R Observatory: Metrics for magi version 1.2.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

magi

1.2.5Package record

MAnifold-Constrained Gaussian Process Inference

0packages depend

3.4Kdownloads / year

63.0%test coverage

8/13flavors OK

Overview

About

Maintained by Shihao YangCRAN page ↗

Provides fast and accurate inference for the parameter estimation problem in Ordinary Differential Equations, including the case when there are unobserved system components. Implements the MAGI method (MAnifold-constrained Gaussian process Inference) of Yang, Wong, and Kou (2021) doi:10.1073/pnas.2020397118. A user guide is provided by the accompanying software paper Wong, Yang, and Kou (2024) doi:10.18637/jss.v109.i04.

Install

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

install.packages("magi", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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-magi

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-magi

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-magi

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:
  magi/tests/testthat/test_loglikR.R (.Dim: 1)
  magi/tests/testthat/test_optimizePhi.R (.Dim: 1)
  magi/tests/testthat/test_xthetasigmallik.R (.Dim: 1)
'.Dim' should be changed to 'dim'.

CRAN check page ↗

Slowest check: 9.3 min · r-devel-windows-x86_64

Status changes

NOTE8 OK, 5 NOTENow
NOTE11 OK, 2 NOTE2026-07-16
OK12 OK2026-04-25
NOTE12 OK, 2 NOTE2026-04-22
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-18
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.2.5

READMEYes · 29 wordsVignettesYes · 1 · evaluation depends on the environmentNEWSNoCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Cites a JSS article

Help pages: 17
Examples that run: 100%15 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 35%

Vignettes (1)

magi-vignette HTML

How these are measured

Downloads

3.4K

CRAN downloads in the past year

Rank #8,917 · ~9/day · ~287/mo

Releases R versions

Daily download trend is not available in this view yet.

44630 days

1.1K90 days

3.4K1 year

Compare downloads with other packages →

Also on383 r2u11 autocran67 c2d4u

How downloads are counted

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Installing magi adds 12 packages (7 with compiled code, 21 MB of source tarballs). Heaviest: BH 14 MB, deSolve 1.9 MB, Rcpp 1.8 MB.

Depends (1)

R >= 3.6.0

Imports (6)

Rcpp gridExtra gridBasegridmethodsdeSolve

LinkingTo (4)

Rcpp RcppArmadillo BH roptim

Suggests (7)

testthat mvtnorm covr knitrMASSrmarkdown markdown

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 (3)

Shihao Yang

Author, Maintainer since 1.0.0 (2021)

Samuel W.K. Wong

Author

S.C. Kou

Contributor, Copyright holder · added in 1.1.3

Contributor of MAGI method development

Listed in earlier versions (2)

Patrick Wieschollek

no longer listed · 1.0.0

Tobias Wood

no longer listed · 1.0.0

Releases (9)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.2.5Latest
record
2025-10-22 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
1.2.4
record
2024-06-22 · diff ↗
1.2.3
record
2024-05-05 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.2.2
record
2023-04-25 · diff ↗ ·
added 2 exports
gpcov, gpmean
R
R 4.3.0 released · 2023-04-21
1.2.1
record
2022-12-19 · diff ↗
1.2.0
record
2022-08-29 · diff ↗ ·
added 14 exports
fnmodelDtheta, fnmodelDx, fnmodelODE, hes1logmodelDtheta, hes1logmodelDx, hes1logmodelODE, hes1modelDtheta, hes1modelDx, hes1modelODE, is.magioutput, magioutput, ptransmodelDtheta, ptransmodelDx, ptransmodelODE
R
R 4.2.0 released · 2022-04-22
1.1.5
record
2022-01-14 · diff ↗
unarchivedReturned to CRAN
2022-01-11
1.1.3
record
2022-01-11 · diff ↗
archivedRemoved from CRAN
2021-08-01
check problems were not corrected in repeated resubmissions
1.0.0
record
2021-07-27

Show 1 earlier eventHide 1 earlier event

R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-07-27
Total releases: 9 / 5 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.6.0
Bundled data: 0.5 KB / 1 file
Download size: 254 KB

Appears in task views

Differential Equations

Cite

Cite this package

Run in R for the authors' entry:

citation("magi")

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

It points to 10.18637/jss.v109.i04.

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 magi version 1.2.5 [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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