R Observatory: Metrics for IsoriX version 0.9.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

IsoriX

0.9.4Package record

Isoscape Computation and Inference of Spatial Origins using Mixed Models

0packages dependsuggested by 1

30.3Kdownloads / year

49.9%test coverage

10/13flavors OK

Overview

About

Maintained by Alexandre CourtiolCRAN page ↗GitHub ↗Website ↗Issues ↗

Building isoscapes using mixed models and inferring the geographic origin of samples based on their isotopic ratios. This package is essentially a simplified interface to several other packages which implements a new statistical framework based on mixed models. It uses 'spaMM' for fitting and predicting isoscapes, and assigning an organism's origin depending on its isotopic ratio. 'IsoriX' also relies heavily on the package 'rasterVis' for plotting the maps produced with 'terra' using 'lattice'.

Changes in 0.9.4

Main release goal

the documentation had to be migrated to another website, so all links were updated.

Minor changes

bookdown.org is being discontinued so the bookdown has been migrated to "https://courtiol-isorix.share.connect.posit.cloud".

Internal (geeky) changes

now explicitly depends on R (>= 4.1.0) since we use pipes (|>).

From NEWS.md in the release

Install

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

install.packages("IsoriX", 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("courtiol/IsoriX")

Development version from courtiol/IsoriX. 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-isorix

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-IsoriX

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-IsoriX

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

1ERROR2NOTE10OK

Check messages

ERRORpackage dependenciesr-release-macos-x86_64

Package required but not available: ‘spaMM’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

NOTERd contentsr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Rd files without \usage:
  ‘IsoriX-defunct.Rd’
\arguments should not be documented without \usage.

CRAN check page ↗

Slowest check: 13.0 min · r-oldrel-windows-x86_64

Status changes

ERROR10 OK, 2 NOTE, 1 ERRORNow
ERROR11 OK, 1 ERROR2026-04-25
OK14 OK2026-04-10
ERROR13 OK, 1 ERROR2026-04-09
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.9.4

READMENoVignettesNoNEWSYes · 100% structured · mentions 0.9.4Citation fileYes · cites a publicationWebsiteYes

Help pages: 35 (1 internal)includes a package overview page
Examples that run: 82%23 run in a plain check · 5 hold no code
Exported functions with examples: 88%
Documented parameters: 91%
Return-value docs: 88%
Help pages citing references: 31%

How these are measured

Downloads

30.3K

CRAN downloads in the past year

Rank #2,656 · ~83/day · ~2.5K/mo

Releases R versions

Daily download trend is not available in this view yet.

2.1K30 days

5.8K90 days

30.3K1 year

Compare downloads with other packages →

Also on88 r2u4 autocran

How downloads are counted

Repository

courtiol/isorix ↗Account: courtiol

15Stars

7Forks

39Open issues

1Open PRs

9Releases

1,016Commits

8Commit identities

1,016 commits · Last activity 2026-01-13

Responsiveness

How these are sampled

PRs merged (all time): 93%
Median days to close, 50 most recently updated closed issues: 276
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-07-16 · 152026-07-07 · 15

How these are measured

PracticesBeta

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

Checks run against github.com/courtiol/isorix on 2026-10-21.

Docs source (1)

GitHub Pages site last deployed 2026-01-13

Reproducibility and dev environment (1)

Makefile

Lint, format, editor (1)

VS Code

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

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Installing IsoriX adds 38 packages (24 with compiled code, 24 MB of source tarballs). Heaviest: sp 4.3 MB, nloptr 2.1 MB, Rcpp 1.8 MB.

Depends (1)

R >= 4.1.0

Imports (14)

graphicsgrDevicesgridlatticelatticeExtramethodsnumDeriv rasterVis spaMMstatsterratoolsutilsviridisLite

LinkingTo (0)

none

Suggests (9)

colorspace elevatr gmp magick rgl spelling testthat webshot2 withr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Suggested by 1

Suggests, most downloaded first

spaMM

How these are counted

Code & Tests

Datasets

People & History

People (4)

Alexandre Courtiol

Author, Maintainer since 0.4-1 (2016)

Stephanie Kramer-Schadt

Author

Marie-Sophie Rohwaeder

Author · added in 0.6

François Rousset

Author · added in 0.5

Listed in earlier versions (2)

François

no longer listed · 0.4-1

Rousset

no longer listed · 0.4-1

Releases (13)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.9.4Latest
record
2026-01-13 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
0.9.3
record
2024-09-08 · diff ↗ ·
removed 1 export
panel.points

added 3 exports
extract, lpolygon, vect
R
R 4.4.0 released · 2024-04-24
0.9.2
record
2023-11-14 · diff ↗ ·
added 1 export
saveRDS_IsoriX
0.9.1
record
2023-09-25 · diff ↗ ·
removed 9 exports
extent<-, projection<-, CRS, area, extent, extract, raster, sp.points, sp.polygons

added 9 exports
crs<-, ext<-, cellSize, crs, ext, plot, points, polys, rast
R
R 4.3.0 released · 2023-04-21
0.9.0
record
2022-09-23 · diff ↗
0.8.3
record
2022-09-12 · diff ↗ ·
removed 1 export
isosim
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
0.8.2
record
2020-09-16 · diff ↗ ·
removed 13 exports
Calibfit, GetElev, Isofit, Isorix, Isoscape, Isosim, QueryGNIP, RElevate, prepdata, prepelev, prepiso, queryGNIP, relevate
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
0.8.1
record
2018-08-29 · diff ↗ ·
removed 2 exports
IsoriX.getOption, IsoriX.options

added 26 exports
extent<-, projection<-, CRS, RdBuTheme, area, downloadfile, extent, extract, getOption_IsoriX, get_ranPars, gpar, grid.text, layer, levelplot, options_IsoriX, panel.points, prepelev, prepiso, prepraster, prepsources, raster, shift, sp.points, sp.polygons, values, xyplot

Show 8 earlier eventsHide 8 earlier events

R
R 3.5.0 released · 2018-04-23
0.7.1
record
2018-04-05 · diff ↗
0.7
record
2017-08-14 · diff ↗ ·
added 1 export
prepdata
0.6
record
2017-07-08 · diff ↗ ·
removed 1 export
pattern:^[[:alpha:]]+

added 23 exports
Calibfit, GetElev, Isofit, IsoriX.getOption, IsoriX.options, Isorix, Isoscape, Isosim, QueryGNIP, RElevate, calibfit, create_aliens, getelev, getprecip, isofind, isofit, isomultifit, isomultiscape, isoscape, isosim, prepcipitate, queryGNIP, relevate
R
R 3.4.0 released · 2017-04-21
0.5
record
2017-04-12 · diff ↗
0.4-1
record
2016-09-11
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2016-09-11
Total releases: 13 / 10 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 4.1.0
Bundled data: 85 KB / 15 files
Download size: 1.5 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("IsoriX")

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

It points to 10.1101/207662.

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 IsoriX version 0.9.4 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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