R Observatory: Metrics for TiPS version 1.3.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

TiPS

1.3.0

Trajectories and Phylogenies Simulator

0packages depend

6.7Kdownloads / year

74.8%test coverage

12/13checks pass

Overview

About

Maintained by Gonche DaneshFirst published 2021-09-138 releasesCRAN page ↗

Generates stochastic time series and genealogies associated with a population dynamics model. Times series are simulated using the Gillespie exact and approximate algorithms and a new algorithm we introduce that uses both approaches to optimize the time execution of the simulations. Genealogies are simulated from a trajectory using a backwards-in-time based approach. Methods are described in Danesh G et al (2022) doi:10.1111/2041-210X.14038.

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("TiPS", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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-tips

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

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-TiPS

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# 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-TiPS

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

Health

CRAN checks

1ERROR12OK

Failing flavors

ERROR r-patched-linux-x86_64

Slowest check: 11.5 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.16

74.8%

Coverage · measured lines

100%

Documentation · exports

9

Dependencies · direct

Check history

ERROR2026-08-13
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 1,404 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 0%
Documented parameters: 100%
Return-value docs: 67%
References docs: 0%

Downloads

6.7K

CRAN downloads in the past year

Rank #6,762 · ~18/day · ~560/mo

Releases R versions

Daily download trend is not available in this view yet.

21330 days

1.2K90 days

6.7K1 year

Compare downloads with other packages →

Also on378 r2u22 autocran

Repository

Repository ↗ ete/tips

Repository practices

Upstream repositoryBeta

Repository gitlab.in2p3.fr/ete/tips is linked, but repository-practices checks have not run for it yet. Checks are GitHub-only for now.

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.0.0

Imports (9)

graphicsgrDevicesgtools inlinemethodsRcpp (>= 0.12.14)statsstringrutils

LinkingTo (2)

Rcpp BH

Suggests (4)

knitr rmarkdown ape testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (5)

Maintainer (1)

Gonche Danesh

Author, Maintainer, Copyright holder

Authors (5)

Gonche Danesh

Author, Maintainer, Copyright holder

Samuel Alizon

Author, Copyright holder, Thesis advisor

Marc Choisy

Author, Copyright holder, Thesis advisor

Olivier Gascuel

Author, Copyright holder · added in 1.1.0

Emma Saulnier

Author, Copyright holder

Copyright holders (5)

Gonche Danesh

Author, Maintainer, Copyright holder

Samuel Alizon

Author, Copyright holder, Thesis advisor

Marc Choisy

Author, Copyright holder, Thesis advisor

Olivier Gascuel

Author, Copyright holder · added in 1.1.0

Emma Saulnier

Author, Copyright holder

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.3.0Latest
2025-05-09 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.2.3
2023-05-23 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.2.2
2023-02-28 · diff ↗
1.2.1
2022-08-26 · diff ↗
1.2.0
2022-08-12 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.1.1
2022-02-01 · diff ↗
unarchivedReturned to CRAN
2022-02-01
archivedRemoved from CRAN
2022-01-15
check problems were not corrected in time
1.1.0
2021-11-12 · diff ↗
1.0
2021-09-13
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-09-13
Total releases: 8 / 5 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 4.0.0
Download size: 1.9 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("TiPS")

Format

Danesh, G., Alizon, S., Choisy, M., Gascuel, O., & Saulnier, E. (2025). TiPS: Trajectories and Phylogenies Simulator (Version 1.3.0) [Computer software]. https://doi.org/10.32614/CRAN.package.TiPS

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 TiPS version 1.3.0 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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