R Observatory: Metrics for spatialAtomizeR version 0.2.8

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

spatialAtomizeR

0.2.8

Spatial Analysis with Misaligned Data Using Atom-Based Regression Models

0packages depend

3.9Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Yunzhe QianCRAN page ↗GitHub ↗Issues ↗

Implements atom-based regression models (ABRM) for analyzing spatially misaligned data. Provides functions for simulating misaligned spatial data, preparing NIMBLE model inputs, running MCMC diagnostics, and providing results. All main functions return S3 objects with print(), summary(), and plot() methods for intuitive result exploration. Methods originally described in Mugglin et al. (2000) doi:10.1080/01621459.2000.10474279, further investigated in Trevisani & Gelfand (2013), and applied in Nethery et al. (2023) doi:10.1101/2023.01.10.23284410.

Changes in 0.2.8

This is a resubmission (v0.2.7) addressing reviewer comments on package quality,

documentation, and replication material. Changes include:

Fixed atom ID column renaming to handle both older sf (which produces ID/ID.1 after raster::intersect()) and newer sf >= 1.0 (which produces ID_1/ID_2). Affected simulate_misaligned_data() and the case example vignette (#issue number if you have one).
Added \examples{} blocks to all exported functions; slow MCMC-based functions use \dontrun{} while lightweight functions (e.g., simulate_misaligned_data(), get_abrm_model(), gen_correlated_spat(), and all S3 methods for misaligned_data) now have fully executable examples
Changed vcov.abrm example from \dontrun{} to \donttest{} per CRAN policy for examples that are valid but too slow for routine checking
Fixed run_abrm() silently writing a PDF to the user's working directory: changed default of save_plots from TRUE to FALSE; diagnostic plots are now obtained explicitly via plot() on the returned object

Show all changes in 0.2.8Hide the rest of the changes in 0.2.8

Added plot.misaligned_data() S3 method for spatial data exploration
Added coef.abrm(), confint.abrm(), fitted.abrm(), waic.abrm(), print.waic_abrm() S3 methods to improve model result inspection without accessing internal object structure directly
Updated vignette to set eval = TRUE for all simulated-data (Example 1) code chunks so the vignette executes and displays output during build
Removed redundant library(nimble) call from vignette (nimble is already loaded as a dependency of spatialAtomizeR)
Fixed man page titles to use title case throughout (e.g., "Print Method for ABRM Objects" instead of "Print method for abrm objects")

Test environments

local: macOS/Windows/Linux (R 4.4.0)
GitHub Actions:
ubuntu-latest (R-release, R-devel)
windows-latest (R-release)
macOS-latest (R-release)
win-builder (R-devel)
R-hub (ubuntu-gcc-release)

R CMD check results

0 errors ✔ | 0 warnings ✔ | 0 notes ✔

Downstream dependencies

There are currently no downstream dependencies for this package.

Previous submission (v0.2.6)

Fixed Editor's comments
Fixed print() statement causing debug output in console
Fixed unable to use S3 plot() function bug
Marked 14 internal helper functions as @keywords internal (no longer exported)
Fixed vignette errors: removed non-existent function parameters and corrected signatures
Improved S3 method output formatting
Enhanced documentation with working code examples
Added vcov() method for variance-covariance matrices
Fixed coefficient naming for beta_x and beta_y parameters

From NEWS.md in the release

Install

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

install.packages("spatialAtomizeR", 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("bellayqian/spatialAtomizeR")

Development version from bellayqian/spatialAtomizeR. 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-spatialatomizer

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-spatialAtomizeR

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-spatialAtomizeR

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: 9.3 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK12 OK2026-04-25

Show 1 earlier changeHide 1 earlier change

NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.2.8

READMEYes · 940 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 0.2.8Citation fileNo

Help pages: 26 (7 internal)includes a package overview page
Examples that run: 28%5 run in a plain check · 13 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 45%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 4%

Vignettes (1)

Getting Started with spatialAtomizeR HTML

How these are measured

Downloads

3.9K

CRAN downloads in the past year

Rank #11,325 · ~11/day · ~322/mo

Releases R versions

Daily download trend is not available in this view yet.

37930 days

92090 days

3.9K1 year

Compare downloads with other packages →

Also on132 r2u9 autocran

How downloads are counted

Repository

bellayqian/spatialatomizer ↗Account: bellayqian

8Stars

0Forks

0Open issues

0Open PRs

0Releases

55Commits

2Commit identities

55 commits · Last activity 2026-03-24 · +33.3% stars, 30d

Responsiveness

not measured

Stars over time

2025-10-22 · 12026-10-08 · 8

How these are measured

PracticesBeta

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

Checks run against github.com/bellayqian/spatialatomizer on 2026-10-11.

Docs source (2)

pkgdown

GitHub Pages site last deployed 2026-03-24

Reproducibility and dev environment (1)

data-raw/

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Installing spatialAtomizeR adds 52 packages (33 with compiled code, 69 MB of source tarballs). Heaviest: stringi 11 MB, sf 9.3 MB, ggplot2 6.0 MB.

Depends (1)

R >= 4.0.0

Imports (16)

nimble sp sf spdepMASSdplyr tidyr ggplot2 reshape2 coda BiasedUrnstatsutilsgrDevicesmethodsraster

LinkingTo (0)

none

Suggests (4)

testthat knitr rmarkdown tigris

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (4)

Yunzhe Qian

Author, Maintainer since 0.2.3 (2025)

Rachel Nethery

Author

Nykesha Johnson

Contributor

Contributed to the project conceptualization and manuscript

Nancy Krieger

Contributor

Contributed to the project conceptualization and manuscript

Releases (6)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.2.8Latest
record
2026-03-24 · current release · diff ↗
0.2.7
record
2026-03-08 · diff ↗ ·
added 1 export
waic
0.2.6
record
2026-02-14 · diff ↗ ·
removed 4 exports
dasymetric_mapping, fit_dasymetric_model, run_both_methods, run_sensitivity_analysis
0.2.5
record
2026-02-09 · diff ↗ ·
removed 9 exports
check_mcmc_diagnostics, create_comparison_plots, create_diagnostic_plots, create_sensitivity_summary_plots, create_summary_statistics, prepare_adjacency_matrices, prepare_nimble_inputs, prepare_spatial_bookkeeping, print_convergence_summary
0.2.4
record
2025-12-17 · diff ↗ ·
added 3 exports
Rmfnchypg, dmfnchypg, rmfnchypg
0.2.3
record
2025-12-10
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-12-10
Total releases: 6 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.0.0
Download size: 4.3 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("spatialAtomizeR")

Format

Qian, Y., Johnson, N., Krieger, N., & Nethery, R. (2026). spatialAtomizeR: Spatial Analysis with Misaligned Data Using Atom-Based Regression Models (Version 0.2.8) [Computer software]. https://doi.org/10.32614/CRAN.package.spatialAtomizeR

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 spatialAtomizeR version 0.2.8 [Data set]. HJJB, LLC. Data release v2026-10-17. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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