diversitree v0.9-9
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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
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 |
depends | ape , methods , R (>= 2.10) |
suggests | caper , expm , geiger , lubridate , minqa , numDeriv |
imports | deSolve (>= 1.7) , graphics , grDevices , Rcpp (>= 0.10.0) , stats , subplex |
Contributors | Richard FitzJohn |
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