paleotree is an R package for transforming, ‘a
posteriori’ time-scaling, and modifying phylogenies containing extinct
(i.e. fossil) lineages. In particular, most users are interested in the
functions timePaleoPhy, bin_timePaleoPhy,
cal3TimePaleoPhy and bin_cal3TimePaleoPhy,
which a posteriori time-scale cladograms of fossil taxa into
dated phylogenies. This package also contains a large number of
likelihood functions for estimating sampling and diversification rates
from different types of data available from the fossil record
(e.g. range data, occurrence data, etc).
paleotree users can also simulate diversification and
sampling in the fossil record using the function
simFossilRecord, which is a detailed simulator for
branching birth-death-sampling processes composed of discrete taxonomic
units arranged in ancestor-descendant relationships. Users can use
simFossilRecord to simulate diversification in incompletely
sampled fossil records, under various models of morphological
differentiation (i.e. the various patterns by which morphotaxa originate
from one another), and with time-dependent, longevity-dependent and/or
diversity-dependent rates of diversification, extinction and
sampling.
Additional functions allow users to translate simulated
ancestor-descendant data from simFossilRecord into standard
time-scaled phylogenies or unscaled cladograms that reflect the
relationships among taxon units.
The most recent public release of the code is on CRAN at:
You can install the most recent public release version of
paleotree in R from CRAN using:
install.packages("paleotree")The latest pre-release version of paleotree can be found
at github:
https://github.com/dwbapst/paleotreeYou can install this latest development version using the R function
install_github in the package devtools:
devtools::install_github("dwbapst/paleotree")The above command will install the master branch (as
the default option), which should be the most recent stable release
(ideally the CRAN release, and thus should be identical to installing
paleotree from CRAN). There will also generally be an
in-development branch where the code may be in a state of change, with
new features and bug-fixes. For example, the current development branch
is named developmentBranch and can be specified with
the ref = argument:
devtools::install_github("dwbapst/paleotree", ref="developmentBranch")Once installed, you can check the version number of your
paleotree install using the R function
packageVersion:
packageVersion("paleotree")If you use paleotree in your research, you can cite my
paper describing paleotree in Methods in Ecology and Evolution:
Bapst, D.W. 2012. `paleotree`: an R package for paleontological and phylogenetic analyses of evolution. Methods in Ecology and Evolution. 3: 803-807. doi: 10.1111/j.2041-210X.2012.00223.x
http://onlinelibrary.wiley.com/doi/10.1111/j.2041-210X.2012.00223.x/abstractYou can also call the citation for paleotree from within
R, using the citation function:
citation("paleotree")This code is mainly authored by David Bapst, with some functions
authored by Peter Wagner, and offered under CC0. Some functions are
strongly based on code from Rich Fitzjohn’s diversitree
package, while others are greatly inspired by code written by Graeme
Lloyd and Gene Hunt.
The current total number of downloads of the paleotree
package from the RStudio CRAN mirror is:
Trying out using GitHub actions instead of Travis CI:
