Update readme

R/lib.csv

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

docs/analysis.outline/Makefile copy

-TARGETS = $(subst md,pdf,$(shell ls *.md))
-
-all: $(TARGETS)
-
-%.pdf: %.md
-	pandoc $< -V linkcolor:black -V geometry:a4paper -V geometry:margin=1in --listings --include-in-header=../include.tex -o $@
-
-clean:
-	rm -f *.pdf

lib.md

+./docs/metadata/knit_site_description.R:library(knitr, quietly  = TRUE)
+./docs/metadata/knit_site_description.R:library(markdown, quietly  = TRUE)
+./docs/metadata/knit_site_description.R:library(rjson, quietly =TRUE)
+./docs/metadata/knit_site_description.R:library(pander, quietly =TRUE)
+./R/find.trait/trait.fun.R:library(MASS, quietly=TRUE)
+./R/find.trait/trait.fun.R:library(doParallel, quietly=TRUE)
+./R/find.trait/trait.fun.R:library(mvoutlier, quietly=TRUE)
+./R/format.data/BCI.R:library(reshape,quietly=TRUE)
+./R/format.data/Canada.R:library(reshape)
+./R/format.data/Canada.R:## library(RColorBrewer)
+./R/format.data/Canada.R:## library(rworldmap)
+./R/format.data/France.R:library(reshape)
+./R/format.data/France.R:library(sp)
+./R/format.data/France.R:library(dismo)
+./R/format.data/France.R:library(rgdal)
+./R/format.data/France.R:## ## plot on world map library(rworldmap) newmap <- getMap(resolution = 'coarse')
+./R/format.data/Fushan.R:library(reshape, quietly=TRUE)
+./R/format.data/NSW.R:library(reshape)
+./R/format.data/NVS.R:library(reshape)
+./R/format.data/NVS.R:library(sp)
+./R/format.data/NVS.R:library(dismo)
+./R/format.data/NVS.R:library(rgdal)
+./R/format.data/NVS.R:# library(RColorBrewer)
+./R/format.data/NVS.R:# library(rworldmap)
+./R/format.data/Paracou.R:library(reshape,quietly=TRUE)
+./R/format.data/Spain.R:library(reshape)
+./R/format.data/Spain.R:library(sp)
+./R/format.data/Spain.R:library(dismo)
+./R/format.data/Spain.R:library(rgdal)
+./R/format.data/Spain.R:## library(rworldmap)
+./R/format.data/Spain.R:# library(RColorBrewer)
+./R/format.data/Sweden.R:library(reshape);
+./R/format.data/Sweden.R:library(sp)
+./R/format.data/Sweden.R:library(dismo)
+./R/format.data/Sweden.R:library(rgdal)
+./R/format.data/Sweden.R:## library(rworldmap)
+./R/format.data/Swiss.R:library(reshape)
+./R/format.data/Swiss.R:library(foreign)
+./R/format.data/Swiss.R:library(sp)
+./R/format.data/Swiss.R:library(dismo)
+./R/format.data/Swiss.R:library(rgdal)
+./R/format.data/Swiss.R:library(maptools)
+./R/format.data/Swiss.R:## library(rworldmap)
+./R/format.data/try.fun.R:library(MASS, quietly=TRUE)
+./R/format.data/try.fun.R:library(doParallel, quietly=TRUE)
+./R/format.data/try.fun.R:library(mvoutlier, quietly=TRUE)
+./R/format.data/TRY.R:library(MASS)
+./R/format.data/TRY.R:library(doParallel)
+./R/format.data/TRY.R:library(mvoutlier)
+./R/format.data/TRY.R:library(quantreg)
+./R/format.data/US.R:library(reshape, quietly=TRUE)
+./R/format.data/US.R:## library(RColorBrewer)
+./R/format.data/US.R:## library(rworldmap)
+./R/format.function.R:## use library(data.table)
+./R/format.function.R:  library(doParallel)
+./R/utils/maps.R:library(RColorBrewer, quietly = TRUE)
+./R/utils/maps.R:library(rworldmap, quietly = TRUE)
+./R/find.trait/trait.fun.R:    require(boot, quietly=TRUE)
+./R/find.trait/trait.fun.R:require(plyr)
+./R/format.data/format.fun.R:require(boot)
+./R/format.data/format.fun.R:    require(boot)
+./R/format.data/try.fun.R:    require(boot, quietly=TRUE)
+./R/format.function.R:require(boot)
+./R/format.function.R:    require(boot)
+./R/format.function.R:require(data.table)
+./R/format.function.R:require(data.table)
+./R/format.function.R:  require(rpud)
+./R/format.function.R:    require(doParallel)
+./R/format.function.R:require(data.table)
+./R/format.function.R:require(data.table)

readme.md

+% 'How are competitive interactions influenced by traits? A global analysis based on tree radial growth',
+% Workshop at Macquarie University September 2013
+
+This is the shared material for an analysis based on following paper, using data from French Alps: Kunstler *et al.* (2012) "Competitive interactions between forest trees are driven by species’ trait hierarchy, not phylogenetic or functional similarity: implications for forest community assembly". Ecology Letters, 15, 831–840. [DOI: 10.1111/j.1461-0248.2012.01803.x]( http://doi.org/10.1111/j.1461-0248.2012.01803.x) [PDF](http://www.wsl.ch/staff/niklaus.zimmermann/papers/EcolLett_Kunstler_2012.pdf).
+
+# Folder structure
+
+The repository has the following basic directories:
+
+- `data`: contains raw data and metadata. Treat this as read-only, i.e. do not save output from R scripts here, these go in outputs.
+- `R`: where all R code used in analysis is saved. The only exception is `*.Rmd` files used in creating some of the documents, which are stored in `docs` directory.
+- `output`: a temporary directory that is used to hold all process data. Material in this directory is not tracked because it can be recreated from scripts.
+- `docs`: contains documents developed for the project.
+
+Some specific folders of likely interest:
+
+- `docs/meeting.agenda`: agenda for workshop
+- `docs/analysis.outline`: theoretical description of analysis
+- `docs/analysis.pipeline`: outline of workflow (code, data etc).
+- `data/raw`: Directory containing all the raw data from different sites. By default, this directory is not available.
+- `docs/metadata`: Contains infomration about the dataset from each site
+- `ms`: eventual home for manuscript materials
+
+# Tools
+
+We are making use of the following tools:
+
+- *R stats program*
+- A number R libraries:
+	```install.packages(knitr,
+
+
+# Git
+
+Documents are kept under version control using git, and stored on github. To access:
+
+1. Sign up to github and send your username to Georges so he can add you to the repository.
+2.
+- https://github.com/kunstler/trait.competition.workshop
+- intro to git: http://nicercode.github.io/git/
+
+To access github first install one of the following then `clone` the workshop repository
+
+- Mac: Install [Github for mac] (http://mac.github.com/)
+- Windows: Install [Github for windows](http://windows.github.com/)
+- [Rstudio](http://www.rstudio.com/): R editor with built in

readme.txt

-# README 15/06/2013 G. Kunstler
-
-Code to format data  for the working group on traits and competition
-Sydney Maquarie University September 2013
-
-Folders structure
-/data/raw
-/data/process
-/data/species.list
-/figs
-/output
-
-