spatPomp

1.1.0

Inference for Spatiotemporal Partially Observed Markov Processes

0packages depend

6.3Kdownloads / year

100.0%test coverage

13/13checks pass

Overview

About

Maintained by Edward IonidesFirst published 2021-04-1216 releasesCRAN page ↗GitHub ↗

Inference on panel data using spatiotemporal partially-observed Markov process (SpatPOMP) models. The 'spatPomp' package extends 'pomp' to include algorithms taking advantage of the spatial structure in order to assist with handling high dimensional processes. See Asfaw et al. (2024) doi:10.48550/arXiv.2101.01157 for further description of the package.

Install

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

install.packages("spatPomp", 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("spatPomp-org/spatPomp")

Development version from spatPomp-org/spatPomp. 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-spatpomp

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-spatPomp

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-spatPomp

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 6.3 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.44

100.0%

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
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 74%
Return-value docs: 85%
References docs: 49%

Downloads

6.3K

CRAN downloads in the past year

Rank #10,085 · ~17/day · ~529/mo

Releases R versions

Daily download trend is not available in this view yet.

30430 days

1.1K90 days

6.3K1 year

Compare downloads with other packages →

Also on422 r2u37 autocran

Repository

GitHub ↗ spatpomp-org/spatpomp

4Stars

2Forks

0Open issues

0Open PRs

1Releases

560Commits

13Contributors

License GPL-3.0 · 560 commits · Last activity 2025-09-03 · 0% stars, 30d

Stars over time

2025-01-09 · 22026-07-07 · 4

Repository practices

Upstream repositoryBeta

4 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/spatpomp-org/spatpomp on 2026-07-19.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

Makefile

CRAN release process (1)

cran-comments.md

Coverage (1)

Codecov

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

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Depends (3)

R >= 4.1pompmethods

Imports (7)

foreach dplyr tidyr stringr abind rlang ggplot2

LinkingTo (1)

pomp

Suggests (3)

doParallelparalleldoRNG

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (11)

Maintainer (1)

Edward Ionides

Maintainer, Author

Authors (3)

Edward Ionides

Maintainer, Author

Kidus Asfaw

Author

Aaron A. King

Author

Contributors (8)

Haogao Gu

Contributor · added in 0.34.0

Kunyang He

Contributor · added in 1.1.0

Allister Ho

Contributor

Gottfried Julian

Contributor · added in 1.1.0

Jifan Li

Contributor · added in 0.30.2.0

Ning Ning

Contributor · added in 0.32.0

Joonha Park

Contributor

Jesse Wheeler

Contributor · added in 0.30.0.1

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.1.0Latest
2025-09-03 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
1.0.0
2024-11-14 · diff ↗
0.36.1
2024-08-20 · diff ↗
0.35.0
2024-05-31 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.34.2
2024-02-18 · diff ↗
0.34.0
2023-12-03 · diff ↗
0.33.0
2023-08-09 · diff ↗
unarchivedReturned to CRAN
2023-08-09
archivedRemoved from CRAN
2023-06-09
issues were not corrected in time
0.32.0
2023-05-18 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.31.0.0
2023-01-16 · diff ↗
0.30.2.0
2022-12-24 · diff ↗

Show 9 earlier events

0.30.0.1
2022-09-06 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.29.0.0
2022-01-15 · diff ↗
0.28.0.0
2021-09-05 · diff ↗
0.25.0.0
2021-07-28 · diff ↗
0.23.0.0
2021-07-09 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.21.0.0
2021-04-12
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2021-04-12
Total releases: 16 / 5 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.1
Bundled data: 343 KB / 6 files
Download size: 2.6 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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