R Observatory: Metrics for crane version 0.3.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

crane

0.3.2Package record

Supplements the 'gtsummary' Package for Pharmaceutical Reporting

1packages dependsuggested by 1

11.7Kdownloads / year

97.1%test coverage

13/13flavors OK

Overview

About

Maintained by Joe ZhuCRAN page ↗GitHub ↗Website ↗Issues ↗Declared funder: F. Hoffmann-La Roche AG

Tables summarizing clinical trial results are often complex and require detailed tailoring prior to submission to a health authority. The 'crane' package supplements the functionality of the 'gtsummary' package for creating these often highly bespoke tables in the pharmaceutical industry.

Changes in 0.3.2

New Functions and Functionality

Added g_lineplot() for creating line plots with optional summary statistics table. Includes helper functions calc_stats(), g_lineplot_table(), and preprocess_lineplot_data().
Added ard_tabulate_abnormal_by_baseline() for creating an Analysis Results Data (ARD) object counting participants with abnormal assessments, stratified by their baseline status.
Added tbl_mmrm() and get_mmrm_results() functions to create regression tables for Mixed Models for Repeated Measures (MMRM). (#163)
Added gg_mmrm_lineplot() to create line plots of MMRM results. (#181)
Added gg_pkc_lineplot() to create line plots for PK data. (#185)
Added annotate_gg_pkc() to add optional summary statistics table to

gg_pkc_lineplot(). (#189)

Refactored the underlying data.frame alignment and rendering methodology used for plot annotations. Functions for table annotation now use a completely rebuilt engine that ensures X-axis synchronization for stacked tables (annotate_riskdf()) and flexible, reliable placement for floating tables (annotate_surv_med(), annotate_coxph()). (#189)
Refactored functions for lineplot plotting - added gg_lineplot() and annotate_gg() to create lineplots and annotate summary statistics table. (#184)
Added functions reverse_ci(), reverse_rate_difference() to reverse confidence intervals and rate differences in tables from add_row_difference(). (#204)
g_lineplot(), g_lineplot_table(), and preprocess_lineplot_data() were deprecated. (#184)

Show all changes in 0.3.2Hide the rest of the changes in 0.3.2

Added tbl_coxph() to render pairwise Cox proportional hazards results as a gtsummary table. (#159)
Added tbl_hierarchical_incidence_rate() which computes the incidence rate of adverse events (#211)
Added adjust_stat_columns_wrap() which keep the presentation of statistics in one row (#219)
get_cox_pairwise_df() now allows for different methods to compute p-value (#191) and to handle ties (#193).
tbl_coxph() now accepts a data.frame created by get_cox_pairwise_df() as input. (#207)
Added add_grade_column() to inject a grade-label column into tbl_hierarchical_rate_by_grade() output. Decoupled from the table builder to prevent Cartesian join explosion in tbl_merge(). (#226)
get_cox_pairwise_df() now fully supports strata() terms in survival formulas (#256).
The "likelihood-ratio" test now intelligently switches between survival::survreg() (for unstratified models) and survival::coxph() (for stratified models) (#256).
Stripped package namespace prefixes (e.g., survival::) from survival formulas to prevent evaluation errors (#256).
Added ... support in get_cox_pairwise_df() for conf.int (e.g., to adjust CI level) and robust = TRUE (for robust standard errors).

Other Updates

tbl_hierarchical_rate_and_count() now emits zero-rows for unobserved factor levels in the first hierarchical variable. (#233)
df2gg_aligned() and df2gg_floating() now preserve original ggplot objects in attr(result, "plotlist") for downstream data extraction after combining with cowplot. (#208)
Remove warning when data has more levels than needed for grade_groups on tbl_hierarchical_rate_by_grade.
Changed the default conf.type from "log" to "plain" (linear) in tbl_survfit_times() and tbl_survfit_quantiles() to align with GDSR guidelines. (#173)
Removed bold from headers when using tbl_strata() (#133).
Unified border width in theme_gtsummary_roche() to 0.5 for header. (#154)
Added example on how to stratify tbl_baseline_chg() by PARAM and split into a list.
Adjusted tbl_mmrm() to allow base_df = NULL.
Fixed two bugs related to summary statistics calculation in ard_tabulate_abnormal_by_baseline(). (#198)
Fixed a bug in gg_pkc_lineplot() causing misplaced error bars on a log scale. (#199)
Adjusted gg_pkc_lineplot() to use tbl_roche_summary() for automatic decimals formatting.
Adjusted tbl_hierarchical_incidence_rate() to handle first event as well as

all events (#217)

Adjusted tbl_baseline_chg() to allow for custiomization of display statistics (#222)
Changed baseline statistic argument in tbl_baseline_chg() (#224)
Adjusted modify_zero_recode() to account for strings comprising regular and non-breaking spaces (#230)
tbl_roche_subgroups() now shows n, Events, and Median per arm when time_to_event is specified. The total column shows Total Events instead of Total n. (#235)
Skip tests if suggested packages are missing (Failing test due to missing suggested package #252, @llrs-roche)
The default "log-rank" test now uses survival::survdiff() instead of coin, aligning output more closely with SAS and rtables

From NEWS.md in the release

Install

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

install.packages("crane", 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("insightsengineering/crane")

Development version from insightsengineering/crane. 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-crane

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-crane

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-crane

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

13OK

Additional issues

donttest

CRAN check page ↗

Slowest check: 7.2 min · r-devel-linux-x86_64-debian-clang

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-07-04
WARNING12 OK, 1 WARNING2026-07-03
OK13 OK2026-06-09

Show 6 earlier changesHide 6 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-09
ERROR12 OK, 1 ERROR2026-05-03
OK13 OK2026-05-02
ERROR11 OK, 1 ERROR2026-04-25
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.3.2

READMEYes · 136 wordsVignettesNoNEWSYes · 100% structured · mentions 0.3.2Citation fileNoWebsiteYes · pkgdown

The repository also keeps web-only articles.

Help pages: 47 (12 internal)includes a package overview page
Examples that run: 89%40 run in a plain check (14 of them under a condition) · 5 never run
Exported functions with examples: 97%
Documented parameters: 79%
Return-value docs: 97%
Help pages citing references: 0%

How these are measured

Downloads

11.7K

CRAN downloads in the past year

Rank #5,747 · ~32/day · ~976/mo

Releases R versions

Daily download trend is not available in this view yet.

48430 days

1.4K90 days

11.7K1 year

Compare downloads with other packages →

Also on123 r2u9 autocran

How downloads are counted

Repository

insightsengineering/crane ↗Organization: insightsengineering

15Stars

7Forks

33Open issues

7Open PRs

5Releases

445Commits

16Commit identities

rreproducible-researchsummary-statisticsgt

445 commits · Last activity 2026-10-15 · 0% stars, 30d · Default branch at 0.4.0.9003, ahead of CRAN 0.3.2 (checked 2026-10-21)

Responsiveness

How these are sampled

PRs merged (all time): 90%
Median days to close, 50 most recently updated closed issues: 8
Median days to close, 50 most recently updated closed PRs: 2

Stars over time

2025-08-20 · 52026-07-07 · 15

How these are measured

PracticesBeta

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

Checks run against github.com/insightsengineering/crane on 2026-10-21.

Continuous integration (3)

GitHub ActionsR CMD check workflowGitLab CI

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

Governance and community (5)

Code of conduct (inherited from insightsengineering)Contributing guideIssue templatesPR template

Funding links: pharmaverse.org

Docs source (3)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-10-15

pkgdown site last built 2026-10-02

Coverage (1)

Coverage reporting

Show all practicesHide 2 practices

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (2)

lintrRStudio project

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

AI coding toolsBeta

This repository shows signs of AI coding tools.

GitHub Copilotfirst seen 2026-02-12
Pull request: opened by its own account
Commits: 3 by its own account · at least 8 crediting it in the message
Claude Codefirst seen 2026-10-14
Commits: at least 1 crediting it in the message

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

30 external dependencies (excludes base and recommended)

Installing crane adds 85 packages (44 with compiled code, 77 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (2)

R >= 4.2gtsummary

Imports (18)

broom cards cardx cli (>= 3.6.4)cowplot dplyr flextable (>= 0.9.7)ggplot2 glue gt labeling lifecycle rlang scales scales (>= 1.3.0)survivaltibble tidyr

LinkingTo (0)

none

Suggests (12)

broom.helpers coin emmeans labelled magick mmrm parameters pharmaverseadam testthat tidyselect withr yaml

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Depends 1

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

cardinalfda

Suggests, most downloaded first

autoslider.core

How these are counted

Code & Tests

People & History

People (8)

Joe Zhu

Maintainer since 0.3.1 (2026) · added in 0.3.1

Davide Garolini

Author

Daniel D. Sjoberg

Author

Original creator of the package

Jan Szczypiński

Author · added in 0.3.2

Chi Zhang

Author · added in 0.3.2

Emily de la Rua

Author

Abinaya Yogasekaram

Contributor

F. Hoffmann-La Roche AG

Copyright holder, Funder

Previously maintained by Daniel D. Sjoberg (0.1.0 to 0.3.0).

Releases (5)

Pick two releases to compare their code metrics.

0.3.2Latest
record
2026-06-03 · current release · diff ↗ ·
removed 1 export
g_forest

added 21 exports
add_forest, add_grade_column, adjust_stat_columns_wrap, annotate_lineplot_df, annotate_pkc_df, ard_tabulate_abnormal_by_baseline, df_add_poolings, g_lineplot, g_lineplot_table, get_mmrm_results, gg_lineplot, gg_mmrm_lineplot, gg_pkc_lineplot, preprocess_lineplot_data, reverse_ci, reverse_rate_difference, tbl_coxph, tbl_hierarchical_incidence_rate, tbl_mmrm, tbl_rmpt, tbl_with_pools
R
R 4.6.0 released · 2026-04-24
0.3.1
record
2026-01-21 · diff ↗ ·
added 8 exports
annotate_coxph, annotate_riskdf, annotate_surv_med, g_forest, get_cox_pairwise_df, gg_km, process_survfit, tbl_roche_subgroups
0.3.0
record
2025-12-06 · diff ↗ ·
removed 1 export
label_style_number

added 4 exports
add_difference_row, label_roche_number, style_roche_number, tbl_null_report
0.2.0
record
2025-08-29 · diff ↗ ·
removed 4 exports
add_blank_row, all_categorical, all_continuous, roche_pvalue

added 22 exports
add_blank_rows, add_hierarchical_count_row, add_overall, filter_hierarchical, label_roche_percent, label_roche_ratio, label_style_number, modify_header_rm_md, modify_zero_recode, remove_duplicate_keys, sort_hierarchical, style_roche_percent, style_roche_pvalue, style_roche_ratio, tbl_baseline_chg, tbl_hierarchical_rate_and_count, tbl_hierarchical_rate_by_grade, tbl_listing, tbl_roche_summary, tbl_shift, tbl_survfit_quantiles, tbl_survfit_times
R
R 4.5.0 released · 2025-04-11
0.1.0
record
2025-02-24
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2025-02-24
Total releases: 5 / 1 yrs
License: Apache License 2.0 OSI
Minimum R: ≥ 4.2
Download size: 271 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("crane")

Format

Zhu, J., F. Hoffmann-La Roche AG, Garolini, D., Sjoberg, D. D., Szczypiński, J., Yogasekaram, A., Zhang, C., & de la Rua, E. (2026). crane: Supplements the 'gtsummary' Package for Pharmaceutical Reporting (Version 0.3.2) [Computer software]. https://doi.org/10.32614/CRAN.package.crane

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 crane version 0.3.2 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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