R Observatory: Metrics for summata version 0.13.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

summata

0.13.0Package record

Publication-Ready Summary Tables and Forest Plots

0packages depend

3.9Kdownloads / year

78.3%test coverage

13/13flavors OK

Overview

About

Maintained by Paul Hsin-ti McClellandCRAN page ↗GitHub ↗Website ↗Issues ↗

A comprehensive framework for descriptive statistics and regression analysis that produces publication-ready tables and forest plots. Provides a unified interface from descriptive statistics through multivariable modeling, with support for linear models, generalized linear models, Cox proportional hazards, and mixed-effects models. Also includes univariable screening, multivariate regression, model comparison, and export to multiple formats including PDF, DOCX, PPTX, 'LaTeX', HTML, and RTF. Built on 'data.table' for computational efficiency.

Changes in 0.13.0

Speed up desctable(), which now computes rank-test *p*-values from a single sort and derives the grouping structure once per table
Pass the arguments in ... of desctable() (*e.g.*, var.equal = TRUE) to the tests that accept them, with a warning for arguments no test accepts; exclude missing and empty categories from categorical tests, falling back to a Monte Carlo *p*-value when Fisher's exact test exceeds its workspace
Fix categorical totals, median survival intervals at nondefault confidence levels, and the formatting of values of 1,000 or more in desctable(), and show the second level of binary variables in condensed tables
Compute the Gehan-Breslow, Tarone-Ware, and Peto-Peto tests that survtable(test_type = ) names, honor p_digits, list groups in order of first appearance as desctable() does, and match survival time quantiles to their groups when a factor level is empty
Show logical predictors by level, with FALSE as the reference, in regression tables and forest plots
Accept non-syntactic variable names (*e.g.*, "tumor stage"), with or without backticks, in fit(), uniscreen(), multifit(), fullfit(), and survtable(), and read factor levels and variable names that contain a colon correctly
Fix the matching, counts, and labels of interaction terms whose variables have non-syntactic, overlapping, or logical names
Order the variables of the tables of models passed to fit(model = ) and m2dt() as the model formula does, and describe mixed models as univariable or multivariable from their fixed-effect terms
Count the events of Cox models from the event argument of Surv(), coded as Surv() codes it; counts were wrong for status coded 1 and 2, counting-process responses, clogit() models, and events written as expressions
Omit aliased coefficients from forest plots and Cox regression tables, show a factor whose first level is empty against its effective reference level, and drop empty factor levels before fitting Cox models
Compute forest plot intervals as the regression tables do, following summata.conf_method, at the requested conf_level in uniforest(), and with the *t* quantile for linear models
Fix forest plot interaction rows under indent_groups and condense_table, coxforest() intervals and interactions for coxme models, and the fixed-effect terms of mixed models (*e.g.*, log(age)) in glmforest() and lmforest(); draw forest plots when knitr is not installed

Show all changes in 0.13.0Hide the rest of the changes in 0.13.0

Report only the predictor's coefficients in multifit(), with observations rather than events as *n* for Cox models and the given order of outcomes and levels under columns = "both"; fit Cox models to Surv() outcomes, as fit() does; draw the table's estimates in multiforest()
Name the predictor or outcome of a failed fit in uniscreen() and multifit(), and use one core when the number of cores cannot be determined
Compare linear mixed models in compfit() on maximum likelihood fits, include the Brier score in the composite score of logistic models, score the Cox global *p*-value independently of the number format, accept candidates with aliased coefficients, and skip profile intervals that are not displayed; use model-level *N* and Events in compfit() and the fit() print method
Bold significant *p*-values in exported tables under every number format, and keep the *p*-values of factor levels in indented and condensed exports
Compute the c-statistic without pROC and name GLM families without stringr; both are removed from Suggests
Documentation and testing suite revisions

From NEWS.md in the release

Install

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

install.packages("summata", 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("phmcc/summata")

Development version from phmcc/summata. 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-summata

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-summata

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-summata

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

CRAN check page ↗

Slowest check: 11.0 min · r-release-macos-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-07-21
ERROR12 OK, 1 ERROR2026-07-14
OK13 OK2026-07-13

Show 2 earlier changesHide 2 earlier changes

ERROR12 OK, 1 ERROR2026-07-10
OK9 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.13.0

READMEYes · 1,230 wordsVignettesYes · 9 · evaluation depends on the environmentNEWSYes · 100% structured · mentions 0.13.0Citation fileYes · computed when R runs itWebsiteYes

Help pages: 194 (169 internal)
Examples that run: 100%24 run in a plain check (3 of them under a condition)
Exported functions with examples: 100%
Documented parameters: 99%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (9)

How these are measured

Downloads

3.9K

CRAN downloads in the past year

Rank #6,835 · ~11/day · ~321/mo

Releases R versions

Daily download trend is not available in this view yet.

47830 days

1.3K90 days

3.9K1 year

Compare downloads with other packages →

Also on90 r2u3 autocran

How downloads are counted

Repository

phmcc/summata ↗Account: phmcc

0Stars

0Forks

2Open issues

0Open PRs

0Releases

Last activity 2026-10-18

Responsiveness

not measured

Issues over time

2026-07-07 · 02026-08-28 · 2

How these are measured

PracticesBeta

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

Checks run against github.com/phmcc/summata 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

Governance and community (1)

Code of conduct

Docs source (2)

pkgdown

GitHub Pages site last deployed 2026-10-18

Coverage (1)

Coverage reporting

Show all practicesHide 2 practices

Reproducibility and dev environment (1)

data-raw/

Lint, format, editor (2)

lintrLint workflow

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

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Installing summata adds 18 packages (8 with compiled code, 19 MB of source tarballs). Heaviest: ggplot2 6.0 MB, data.table 5.7 MB, isoband 1.5 MB.

Depends (1)

R >= 4.2.0

Imports (8)

data.tablesurvivalggplot2statsgrDevicesparalleltoolsutils

LinkingTo (0)

none

Suggests (17)

MASScoxme flextablegridknitr lme4 MuMIn officer ragg ResourceSelection reformulas rmarkdown systemfonts testthat tinytex withr xtable

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (1)

Paul Hsin-ti McClelland

Listed in earlier versions (1)

McClelland

no longer listed · 0.11.3 to 0.13.0

Releases (5)

Pick two releases to compare their code metrics.

0.13.0Latest
record
2026-10-19 · current release · diff ↗ ·
listed once in CRAN's queue
Seen in one reading of CRAN's incoming queue, at 2026-10-19 00:39 UTC, so it stayed less than the time between readings.
0.12.0
record
2026-05-07 · diff ↗ ·
added 3 exports
forestsave, recdims, tablesave
0.11.5
record
2026-05-07 · diff ↗
R
R 4.6.0 released · 2026-04-24
0.11.4
record
2026-03-20 · diff ↗
0.11.3
record
2026-03-08
R
R 4.5.0 released · 2025-04-11

Across CRAN, the median accepted release of the past year spent 23 hours in the queue, 90% under 11 days.How queue time is measured

Package metadata

First published: 2026-03-08
Total releases: 5 / 1 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.2.0
Bundled data: 20 KB / 2 files
Download size: 2.4 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("summata")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

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 summata version 0.13.0 [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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