diversitree v0.9-9

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by Rich FitzJohn

Comparative 'Phylogenetic' Analyses of Diversification

Contains a number of comparative 'phylogenetic' methods, mostly focusing on analysing diversification and character evolution. Contains implementations of 'BiSSE' (Binary State 'Speciation' and Extinction) and its unresolved tree extensions, 'MuSSE' (Multiple State 'Speciation' and Extinction), 'QuaSSE', 'GeoSSE', and 'BiSSE-ness' Other included methods include Markov models of discrete and continuous trait evolution and constant rate 'speciation' and extinction.

Readme

diversitree: comparative phylogenetic analyses of diversification

Build Status

This repository contains "diversitree". It is my experimental sources though, and may not compile or work for you. You may prefer the released version from CRAN:

> install.packages("diversitree")

The interesting directories are:

  • inst/tests: testing functions that exercise most of the package's main features. Running ./run_tests.R will run the tests. These take too long to run on CRAN (over a minute), so are not set up in the usual way.
  • doc: Vignettes, and their required data files.

Installing diversitree

Clone the repository with

git clone git://github.com/richfitz/diversitree.git

The package should then be installable the usual way. You'll need a C, C++ and Fortran compiler.

To install and specify the location of the fftw library in a non-standard place, a line like this is required: R CMD INSTALL diversitree --configure-args='--with-fftw=/path/to/fftw' where the path will be the path so that the files /path/to/fftw/include/fftw3.h /path/to/fftw/lib/lib/fftw3.so exist.

On Windows, set the environment variable LIB_FFTW to point to the directory that contains include/fftw.h, and install the package.

If fftw is not found, installation will continue, but the (relatively) fast C based QuaSSE integration will not be available. The R based fft integrator and the method-of-lines integrator will be available.

Branches

The "master" branch contains the bleeding edge version of diversitree. It may or may not work for you. The "release" branch contains stable releases.

Functions in diversitree

Name Description
diversitree-deprecated Deprecated and Defunct Functions in Diversitree
big.brother Verbosely Track Function Evaluations
asr-mkn Ancestral State Reconstruction Under Mk2/Mkn
Constants Constants Used by Diversitree
asr-bisse Ancestral State Reconstruction Under BiSSE
asr Ancestral State Reconstruction
argnames Argument Names for Vector-Argument Functions
check Check Capabilities of the Diversitree Install
combine Combine Several Likelihood Functions Multiplicatively
constrain Constrain Parameters of a Model
make.bd Constant Rate Birth-Death Models
make.bd.split Constant Rate Birth-Death Models: Split Models
diversitree-package \Sexpr[results=rd,stage=build]{tools:::Rd_package_title("#1")}diversitreeComparative 'Phylogenetic' Analyses of Diversification
history.from.sim Extract Character Histories From Simulations
find.mle Maximimum Likelihood Inference
make.bd.t Time-varing Birth-Death Models
make.bisse.split Binary State Speciation and Extinction Model: Split Models
make.bisse.td Binary State Speciation and Extinction Model: Time Dependant Models
geosse.phy Example GeoSSE Tree
make.bisse Binary State Speciation and Extinction Model
make.clade.tree Make a "Clade Tree"
make.geosse.t Geographic State Speciation and Extinction Model: Time Dependent Models
make.geosse Geographic State Speciation and Extinction Model
make.classe Cladogenetic State change Speciation and Extinction Model
make.mkn Mk2 and Mk-n Models of character evolution
make.bm Brownian Motion and Related Models of Character Evolution
make.bisseness Binary State Speciation and Extinction (Node Enhanced State Shift) Model
make.geosse.split Geographic State Speciation and Extinction Model: Split Models
make.musse.multitrait MuSSE: Multi-State Speciation and Extinction (Multiple Binary Traits Version)
make.musse MuSSE: Multi-State Speciation and Extinction
make.musse.split Multiple State Speciation and Extinction Model: Split Models
make.quasse.split Quantitative State Speciation and Extinction Model: Split Models
profiles.plot Plot Marginal Distributions from MCMC
make.pgls Phylogenetic Generalised Least Squares
protect Protect Function Evaluations
plot.history Plot Character History
make.prior Simple Prior Functions
make.musse.td Multiple State Speciation and Extinction Model: Time Dependent Models
make.quasse Quantitative State Speciation and Extinction Model
mcmc Simple Markov Chain Monte Carlo with Slice Sampling
set.defaults Set Default Arguments of a Function
quasse-common Support Functions for QuaSSE Models
trait.plot Plot a Phylogeny and Traits
simulate Evolve Birth-Death Trees
utilities Utility Functions
sim.character Simulate a Character Distribution on a Tree
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Details

LinkingTo Rcpp
RcppModules diversitree
SystemRequirements fftw3 (>= 3.1.2), gsl (>= 1.15)
License GPL (>= 2)
URL http://www.zoology.ubc.ca/prog/diversitree
NeedsCompilation yes
Packaged 2016-10-05 09:03:42 UTC; rich
Repository CRAN
Date/Publication 2016-10-05 11:30:53

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