R Observatory: Metrics for reportRmd version 0.1.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

CRAN requires the check problems on this package to be fixed before Nov 14 or it will be archived. See the check details

reportRmd

0.1.3Package record

Tidy Presentation of Clinical Reporting

1packages depend

4.6Kdownloads / year

14.1%test coverage

8/13flavors OK

Overview

About

Maintained by Lisa AveryCRAN page ↗Website ↗

Streamlined statistical reporting in 'Rmarkdown' environments. Facilitates the automated reporting of descriptive statistics, multiple univariate models, multivariable models and tables combining these outputs. Plotting functions include customisable survival curves, forest plots from logistic and ordinal regression and bivariate comparison plots.

Changes in 0.1.3

New features

rm_mvsum() and forestplotMV() now support include_unadjusted parameter to display univariate (unadjusted) estimates alongside multivariable (adjusted) estimates in a single table or plot
forestplotMV() data parameter is now optional - data will be automatically extracted from the model object if not provided
new extract_package_details() function to extract R packages used by a script or markdown file, along with citations.
new scrolling_table() creates scrollable HTML tables for long outputs or keeps regular tables for non-HTML formats

Minor improvements and fixes

improved plotting of survival curves
Cox proportional hazards clustering: fixed bug when clustering is used in coxph models
Date handling in Word tables fixed bug where tables with date columns containing NA values caused errors in Word output
rm_compactsum improvements: fixed output formatting issues, fixed bug with difftime variable handling, improved bolding for corrected p-values, better handling of negative numbers
rm_uvsum fixes: fixed handling of integer predictors, various bug fixes for edge cases
more robust handling of tidy evaluation

Show all changes in 0.1.3Hide the rest of the changes in 0.1.3

HTML output improvements: improved display for special characters in HTML rendered tables

From NEWS.md in the release

Install

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

install.packages("reportRmd", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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-reportrmd

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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-reportRmd

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-reportRmd

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

4ERROR1NOTE8OK

Check messages

ERRORtestsr-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-release-linux-x86_64

r-devel-linux-x86_64-debian-gcc

Running ‘testthat.R’ [7s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(reportRmd)
  > 
  > test_check("reportRmd")
  Using MC sim. Use set.seed() prior to function for reproducible results.
  Using MC sim. Use set.seed() prior to function for reproducible results.
  Saving _problems/test_calculations-348.R
  boundary (singular) fit: see help('isSingular')
  boundary (singular) fit: see help('isSingular')
  boundary (singular) fit: see help('isSingular')
  boundary (singular) fit: see help('isSingular')
  boundary (singular) fit: see help('isSingular')
  
  [ FAIL 1 | WARN 3 | SKIP 0 | PASS 66 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_calculations.R:348:3'): rm_mvsum outputs glmer binomial model with ORs correctly ──
  Expected `output[, 2]` to equal `est`.
  Differences:
      actual              | expected               
  [1] NA                  | NA                  [1]
  [2] "Reference"         | "Reference"         [2]
  [3] "0.37 (0.20, 0.68)" - "0.37 (0.20, 0.67)" [3]
  [4] "0.32 (0.17, 0.61)" | "0.32 (0.17, 0.61)" [4]
  [5] "0.21 (0.09, 0.48)" - "0.21 (0.09, 0.47)" [5]
  
  
  [ FAIL 1 | WARN 3 | SKIP 0 | PASS 66 ]
  Error:
  ! Test failures.
  Execution halted

r-devel-linux-x86_64-fedora-clang

Running ‘testthat.R’ [8s/20s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(reportRmd)
  > 
  > test_check("reportRmd")
  Using MC sim. Use set.seed() prior to function for reproducible results.
  Using MC sim. Use set.seed() prior to function for reproducible results.
  Saving _problems/test_calculations-348.R
  boundary (singular) fit: see help('isSingular')
  boundary (singular) fit: see help('isSingular')
  boundary (singular) fit: see help('isSingular')
  boundary (singular) fit: see help('isSingular')
  boundary (singular) fit: see help('isSingular')
  
  [ FAIL 1 | WARN 3 | SKIP 0 | PASS 66 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_calculations.R:348:3'): rm_mvsum outputs glmer binomial model with ORs correctly ──
  Expected `output[, 2]` to equal `est`.
  Differences:
      actual              | expected               
  [1] NA                  | NA                  [1]
  [2] "Reference"         | "Reference"         [2]
  [3] "0.37 (0.20, 0.68)" - "0.37 (0.20, 0.67)" [3]
  [4] "0.32 (0.17, 0.61)" | "0.32 (0.17, 0.61)" [4]
  [5] "0.21 (0.09, 0.48)" - "0.21 (0.09, 0.47)" [5]
  
  
  [ FAIL 1 | WARN 3 | SKIP 0 | PASS 66 ]
  Error:
  ! Test failures.
  Execution halted

r-devel-linux-x86_64-fedora-gcc

Running ‘testthat.R’ [7s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(reportRmd)
  > 
  > test_check("reportRmd")
  Using MC sim. Use set.seed() prior to function for reproducible results.
  Using MC sim. Use set.seed() prior to function for reproducible results.
  Saving _problems/test_calculations-348.R
  boundary (singular) fit: see help('isSingular')
  boundary (singular) fit: see help('isSingular')
  boundary (singular) fit: see help('isSingular')
  boundary (singular) fit: see help('isSingular')
  boundary (singular) fit: see help('isSingular')
  
  [ FAIL 1 | WARN 3 | SKIP 0 | PASS 66 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_calculations.R:348:3'): rm_mvsum outputs glmer binomial model with ORs correctly ──
  Expected `output[, 2]` to equal `est`.
  Differences:
      actual              | expected               
  [1] NA                  | NA                  [1]
  [2] "Reference"         | "Reference"         [2]
  [3] "0.37 (0.20, 0.68)" - "0.37 (0.20, 0.67)" [3]
  [4] "0.32 (0.17, 0.61)" | "0.32 (0.17, 0.61)" [4]
  [5] "0.21 (0.09, 0.48)" - "0.21 (0.09, 0.47)" [5]
  
  
  [ FAIL 1 | WARN 3 | SKIP 0 | PASS 66 ]
  Error:
  ! Test failures.
  Execution halted

r-release-linux-x86_64

Running ‘testthat.R’ [11s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(reportRmd)
  > 
  > test_check("reportRmd")
  Using MC sim. Use set.seed() prior to function for reproducible results.
  Using MC sim. Use set.seed() prior to function for reproducible results.
  Saving _problems/test_calculations-348.R
  boundary (singular) fit: see help('isSingular')
  boundary (singular) fit: see help('isSingular')
  boundary (singular) fit: see help('isSingular')
  boundary (singular) fit: see help('isSingular')
  boundary (singular) fit: see help('isSingular')
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 66 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_calculations.R:348:3'): rm_mvsum outputs glmer binomial model with ORs correctly ──
  Expected `output[, 2]` to equal `est`.
  Differences:
      actual              | expected               
  [1] NA                  | NA                  [1]
  [2] "Reference"         | "Reference"         [2]
  [3] "0.37 (0.20, 0.68)" - "0.37 (0.20, 0.67)" [3]
  [4] "0.32 (0.17, 0.61)" | "0.32 (0.17, 0.61)" [4]
  [5] "0.21 (0.09, 0.48)" - "0.21 (0.09, 0.47)" [5]
  
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 66 ]
  Error:
  ! Test failures.
  Execution halted

NOTERd contentsr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Rd files without \usage:
  ‘ggkmcif2_2025.Rd’
\arguments should not be documented without \usage.

CRAN check page ↗

Slowest check: 6.1 min · r-release-macos-x86_64

Status changes

ERROR8 OK, 1 NOTE, 4 ERRORNow
ERROR9 OK, 1 NOTE, 3 ERROR2026-10-24
NOTE12 OK, 1 NOTE2026-07-11
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK12 OK2026-04-25

Show 2 earlier changesHide 2 earlier changes

ERROR13 OK, 1 ERROR2026-03-21
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.3

READMEYes · 3,147 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 0.1.3Citation fileNoWebsiteYes · pkgdown

Help pages: 101 (37 internal)
Examples that run: 81%22 run in a plain check · 5 never run
Exported functions with examples: 57%
Documented parameters: 97%
Return-value docs: 78%
Help pages citing references: 6%

Vignettes (1)

reportRmd Package HTML

How these are measured

Downloads

4.6K

CRAN downloads in the past year

Rank #9,112 · ~13/day · ~383/mo

Releases R versions

Daily download trend is not available in this view yet.

38030 days

1.1K90 days

4.6K1 year

Compare downloads with other packages →

Also on111 r2u4 autocran

How downloads are counted

Repository

biostatspmh/reportrmd ↗Organization: biostatsPMH

6Stars

0Forks

1Open issues

0Open PRs

0Releases

388Commits

7Commit identities

388 commits · Last activity 2026-03-23 · +20% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 50%
Median days to close, 50 most recently updated closed issues: 20
Median days to close, 50 most recently updated closed PRs: 218

Stars over time

2025-06-22 · 52026-10-09 · 6

How these are measured

PracticesBeta

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

Checks run against github.com/biostatspmh/reportrmd on 2026-10-22.

Continuous integration (1)

GitHub Actions

Docs source (3)

README.Rmd

GitHub Pages site last deployed 2026-03-23 · The repository has a site deploy workflow

Reproducibility and dev environment (1)

data-raw/

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Show all practicesHide 1 practice

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

22 external dependencies (excludes base and recommended)

Installing reportRmd adds 98 packages (51 with compiled code, 84 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, bslib 5.6 MB.

Depends (1)

R >= 4.2

Imports (18)

aodbootcmprsk cowplot dplyr ggplot2 ggpubr kableExtra knitr lifecycle pander rlang rstudioapi scalesstatssurvivaltidyr tidyselect

LinkingTo (0)

none

Suggests (9)

geepack lme4 lmerTestMASSmicenlmetidycmprsk rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Depends, Imports or LinkingTo, most downloaded first

BiostatsUHNplus

How these are counted

Code & Tests

Datasets

People & History

People (10)

Lisa Avery

Maintainer since 0.0.1 (2022), Author

Ryan Del Bel

Author

Osvaldo Espin-Garcia

Author

Katherine Lajkosz

Author · added in 0.1.0

Clarina Ong

Author · added in 0.1.1

Tyler Pittman

Author

Anna Santiago

Author · added in 0.1.0

Jessica Weiss

Author

Wei Xu

Author

Yanning Wang

Contractor

Releases (5)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.1.3Latest
record
2026-03-20 · current release · diff ↗ ·
removed 1 export
ggkmcif_paste

added 13 exports
autoreg, coeffSum, delta_l, delta_u, extract_package_details, get_cluster_ids, get_event_counts, get_model_coef, get_model_data, ggkmcif2Parameters, gp, mterms, xvar_function
R
R 4.5.0 released · 2025-04-11
0.1.1
record
2025-01-24 · diff ↗ ·
added 3 exports
replace_plot_labels, rm_compactsum, scrolling_table
R
R 4.4.0 released · 2024-04-24
0.1.0
record
2023-11-16 · diff ↗ ·
added 10 exports
clear_labels, excelColLetters, extract_labels, forestplotMV, forestplotUV, forestplotUVMV, ggkmcif2, rm_cifsum, set_labels, set_var_labels
R
R 4.3.0 released · 2023-04-21
0.0.2
record
2023-01-13 · diff ↗
0.0.1
record
2022-10-17
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-10-17
Total releases: 5 / 4 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.2
Bundled data: 7.4 KB / 2 files
Download size: 2.0 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("reportRmd")

Format

Avery, L., Del Bel, R., Espin-Garcia, O., Lajkosz, K., Ong, C., Pittman, T., Santiago, A., Wang, Y., Weiss, J., & Xu, W. (2026). reportRmd: Tidy Presentation of Clinical Reporting (Version 0.1.3) [Computer software]. https://doi.org/10.32614/CRAN.package.reportRmd

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.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for reportRmd version 0.1.3 [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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