Package: Publish 2023.01.17

Publish: Format Output of Various Routines in a Suitable Way for Reports and Publication

A bunch of convenience functions that transform the results of some basic statistical analyses into table format nearly ready for publication. This includes descriptive tables, tables of logistic regression and Cox regression results as well as forest plots.

Authors:Thomas A. Gerds [aut, cre], Christian Torp-Pedersen [ctb], Klaus K Holst [ctb], Brice Ozenne [aut]

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Publish.pdf |Publish.html✨
Publish/json (API)

# Install 'Publish' in R:

install.packages('Publish', repos = c('https://tagteam.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/tagteam/publish/issues

Datasets:

CiTable - CiTable data
Diabetes - Diabetes data of Dr John Schorling
SpaceT - A study was made of all 26 astronauts on the first eight space shuttle flights (Bungo et.al., 1985). On a voluntary basis 17 astronauts consumed large quantities of salt and fluid prior to landing as a countermeasure to space deconditioning, while nine did not.
trace - Trace data
traceR - TraceR data

On CRAN:

29 exports 15 stars 6.04 score 27 dependencies 32 dependents 53 mentions 199 scripts 6.3k downloads

Last updated 2 years agofrom:b027ce49f8. Checks:OK: 3 NOTE: 2 ERROR: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 05 2024
R-4.5-win	NOTE	Sep 05 2024
R-4.5-linux	NOTE	Sep 05 2024
R-4.4-win	OK	Sep 05 2024
R-4.4-mac	OK	Sep 05 2024
R-4.3-win	ERROR	Sep 05 2024
R-4.3-mac	ERROR	Sep 05 2024

Exports:acut ci.mean coxphSeries fixRegressionTable followupTable formatCI glmSeries labelUnits lazyDateCoding lazyFactorCoding org parseInteractionTerms plotConfidence pubformat publish regressionTable spaghettiogram Spaghettiogram specialFrame splinePlot.lrm stripes subgroupAnalysis summary.univariateTable summary.utable sutable table2x2 Units univariateTable utable

Dependencies:cli codetools data.table diagram digest future future.apply globals KernSmooth lattice lava listenv MASS Matrix multcomp mvtnorm numDeriv parallelly prodlim progressr Rcpp sandwich shape SQUAREM survival TH.data zoo

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Publish package	Publish-package
Automatic selection and formatting of breaks in 'cut'	acut
Compute mean values with confidence intervals	ci.mean
Compute mean values with confidence intervals	ci.mean.default
CiTable data	CiTable
Run a series of Cox regression models	coxphSeries
Diabetes data of Dr John Schorling	Diabetes
Expand regression coefficient table	fixRegressionTable
Summary tables for a given followup time point.	followupTable
Formatting confidence intervals	formatCI
Run a series of generalized linear regression analyses	glmSeries
labelUnits	labelUnits
Efficient coding of date variables	lazyDateCoding
Efficient coding of factor levels	lazyFactorCoding
Wrapper function for publish with output format org	org
Parse interaction terms	parseInteractionTerms
Plot confidence intervals	plot.ci
Plotting regression coefficients with confidence limits	plot.regressionTable
plot.subgroupAnalysis	plot.subgroupAnalysis
Plot confidence intervals	plotConfidence
Print confidence intervals	print.ci
Printing univariate tables	print.subgroupAnalysis
print results of 2x2 contingency table analysis	print.table2x2
Printing univariate tables	print.univariateTable
Format numbers for publication	pubformat
Publishing tables and figures	publish
Tabulizing cause-specific hazard ratio from all causes with confidence limits and Wald test p-values.	publish.CauseSpecificCox
Publish tables with confidence intervals	publish.ci
Tabulize hazard ratios with confidence intervals and p-values.	publish.coxph
Tabulize regression coefficients with confidence intervals and p-values.	publish.glm
Pretty printing of test results.	publish.htest
Publishing a matrix in raw, org, latex, or muse format	publish.matrix
Present logistic regression and Cox regression obtained with mitools::MIcombine based on smcfcs::smcfcs multiple imputation analysis	publish.MIresult
Publishing results of riskRegression	publish.riskRegression
Publish predictive accuracy results	publish.Score
Format summary table of aov results	publish.summary.aov
Alternative summary of survdiff results	publish.survdiff
Regression table	regressionTable
A study was made of all 26 astronauts on the first eight space shuttle flights (Bungo et.al., 1985). On a voluntary basis 17 astronauts consumed large quantities of salt and fluid prior to landing as a countermeasure to space deconditioning, while nine did not.	SpaceT
Spaghettiogram	Spaghettiogram spaghettiogram
Special frame	specialFrame
Plot predictions of logistic regression	splinePlot.lrm
Background and grid color control.	stripes
Subgroup Analysis - Interactions and estimates	subgroupAnalysis
Summarize confidence intervals	summary.ci
Formatting regression tables	print.summary.regressionTable summary.regressionTable
summary.subgroupAnalysis	summary.subgroupAnalysis
Preparing univariate tables for publication	summary.univariateTable summary.utable
Fast summary of a univariate table	sutable
2x2 table calculus for teaching	table2x2
trace data	trace
traceR data	traceR
Add units to data set	Units
Univariate table	univariateTable utable