R Observatory: Metrics for MCseqReplic version 1.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

MCseqReplic

1.1.0Package record

Monte Carlo Simulations of Time Changes in Sequences

0packages depend

1.9Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Gilbert RitschardCRAN page ↗Website ↗

Generates replicated sets of sequences with Monte Carlo simulated timing changes and computes various indicators for evaluating effects of timing uncertainty on sequence analysis results. See Ritschard, G. and Liao, T.F. (2026): "Assessing the Impact of Timing Errors in Sequence Analysis". International Journal of Social Research Methodology doi:10.1080/13645579.2026.2666297.

Changes in 1.1.0

New functions

MCcompgrp collects group comparison statistics per MC-sets.
ggplotMCcqi ggplot, by MC-sets, the selected range values of a CQI selected in a MCclustQ object.
print method for MCclustQ objects returned by MCclustqual.

Changes in existing functions

MCclustqual elements $qual.max and $qual.tab now include results for observed sequences when attribute "obs" of disslist is TRUE. Element qual.obs has been suppressed from the outcome.
MCclustqual and MCmdscorr: argument verbose in place of silent.
MCclustqual and MCmdscorr: argument core now can be "auto".
MCclustcomp new logical argument AMI to specify if the costly AMI should be computed.

Misc.

Added vignette.
Added REFERENCES.bib

Show all changes in 1.1.0Hide the rest of the changes in 1.1.0

Outdated function seqdistMCSE suppressed, use MCseqdistSE instead.
Now requires version >= 1.1.0 of aricode.

From inst/NEWS.Rd in the release

Install

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

install.packages("MCseqReplic", 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-mcseqreplic

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-MCseqReplic

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-MCseqReplic

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: 3.1 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK5 OK2026-04-30

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.0

READMENoVignettesYes · 1 · dynamicNEWSYes · mentions 1.1.0Citation fileYes · cites a publicationWebsiteYes

Help pages: 17
Examples that run: 100%9 run in a plain check
Exported functions with examples: 69%
Documented parameters: 100%
Return-value docs: 92%
Help pages citing references: 24% with a bibliography file

Vignettes (1)

Assessing Effects of Timing Errors on Sequence Analaysis Outcomes with MCseqReplic HTML

How these are measured

Downloads

1.9K

CRAN downloads in the past year

Rank #14,061 · ~5/day · ~157/mo

Releases R versions

Daily download trend is not available in this view yet.

32630 days

82390 days

1.9K1 year

Compare downloads with other packages →

Also on50 r2u7 autocran

How downloads are counted

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Installing MCseqReplic adds 65 packages (34 with compiled code, 60 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (3)

R >= 3.0.0TraMineR ggplot2

Imports (14)

WeightedCluster aricode doParallel parallelly foreach doSNOWstatsvegan wCorr Rdpack TraMineRextras dplyr tidyr magrittr

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (2)

Gilbert Ritschard

Tim F. Liao

Contributor · added in 1.1.0

Releases (2)

Pick two releases to compare their code metrics.

1.1.0Latest
record
2026-04-29 · current release · diff ↗ ·
removed 1 export
seqdistMCSE

added 2 exports
MCcompgrp, ggplotMCcqi
1.0.0
record
2026-04-29
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-04-29
Total releases: 2 / 1 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.0.0
Download size: 91 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("MCseqReplic")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

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 MCseqReplic version 1.1.0 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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