SDALGCP2
Fast Spatially Discrete Approximation to Log-Gaussian Cox Processes for Aggregated Disease Count Data
Description
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, '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 'MCML'.
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CRAN Check Status
Show all 9 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | ERROR |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | OK |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check details (1 non-OK)
re-building of vignette outputs
Error(s) in re-building vignettes: --- re-building ‘SDALGCP2-intro.Rmd’ using rmarkdown OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead. OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set). --- re-building ‘misaligned-covariates.Rmd’ using rmarkdown --- finished re-building ‘misaligned-covariates.Rmd’ --- re-building ‘raster-covariates.Rmd’ using rmarkdown --- finished re-building ‘raster-covariates.Rmd’ --- re-building ‘scale-grid-vs-continuous.Rmd’ using rmarkdown --- finished re-building ‘scale-grid-vs-continuous.Rmd’ --- re-building ‘spatial-confounding.Rmd’ using rmarkdown --- finished re-building ‘spatial-confounding.Rmd’ --- re-building ‘spatio-temporal.Rmd’ using rmarkdown --- finished re-building ‘spatio-temporal.Rmd’ SUMMARY: processing the following file failed: ‘SDALGCP2-intro.Rmd’ Error: Vignette re-building failed. Execution halted
Check History
ERROR 5 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Jul 3, 2026
re-building of vignette outputs
Error(s) in re-building vignettes: --- re-building ‘SDALGCP2-intro.Rmd’ using rmarkdown OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead. OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LI ...[truncated]... patial-confounding.Rmd’ --- re-building ‘spatio-temporal.Rmd’ using rmarkdown --- finished re-building ‘spatio-temporal.Rmd’ SUMMARY: processing the following file failed: ‘SDALGCP2-intro.Rmd’ Error: Vignette re-building failed. Execution halted
Code
Structure
Lines of code
7,277
Files
145
Compiled share
8.2%
Has compiled src
Yes
Language breakdown
API
Exported functions
18
Internal functions
60
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.28
testthat edition
3
CI present
No
CI type
[]
PR gated
No
Docs
Return-value doc rate
100%
\dontrun example ratio
85.7%
Roxygen coverage
100%
Has pkgdown
No
NEWS present
Yes
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.2.0
System requirements
–
C++ standard
–
License
GPL-2 | GPL-3
License flags
SPDX valid, OSI approved
History
Versions
1
First release
2026-07-02
Latest release
2026-07-02
Avg cadence
–
Cold removal rate
–
Dep drift
0
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/cran-code-metrics.