Dear All
I’m sending you some information regarding the material to be used in the course
"PHYLOGENETIC COMPARATIVE METHODS IN (MACRO)ECOLOGY", 16-20 July. You
already had some instructions regarding R packages that can be used in course.
All the material are available by the link www.ecoevol.ufg.br/diniz, in the folder COMPBIO.
Studying this material in advance is actually not required, but may be useful, if you have time. In
the folder you will found a zipped file with some PDFs of selected papers, and within this file
another zipped with the most “important” (“key papers”) readings.
You also will have the three powerpoints (PDFs) that we’ll use during the next week.
You also will have two zipped files regarding our PAM software, as well as a PDF with tutorial.
In one zipped file you’ll find the PAM software (the pam.exe file) and all the necessary dll files,
and others. Just copy the zipped files to a new folder and unzip it there. The pGLS module in
PAM is not ready yet, so we’ll probably will have to replace the *.exe file next week. But, even
so, the other modules are working well and, more important, you can take a look in the files that
PAM will need and their format.
In the other PAM zipped file you will have different files with datasets (many files, and a PAM
file). You have several G47 files, and wolverines files. Take a look in the tutorial before working
with the files. But anyway you do not need to open all these files to use PAM, you can go
directly and open a PAM file (Tadpoles and wolverines). But these *.pam files are built as a
“project” inside PAM using all these independent files (you’ll need to look at each one if you
want to put your own dataset in PAM format). You also have an angiosperm tree file, and a big
dataset with mammals phylogeny and body size (just for illustrative purposes).
Finally, inside the zipped file you will find another zipped file with our PVR R package, including
instructions and data used in the text.
Do not worry too much about all this if you are running against time, we’ll have the opportunity
to explore together all this.
See you all next week.
Cheers,
Alexandre
It would be great if you could
install them before the beginning of the course. If you cannot achieve
this by yourself, a technical support will be available on site but of
course this may slow a bit down the whole process.
The basic command to install a package is : install.packages("package.name")
for example, to install the ape package : install.packages("ape")
ade4 (Analysis of Ecological Data : Exploratory and Euclidean methods
in Environmental sciences)
adephylo (exploratory analyses for the phylogenetic comparative method)
ape (Analyses of Phylogenetics and Evolution)
apTreeshape (Analyses of Phylogenetic Treeshape)
caper (Comparative Analyses of Phylogenetics and Evolution in R)
ecodist (Dissimilarity-based functions for ecological analysis)
geiger (Analysis of evolutionary diversification)
laser (Likelihood Analysis of Speciation/Extinction Rates from Phylogenies)
motmot (Models of Trait Macroevolution on Trees)
ouch (Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses)
pGLS (Generalized Least Square in comparative Phylogenetics)
phylobase (Base package for phylogenetic structures and comparative data)
PHYLOGR (functions for phylogenetically based statistical analyses)
phylotools (Phylogenetic tools for Eco-phylogenetics)
phytools (Phylogenetic Tools for comparative biology and other things)
picante (R tools for integrating phylogenies and ecology)
pls (Partial Least Squares and Principal Component regression)
PVR (Computes PVR and PSR)
splancs (Spatial and Space-Time Point Pattern Analysis)
SYNCSA (Analysis of functional and phylogenetic patterns in metacommunities)
vegan (Community Ecology Package)