From 0bc332d79e2e512fe23f9bcb1ff08bcf55bd3a0b Mon Sep 17 00:00:00 2001
From: Daniel Falster <daniel.falster@mq.edu.au>
Date: Tue, 17 Sep 2013 09:21:03 +1000
Subject: [PATCH] Fix TRY make, remove libs file
---
.gitignore | 2 +-
R/format.data/Makefile | 4 +++-
R/format.data/TRY.R | 22 +++++++++++-----------
R/lib.csv | 18 ------------------
4 files changed, 15 insertions(+), 31 deletions(-)
delete mode 100644 R/lib.csv
diff --git a/.gitignore b/.gitignore
index 27c1c3f..4213df5 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,7 +1,7 @@
output
output_cluster
ignore
-data/raw
+data/raw*
figs
*.xls
*.xlsx
diff --git a/R/format.data/Makefile b/R/format.data/Makefile
index 61a7603..487cc9e 100644
--- a/R/format.data/Makefile
+++ b/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
diff --git a/R/format.data/TRY.R b/R/format.data/TRY.R
index af9c8a8..7a995ae 100644
--- a/R/format.data/TRY.R
+++ b/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()
diff --git a/R/lib.csv b/R/lib.csv
deleted file mode 100644
index 636cae5..0000000
--- a/R/lib.csv
+++ /dev/null
@@ -1,18 +0,0 @@
-x
-data.table
-dismo
-doParallel
-foreign
-knitr
-maptools
-markdown
-MASS
-mvoutlier
-pander
-quantreg
-RColorBrewer
-reshape
-rgdal
-rjson
-rworldmap
-sp
--
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