Files
This directory contains files used to run the examples in the
diversitree tutorial document:
- Lislevand-states.csv: Measures of
sexual dimorphism. Data are from Lislevand T., Figuerola J.,
and Székely T. 2007. Avian body sizes in relation to fecundity,
mating system, display behavior, and resource sharing. Ecology
88:1605.
- Redding-2010.csv: Primate body size data.
From Redding D.W., DeWolff C., Mooers A.Ø. 2010. Evolutionary
distinctiveness, threat status and ecological oddity in
primates. Conserv. Biol. 24:1052–1058.
- Thomas-tree.nex: Shorebird
phylogeny, from Thomas G.H., Wills M.A., and Székely T. 2004. A
supertree approach to shorebird phylogeny. BMC Evolutionary Biology
4:28.
- Thomas-tree-exemplar.nex: Shorebird
phylogeny, but trimmed down to only "exemplar" species.
- Thomas-unresolved.csv: Unresolved
clade information for the exemplar tree. This is derived from
the Lislevand et al. sexual dimorphism data, assuming a 15%
cut-off.
- Vos-2006.nex:
Phylogenetic tree of Primates, with polytomies randomly resolved
and branch lengths simulated from a birth death. From Vos R.A.,
Mooers A.Ø. 2006. A new dated supertree of the Primates.
Chapter 5. In Inferring large phylogenies: the big tree
problem (R Vos, Ph.D. thesis) Simon Fraser University.
-
arc.dat,
arc.tre,
cea.dat and
cea.tre. Phylogenies
and data for the GeoSSE multi-tree example.
If you want to recompile the tutorial document, you will need
these files placed into a directory "data". You can
get all the files at once here.
To compile, run R CMD Sweave
diversitree-tutorial.Rnw to create the LaTeX source file,
then run pdflatex, bibtex, pdflatex and pdflatex on the file
diversitree-tutorial.tex that is produced
However, because some of the examples are computationally
intensive, regenerating the file takes many hours (27 hours on a
2008 MacPro). If you use cacheSweave
with Sweave.sh,
subsequent compilations are very fast (< 1 min).