRY.sd.update[[sd.names[i]]][data.TRY.sd.update[[genus.names[i]]]] ##
+# ## points(rep(r[i,1],length(sd.obs)),sd.obs,col='red',pch=4) print(sd.obs) }
+# dev.off() 

R/lib.csv

-x
-data.table
-dismo
-doParallel
-foreign
-knitr
-maptools
-markdown
-MASS
-mvoutlier
-pander
-quantreg
-RColorBrewer
-reshape
-rgdal
-rjson
-rworldmap
-sp