R Observatory: Metrics for ampir version 1.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ampir

1.1.0Package record

Predict Antimicrobial Peptides

0packages depend

4.1Kdownloads / year

98.7%test coverage

11/13flavors OK

Overview

About

Maintained by Legana FingerhutCRAN page ↗GitHub ↗

A toolkit to predict antimicrobial peptides from protein sequences on a genome-wide scale. It incorporates two support vector machine models ("precursor" and "mature") trained on publicly available antimicrobial peptide data using calculated physico-chemical and compositional sequence properties described in Meher et al. (2017) doi:10.1038/srep42362. In order to support genome-wide analyses, these models are designed to accept any type of protein as input and calculation of compositional properties has been optimised for high-throughput use. For best results it is important to select the model that accurately represents your sequence type: for full length proteins, it is recommended to use the default "precursor" model. The alternative, "mature", model is best suited for mature peptide sequences that represent the final antimicrobial peptide sequence after post-translational processing. For details see Fingerhut et al. (2020) doi:10.1093/bioinformatics/btaa653. The 'ampir' package is also available via a Shiny based GUI at https://ampir.marine-omics.net/.

Changes in 1.1.0

ampir now has a Shiny based web interface! <https://ampir.marine-omics.net/>
updated both classification models (ampir_precursor and ampir_mature) with additional AMPs
fixed an example in the README which resulted in NAs output (@Ebedthan, #20)
converted input for calculate_features.R to a dataframe, in case it was not a dataframe

From NEWS.md in the release

Install

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

install.packages("ampir", 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("Legana/ampir")

Development version from Legana/ampir. 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-ampir

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-ampir

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-ampir

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

2NOTE11OK

Check messages

NOTEdependencies in R coder-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Namespace in Imports field not imported from:
  ‘kernlab’
All declared Imports should be used.

CRAN check page ↗

Slowest check: 4.6 min · r-devel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTE2026-09-08
ERROR11 OK, 1 NOTE, 1 ERROR2026-09-07
NOTE11 OK, 2 NOTE2026-06-09
ERROR10 OK, 2 NOTE, 1 ERROR2026-06-08
NOTE12 OK, 2 NOTE2026-04-22

Show 3 earlier changesHide 3 earlier changes

ERROR11 OK, 2 NOTE, 1 ERROR2026-04-18
NOTE12 OK, 2 NOTE2026-03-30
ERROR11 OK, 2 NOTE, 1 ERROR2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.0

READMEYes · 494 wordsVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 1.1.0Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 14
Examples that run: 100%5 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 50%

Vignettes (2)

Introduction to ampir HTML
How to train your model HTML

How these are measured

Downloads

4.1K

CRAN downloads in the past year

Rank #6,410 · ~11/day · ~339/mo

Releases R versions

Daily download trend is not available in this view yet.

47330 days

1.3K90 days

4.1K1 year

Compare downloads with other packages →

Also on431 r2u33 autocran3K conda_forge62 c2d4u

How downloads are counted

Repository

legana/ampir ↗Account: Legana

35Stars

6Forks

0Open issues

0Open PRs

0Releases

240Commits

5Commit identities

240 commits · Last activity 2021-06-29 · -2.8% stars, 30d · Discussions: 2 posts

Responsiveness

How these are sampled

PRs merged (all time): 81%
Median days to close, 50 most recently updated closed issues: 7
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2025-07-25 · 332026-10-04 · 35

How these are measured

PracticesBeta

5 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/legana/ampir on 2026-10-18.

Continuous integration (1)

Travis CI (config file)

Docs source (1)

README.Rmd

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Show all practicesHide 1 practice

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Installing ampir adds 65 packages (36 with compiled code, 50 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 3.5.0

Imports (5)

Peptides caret kernlab Rcppparallel

LinkingTo (1)

Rcpp

Suggests (4)

testthat knitr rmarkdown e1071

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 (4)

Legana Fingerhut

Author, Maintainer since 0.1.0 (2019)

Ira Cooke

Author

Nan Xiao

Contributor

R/calc_pseudo_comp.R

Jinlong Zhang

Contributor

R/read_faa.R

Releases (3)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
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
1.1.0Latest
record
2021-06-29 · current release · diff ↗
R
R 4.1.0 released · 2021-05-18
1.0.0
record
2020-05-11 · diff ↗ ·
added 2 exports
calculate_features, remove_nonstandard_aa
R
R 4.0.0 released · 2020-04-24
0.1.0
record
2019-12-06
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-12-06
Total releases: 3 / 7 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.5.0
Download size: 1.6 MB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ampir")

Format

Fingerhut, L., Cooke, I., Xiao, N., & Zhang, J. (2021). ampir: Predict Antimicrobial Peptides (Version 1.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.ampir

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 ampir version 1.1.0 [Data set]. HJJB, LLC. Data release v2026-10-20. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-20, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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