R Observatory: Metrics for SiPhyNetwork version 1.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SiPhyNetwork

1.1.0

A Phylogenetic Simulator for Reticulate Evolution

0packages depend

7.9Kdownloads / year

58.4%test coverage

0/13checks pass

Overview

About

Maintained by Joshua JustisonFirst published 2022-09-203 releasesCRAN page ↗

A simulator for reticulate evolution under a birth-death-hybridization process. Here the birth-death process is extended to consider reticulate Evolution by allowing hybridization events to occur. The general purpose simulator allows the modeling of three different reticulate patterns: lineage generative hybridization, lineage neutral hybridization, and lineage degenerative hybridization. Users can also specify hybridization events to be dependent on a trait value or genetic distance. We also extend some phylogenetic tree utility and plotting functions for networks. We allow two different stopping conditions: simulated to a fixed time or number of taxa. When simulating to a fixed number of taxa, the user can simulate under the Generalized Sampling Approach that properly simulates phylogenies when assuming a uniform prior on the root age.

Install

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

install.packages("SiPhyNetwork", 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-siphynetwork

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-SiPhyNetwork

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-SiPhyNetwork

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

Health

CRAN checks

2ERROR11NOTE

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc
NOTE r-devel-windows-x86_64
ERROR r-oldrel-macos-arm64
ERROR r-oldrel-macos-x86_64
NOTE r-oldrel-windows-x86_64
NOTE r-patched-linux-x86_64
NOTE r-release-linux-x86_64
NOTE r-release-macos-arm64
NOTE r-release-macos-x86_64
NOTE r-release-windows-x86_64

Slowest check: 3.3 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.04

58.4%

Coverage · measured lines

100%

Documentation · exports

5

Dependencies · direct

Check history

ERROR2026-03-10
0 OK · 12 NOTE · 0 WARNING · 2 ERROR · 0 FAILURE

Documentation

READMEYes · 82 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

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

Downloads

7.9K

CRAN downloads in the past year

Rank #5,431 · ~22/day · ~656/mo

Releases R versions

Daily download trend is not available in this view yet.

24830 days

1.4K90 days

7.9K1 year

Compare downloads with other packages →

Also on379 r2u24 autocran

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (5)

statsape Rcpp rstackdeque lifecycle

LinkingTo (1)

Rcpp

Suggests (4)

testthat knitr rmarkdown markdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (6)

Maintainer (1)

Joshua Justison

Author, Maintainer, Copyright holder

Authors (3)

Joshua Justison

Author, Maintainer, Copyright holder

Claudia Solis-Lemus

Author, Copyright holder

Tracy A. Heath

Author, Copyright holder

Copyright holders (6)

Joshua Justison

Author, Maintainer, Copyright holder

Claudia Solis-Lemus

Author, Copyright holder

Tracy A. Heath

Author, Copyright holder

Daniel Lawson

Copyright holder

Emmanuel Paradis

Copyright holder

Klaus Schliep

Copyright holder

Listed in earlier versions (1)

Tracy A.

no longer listed · 1.0.0 to 1.1.0

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
1.1.0Latest
2023-04-14 · current release · diff ↗
1.0.1
2022-09-29 · diff ↗
1.0.0
2022-09-20
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-09-20
Total releases: 3 / 4 yrs
License: GPL-3 OSI
Download size: 673 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("SiPhyNetwork")

Format

Justison, J., Claudia Solis-Lemus, Heath, T. A., Lawson, D., Paradis, E., & Schliep, K. (2023). SiPhyNetwork: A Phylogenetic Simulator for Reticulate Evolution (Version 1.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.SiPhyNetwork

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 SiPhyNetwork version 1.1.0 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →