R Observatory: Metrics for PointedSDMs version 2.1.6

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PointedSDMs

2.1.6Package record

Fit Models Derived from Point Processes to Species Distributions using 'inlabru'

1packages depend

5.2Kdownloads / year

23.4%test coverage

13/13flavors OK

Overview

About

Maintained by Philip MostertCRAN page ↗GitHub ↗Issues ↗

Integrated species distribution modeling is a rising field in quantitative ecology thanks to significant rises in the quantity of data available, increases in computational speed and the proven benefits of using such models. Despite this, the general software to help ecologists construct such models in an easy-to-use framework is lacking. We therefore introduce the R package 'PointedSDMs': which provides the tools to help ecologists set up integrated models and perform inference on them. There are also functions within the package to help run spatial cross-validation for model selection, as well as generic plotting and predicting functions. An introduction to these methods is discussed in Issac, Jarzyna, Keil, Dambly, Boersch-Supan, Browning, Freeman, Golding, Guillera-Arroita, Henrys, Jarvis, Lahoz-Monfort, Pagel, Pescott, Schmucki, Simmonds and O’Hara (2020) doi:10.1016/j.tree.2019.08.006.

Install

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

install.packages("PointedSDMs", 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("PhilipMostert/PointedSDMs")

Development version from PhilipMostert/PointedSDMs. 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-pointedsdms

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-PointedSDMs

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-PointedSDMs

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

13OK

CRAN check page ↗

Slowest check: 9.2 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-30
ERROR11 OK, 2 ERROR2026-08-21
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09

Show 5 earlier changesHide 5 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-14
NOTE12 OK, 1 NOTE2026-05-07
OK12 OK2026-04-25
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.1.6

READMEYes · 558 wordsVignettesYes · 4 · dynamicNEWSYes · 67% structured · does not mention 2.1.6Citation fileYes · cites a publication

Help pages: 58
Examples that run: 23%3 run in a plain check (3 of them under a condition) · 10 never run
Exported functions with examples: 65%
Documented parameters: 95%
Return-value docs: 53%
Help pages citing references: 12%

Vignettes (4)

Example of PointedSDMs for the solitary tinamou HTML
Marked Point Process HTML
Setophaga example HTML
Spatiotemporal example HTML

How these are measured

Downloads

5.2K

CRAN downloads in the past year

Rank #7,350 · ~14/day · ~435/mo

Releases R versions

Daily download trend is not available in this view yet.

39730 days

1.2K90 days

5.2K1 year

Compare downloads with other packages →

Also on121 r2u3 autocran

How downloads are counted

Repository

philipmostert/pointedsdms ↗Account: PhilipMostert

29Stars

6Forks

4Open issues

0Open PRs

4Releases

1,429Commits

44Commit identities

1,429 commits · Last activity 2026-10-23 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 4
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-03-19 · 262026-07-25 · 29

How these are measured

PracticesBeta

10 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/philipmostert/pointedsdms on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (3)

README.Rmd

GitHub Pages site last deployed 2024-06-04 · The repository has a site deploy workflow

Coverage (1)

Coverage reporting (Codecov)

Reproducibility and dev environment (1)

data-raw/

Show all practicesHide 2 practices

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

25 external dependencies (excludes base and recommended)

Installing PointedSDMs adds 60 packages (34 with compiled code, 60 MB of source tarballs). Heaviest: sf 9.3 MB, ggplot2 6.0 MB, blockCV 4.5 MB.

Depends (6)

R >= 4.1statssf inlabru R6methods

Imports (10)

terra ggplot2 fmesher raster sp R.devices blockCV FNN dplyr lifecycle

LinkingTo (0)

none

Suggests (12)

testthat sn INLA rasterVis ggmap RColorBrewer cowplot knitr kableExtra rmarkdown spocc covr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Depends 1

Depends, Imports or LinkingTo, most downloaded first

intSDM

How these are counted

Code & Tests

Datasets

People & History

People (2)

Philip Mostert

Author, Maintainer since 1.0.5 (2022)

Bob O'hara

Author

Releases (15)

Pick two releases to compare their code metrics.

2.1.6Latest
record
2026-08-24 · current release · diff ↗ ·
added 3 exports
print.blockedCV, print.blockedCVpred, print.datasetOut
R
R 4.6.0 released · 2026-04-24
2.1.5
record
2026-02-18 · diff ↗
unarchivedReturned to CRAN
2025-08-29
2.1.4
record
2025-08-29 · diff ↗
archivedRemoved from CRAN
2025-07-30
required archived package 'blockCV'
R
R 4.5.0 released · 2025-04-11
2.1.3
record
2025-01-13 · diff ↗ ·
added 1 export
nearestValue
2.1.2
record
2024-08-22 · diff ↗
2.1.0
record
2024-07-08 · diff ↗ ·
removed 1 export
dataSDM

added 6 exports
specifyISDM, specifyMarks, specifySpecies, startISDM, startMarks, startSpecies
R
R 4.4.0 released · 2024-04-24
1.3.2
record
2024-02-02 · diff ↗
1.3.1
record
2023-10-10 · diff ↗
1.3
record
2023-08-10 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.2.1
record
2023-02-07 · diff ↗

Show 6 earlier eventsHide 6 earlier events

1.2.0
record
2023-01-16 · diff ↗
1.1.1
record
2022-09-05 · diff ↗ ·
added 1 export
fitISDM
1.1.0
record
2022-08-31 · diff ↗
1.0.6
record
2022-06-15 · diff ↗
1.0.5
record
2022-06-14
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-06-14
Total releases: 15 / 4 yrs
License: GPL (>= 3) OSI
Additional repositories: inla.r-inla-download.org
Minimum R: ≥ 4.1
Bundled data: 197 KB / 4 files
Download size: 1.5 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("PointedSDMs")

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

It points to 10.1111/2041-210x.14091.

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 PointedSDMs version 2.1.6 [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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