R Observatory: Metrics for psfmi version 1.4.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

psfmi

1.4.0

Prediction Model Pooling, Selection and Performance Evaluation Across Multiply Imputed Datasets

0packages depend

5.8Kdownloads / year

0.0%test coverage

13/13checks pass

Overview

About

Maintained by Martijn HeymansFirst published 2019-05-168 releasesCRAN page ↗GitHub ↗

Pooling, backward and forward selection of linear, logistic and Cox regression models in multiply imputed datasets. Backward and forward selection can be done from the pooled model using Rubin's Rules (RR), the D1, D2, D3, D4 and the median p-values method. This is also possible for Mixed models. The models can contain continuous, dichotomous, categorical and restricted cubic spline predictors and interaction terms between all these type of predictors. The stability of the models can be evaluated using (cluster) bootstrapping. The package further contains functions to pool model performance measures as ROC/AUC, Reclassification, R-squared, scaled Brier score, H&L test and calibration plots for logistic regression models. Internal validation can be done across multiply imputed datasets with cross-validation or bootstrapping. The adjusted intercept after shrinkage of pooled regression coefficients can be obtained. Backward and forward selection as part of internal validation is possible. A function to externally validate logistic prediction models in multiple imputed datasets is available and a function to compare models. For Cox models a strata variable can be included. Eekhout (2017) doi:10.1186/s12874-017-0404-7. Wiel (2009) doi:10.1093/biostatistics/kxp011. Marshall (2009) doi:10.1186/1471-2288-9-57.

Install

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

install.packages("psfmi", 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("mwheymans/psfmi")

Development version from mwheymans/psfmi. 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-psfmi

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-psfmi

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-psfmi

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

Health

CRAN checks

13OK

Slowest check: 7.3 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.00

0.0%

Coverage · measured lines

100%

Documentation · exports

18

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
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-07
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-02
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

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 · 279 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 96%
Documented parameters: 92%
Return-value docs: 58%
References docs: 35%

Downloads

5.8K

CRAN downloads in the past year

Rank #7,397 · ~16/day · ~479/mo

Releases R versions

Daily download trend is not available in this view yet.

28830 days

1.2K90 days

5.8K1 year

Compare downloads with other packages →

Also on127 r2u58 c2d4u

Repository

GitHub ↗ mwheymans/psfmi

12Stars

7Forks

3Open issues

1Open PRs

1Releases

427Commits

5Contributors

predictorselectionlogisticregressionimputationimputed-datasetssplinepool

427 commits · Last activity 2025-10-26 · 0% stars, 30d

Stars over time

2025-05-06 · 112026-07-07 · 12

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/mwheymans/psfmi on 2026-08-16.

Continuous integration (1)

GitHub Actions

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

Show all practices

Coverage (1)

Codecov

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

Dependencies

Declared dependencies

24 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.0.0

Imports (18)

ggplot2 normsurvivalmitools pROC rms magrittr rsample mice mitml cvAUC dplyr purrr tidyr tibble stringr lme4 car

LinkingTo (0)

none

Suggests (8)

foreignknitr rmarkdown testthat bookdown readr gtools covr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Martijn Heymans

Maintainer, Author

Authors (1)

Martijn Heymans

Maintainer, Author

Contributors (1)

Iris Eekhout

Contributor

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
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.4.0Latest
2023-06-18 · current release · diff ↗
1.3.0
2023-06-16 · diff ↗
unarchivedReturned to CRAN
2023-06-16
archivedRemoved from CRAN
2023-06-12
issues were not corrected in time
R
R 4.3.0 released · 2023-04-21
1.1.0
2022-11-06 · diff ↗
unarchivedReturned to CRAN
2022-11-06
archivedRemoved from CRAN
2022-11-06
issues were not corrected in time
R
R 4.2.0 released · 2022-04-22
1.0.0
2021-09-23 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.7.1
2021-01-13 · diff ↗
0.5.0
2020-09-24 · diff ↗

Show 4 earlier events

R
R 4.0.0 released · 2020-04-24
0.2.0
2020-02-03 · diff ↗
0.1.0
2019-05-16
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-05-16
Total releases: 8 / 7 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 4.0.0
Bundled data: 256 KB / 24 files
Download size: 431 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Missing Data

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("psfmi")

Format

Heymans, M., & Eekhout, I. (2023). psfmi: Prediction Model Pooling, Selection and Performance Evaluation Across Multiply Imputed Datasets (Version 1.4.0) [Computer software]. https://doi.org/10.32614/CRAN.package.psfmi

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 psfmi version 1.4.0 [Data set]. HJJB, LLC. Data release v2026-08-16. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-16, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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