R Observatory: Metrics for BIDistances version 1.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

BIDistances

1.0.1Package record

Bioinformatic Distances

0packages depend

2.9Kdownloads / year

50.9%test coverage

13/13flavors OK

Overview

About

Maintained by Michael ThrunCRAN page ↗GitHub ↗Issues ↗

Provides a unified interface for computing, comparing, and examining distances, dissimilarities, divergences, and selected similarities for bioinformatics data. The core installation exposes 60 canonical named routes for numerical data and more than 90 when the suggested 'philentropy' backend is installed; aliases, user-defined functions, and mixed-data combinations are not included in these counts. Weighted Minkowski distances can be computed through 'parallelDist', an internal multicore implementation, or optional 'OpenCL' kernels, while the established weighted Euclidean GPU implementation is retained as the optimized p = 2 route. The package also supports theory-guided comparison of distance distributions for clustering, explicit mathematical property classifications, mixed-data constructions through 'manydist', and a specialized Gene Ontology-derived TF-IDF distance.

Install

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

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

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

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("Mthrun/BIDistances")

Development version from Mthrun/BIDistances. Installs pak first if it is not already available.

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-bidistances

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-BIDistances

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-BIDistances

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: 4.2 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-22
WARNING12 OK, 1 WARNING2026-08-21
ERROR10 OK, 2 WARNING, 1 ERROR2026-08-20
WARNING6 OK, 2 NOTE, 5 WARNING2026-08-05
NOTE12 OK, 1 NOTE2026-07-11

Show 4 earlier changesHide 4 earlier changes

OK12 OK2026-04-25
NOTE11 OK, 3 NOTE2026-04-22
ERROR10 OK, 3 NOTE, 1 ERROR2026-04-18
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.1

READMEYes · 1,263 wordsVignettesYes · 1 · dynamicNEWSNoCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 39 (1 internal)
Examples that run: 86%32 run in a plain check (2 of them under a condition) · 3 only when donttest examples are enabled (R CMD check --as-cran) · 2 never run
Exported functions with examples: 100%
Documented parameters: 99%
Return-value docs: 100%
Help pages citing references: 46%

Vignettes (1)

BIDistances: From distance computation to theory-guided selection HTML

How these are measured

Downloads

2.9K

CRAN downloads in the past year

Rank #8,365 · ~8/day · ~242/mo

Releases R versions

Daily download trend is not available in this view yet.

32330 days

1.1K90 days

2.9K1 year

Compare downloads with other packages →

Also on470 r2u34 autocran

How downloads are counted

Repository

mthrun/bidistances ↗Account: Mthrun

0Stars

0Forks

0Open issues

0Open PRs

0Releases

Last activity 2026-08-20

Responsiveness

not measured

How these are measured

PracticesBeta

3 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/mthrun/bidistances on 2026-10-22.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

22 external dependencies (excludes base and recommended)

Installing BIDistances adds 32 packages (20 with compiled code, 38 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, sp 4.3 MB.

Depends (1)

R >= 3.5.0

Imports (9)

Rcpp RcppParallel parallelDistparallelDataVisualizations diptest e1071 pracma ggplot2

LinkingTo (2)

Rcpp RcppParallel

Suggests (12)

knitr rmarkdown OpenCL transport ineq ScatterDensity memshare philentropy dtw proxy manydist (>= 0.5.0)testthat

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 (3)

Michael Thrun

Author, Maintainer since 0.1.5 (2026)

Quirin Stier

Author, Reviewer, Contributor

Luca Brinkmann

Contributor

Previously maintained by Quirin Stier (0.0.2 to 0.1.3).

Releases (5)

Pick two releases to compare their code metrics.

1.0.1Latest
record
2026-08-19 · current release · diff ↗
1.0.0
record
2026-08-19 · diff ↗ ·
removed 17 exports
CosinusDistance, Dist2All, EuclideanDistances_GPU, fastPdist, FractionalDistance, GiniDist, Hellinger4ConditionalPDF, jaccard, knneighborDistances, Mahalanobis, msmd, nearest, pdistToroid, SharedNeighborDistance, ToroidDist2All, twed, WassersteinDist

added 31 exports
Cosine_Distance, DistanceOneToAll, DistanceDistributionAnalysis, DistanceProperties, DTW_Distance, endresSchindelin_TwoSamplePDF, endresSchindelin_Distribution, EndresSchindelin_Distance, EuclideanGPU_Distance, EuclideanMulticore_Distance, Fractional_Distance, Gini_Distance, Hellinger_Distance, IntraClusterBoundaryCounts, Jaccard_Distance, KNearestNeighborsFromDistance, Mahalanobis_Distance, MSMD_Distance, Minkowski_Distance, NearestNeighborIndex, ToroidalEuclidean_Distance, SharedNeighbor_Distance, Tfidf_Distance, ToroidalEuclideanDistanceOneToAll, TWED_Distance, Wasserstein_Distance, fast_dip_stat, fast_dip_test, fast_dip_test_matrix, dip.test.fast and 1 more
0.1.5
record
2026-08-04 · diff ↗ ·
added 6 exports
calculateMemoryDemandGPU, EuclideanDistances_GPU, Hellinger4ConditionalPDF, knneighborDistances, Kullback_Leibler_div, pdistToroid
R
R 4.6.0 released · 2026-04-24
unarchivedReturned to CRAN
2025-05-11
0.1.3
record
2025-05-11 · diff ↗ ·
removed 1 export
pattern:^[[:alpha:]]+

added 18 exports
CosinusDistance, Dist2All, DistanceDistributions, DistanceMatrix, fastPdist, FractionalDistance, GiniDist, jaccard, Mahalanobis, msmd, nearest, SharedNeighborDistance, Tfidf_dist, ToroidDist2All, TransformSimilarity2MetricDistance, twed, VariablePrecision, WassersteinDist
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
archivedRemoved from CRAN
2023-06-01
issues were not corrected in time OpenCL on macOS, also Fedora 34
0.0.2
record
2023-05-18
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-05-18
Total releases: 5 / 3 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 14 KB / 2 files
Download size: 154 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("BIDistances")

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

It points to 10.1142/s1469026821500164, 10.15388/23-infor517.

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 BIDistances version 1.0.1 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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