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rbmiUtils

0.3.0Package record

Utility Functions to Support and Extend the 'rbmi' Package

0packages depend
3.4Kdownloads / year
91.0%test coverage
10/13flavors OK

Overview

About

Provides utility functions that extend the capabilities of the reference-based multiple imputation package 'rbmi'. It supports clinical trial analysis workflows with functions for managing imputed datasets, applying analysis methods across imputations, and tidying results for reporting.

Changes in 0.3.0

CRAN Release

From NEWS.md in the release

Install

Health

CRAN checks
3ERROR10OK
Check messages
ERRORre-building of vignette outputsr-devel-windows-x86_64, r-oldrel-windows-x86_64, r-release-windows-x86_64

r-devel-windows-x86_64

Error(s) in re-building vignettes:
--- re-building 'analyse2.Rmd' using rmarkdown
specified C++17
make cmd is
  make -f "D:/RCompile/recent/R/etc/x64/Makeconf" -f "D:/RCompile/recent/R/share/make/winshlib.mk" CXX='$(CXX17) $(CXX17STD)' CXXFLAGS='$(CXX17FLAGS)' CXXPICFLAGS='$(CXX17PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX17LDFLAGS)' SHLIB_LD='$(SHLIB_CXX17LD)' SHLIB="file1db8435bc6674.dll" WIN=64 TCLBIN= OBJECTS="file1db8435bc6674.o"

make would use
if test "zfile1db8435bc6674.o" != "z"; then \
  if test -e "file1db8435bc6674-win.def"; then \
    echo g++   -shared  -s -static-libgcc -o file1db8435bc6674.dll file1db8435bc6674-win.def file1db8435bc6674.o  "D:/RCompile/CRANpkg/lib/4.7/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.7/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.7/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.7/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.7/RcppParallel/lib/x64 -ltbb -ltbbmalloc -L"d:/rtools45/x86
...[truncated]...
six/lib"  -L"D:/RCompile/recent/R/bin/x64" -lR ; \
    rm -f tmp.def; \
  fi \
fi

Quitting from pipeline.Rmd:160-165 [draws]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `sink()`:
! invalid connection
---
Backtrace:
    ▆
 1. ├─rbmi::draws(data = dat, vars = vars, method = method)
 2. └─rbmi:::draws.bayes(data = dat, vars = vars, method = method)
 3.   └─rbmi:::fit_mcmc(...)
 4.     └─rbmi:::get_stan_model(covariance = method$covariance, prior_cov = method$prior_cov)
 5.       └─rstan::stan_model(...)
 6.         └─rstan:::cxxfunctionplus(...)
 7.           └─base::sink(type = "output")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'pipeline.Rmd' failed with diagnostics:
invalid connection
--- failed re-building 'pipeline.Rmd'

SUMMARY: processing the following files failed:
  'analyse2.Rmd' 'pipeline.Rmd'

Error: Vignette re-building failed.
Execution halted

r-oldrel-windows-x86_64

Error(s) in re-building vignettes:
--- re-building 'analyse2.Rmd' using rmarkdown
make cmd is
  make -f "D:/RCompile/recent/R-4.5.3/etc/x64/Makeconf" -f "D:/RCompile/recent/R-4.5.3/share/make/winshlib.mk" CXX='$(CXX17) $(CXX17STD)' CXXFLAGS='$(CXX17FLAGS)' CXXPICFLAGS='$(CXX17PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX17LDFLAGS)' SHLIB_LD='$(SHLIB_CXX17LD)' SHLIB="file54f9860c55ddc.dll" WIN=64 TCLBIN= OBJECTS="file54f9860c55ddc.o"

make would use
if test "zfile54f9860c55ddc.o" != "z"; then \
  if test -e "file54f9860c55ddc-win.def"; then \
    echo g++  -shared -s -static-libgcc -o file54f9860c55ddc.dll file54f9860c55ddc-win.def file54f9860c55ddc.o  "D:/RCompile/CRANpkg/lib/4.5/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.5/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.5/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.5/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.5/RcppParallel/lib/x64 -ltbb -ltbbmalloc -L"d:/rtools45/x86_64-w6
...[truncated]...
b"  -L"D:/RCompile/recent/R-4.5.3/bin/x64" -lR ; \
    rm -f tmp.def; \
  fi \
fi

Quitting from pipeline.Rmd:160-165 [draws]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `sink()`:
! invalid connection
---
Backtrace:
    ▆
 1. ├─rbmi::draws(data = dat, vars = vars, method = method)
 2. └─rbmi:::draws.bayes(data = dat, vars = vars, method = method)
 3.   └─rbmi:::fit_mcmc(...)
 4.     └─rbmi:::get_stan_model(covariance = method$covariance, prior_cov = method$prior_cov)
 5.       └─rstan::stan_model(...)
 6.         └─rstan:::cxxfunctionplus(...)
 7.           └─base::sink(type = "output")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'pipeline.Rmd' failed with diagnostics:
invalid connection
--- failed re-building 'pipeline.Rmd'

SUMMARY: processing the following files failed:
  'analyse2.Rmd' 'pipeline.Rmd'

Error: Vignette re-building failed.
Execution halted

r-release-windows-x86_64

Error(s) in re-building vignettes:
--- re-building 'analyse2.Rmd' using rmarkdown
specified C++17
make cmd is
  make -f "D:/RCompile/recent/R-4.6.1/etc/x64/Makeconf" -f "D:/RCompile/recent/R-4.6.1/share/make/winshlib.mk" CXX='$(CXX17) $(CXX17STD)' CXXFLAGS='$(CXX17FLAGS)' CXXPICFLAGS='$(CXX17PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX17LDFLAGS)' SHLIB_LD='$(SHLIB_CXX17LD)' SHLIB="file571ac57455045.dll" WIN=64 TCLBIN= OBJECTS="file571ac57455045.o"

make would use
if test "zfile571ac57455045.o" != "z"; then \
  if test -e "file571ac57455045-win.def"; then \
    echo g++   -shared  -s -static-libgcc -o file571ac57455045.dll file571ac57455045-win.def file571ac57455045.o  "D:/RCompile/CRANpkg/lib/4.6/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.6/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.6/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.6/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.6/RcppParallel/lib/x64 -ltbb -ltbbmalloc -L"d:/
...[truncated]...
b"  -L"D:/RCompile/recent/R-4.6.1/bin/x64" -lR ; \
    rm -f tmp.def; \
  fi \
fi

Quitting from pipeline.Rmd:160-165 [draws]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `sink()`:
! invalid connection
---
Backtrace:
    ▆
 1. ├─rbmi::draws(data = dat, vars = vars, method = method)
 2. └─rbmi:::draws.bayes(data = dat, vars = vars, method = method)
 3.   └─rbmi:::fit_mcmc(...)
 4.     └─rbmi:::get_stan_model(covariance = method$covariance, prior_cov = method$prior_cov)
 5.       └─rstan::stan_model(...)
 6.         └─rstan:::cxxfunctionplus(...)
 7.           └─base::sink(type = "output")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'pipeline.Rmd' failed with diagnostics:
invalid connection
--- failed re-building 'pipeline.Rmd'

SUMMARY: processing the following files failed:
  'analyse2.Rmd' 'pipeline.Rmd'

Error: Vignette re-building failed.
Execution halted
ERRORtestsr-devel-windows-x86_64, r-oldrel-windows-x86_64, r-release-windows-x86_64

r-devel-windows-x86_64

Running 'spelling.R' [0s]
  Running 'testthat.R' [132s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(rbmiUtils)
  > 
  > test_check("rbmiUtils")
  
  Attaching package: 'dplyr'
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  v All outcome values are complete -- no missing data to impute.
  i You may not need `data_ice` for `rbmi::draws()`.
  v All outcome values are complete -- no missing data to impute.
  i You may not need `data_i
...[truncated]...
an::stan_model(...)
    6.         └─rstan:::cxxfunctionplus(...)
    7.           ├─pkgbuild::with_build_tools(...)
    8.           │ └─pkgbuild:::withr_with_path(rtools_path(), code)
    9.           │   └─base::force(code)
   10.           └─inline::cxxfunction(...)
   11.             └─inline:::compileCode(f, code, language = language, verbose = verbose)
  ── Error ('test-utils.R:39:3'): positive test get_imputed_data (from vignettes) ──
  Error in `sink(type = "output")`: invalid connection
  Backtrace:
      ▆
   1. ├─rbmi::draws(data = dat, vars = vars, method = method, quiet = TRUE) at test-utils.R:39:3
   2. └─rbmi:::draws.bayes(...)
   3.   └─rbmi:::fit_mcmc(...)
   4.     └─rbmi:::get_stan_model(covariance = method$covariance, prior_cov = method$prior_cov)
   5.       └─rstan::stan_model(...)
   6.         └─rstan:::cxxfunctionplus(...)
   7.           └─base::sink(type = "output")
  
  [ FAIL 2 | WARN 16 | SKIP 2 | PASS 1024 ]
  Error:
  ! Test failures.
  Execution halted

r-oldrel-windows-x86_64

Running 'spelling.R' [0s]
  Running 'testthat.R' [173s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(rbmiUtils)
  > 
  > test_check("rbmiUtils")
  
  Attaching package: 'dplyr'
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  v All outcome values are complete -- no missing data to impute.
  i You may not need `data_ice` for `rbmi::draws()`.
  v All outcome values are complete -- no missing data to impute.
  i You may not need `data_i
...[truncated]...
an::stan_model(...)
    6.         └─rstan:::cxxfunctionplus(...)
    7.           ├─pkgbuild::with_build_tools(...)
    8.           │ └─pkgbuild:::withr_with_path(rtools_path(), code)
    9.           │   └─base::force(code)
   10.           └─inline::cxxfunction(...)
   11.             └─inline:::compileCode(f, code, language = language, verbose = verbose)
  ── Error ('test-utils.R:39:3'): positive test get_imputed_data (from vignettes) ──
  Error in `sink(type = "output")`: invalid connection
  Backtrace:
      ▆
   1. ├─rbmi::draws(data = dat, vars = vars, method = method, quiet = TRUE) at test-utils.R:39:3
   2. └─rbmi:::draws.bayes(...)
   3.   └─rbmi:::fit_mcmc(...)
   4.     └─rbmi:::get_stan_model(covariance = method$covariance, prior_cov = method$prior_cov)
   5.       └─rstan::stan_model(...)
   6.         └─rstan:::cxxfunctionplus(...)
   7.           └─base::sink(type = "output")
  
  [ FAIL 2 | WARN 16 | SKIP 2 | PASS 1024 ]
  Error:
  ! Test failures.
  Execution halted

r-release-windows-x86_64

Running 'spelling.R' [0s]
  Running 'testthat.R' [128s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(rbmiUtils)
  > 
  > test_check("rbmiUtils")
  
  Attaching package: 'dplyr'
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  v All outcome values are complete -- no missing data to impute.
  i You may not need `data_ice` for `rbmi::draws()`.
  v All outcome values are complete -- no missing data to impute.
  i You may not need `data_i
...[truncated]...
an::stan_model(...)
    6.         └─rstan:::cxxfunctionplus(...)
    7.           ├─pkgbuild::with_build_tools(...)
    8.           │ └─pkgbuild:::withr_with_path(rtools_path(), code)
    9.           │   └─base::force(code)
   10.           └─inline::cxxfunction(...)
   11.             └─inline:::compileCode(f, code, language = language, verbose = verbose)
  ── Error ('test-utils.R:39:3'): positive test get_imputed_data (from vignettes) ──
  Error in `sink(type = "output")`: invalid connection
  Backtrace:
      ▆
   1. ├─rbmi::draws(data = dat, vars = vars, method = method, quiet = TRUE) at test-utils.R:39:3
   2. └─rbmi:::draws.bayes(...)
   3.   └─rbmi:::fit_mcmc(...)
   4.     └─rbmi:::get_stan_model(covariance = method$covariance, prior_cov = method$prior_cov)
   5.       └─rstan::stan_model(...)
   6.         └─rstan:::cxxfunctionplus(...)
   7.           └─base::sink(type = "output")
  
  [ FAIL 2 | WARN 16 | SKIP 2 | PASS 1024 ]
  Error:
  ! Test failures.
  Execution halted

CRAN check page ↗

Slowest check: 23.5 min · r-oldrel-macos-x86_64
Status changes
  • ERROR10 OK, 3 ERRORNow
  • ERROR12 OK, 1 ERROR2026-09-04
  • OK13 OK2026-08-05
  • NOTE12 OK, 1 NOTE2026-08-01
  • OK14 OK2026-04-22
  • ERROR13 OK, 1 ERROR2026-04-18
Show 1 earlier changeHide 1 earlier change
  • OK14 OK2026-03-10
Advisories

none known

Documentation

In release 0.3.0
READMEYes · 335 wordsVignettesYes · 6 · evaluation depends on the environmentNEWSYes · 100% structured · mentions 0.3.0Citation fileNo
Help pages
36 (4 internal)includes a package overview page
Examples that run
40%12 run in a plain check · 14 only when donttest examples are enabled (R CMD check --as-cran) · 4 never run
Exported functions with examples
100%
Documented parameters
100%
Return-value docs
100%
Help pages citing references
0%

Downloads

3.4K
CRAN downloads in the past year
Rank #17,265 · ~9/day · ~283/mo
Daily download trend is not available in this view yet.
25230 days
74390 days
3.4K1 year
Compare downloads with other packages →
Also on105 r2u6 autocran

Repository

4Stars
1Forks
2Open issues
2Open PRs
5Releases
146Commits
2Commit identities
multiple-imputationrrbmiutils
License file reads as GPL-3.0 · 146 commits · Last activity 2026-02-16 · 0% stars, 30d · Default branch at 0.3.0.9000, ahead of CRAN 0.3.0 (checked 2026-10-21)
Responsiveness
How these are sampled
PRs merged (all time)
100%
Median days to close, 50 most recently updated closed issues
1
Median days to close, 50 most recently updated closed PRs
0

Stars over time

2025-10-11 · 42026-07-07 · 4
PracticesBeta

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

Checks run against github.com/openpharma/rbmiutils on 2026-10-21.

Continuous integration (2)
GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (4)
README.Rmdpkgdown

GitHub Pages site last deployed 2026-02-16 · The repository has a site deploy workflow

Coverage (1)
Coverage reporting
Reproducibility and dev environment (1)
data-raw/
Show all practicesHide 2 practices
CRAN release process (1)
cran-comments.md
Lint, format, editor (1)
RStudio project
How this is detected·Detection ruleset v4 (2026-10-20)
AI coding toolsBeta

This repository shows signs of AI coding tools.

  • Claude Codefirst seen 2026-01-24
    Named in .Rbuildignore: .claude
    Commits: 5 by its own account · at least 7 crediting it in the message
From outside contributors
  • Claude Code
    Pull requests: 2 from outside contributors, first on 2026-01-25, 2 from forks
Models named in its commits
  • Claude Sonnet 4.54 commits · Jan 2026
  • Claude Opus 4.53 commits · Jan 2026
Counts are commits, not lines of code. Commits by a tool's accounts count once across all of its accounts. Commits crediting it are the largest count among its credit lines, a minimum.How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies
20 external dependencies (excludes base and recommended)

Installing rbmiUtils adds 51 packages (28 with compiled code, 32 MB of source tarballs). Heaviest: stringi 11 MB, Rcpp 1.8 MB, RcppEigen 1.7 MB.

Depends (1)
R >= 4.1
LinkingTo (0)
none
Enhances (0)
none
Reverse dependencies
0direct
0indirect

Nothing depends on this yet.

Datasets

People & History

People (4)
Author, Maintainer since 0.1.4 (2025), Copyright holder
Author · added in 0.3.0
Contributor
Listed in earlier versions (1)
no longer listed · 0.1.4 to 0.1.8
Releases (4)

Pick two releases to compare their code metrics.

  • R
    R 4.6.0 released · 2026-04-24
  • 0.3.0Latest
    record
    2026-02-16 · current release · diff ↗ ·
    added 18 exports
    combine_results, create_impid, describe_draws, describe_imputation, efficacy_table, expand_imputed_data, extract_lsm, extract_trt_effects, format_estimate, format_pvalue, format_results, format_results_table, plot_forest, pool_to_ard, prepare_data_ice, reduce_imputed_data, summarise_missingness, validate_data
  • unarchivedReturned to CRAN
    2026-01-24
  • 0.1.8
    record
    2026-01-24 · diff ↗
  • archivedRemoved from CRAN
    2025-11-19
    requires archived package 'rbmi'
  • 0.1.6
    record
    2025-09-13 · diff ↗
  • 0.1.4
    record
    2025-05-23
  • R
    R 4.5.0 released · 2025-04-11

Package metadata

First published
2025-05-23
Total releases
4 / 1 yrs
License
GPL (>= 3) OSI
Minimum R
≥ 4.1
Bundled data
63 KB / 2 files
Download size
3.0 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("rbmiUtils")
Baillie, M., Muetze, T., Talboys, J., & Widmer, L. A. (2026). rbmiUtils: Utility Functions to Support and Extend the 'rbmi' Package (Version 0.3.0) [Computer software]. https://doi.org/10.32614/CRAN.package.rbmiUtils

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.

APA

Balamuta, J. J. (2026). R Observatory: Metrics for rbmiUtils version 0.3.0 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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