R Observatory: Metrics for shapeR version 1.0-2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

shapeR

1.0-2

Collection and Analysis of Otolith Shape Data

0packages depend

3.5Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Lisa Anne LibunganFirst published 2015-04-034 releasesCRAN page ↗GitHub ↗

Studies otolith shape variation among fish populations. Otoliths are calcified structures found in the inner ear of teleost fish and their shape has been known to vary among several fish populations and stocks, making them very useful in taxonomy, species identification and to study geographic variations. The package extends previously described software used for otolith shape analysis by allowing the user to automatically extract closed contour outlines from a large number of images, perform smoothing to eliminate pixel noise described in Haines and Crampton (2000) doi:10.1111/1475-4983.00148, choose from conducting either a Fourier or wavelet see Gençay et al (2001) doi:10.1016/S0378-4371(00)00463-5 transform to the outlines and visualize the mean shape. The output of the package are independent Fourier or wavelet coefficients which can be directly imported into a wide range of statistical packages in R. The package might prove useful in studies of any two dimensional objects.

Install

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

install.packages("shapeR", 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("lisalibungan/shapeR")

Development version from lisalibungan/shapeR. 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-shaper

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

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-shapeR

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-shapeR

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 2.6 min · r-oldrel-macos-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

7

Dependencies · direct

Check history

OK2026-08-04
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-08
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 1 FAILURE
NOTE2026-06-07
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

Examples that run: 47%
Documented parameters: 97%
Return-value docs: 100%
References docs: 41%

Downloads

3.5K

CRAN downloads in the past year

Rank #11,355 · ~10/day · ~292/mo

Releases R versions

Daily download trend is not available in this view yet.

19830 days

85790 days

3.5K1 year

Compare downloads with other packages →

Also on186 r2u20 autocran

Repository

GitHub ↗ lisalibungan/shaper

10Stars

22Forks

1Open issues

0Open PRs

0Releases

14Commits

1Contributors

License GPL-2.0 · 14 commits · Last activity 2019-06-28 · +11.1% stars, 30d

Stars over time

2024-01-05 · 92026-08-21 · 10

Repository practices

Upstream repositoryBeta

Checks run against github.com/lisalibungan/shaper on 2026-08-16.

No development-tooling practices detected in the upstream repository.

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.0.2

Imports (7)

plotrix jpeg pixmap wavethreshmethodsveganMASS

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Lisa Anne Libungan

Author, Maintainer

Authors (2)

Lisa Anne Libungan

Author, Maintainer

Snaebjorn Palsson

Author, Thesis advisor

Package Timeline

4 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.0-2Latest
2025-10-28 · current release · diff ↗
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
1.0-1
2022-11-21 · diff ↗
unarchivedReturned to CRAN
2022-11-21
archivedRemoved from CRAN
2022-06-20
check problems were not corrected despite reminders
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
0.1-5
2015-05-20 · diff ↗

Show 3 earlier events

R
R 3.2.0 released · 2015-04-16
0.1-3
2015-04-03
R
R 3.1.0 released · 2014-04-10

Package metadata

First published: 2015-04-03
Total releases: 4 / 11 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.0.2
Bundled data: 3.2 MB / 3 files
Download size: 3.2 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("shapeR")

Format

Libungan, L. A., & Palsson, S. (2025). shapeR: Collection and Analysis of Otolith Shape Data (Version 1.0-2) [Computer software]. https://doi.org/10.32614/CRAN.package.shapeR

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 shapeR version 1.0-2 [Data set]. HJJB, LLC. Data release v2026-08-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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