R Observatory: Metrics for dowser version 2.5.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

dowser

2.5.2Package record

B Cell Receptor Phylogenetics Toolkit

0packages depend

8.2Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Kenneth HoehnCRAN page ↗GitHub ↗Website ↗Issues ↗

Provides a set of functions for inferring, visualizing, and analyzing B cell phylogenetic trees. Provides methods to 1) reconstruct unmutated ancestral sequences, 2) build B cell phylogenetic trees using multiple methods, 3) visualize trees with metadata at the tips, 4) reconstruct intermediate sequences, 5) detect biased ancestor-descendant relationships among metadata types Workflow examples available at documentation site (see URL). Citations: Hoehn et al (2022) doi:10.1371/journal.pcbi.1009885, Hoehn et al (2021) doi:10.1101/2021.01.06.425648.

Changes in 2.5.2

Fix error from rmarkdown update
Removed vignettes from CRAN versions, now redirect to readthedocs.
Minor bug fixes

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("dowser", 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("immcantation/dowser")

Development version from immcantation/dowser. 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-dowser

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

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 12.1 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-30
ERROR11 OK, 2 ERROR2026-09-02
OK13 OK2026-08-26
ERROR11 OK, 2 ERROR2026-07-11
OK13 OK2026-06-09

Show 5 earlier changesHide 5 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-10
ERROR12 OK, 1 ERROR2026-05-03
OK12 OK2026-04-25
ERROR9 OK, 1 NOTE, 4 ERROR2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.5.2

READMEYes · 297 wordsVignettesYes · 12 · staticNEWSYes · 100% structured · mentions 2.5.2Citation fileYes · cites a publicationWebsiteYes

Help pages: 104 (1 internal)includes a package overview page
Examples that run: 57%8 run in a plain check · 6 never run
Exported functions with examples: 19%
Documented parameters: 100%
Return-value docs: 84%
Help pages citing references: 4%

Vignettes (12)

Show 2 moreHide 2 vignettes

How these are measured

Downloads

8.2K

CRAN downloads in the past year

Rank #3,666 · ~22/day · ~682/mo

Releases R versions

Daily download trend is not available in this view yet.

1.2K30 days

2.7K90 days

8.2K1 year

Compare downloads with other packages →

Also on301 r2u564 bioconda

How downloads are counted

Repository

immcantation/dowser ↗Organization: immcantation

3Stars

1Forks

2Open issues

0Open PRs

0Releases

786Commits

16Commit identities

License file reads as AGPL-3.0 · 786 commits · Last activity 2026-09-15 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 0
Median days to close, 50 most recently updated closed PRs: 2

Stars over time

2026-07-14 · 12026-08-06 · 3

How these are measured

PracticesBeta

7 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/immcantation/dowser on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux

Governance and community (3)

Code of conduct (inherited from immcantation)Contributing guideIssue templates

Reproducibility and dev environment (1)

data-raw/

For agents and models (1)

llms.txt

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

24 external dependencies (excludes base and recommended)

Installing dowser adds 69 packages (38 with compiled code, 59 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, igraph 4.8 MB. 6 more not on CRAN are not measured.

Depends (2)

R >= 4.4ggplot2

Imports (23)

airr alakazam ape coda dplyr ggtreegraphicsgridExtra markdownmethodsphangorn (>= 2.7.1)phylotate RColorBrewer rlang shazamstatsstringr tidyselect tidyrutilspwalign treeio jsonlite

LinkingTo (0)

none

Suggests (4)

knitr rmarkdown testthat BiocManager

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 (8)

Kenneth Hoehn

Author, Maintainer since 0.1.0 (2021)

Jessie Fielding

Author · added in 2.4.0

Cole Jensen

Author · added in 1.2.0

Steven Kleinstein

Author, Copyright holder

Hunter Melton

Author · added in 2.4.0

Susanna Marquez

Contributor

Erick Matsen

Contributor · added in 2.5.1

Jason Vander Heiden

Contributor

Releases (12)

Pick two releases to compare their code metrics.

2.5.2Latest
record
2026-09-16 · current release · diff ↗ ·
added 2 exports
getDiffPoint, getHeightsAndLengths
R
R 4.6.0 released · 2026-04-24
2.5.1
record
2026-03-26 · diff ↗ ·
added 16 exports
buildAllClonalGermlines, checkNodeDivergences, createAllGermlines, dowserObjectEquivalent, filterCombs, filterPartialSeqs, getDiffPoints, getSeqPath, getTreesAndUCAs, mapSubtrees, plotMSA, readTreesJSON, setNodeDivergences, treesEquivalent, writeFasta, writeTreesJSON
2.4.1
record
2026-03-26 · diff ↗
2.4.0
record
2025-10-15 · diff ↗ ·
added 9 exports
buildBeast, checkDivergence, getSkylines, getTimeTrees, getTimeTreesIterate, makeSkyline, plotSkylines, readBEAST, sampleClones
R
R 4.5.0 released · 2025-04-11
2.3
record
2024-10-22 · diff ↗ ·
added 4 exports
dfToFasta, exportTrees, getAllSeqs, writeCloneSequences
2.2.0
record
2024-05-09 · diff ↗
R
R 4.4.0 released · 2024-04-24
2.1.0
record
2023-12-22 · diff ↗
2.0.0
record
2023-09-27 · diff ↗ ·
added 1 export
resolveLightChains
1.2.0
record
2023-05-31 · diff ↗ ·
added 4 exports
buildRAxML, calcRF, getBootstraps, getSubTaxa
R
R 4.3.0 released · 2023-04-21
1.1.0
record
2022-10-05 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.0.0
record
2022-04-13 · diff ↗ ·
added 3 exports
findSwitches, getNodeSeq, reconIgPhyML

Show 2 earlier eventsHide 2 earlier events

0.1.0
record
2021-07-22
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-07-22
Total releases: 12 / 5 yrs
License: AGPL-3 OSI
Minimum R: ≥ 4.4
Bundled data: 276 KB / 9 files
Download size: 1.7 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("dowser")

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

It points to 10.1371/journal.pcbi.1009885, 10.7554/elife.70873, 10.4049/jimmunol.2300851, 10.1073/pnas.1906020116.

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 dowser version 2.5.2 [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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