Package: diversitree 0.10-1
Richard G. FitzJohn
diversitree: 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.
Authors:
diversitree_0.10-1.tar.gz
diversitree_0.10-1.tar.gz(r-4.5-noble)diversitree_0.10-1.tar.gz(r-4.4-noble)
diversitree.pdf |diversitree.html✨
diversitree/json (API)
| # Install 'diversitree' in R: |
| install.packages('diversitree', repos = 'https://cloud.r-project.org') |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 6 months agofrom:dd3ceae86a. Checks:3 OK. Indexed: no.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Apr 01 2025 |
| R-4.5-linux-x86_64 | OK | Apr 01 2025 |
| R-4.4-linux-x86_64 | OK | Apr 01 2025 |
Exports:argnamesargnames<-asr.jointasr.marginalasr.stochbig.brothercheck.fftCclades.from.classificationclades.from.polytomiescombineconstant.xconstrainconstrain.idrop.likelihoodexpand.parametersfind.mleget.descendantsget.likelihoodhistory.from.sim.discreteinvertmake.asr.jointmake.asr.marginalmake.asr.stochmake.bdmake.bd.splitmake.bd.tmake.bissemake.bisse.splitmake.bisse.tmake.bisse.tdmake.bisse.unevenmake.bissenessmake.bmmake.brownian.with.driftmake.clade.treemake.classemake.ebmake.geossemake.geosse.splitmake.geosse.tmake.geosse.unevenmake.lambdamake.linear.xmake.mk2make.mknmake.mkn.meristicmake.mkn.multitraitmake.mussemake.musse.multitraitmake.musse.splitmake.musse.tmake.musse.tdmake.oumake.pglsmake.prior.exponentialmake.prior.uniformmake.quassemake.quasse.splitmake.sim.charactermake.yulemcmcmkn.multitrait.translatemusse.multitrait.translatenoroptimal.xpolytomies.to.cladesprofiles.plotprotectpruneROOT.ALLROOT.BOTHROOT.EQUIROOT.FLATROOT.GIVENROOT.MAXROOT.OBSrun.cachedsampler.normsampler.sliceset.defaultssigmoid.xsigmoid2.xsim.characterstarting.point.bdstarting.point.bissestarting.point.classestarting.point.geossestarting.point.mussestarting.point.musse.multitraitstarting.point.quassestepf.xtrait.plottree.bdtree.bissetree.bissenesstree.classetree.geossetree.mussetree.musse.multitraittree.quassetree.yuletrees
Citation
To cite diversitree in a publication, please use:
FitzJohn, R.G. 2012. Diversitree: Comparative Phylogenetic Analyses of Diversification in R. Methods in Ecology and Evolution 3: 1084-1092<doi:10.1111/j.2041-210X.2012.00234.x>
Corresponding BibTeX entry:
@Article{,
title = {Diversitree: Comparative Phylogenetic Analyses of
Diversification in R},
author = {Richard G FitzJohn},
journal = {Methods in Ecology and Evolution},
year = {2012},
volume = {3},
pages = {1084-1092},
doi = {10.1111/j.2041-210X.2012.00234.x},
}
Readme and manuals
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.Rwill 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.
Unresolved clades
As of version 0.10.0, diversitree can no longer work with unresolved clades (FitzJohn, Maddison and Otto 2009's method), due to the package being long in retirement from development and difficulties adapting the Fortran code to meet CRAN's requirements. Users can install an older package from github (e.g., with remotes::install_github("mrc-ide/diversitree@e587755") to install the last released version that contained this code). This will require a working Fortran compiler. Alternatively, a suitably motivated person could restore the code (reverting changes contained in aaaa) and patch the code to work with the current version of flang as used by CRAN.
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.
