R Observatory: Metrics for Morpho version 2.13

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

Morpho

2.13Package record

Calculations and Visualisations Related to Geometric Morphometrics

11packages dependsuggested by 4

25Kdownloads / year

16.3%test coverage

8/13flavors OK

Overview

About

Maintained by Stefan SchlagerCRAN page ↗GitHub ↗Issues ↗

A toolset for Geometric Morphometrics and mesh processing. This includes (among other stuff) mesh deformations based on reference points, permutation tests, detection of outliers, processing of sliding semi-landmarks and semi-automated surface landmark placement.

Changes in 2.13

NEW: inscribeEllipse/inscribeEllipseRot: fit a maximum area ellipse into a 2D outline. Published in Torres et al. (2025)
NEW: ILDS, ILDSR2: functions to assess meaningful subsets of interlandmark distances (Cardini et al (2025) - under review).
icpmat: add functionality to avoid excessive scaling in case of similarity transform.
meshDist: fix heatmap colors for case matrix

From inst/NEWS.Rd in the release

Install

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

install.packages("Morpho", 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("zarquon42b/Morpho")

Development version from zarquon42b/Morpho. 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-morpho

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-Morpho

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-Morpho

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

5NOTE8OK

Check messages

NOTER code for possible problemsr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64

Found calls to structure() using deprecated special names:
  Morpho/tests/testthat/test-mirror.r (.Dim: 1)
'.Dim' should be changed to 'dim'.

CRAN check page ↗

Slowest check: 10.1 min · r-oldrel-windows-x86_64

Status changes

NOTE8 OK, 5 NOTE2026-09-08
ERROR8 OK, 4 NOTE, 1 ERROR2026-09-07
NOTE10 OK, 3 NOTE2026-07-16
OK12 OK2026-04-25
NOTE11 OK, 3 NOTE2026-04-22

Show 2 earlier changesHide 2 earlier changes

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 2.13

README· In the repository, left out of the releaseVignettesNoNEWSYes · mentions 2.13Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 155 (1 internal)includes a package overview page
Examples that run: 92%106 run in a plain check (1 of them under a condition) · 8 never run · 1 hold no code
Exported functions with examples: 77%
Documented parameters: 99%
Return-value docs: 89%
Help pages citing references: 21%

How these are measured

Downloads

25K

CRAN downloads in the past year

Rank #2,999 · ~68/day · ~2.1K/mo

Releases R versions

Daily download trend is not available in this view yet.

1.9K30 days

4.5K90 days

25K1 year

Compare downloads with other packages →

Also on704 r2u240 c2d4u

How downloads are counted

Repository

zarquon42b/morpho ↗Account: zarquon42b

54Stars

18Forks

8Open issues

1Open PRs

9Releases

1,731Commits

13Commit identities

1,731 commits · Last activity 2026-04-24 · +1.9% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 69%
Median days to close, 50 most recently updated closed issues: 8
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2025-10-21 · 522026-09-26 · 54

How these are measured

PracticesBeta

3 development-tooling and community-health practices detected across 1 family in the upstream repository

Checks run against github.com/zarquon42b/morpho on 2026-10-18.

Continuous integration (3)

GitHub ActionsR CMD check workflowTravis CI (config file)

The R CMD check workflow runs on Linux

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

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Installing Morpho adds 39 packages (21 with compiled code, 33 MB of source tarballs). Heaviest: bslib 5.6 MB, rgl 4.0 MB, sass 2.9 MB.

Depends (1)

R >= 3.2.0

Imports (18)

Rvcg rgl foreachMatrixMASSparalleldoParallel colorRamps RcppgraphicsgrDevicesmethodsstatsutilsjsonlite bezier crayon mclust

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (6)

carlatticeshapes sf testthat DescTools

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

11direct

0indirect

Imports 11

Suggested by 4

Show all 15 packagesHide all 15 packages

Depends, Imports or LinkingTo, most downloaded first

evolqg ETRep Arothron doolkit pressuRe morphomap TestDimorph patternize RRmorph prWarp Toothnroll

Suggests, most downloaded first

Rvcg RRphylo nat.templatebrains GeometricMorphometricsMix

How these are counted

Code & Tests

Datasets

People & History

People (3)

Stefan Schlager

Gregory Jefferis

Contributor · added in 2.3.0

Dryden Ian

Copyright holder · added in 2.6

Releases (29)

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
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
R
R 3.2.0 released · 2015-04-16
R
R 3.1.0 released · 2014-04-10
3.0.3Latest
record
2014-02-24 · current release · diff ↗
3.0.2
record
2013-08-02 · diff ↗
R
R 3.0.0 released · 2013-04-03

Show 28 earlier eventsHide 28 earlier events

3.0.0
record
2013-03-21 · diff ↗
2.13
record
2025-09-04 · diff ↗ ·
added 6 exports
ILDS, ILDSR2, inscribeEllipse, inscribeEllipseRot, visualise, visualize
2.12
record
2023-12-06 · diff ↗
2.11
record
2023-01-27 · diff ↗
2.10
record
2022-09-09 · diff ↗ ·
added 1 export
computeArea
2.9
record
2021-09-09 · diff ↗ ·
added 11 exports
LPS2RAS, array2list, checkNA, getPointAlongOutline, getSides, read.slicerjson, resampleCurve, restoreFromPCA, restoreShapes, updateIndices, write.slicerjson
2.8
record
2020-03-09 · diff ↗
2.7
record
2019-05-16 · diff ↗
2.6
record
2018-04-24 · diff ↗ ·
added 7 exports
data2platonic, getOuterViewpoints, getPCscores, getPLSCommonShape, getVisibleVertices, plsCoVarCommonShape, virtualMeshScan
2.5.1
record
2017-04-21 · diff ↗
2.5
record
2017-04-05 · diff ↗ ·
added 4 exports
align2procSym, predictRelWarps, slider2d, tps2d
2.4.1.1
record
2016-09-13 · diff ↗
2.4
record
2016-08-01 · diff ↗ ·
added 6 exports
equidistantCurve, fastKmeans, prcompfast, read.fcsv, sortCurve, write.fcsv
2.3.1.1
record
2016-01-22 · diff ↗
2.3.1
record
2015-12-15 · diff ↗ ·
added 4 exports
angleTest, areaSphere, areaSpherePart, mirror2plane
2.3.0
record
2015-06-23 · diff ↗ ·
removed 1 export
meanMat

added 10 exports
armaGinv, getMeaningfulPCs, getPCtol, getPLSfromScores, getPLSscores, line2plane, list2array, plsCoVar, predictPLSfromData, predictPLSfromScores
2.2
record
2014-12-16 · diff ↗ ·
added 8 exports
createMissingList, crossProduct, deformGrid2d, invertFaces, pcAlign, points2plane, symmetrize, tangentPlane
2.1
record
2014-09-25 · diff ↗ ·
added 11 exports
applyTransform, classify, computeTransform, getFaces, getTrafo4x4, getTrafoRotaxis, icpmat, meshPlaneIntersect, mirror, retroDeform3d, retroDeformMesh
2.0.3-1
record
2014-05-13 · diff ↗ ·
added 4 exports
cutMeshPlane, cutSpace, quad2trimesh, solutionSpace
2.0.2
record
2014-02-24 · diff ↗ ·
added 2 exports
arrMean3, fixLMmirror
2.0.1
record
2014-02-07 · diff ↗
2.0
record
2014-02-06 · diff ↗ ·
removed 8 exports
exVar.lm, exVar.mvr, mesh2mesh, c.extract, c.size, mc.CVA, mc.procSym, mc.slider3d

added 5 exports
CAC, RegScore, asymPermute, meanMat, updateNormals
1.0-1
record
2013-11-04 · diff ↗ ·
removed 1 export
pattern:^[^\\.]

added 108 exports
meshDist, meshres, pcaplot3d, warpmovie3d, render, export, adnormals, angle.calc, anonymize, barycenter, bindArr, bone1, bone2, bone3, cExtract, checkLM, closemeshKD, conv2backf, covDist, covPCA, covW, createAtlas, CreateL, crossp, cSize, CVA, deformGrid3d, exVar, exVar.lm, exVar.mvr and 78 more
0.25-1
record
2013-08-02 · diff ↗
0.25
record
2013-07-24 · diff ↗
0.24.1
record
2013-06-17 · diff ↗
0.23.3
record
2013-03-21
R
R 2.15.0 released · 2012-03-30

Package metadata

First published: 2013-03-21
Total releases: 29 / 13 yrs
License: GPL-2 OSI
Copyright: see COPYRIGHTS file for details
Minimum R: ≥ 3.2.0
Bundled data: 2.0 MB / 3 files
Download size: 2.8 MB

Appears in task views

Anomaly Detection Medical Image Analysis

Cite

Cite this package

Run in R for the authors' entry:

citation("Morpho")

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

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 Morpho version 2.13 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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