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rbmi

rbmi: A R package for standard and reference-based multiple imputation methods - Published in JOSS (2022)

https://github.com/insightsengineering/rbmi

Science Score: 93.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 1 DOI reference(s) in JOSS metadata
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Scientific Fields

Engineering Computer Science - 60% confidence
Last synced: 6 months ago · JSON representation

Repository

Reference based multiple imputation R package

Basic Info
Statistics
  • Stars: 20
  • Watchers: 4
  • Forks: 11
  • Open Issues: 40
  • Releases: 17
Created over 4 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing License

README.md

CRAN status R-CMD-check <!-- badges: end -->

Reference Based Multiple Imputation (rbmi)

Overview

The rbmi package is used for the imputation of missing data in clinical trials with continuous multivariate normal longitudinal outcomes. It supports imputation under a missing at random (MAR) assumption, reference-based imputation methods, and delta adjustments (as required for sensitivity analysis such as tipping point analyses). The package implements both Bayesian and approximate Bayesian multiple imputation combined with Rubin's rules for inference, and frequentist conditional mean imputation combined with (jackknife or bootstrap) resampling.

Installation

The package can be installed directly from CRAN via:

install.packages("rbmi")

Note that the usage of Bayesian multiple imputation requires the installation of the suggested package rstan. install.packages("rstan")

Usage

The package is designed around its 4 core functions:

  • draws() - Fits multiple imputation models
  • impute() - Imputes multiple datasets
  • analyse() - Analyses multiple datasets
  • pool() - Pools multiple results into a single statistic

The basic usage of these core functions is described in the quickstart vignette:

vignette(topic = "quickstart", package = "rbmi")

Validation

For clarification on the current validation status of rbmi please see the FAQ vignette.

Support

For any help with regards to using the package or if you find a bug please create a GitHub issue

Owner

  • Name: Roche/Genentech - Insights Engineering
  • Login: insightsengineering
  • Kind: organization
  • Location: Switzerland

Roche/Genentech - Insights Engineering

JOSS Publication

rbmi: A R package for standard and reference-based multiple imputation methods
Published
June 15, 2022
DOI
Volume 7, Issue 74, Page 4251
Authors
Craig Gower-Page
Data and Statistical Sciences, Pharma Development, Roche, Welwyn Garden City, UK
Alessandro Noci
Data and Statistical Sciences, Pharma Development, Roche, Basel, Switzerland
Marcel Wolbers
Data and Statistical Sciences, Pharma Development, Roche, Basel, Switzerland
Editor
Frederick Boehm ORCID
Tags
Biostatistics Clinical Trials Estimands Missing Data Multiple Imputation Reference-based Methods
View PDF Review Thread Software Archive

GitHub Events

Total
  • Create event: 6
  • Release event: 1
  • Issues event: 11
  • Watch event: 2
  • Delete event: 2
  • Issue comment event: 68
  • Member event: 3
  • Push event: 92
  • Pull request review comment event: 65
  • Pull request event: 11
  • Pull request review event: 81
  • Fork event: 4
Last Year
  • Create event: 6
  • Release event: 1
  • Issues event: 11
  • Watch event: 2
  • Delete event: 2
  • Issue comment event: 68
  • Member event: 3
  • Push event: 92
  • Pull request review comment event: 65
  • Pull request event: 11
  • Pull request review event: 81
  • Fork event: 4

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 803
  • Total Committers: 12
  • Avg Commits per committer: 66.917
  • Development Distribution Score (DDS): 0.403
Past Year
  • Commits: 54
  • Committers: 5
  • Avg Commits per committer: 10.8
  • Development Distribution Score (DDS): 0.296
Top Committers
Name Email Commits
Craig Gower-Page c****e@r****m 479
Alessandro Noci a****i@r****m 248
wolbersm 9****m 47
Daniel Sabanes Bove d****e 7
Isaac Gravestock i****k@r****m 6
cicdguy 2****y 4
Dinakar 2****9 4
James Black j****2@r****m 3
Pawel Rucki p****i@g****m 2
walkowif 5****f 1
Arfon Smith a****n 1
Andrew Johnson a****n@a****m 1
Committer Domains (Top 20 + Academic)
roche.com: 4 arjohnsonau.com: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 121
  • Total pull requests: 132
  • Average time to close issues: 4 months
  • Average time to close pull requests: 6 days
  • Total issue authors: 19
  • Total pull request authors: 11
  • Average comments per issue: 1.74
  • Average comments per pull request: 1.28
  • Merged pull requests: 109
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 47
  • Pull requests: 53
  • Average time to close issues: 5 days
  • Average time to close pull requests: 2 days
  • Issue authors: 10
  • Pull request authors: 5
  • Average comments per issue: 1.53
  • Average comments per pull request: 1.38
  • Merged pull requests: 39
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • gowerc (70)
  • nociale (19)
  • tobiasmuetze (7)
  • wolbersm (3)
  • Generalized (2)
  • danielinteractive (2)
  • pawelru (2)
  • harriscw (2)
  • luwidmer (2)
  • gravesti (2)
  • tronieri (1)
  • MayFine (1)
  • osamaidais (1)
  • adrianolszewski (1)
  • clarkliming (1)
Pull Request Authors
  • gowerc (75)
  • nociale (17)
  • danielinteractive (15)
  • pengguanya (6)
  • gravesti (6)
  • cicdguy (5)
  • wolbersm (2)
  • epijim (2)
  • arfon (1)
  • AKlebus (1)
Top Labels
Issue Labels
enhancement (54) bug (42) To be evaluated (9) documentation (7) priority (1) To be done (1) question (1) good first issue (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 421 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 12
  • Total maintainers: 1
cran.r-project.org: rbmi

Reference Based Multiple Imputation

  • Versions: 12
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 421 Last month
Rankings
Forks count: 14.2%
Stargazers count: 15.1%
Average: 21.1%
Downloads: 23.6%
Dependent repos count: 23.9%
Dependent packages count: 28.7%
Maintainers (1)
isaac.gravestock@roche.com
Last synced: 6 months ago

Dependencies

.github/actions/build-src/action.yml actions
  • actions/cache v3 composite
.github/workflows/build_docker.yaml actions
  • actions/cache v3 composite
  • actions/checkout v3 composite
  • docker/build-push-action v3 composite
  • docker/login-action v2 composite
  • docker/setup-buildx-action v2 composite
.github/workflows/build_docker_latest.yaml actions
  • actions/cache v3 composite
  • actions/checkout v3 composite
  • docker/build-push-action v3 composite
  • docker/login-action v2 composite
  • docker/setup-buildx-action v2 composite
.github/workflows/check_for_cran.yaml actions
  • ./.github/actions/rcmdcheck * composite
  • actions/checkout v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
.github/workflows/on_biweekly.yaml actions
  • ./.github/actions/rcmdcheck * composite
  • actions/checkout v3 composite
.github/workflows/on_pr_main.yaml actions
  • ./.github/actions/build-src * composite
  • ./.github/actions/rcmdcheck * composite
  • actions/checkout v3 composite
.github/workflows/on_push.yaml actions
  • ./.github/actions/build-src * composite
  • actions/checkout v3 composite
.github/workflows/validate_generic_master.yaml actions
  • actions/checkout v3 composite
  • insightsengineering/thevalidatoR v1.2.1 composite
  • svenstaro/upload-release-action v2 composite
DESCRIPTION cran
  • R >= 3.4.0 depends
  • Matrix * imports
  • R6 * imports
  • Rcpp >= 0.12.0 imports
  • RcppParallel >= 5.0.1 imports
  • assertthat * imports
  • methods * imports
  • mmrm * imports
  • pkgload * imports
  • rstan >= 2.18.1 imports
  • rstantools >= 2.1.1 imports
  • R.rsp * suggests
  • bookdown * suggests
  • dplyr * suggests
  • emmeans * suggests
  • ggplot2 * suggests
  • knitr * suggests
  • lubridate * suggests
  • mvtnorm * suggests
  • nlme * suggests
  • purrr * suggests
  • rmarkdown * suggests
  • testthat * suggests
  • tibble * suggests
  • tidyr * suggests
misc/docker/Dockerfile docker
  • ${IMAGE} latest build