R Observatory: Metrics for SDALGCP2 version 0.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SDALGCP2

0.1.1

Discrete Log-Gaussian Cox Processes for Aggregated Disease Counts

0packages depend

537downloads / year

86.6%test coverage

13/13checks pass

Overview

About

Maintained by Olatunji JohnsonFirst published 2026-07-032 releasesCRAN page ↗GitHub ↗

Fits a spatially discrete approximation to a log-Gaussian Cox process model for spatially aggregated disease count data, estimated by Monte Carlo Maximum Likelihood as in Christensen (2004) doi:10.1198/106186004X2525 and Johnson, Diggle and Giorgi (2019) doi:10.1002/sim.8339. Performance-critical steps (aggregated correlation assembly, Metropolis-adjusted Langevin algorithm (MALA) sampling, the Monte Carlo likelihood, and the Kronecker-structured space-time likelihood) are implemented in C++ via 'RcppArmadillo'. Provides a one-line, 'glm'-like interface and statistical extensions including a nugget term, general 'Matern' smoothness, raster and misaligned covariates, restricted spatial regression, importance-sampling diagnostics and re-anchored Monte Carlo maximum likelihood (MCML).

Install

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

install.packages("SDALGCP2", 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("olatunjijohnson/SDALGCP2")

Development version from olatunjijohnson/SDALGCP2. 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-sdalgcp2

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-SDALGCP2

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

Health

CRAN checks

13OK

Slowest check: 5.1 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.27

86.6%

Coverage · measured lines

100%

Documentation · exports

9

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-07-08
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-07-03
5 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Documentation

READMEYes · 396 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 14%
Documented parameters: 91%
Return-value docs: 100%
References docs: 0%

Downloads

537

CRAN downloads in the past year

Rank #21,244 · ~1/day · ~45/mo

Releases R versions

Daily download trend is not available in this view yet.

19530 days

53790 days

5371 year

Compare downloads with other packages →

Also on34 r2u

Repository

GitHub ↗ olatunjijohnson/sdalgcp2

0Stars

0Forks

0Open issues

0Open PRs

2Releases

49Commits

1Contributors

49 commits · Last activity 2026-07-07

Releases over time

2026-06-26 · 12026-07-07 · 2

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/olatunjijohnson/sdalgcp2 on 2026-08-23.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

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

Development tooling

AI-assisted toolingBeta

Uses AI-assisted development tooling (declared in repo)

Earliest detected marker: claude on 2026-07-06

claude

Most recent: claude on 2026-07-06

Evidence

claude: on 2026-07-06 · evidence B, D

How this is detected·Detection ruleset v2 (updated 2026-07-29)

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.2.0

Imports (9)

Rcpp sf terra spatstat.geom spatstat.random ggplot2 progressstatsutils

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (4)

knitr rmarkdown testthat numDeriv

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (3)

Maintainer (1)

Olatunji Johnson

Author, Maintainer

Authors (3)

Olatunji Johnson

Author, Maintainer

Peter Diggle

Author

Emanuele Giorgi

Author

Package Timeline

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

0.1.1Latest
2026-07-07 · current release · diff ↗
0.1.0
2026-07-03
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-07-03
Total releases: 2 / 1 yrs
License: GPL-2 | GPL-3 OSI
Minimum R: ≥ 4.2.0
Bundled data: 551 KB / 2 files
Download size: 1.6 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("SDALGCP2")

Format

Johnson, O., Diggle, P., & Giorgi, E. (2026). SDALGCP2: Discrete Log-Gaussian Cox Processes for Aggregated Disease Counts (Version 0.1.1) [Computer software]. https://doi.org/10.32614/CRAN.package.SDALGCP2

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 SDALGCP2 version 0.1.1 [Data set]. HJJB, LLC. Data release v2026-08-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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