R Observatory: Metrics for BioGeoBEARS version 0.2.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2019-01-28. Its history is shown below.

Reason: check issues were not corrected despite reminder

Details below reflect version 0.2.1, its last release before removal.

BioGeoBEARS

0.2.1Package record

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

0packages dependsuggested by 1

–downloads / year

–test coverage

–flavors OK

Overview

About

Maintained by Nicholas J. MatzkeCRAN page ↗Website ↗

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.

Install

R (source archive)

url <- "https://cran.r-project.org/src/contrib/Archive/BioGeoBEARS/BioGeoBEARS_0.2.1.tar.gz"
pkgFile <- "BioGeoBEARS_0.2.1.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (0.2.1) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

Health

CRAN checks

CRAN check results are not tracked yet.

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.2.1

READMENoVignettesNoNEWSYes · 0% structuredCitation fileYes · computed when R runs itWebsiteYes

Help pages: 248includes a package overview page
Examples that run: 100%247 run in a plain check · 1 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 95% with a bibliography file

How these are measured

Downloads

BioGeoBEARS Releases R versions

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Also on115 c2d4u

How downloads are counted

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Depends (5)

rexpokit cladoRcpp ape phylobasemethods

Imports (6)

optimx FDparallelxtable plotrix gdata

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Suggested by 1

Suggests, most downloaded first

deepSTRAPP

How these are counted

Code & Tests

Datasets

People & History

People (1)

Nicholas J. Matzke

Releases (3)

Pick two releases to compare their code metrics.

R
R 3.6.0 released · 2019-04-26
archivedRemoved from CRAN
2019-01-28
check issues were not corrected despite reminder
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16
R
R 3.1.0 released · 2014-04-10
0.2.1
record
2013-07-27 · diff ↗ ·
added 13 exports
Pdata_given_rangerow, Pdata_given_rangerow_dp, calc_obs_like, calc_post_prob_presence, cornerpies, mapply_calc_obs_like, mapply_calc_post_prob_presence, post_prob_states, post_prob_states_matrix, prob_of_states_from_prior_prob_areas, read_controls, read_detections, tiplikes_wDetectionModel
0.2
record
2013-07-25 · diff ↗ ·
removed 9 exports
LapDem_Model_calc_logPP, LapDem_Model_calc_logPP_orig, change_burnin, invtransform_with_logistic, make_all_tips_come_to_0, plot_demonoid2, plotlp, reparam_LapDem_output, transform_with_logistic

added 18 exports
BioGeoBEARS_model_object_to_est_params, average_tr_tips, check_BioGeoBEARS_run, extend_tips_to_ultrametricize, get_indices_of_branches_under_tips, get_indices_of_tip_nodes, get_indices_where_list1_occurs_in_list2_noNA, get_perEvent_probs, np, parse_lagrange_output_old, parse_lagrange_python_output_old, plot_BioGeoBEARS_model, plot_BioGeoBEARS_results, plot_cladogenesis_size_probabilities, printall, prune_specimens_to_species, prune_states_list, return_items_not_NA
0.1.1
record
2013-06-23
R
R 3.0.0 released · 2013-04-03

Package metadata

First published: 2013-06-23
Total releases: 3 / 13 yrs
License: GPL (>= 2) OSI

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("BioGeoBEARS")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for BioGeoBEARS version 0.2.1 [Data set]. HJJB, LLC. Data release v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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