R Observatory: Metrics for sidier version 4.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

sidier

4.1.1Package record

Substitution and Indel Distances to Infer Evolutionary Relationships

0packages depend

2.7Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by A.J. Muñoz-PajaresCRAN page ↗

Evolutionary reconstruction based on substitutions and insertion-deletion (indels) analyses in a distance-based framework as described in Muñoz-Pajares (2013) doi:10.1111/2041-210X.12118.

Install

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

install.packages("sidier", 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-sidier

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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-sidier

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-sidier

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 2.5 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 4.1.1

READMENoVignettesNoNEWSNoCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 41includes a package overview page
Examples that run: 18%7 run in a plain check · 32 hold no code
Exported functions with examples: 97%
Documented parameters: 95%
Return-value docs: 71%
Help pages citing references: 24%

How these are measured

Downloads

2.7K

CRAN downloads in the past year

Rank #13,789 · ~7/day · ~225/mo

Releases R versions

Daily download trend is not available in this view yet.

31930 days

85390 days

2.7K1 year

Compare downloads with other packages →

Also on64 r2u4 autocran

How downloads are counted

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Installing sidier adds 49 packages (31 with compiled code, 45 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, igraph 4.8 MB.

Depends (1)

R >= 3.5.0

Imports (7)

ape network igraph gridBasegridggmap ggplot2

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (1)

A.J. Muñoz-Pajares

Maintainer, Author · added in 4.1.1

Maintainer since 1.0 (2013)

Listed in earlier versions (2)

A.J. Munoz-Pajares

no longer listed · 1.0 to 2.3

A. Jesus Muñoz Pajares

no longer listed · 3.0 to 4.1.0

Releases (11)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
4.1.1Latest
record
2025-06-06 · current release · diff ↗
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
R
R 4.2.0 released · 2022-04-22
4.1.0
record
2021-06-25 · diff ↗ ·
added 3 exports
assign.whole.taxo, filter.whole.taxo, get.majority.taxo
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
4.0.3
record
2018-07-09 · diff ↗
R
R 3.5.0 released · 2018-04-23
4.0.2
record
2017-06-08 · diff ↗
4.0.1
record
2017-06-07 · diff ↗ ·
added 9 exports
barcode.gap, barcode.quality, barcode.summary, compare.dist, FilterHaplo, genbank.sp.names, inter.intra.plot, rule, single.network.module
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03

Show 10 earlier eventsHide 10 earlier events

R
R 3.2.0 released · 2015-04-16
3.0.1
record
2015-02-28 · diff ↗
3.0
record
2014-11-18 · diff ↗ ·
added 9 exports
colour.scheme, NINA.thr, double.plot, mergeNodes, mutation.network, pie.network, zero.thr, simplify.network, spatial.plot
R
R 3.1.0 released · 2014-04-10
2.3
record
2013-08-09 · diff ↗ ·
removed 1 export
pattern:.

added 14 exports
BARRIEL, GetHaplo, nt.gap.comb, simuEvolution, distance.comb, HapPerPop, perc.thr, single.network, FIFTH, MCIC, pop.dist, FindHaplo, mutationSummary, SIC
2.2
record
2013-07-02 · diff ↗
R
R 3.0.0 released · 2013-04-03
2.0
record
2013-03-30 · diff ↗ ·
removed 8 exports
pattern:^[[:alpha:]]+, FindHaplo, HapPerPop, nt.gap.comb, pop.dist, GetHaplo, MCIC, perc.thr

added 1 export
pattern:.
1.0
record
2013-02-19
R
R 2.15.0 released · 2012-03-30

Package metadata

First published: 2013-02-19
Total releases: 11 / 13 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.5.0
Bundled data: 3.3 KB / 4 files
Download size: 81 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("sidier")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1111/2041-210x.12118.

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 sidier version 4.1.1 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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