BioGeoBEARS-package: BioGeography with Bayesian (and likelihood) Evolutionary...

In BioGeoBEARS: BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts

Description

BioGeoBEARS: BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts

Details

Package:	BioGeoBEARS
Type:	Package
Version:	0.2.1
Date:	2012-07-27
License:	GPL (>= 3)
LazyLoad:	yes

Summary: This package performs model-based statistical inference for historical biogeography. This includes inference of model parameters, ancestral states, and model comparison. This package performs ML (maximum-likelihood) based inference, but the same functions can easily be integrated into a Bayesian analysis via use of MCMC sampling functions from other packages.

Details: BioGeoBEARS allows probabilistic inference of both historical biogeography (ancestral geographic ranges on a phylogeny) as well as comparison of different models of range evolution. It reproduces the model available in LAGRANGE (Ree and Smith 2008), as well as making available numerous additional models. For example, LAGRANGE as typically run has two free parameters, d (dispersal rate, i.e. the rate of range addition along a phylogenetic branch) and e (extinction rate, really the rate of local range loss along a phylogenetic branch). LAGRANGE also has a fixed cladogenic model which gives equal probability to a number of allowed range inheritance events, e.g.: (1) vicariance, (2) a new species starts in a subset of the ancestral range, (3) the ancestral range is copied to both species; in all cases, at least one species must have a starting range of size 1. LAGRANGE assigns equal probability to each of these events, and zero probability to other events. BioGeoBEARS adds an additional cladogenic event: founder-event speciation (the new species jumps to a range outside of the ancestral range), and also allows the relative weighting of the different sorts of events to be made into free parameters, allowing optimization and standard model choice procedures to pick the best model. The relative probability of different descendent range sizes is also parameterized and thus can also be specified or estimated. The flexibility available in BioGeoBEARS also enables the natural incorporation of (1) imperfect detection of geographic ranges in the tips, and (2) inclusion of fossil geographic range data, when the fossils are tips on the phylogeny. Bayesian analysis has been implemented through use of the "LaplacesDemon" package, however this package is now maintained off of CRAN, so its usage is not formally included in BioGeoBEARS at the current time.

CITATION INFO: This package is the result of my Ph.D. research, please cite the package if you use it! Type: citation(package="BioGeoBEARS") to get the citation information.

See also the citation information for the sister packages, citation(package="rexpokit") and citation(package="cladoRcpp").

Note

Go BEARS!

Author(s)

Nicholas J. Matzke [e-mail]

References

http://phylo.wikidot.com/matzke-2013-international-biogeography-society-poster https://code.google.com/p/lagrange/

Matzke_2012_IBS

ReeSmith2008

See Also

rexpokit cladoRcpp

Examples

test=1

# To get citation information for BioGeoBEARS, type:
citation(package="BioGeoBEARS")

# Please also cite the accessory packages I created to make BioGeoBEARS work:
citation(package="cladoRcpp")
citation(package="rexpokit")		# Roger Sidje is a coauthor of rexpokit
                                 # and author of the FORTRAN EXPOKIT

Example output

Loading required package: rexpokit
Loading required package: cladoRcpp
Loading required package: ape
Loading required package: phylobase

Attaching package: 'phylobase'

The following object is masked from 'package:ape':

    edges


To cite package 'BioGeoBEARS' in publications use:

Matzke N (2013). _BioGeoBEARS: BioGeography with Bayesian (and
Likelihood) Evolutionary Analysis in R Scripts_. University of
California, Berkeley, Berkeley, CA. The rexpokit/cladoRcpp/BioGeoBEARS
packages were first published in: Matzke, Nicholas J. (2012).
Founder-event speciation in BioGeoBEARS package dramatically improves
likelihoods and alters parameter inference in
Dispersal-Extinction-Cladogenesis (DEC) analyses. Frontiers of
Biogeography, 4(suppl. 1): 210, December 2012.  Link to abstract and
PDF of poster:
http://phylo.wikidot.com/matzke-2013-international-biogeography-society-poster
. (Poster abstract published in the Conference Program and Abstracts of
the International Biogeography Society 6th Biannual Meeting, Miami,
Florida. Poster Session P10: Historical and Paleo-Biogeography. Poster
129B. January 11, 2013.), <URL:
http://CRAN.R-project.org/package=BioGeoBEARS>.

A BibTeX entry for LaTeX users is

  @Manual{,
    title = {BioGeoBEARS: BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts},
    author = {Nicholas J. Matzke},
    organization = {University of California, Berkeley},
    address = {Berkeley, CA},
    year = {2013},
    note = {The rexpokit/cladoRcpp/BioGeoBEARS packages were first published in: Matzke, Nicholas J. (2012). Founder-event speciation in BioGeoBEARS package dramatically improves likelihoods and alters parameter inference in Dispersal-Extinction-Cladogenesis (DEC) analyses. Frontiers of Biogeography, 4(suppl. 1): 210, December 2012.  Link to abstract and PDF of poster: 
http://phylo.wikidot.com/matzke-2013-international-biogeography-society-poster . (Poster abstract 
published in the Conference Program and Abstracts of the International Biogeography Society 6th Biannual 
Meeting, Miami, Florida. Poster Session P10: Historical and Paleo-Biogeography. Poster 129B. January 11, 
2013.)},
    url = {http://CRAN.R-project.org/package=BioGeoBEARS},
  }

A lot of time and effort in creating BioGeoBEARS, as well as the sister
packages 'rexpokit' and 'cladoRcpp', please cite it and the other
packages when using it for publication. See also 'citation("pkgname")'
for citing R packages.


To cite package 'cladoRcpp' in publications use:

Matzke N (2018). _cladoRcpp v0.15.1: C++ Implementations of
Phylogenetic Cladogenesis Calculations_. University of Auckland, New
Zealand. In addition to citing the CRAN packages, please cite these
when using the rexpokit/cladoRcpp/BioGeoBEARS packages:

Matzke, Nicholas J. (2013). Probabilistic historical biogeography: new
models for founder-event speciation, imperfect detection, and fossils
allow improved accuracy and model-testing. Frontiers of Biogeography,
5(4), 242-248. http://escholarship.org/uc/item/44j7n141

Others:

Matzke, Nicholas Joseph (2014). Model Selection in Historical
Biogeography Reveals that Founder-event Speciation is a Crucial Process
in Island Clades. Systematic Biology, 63(6), 951-970 , <URL:
https://cran.r-project.org/package=cladoRcpp>.

A BibTeX entry for LaTeX users is

  @Manual{,
    title = {cladoRcpp v0.15.1: C++ Implementations of Phylogenetic Cladogenesis Calculations},
    author = {Nicholas J. Matzke},
    organization = {University of Auckland},
    address = {New Zealand},
    year = {2018},
    note = {In addition to citing the CRAN packages, please cite these when using the rexpokit/cladoRcpp/BioGeoBEARS packages: 

Matzke, Nicholas J. (2013). Probabilistic historical biogeography: new models for founder-event speciation, imperfect detection, and fossils allow improved accuracy and model-testing. Frontiers of Biogeography, 5(4), 242-248. http://escholarship.org/uc/item/44j7n141

Others:

Matzke, Nicholas Joseph (2014). Model Selection in Historical Biogeography Reveals that Founder-event Speciation is a Crucial Process in Island Clades. Systematic Biology, 63(6), 951-970
},
    url = {https://cran.r-project.org/package=cladoRcpp},
  }

A lot of time and effort in creating cladoRcpp, as well as the sister
packages 'rexpokit' and 'BioGeoBEARS', please cite it and the other
packages when using it for publication. See also
'citation("cladoRcpp")' for citing R packages.


To cite R in publications use:

Matzke N, Sidje R and Schmidt D (2013). _rexpokit: R wrappers for
EXPOKIT; other matrix functions_. University of California, Berkeley,
Berkeley, CA. NOTE: The EXPOKIT FORTRAN library was published in:
Sidje, R.B. (1998). A Software Package for Computing Matrix
Exponentials.  ACM-Transactions on Mathematical Software,
24(1):130-156.  http://tinyurl.com/bwa87rq ; Also, the rexpokit R
package was first published in: Matzke, Nicholas J. (2013).
Probabilistic historical biogeography: new models for founder-event
speciation, imperfect detection, and fossils allow improved accuracy
and model-testing. Frontiers of Biogeography, 5(4), 242-248.
http://escholarship.org/uc/item/44j7n141 , <URL:
http://phylo.wikidot.com/rexpokit>.

A BibTeX entry for LaTeX users is

  @Manual{,
    title = {rexpokit: R wrappers for EXPOKIT; other matrix functions},
    author = {Nicholas J. Matzke and Roger B. Sidje and Drew Schmidt},
    organization = {University of California, Berkeley},
    address = {Berkeley, CA},
    year = {2013},
    note = {NOTE: The EXPOKIT FORTRAN library was published in: Sidje, 
R.B. (1998). A Software Package for Computing Matrix Exponentials. 
ACM-Transactions on Mathematical Software, 24(1):130-156. 
http://tinyurl.com/bwa87rq ; Also, the rexpokit R package was first published in: 
Matzke, Nicholas J. (2013). Probabilistic historical biogeography: 
      new models for founder-event speciation, imperfect detection, and fossils allow 
      improved accuracy and model-testing. Frontiers of Biogeography, 5(4), 242-248. 
      http://escholarship.org/uc/item/44j7n141 },
    url = {http://phylo.wikidot.com/rexpokit},
  }

A lot of time and effort in creating EXPOKIT and rexpokit, please cite
it, Sidje (1998), and Matzke (2013) when using it for publication. See
also 'citation("pkgname")' for citing R packages.

BioGeoBEARS documentation built on May 29, 2017, 8:36 p.m.