PointedSDMs

2.1.5

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

1packages depend

6.1Kdownloads / year

23.4%test coverage

13/13checks pass

Overview

About

Maintained by Philip MostertFirst published 2022-06-1414 releasesCRAN page ↗GitHub ↗

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.

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).

Health

CRAN checks

13OK

Slowest check: 12.5 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.29

23.4%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-14
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-05-07
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 1 earlier snapshots

NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 558 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 54%
Documented parameters: 95%
Return-value docs: 64%
References docs: 12%

Downloads

6.1K

CRAN downloads in the past year

Rank #11,723 · ~17/day · ~504/mo

Releases R versions

Daily download trend is not available in this view yet.

26430 days

90990 days

6.1K1 year

Compare downloads with other packages →

Also on134 r2u18 autocran

Repository

GitHub ↗ philipmostert/pointedsdms

28Stars

6Forks

4Open issues

0Open PRs

4Releases

1,401Commits

44Contributors

1,401 commits · Last activity 2026-07-20 · 0% stars, 30d

Stars over time

2025-03-19 · 262026-07-07 · 28

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/philipmostert/pointedsdms on 2026-07-19.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Docs source (1)

README.Rmd

Show all practices

Lint, format, editor (1)

RStudio project

Coverage (1)

Codecov

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

Dependencies

Declared dependencies

25 external dependencies (excludes base and recommended)

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

intSDM

Code & Tests

Code Composition

R 16,213 (72%)Rd 5,033 (22%)Vignettes 1,225 (5%)

Code characteristics

Object systems

S319S4 class11R64

Cyclomatic complexity: 12.5 median / 79 max
Test cases: 50 / 0.29 per code line

Test coverage

Line coverage

23%

Expression

22.2%

Tests / Examples

23.4% / – ex

Functions

42 10 exported

Complexity

17.4 avg / 79 max

Call network

42 nodes / 12 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

42 functions

Function	Cyclo	Coverage
datasetOut exp	21	0%
intModel exp	11	0%
runModel exp	1	0%
makeData	19	0%
makeMarks	9	0%
plot.bruSDM_predict	26	0%

People & History

People (2)

Maintainer (1)

Philip Mostert

Author, Maintainer

Authors (2)

Philip Mostert

Author, Maintainer

Bob O'hara

Author

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
2.1.5Latest
2026-02-18 · current release · diff ↗
2.1.4
2025-08-29 · diff ↗
unarchivedReturned to CRAN
2025-08-29
archivedRemoved from CRAN
2025-07-30
required archived package 'blockCV'
R
R 4.5.0 released · 2025-04-11
2.1.3
2025-01-13 · diff ↗
2.1.2
2024-08-22 · diff ↗
2.1.0
2024-07-08 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.3.2
2024-02-02 · diff ↗
1.3.1
2023-10-10 · diff ↗
1.3
2023-08-10 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.2.1
2023-02-07 · diff ↗
1.2.0
2023-01-16 · diff ↗

Show 5 earlier events

1.1.1
2022-09-05 · diff ↗
1.1.0
2022-08-31 · diff ↗
1.0.6
2022-06-15 · diff ↗
1.0.5
2022-06-14
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-06-14
Total releases: 14 / 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
Installed size: not tracked yet
With dependencies: not tracked yet

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