R Observatory: Metrics for phylotypr version 0.2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

phylotypr

0.2.0Package record

Classifying DNA Sequences to Taxonomic Groupings

0packages dependsuggested by 1

2.6Kdownloads / year

97.6%test coverage

13/13flavors OK

Overview

About

Maintained by Pat SchlossCRAN page ↗GitHub ↗Website ↗Issues ↗

Classification based analysis of DNA sequences to taxonomic groupings. This package primarily implements Naive Bayesian Classifier from the Ribosomal Database Project. This approach has traditionally been used to classify 16S rRNA gene sequences to bacterial taxonomic outlines; however, it can be used for any type of gene sequence. The method was originally described by Wang, Garrity, Tiedje, and Cole in Applied and Environmental Microbiology 73(16):5261-7 doi:10.1128/AEM.00062-07. The package also provides functions to read in 'FASTA'-formatted sequence data.

Changes in 0.2.0

New features

Add new function classify_sequences(), which has confidence score filtering built-in as an option and is multithreaded by default. Can be run by giving the function the name of a data frame and the columns corresponding to the sequence id and sequences or as a {strollur} object and function will be output results as appropriate

Improvements

Update vignettes and documentation for new functions and features
Core functions can now process more than one sequence at a time
Added type checking and check for column names in classify_sequences(), filter_taxonomy(), print_taxonomy()
build_kmer_database() now includes reference_data argument

Show all changes in 0.2.0Hide the rest of the changes in 0.2.0

modified filter_taxonomy() to take a data frame rather than a list
modified print_taxonomy() to take a data frame rather than a list and then output mothur-like taxonomy string to user specified depth. If specified depth is shorter than observed, string gets truncated. If depth is longer than specified it adds "_unclassified". User can turn off confidence scores
rdp_trainset9_pds and rdp_trainset9 now include reference data as a data frame in the reference_data slot; will be incorporated in databases provided by {phylotyprrefdata}. These were renamed from trainset9_rdp and trainset9_pds
Changed id to sequence_name across functions
Modify read_fasta to convert non-ATGCU-. to N; force capitalization. This was also applied to built in reference data
Remove use of set.seed() to be within call to classify_sequences()
Optimized build_kmer_database() and classify_sequences() for performance making both significantly faster

Deprecated functions

classify_sequence()

Bug fixes

Nothing to repair - if you find something let us know!

From NEWS.md in the release

Install

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

install.packages("phylotypr", 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("mothur/phylotypr")

Development version from mothur/phylotypr. 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-phylotypr

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-phylotypr

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-phylotypr

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: 5.2 min · r-release-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK12 OK2026-04-25
NOTE11 OK, 3 NOTE2026-04-22
ERROR10 OK, 3 NOTE, 1 ERROR2026-04-18

Show 1 earlier changeHide 1 earlier change

NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.2.0

READMEYes · 278 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 0.2.0Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 11
Examples that run: 100%10 run in a plain check
Exported functions with examples: 100%
Documented parameters: 99%
Return-value docs: 100%
Help pages citing references: 18%

Vignettes (1)

phylotypr HTML

How these are measured

Downloads

2.6K

CRAN downloads in the past year

Rank #16,287 · ~7/day · ~215/mo

Releases R versions

Daily download trend is not available in this view yet.

29330 days

77390 days

2.6K1 year

Compare downloads with other packages →

Also on354 r2u5 autocran

How downloads are counted

Repository

mothur/phylotypr ↗Organization: mothur

10Stars

4Forks

1Open issues

0Open PRs

1Releases

129Commits

1Commit identities

License file reads as GPL-3.0 · 129 commits · Last activity 2026-10-21 · +11.1% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 0%
Median days to close, 50 most recently updated closed issues: 164
Median days to close, 50 most recently updated closed PRs: 16

Stars over time

2025-01-23 · 82026-10-02 · 10

How these are measured

PracticesBeta

12 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/mothur/phylotypr on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-10-21 · The repository has a site deploy workflow

pkgdown site last built 2026-10-21, before release 0.2.0 (2026-10-22)

Coverage (1)

Coverage reporting

Reproducibility and dev environment (1)

data-raw/

Show all practicesHide 2 practices

CRAN release process (2)

cran-comments.mdrevdep/

Lint, format, editor (2)

lintrRStudio project

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

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Installing phylotypr adds 28 packages (17 with compiled code, 20 MB of source tarballs). Heaviest: stringi 11 MB, Rcpp 1.8 MB, vctrs 1.0 MB.

Depends (1)

R >= 4.2

Imports (5)

Rcpp readr stringistatsparallelly

LinkingTo (2)

Rcpp RcppThread

Suggests (6)

knitr rmarkdown purrr dplyr testthat strollur

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Suggested by 1

Suggests, most downloaded first

strollur

How these are counted

Code & Tests

Datasets

People & History

People (1)

Pat Schloss

Releases (3)

Pick two releases to compare their code metrics.

0.2.0Latest
record
2026-10-22 · current release · diff ↗ ·
added 2 exports
classify_sequences, create_database
R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
0.1.1
record
2025-02-21 · diff ↗ ·
added 1 export
write_fasta
0.1.0
record
2024-10-14
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-10-14
Total releases: 3 / 2 yrs
License: GPL-3 OSI · relicensed from MIT + file LICENSE in 0.1.1
Minimum R: ≥ 4.2
Bundled data: 1.6 MB / 2 files
Download size: 1.8 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("phylotypr")

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

It points to 10.1128/mra.01144-24.

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 phylotypr version 0.2.0 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, 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 →