Commit 0bc332d7 authored by Daniel Falster's avatar Daniel Falster
Browse files

Fix TRY make, remove libs file

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Showing with 15 additions and 31 deletions
+15 -31
output output
output_cluster output_cluster
ignore ignore
data/raw data/raw*
figs figs
*.xls *.xls
*.xlsx *.xlsx
......
...@@ -5,7 +5,9 @@ D2 := $(ROOT)/output/formatted ...@@ -5,7 +5,9 @@ D2 := $(ROOT)/output/formatted
all: TRY Canada France NVS Spain Sweden Swiss US all: TRY Canada France NVS Spain Sweden Swiss US
# BCI Fushan NSW Paracou # 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 Rscript TRY.R
BCI: $(D2)/BCI/traits.csv BCI: $(D2)/BCI/traits.csv
......
...@@ -153,14 +153,14 @@ saveRDS(sd.vec.sp, file = file.path(out.dir, "sd.vec.sp.rds")) ...@@ -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")) saveRDS(sd.vec.genus, file = file.path(out.dir, "sd.vec.genus.rds"))
### plot sd to show mark # ### plot sd to show mark
pdf(file.path(out.dir, "sd.traits.pdf")) # pdf(file.path(out.dir, "sd.traits.pdf"))
r <- barplot(sd.vec.sp, names.arg = c("Leaf.N", "SM", "SLA", "WD", "Vessel", "LL"), # 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") # las = 2, ylim = c(0, 0.9), ylab = "sd log10")
points(r[, 1], sd.vec.genus, col = "red", pch = 16, cex = 2) # points(r[, 1], sd.vec.genus, col = "red", pch = 16, cex = 2)
## for (i in 1:length(nobs.names)){ ## sd.obs <- # ## for (i in 1:length(nobs.names)){ ## sd.obs <-
## data.TRY.sd.update[[sd.names[i]]][!data.TRY.sd.update[[genus.names[i]]]] ## # ## 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 <- # ## 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]]]] ## # ## 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) } # ## points(rep(r[i,1],length(sd.obs)),sd.obs,col='red',pch=4) print(sd.obs) }
dev.off() # dev.off()
x
data.table
dismo
doParallel
foreign
knitr
maptools
markdown
MASS
mvoutlier
pander
quantreg
RColorBrewer
reshape
rgdal
rjson
rworldmap
sp
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