poems

1.4.0

Pattern-Oriented Ensemble Modeling System

2packages depend

4.8Kdownloads / year

88.5%test coverage

13/13checks pass

Overview

About

Maintained by July PilowskyFirst published 2021-03-298 releasesCRAN page ↗GitHub ↗

A framework of interoperable R6 classes (Chang, 2020, https://CRAN.R-project.org/package=R6) for building ensembles of viable models via the pattern-oriented modeling (POM) approach (Grimm et al.,2005, doi:10.1126/science.1116681). The package includes classes for encapsulating and generating model parameters, and managing the POM workflow. The workflow includes: model setup; generating model parameters via Latin hyper-cube sampling (Iman & Conover, 1980, doi:10.1080/03610928008827996); running multiple sampled model simulations; collating summary results; and validating and selecting an ensemble of models that best match known patterns. By default, model validation and selection utilizes an approximate Bayesian computation (ABC) approach (Beaumont et al., 2002, doi:10.1093/genetics/162.4.2025), although alternative user-defined functionality could be employed. The package includes a spatially explicit demographic population model simulation engine, which incorporates default functionality for density dependence, correlated environmental stochasticity, stage-based transitions, and distance-based dispersal. The user may customize the simulator by defining functionality for translocations, harvesting, mortality, and other processes, as well as defining the sequence order for the simulator processes. The framework could also be adapted for use with other model simulators by utilizing its extendable (inheritable) base classes.

Install

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

install.packages("poems", 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("GlobalEcologyLab/poems")

Development version from GlobalEcologyLab/poems. 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-poems

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-poems

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-poems

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

Health

CRAN checks

13OK

Slowest check: 21.6 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.46

88.5%

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
OK2026-05-02
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-25
11 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 595 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 25%
References docs: 0%

Downloads

4.8K

CRAN downloads in the past year

Rank #12,414 · ~13/day · ~403/mo

Releases R versions

Daily download trend is not available in this view yet.

33830 days

86090 days

4.8K1 year

Compare downloads with other packages →

Also on188 r2u12 autocran

Repository

GitHub ↗ globalecologylab/poems

13Stars

2Forks

0Open issues

0Open PRs

15Releases

180Commits

4Contributors

biogeographypopulation-modelprocess-basedrr-packagerstats

180 commits · Last activity 2025-11-11 · 0% stars, 30d

Stars over time

2024-09-28 · 102026-07-07 · 13

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/globalecologylab/poems on 2026-07-19.

Continuous integration (1)

GitHub Actions

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Docs source (1)

README.Rmd

Research and citation (1)

codemeta.json

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

18 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (12)

abc doParallel foreach fossil lhs metRology R6 raster trend truncnorm (>= 1.0)gdistance qs2

LinkingTo (0)

none

Suggests (6)

knitr rmarkdown sf scales stringi testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

0indirect

epizootic paleopop

Code & Tests

Code Composition

R 25,011 (67%)Rd 5,725 (15%)Vignettes 3,468 (9%)HTML 2,879 (8%)Other 44 (0%)

Code characteristics

Object systems

R621

Cyclomatic complexity: 29.0 median / 82 max
Test cases: 142 / 0.46 per code line

Test coverage

Line coverage

89%

Expression

87.1%

Tests / Examples

88.5% / 47% ex

Functions

7 7 exported

Complexity

42 avg / 82 max

Call network

7 nodes / 6 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

7 functions

Function	Cyclo	Coverage
population_simulator exp	82	86%
population_dispersal exp	79	86%
population_density exp	29	92%
population_env_stoch exp	10	94%
population_transformation exp	12	94%
population_results exp	68	99%

Datasets

Bundled datasets · 4

Name	Class	Rows × Cols	Also ships in
tasmania_ibra_data	data.frame	9 × 4	–
thylacine_bounty_record	data.frame	22 × 11	–
thylacine_example_metrics	data.frame	20,000 × 4	–
thylacine_example_metrics_rerun	data.frame	2,000 × 4	–

People & History

People (6)

Maintainer (1)

July Pilowsky

Author, Maintainer · added in 1.1.0

Authors (6)

July Pilowsky

Author, Maintainer · added in 1.1.0

Author

Author

Author

Author

Author

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.4.0Latest
2025-11-12 · current release · diff ↗
1.3.3
2025-05-07 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.3.2
2025-02-24 · diff ↗
1.3.1
2024-09-19 · diff ↗
unarchivedReturned to CRAN
2024-09-19
R
R 4.4.0 released · 2024-04-24
archivedRemoved from CRAN
2023-12-20
issues were not corrected on re-submission
1.1.0
2023-10-07 · diff ↗
unarchivedReturned to CRAN
2023-10-07
archivedRemoved from CRAN
2023-07-07
issues were not corrected in time
R
R 4.3.0 released · 2023-04-21
1.0.4
2022-09-30 · diff ↗
unarchivedReturned to CRAN
2022-09-30
archivedRemoved from CRAN
2022-09-10
email to the maintainer is undeliverable

Show 5 earlier events

R
R 4.2.0 released · 2022-04-22
1.0.2
2022-01-17 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.0.1
2021-03-29
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2021-03-29
Total releases: 8 / 5 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.1.0
Bundled data: 711 KB / 10 files
Download size: 4.2 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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