R Observatory: Metrics for TreePar version 3.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2022-04-27. Its history is shown below.

Reason: check issues were not corrected in time. length > 1 in && or ||

Details below reflect version 3.3, its last release before removal.

TreePar

3.3

Estimating birth and death rates based on phylogenies

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by Tanja Stadler14 releasesCRAN page ↗

(i) For a given species phylogeny on present day data which is calibrated to calendar-time, a method for estimating maximum likelihood speciation and extinction processes is provided. The method allows for non-constant rates. Rates may change (1) as a function of time, i.e. rate shifts at specified times or mass extinction events (likelihood implemented as LikShifts, optimization as bd.shifts.optim and visualized as bd.shifts.plot) or (2) as a function of the number of species, i.e. density-dependence (likelihood implemented as LikDD and optimization as bd.densdep.optim) or (3) extinction rate may be a function of species age (likelihood implemented as LikAge and optimization as bd.age.optim.matlab). Note that the methods take into account the whole phylogeny, in particular it accounts for the "pull of the present" effect. (1-3) can take into account incomplete species sampling, as long as each species has the same probability of being sampled. For a given phylogeny on higher taxa (i.e. all but one species per taxa are missing), where the number of species is known within each higher taxa, speciation and extinction rates can be estimated under model (1) (implemented within LikShifts and bd.shifts.optim with groups !=0). (ii) For a given phylogeny with sequentially sampled tips, e.g. a virus phylogeny, rates can be estimated under a model where rates vary across time using bdsky.stt.optim based on likelihood LikShiftsSTT (extending LikShifts and bd.shifts.optim). Furthermore, rates may vary as a function of host types using LikTypesSTT (multitype branching process extending functions in R package diversitree). This function can furthermore calculate the likelihood under an epidemiological model where infected individuals are first exposed and then infectious.

Install

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

url <- "https://cran.r-project.org/src/contrib/Archive/TreePar/TreePar_3.3.tar.gz"
pkgFile <- "TreePar_3.3.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 (3.3) 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-treepar

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-TreePar

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

5

Dependencies · direct

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 88%
Return-value docs: 88%
References docs: 94%

Downloads

Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on18 r2u10 autocran85 c2d4u

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Depends (5)

apeMatrixsubplex TreeSim deSolve

Imports (0)

none

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Other (1)

Tanja Stadler

Contributor

Package Timeline

14 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.3.0 released · 2023-04-21
archivedRemoved from CRAN
2022-04-27
check issues were not corrected in time length > 1 in && or ||
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
R
R 3.6.0 released · 2019-04-26
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
3.3
2015-01-02 · diff ↗
3.2
2014-11-01 · diff ↗
3.1
2014-09-18 · diff ↗
3.0
2014-07-28 · diff ↗
R
R 3.1.0 released · 2014-04-10
2.5
2013-05-07 · diff ↗

Show 15 earlier events

R
R 3.0.0 released · 2013-04-03
2.3
2012-08-05 · diff ↗
R
R 2.15.0 released · 2012-03-30
2.2
2011-11-01 · diff ↗
R
R 2.14.0 released · 2011-10-31
2.1.2
2011-08-22 · diff ↗
2.1
2011-07-12 · diff ↗
1.4
2011-05-09 · diff ↗
R
R 2.13.0 released · 2011-04-13
1.3
2011-03-21 · diff ↗
1.2
2011-03-20 · diff ↗
R
R 2.12.0 released · 2010-10-15
1.1
2010-06-17 · diff ↗
1.0
2010-06-17
R
R 2.11.0 released · 2010-04-22

Package metadata

Total releases: 14
License: GPL-2 OSI
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("TreePar")

Format

Stadler, T. (n.d.). TreePar: Estimating birth and death rates based on phylogenies (Version 3.3) [Computer software]. Retrieved August 13, 2026, from https://CRAN.R-project.org/package=TreePar

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 TreePar version 3.3 [Data set]. HJJB, LLC. Data release v2026-08-11. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-11, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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