R Observatory: Metrics for bite version 0.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2024-08-23. Its history is shown below.

Reason: issues were not corrected in time

Details below reflect version 0.3, its last release before removal.

bite

0.3

Bayesian Integrative Models of Trait Evolution

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by Theo Gaboriau1 releasesCRAN page ↗

Contains the JIVE (joint inter and intra-specific model of variance evolution) model and other Bayesian models aimed at understanding trait evolution. The goal of the package is to join phylogenetic comparative models (PCM) that tend to integrate various type of data (individual observations, environmental data, fossil data) into a hierarchical Bayesian framework. It contains various PCMs as well as functions to join those models into a hierarchical Bayesian framework in a flexible and user friendly way. It contains various Markov chain Monte-Carlo (MCMC) algorithms, methods for model comparison and many plotting function for pre- and post-processing data visualization. Finally, this package integrates functions allowing bridges between 'R' and the 'BEAST2' implementations of PCMs. Kostikova A, Silvestro D, Pearman PB, Salamin N (2016) doi:10.1093/sysbio/syw010. Gaboriau T, Mendes FK, Joly S, Silvestro D, Salamin N (in prep).

Install

R (source archive)Ubuntu (r2u)openSUSE (OBS)

url <- "https://cran.r-project.org/src/contrib/Archive/bite/bite_0.3.tar.gz"
pkgFile <- "bite_0.3.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 (0.3) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-bite

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-bite

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

CRAN check results are not tracked yet.

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

7

Dependencies · direct

Documentation

READMENoVignettesNopkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 81%
Return-value docs: 67%
References docs: 11%

Downloads

Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on1.3K r2u33 autocran

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.0.3

Imports (7)

apeMASSphytools coda sm vioplot xml2

LinkingTo (0)

none

Suggests (1)

mvMORPH

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (9)

Maintainer (1)

Theo Gaboriau

Author, Maintainer

Authors (4)

Author, Maintainer

Author

Author

Author

Other (5)

crt

crt

crt

crt

crt

Package Timeline

1 release. R releases are shown for context.

R
R 4.5.0 released · 2025-04-11
archivedRemoved from CRAN
2024-08-23
issues were not corrected in time
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
0.3
2020-04-22
R
R 3.6.0 released · 2019-04-26

Package metadata

Total releases: 1
License: GPL-2 OSI
Minimum R: ≥ 3.0.3
Bundled data: 6.0 KB / 3 files
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("bite")

Format

Gaboriau, T., Kostikova, A., Silvestro, D., Laurent, S., Serrano, M., Litsios, G., Hordijk, W., Joly, S., & Salamin, N. (n.d.). bite: Bayesian Integrative Models of Trait Evolution (Version 0.3) [Computer software]. Retrieved August 15, 2026, from https://CRAN.R-project.org/package=bite

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 bite version 0.3 [Data set]. HJJB, LLC. Data release v2026-08-15. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-15, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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