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'))

Peer review:

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:

9.72 score 15 stars 33 packages 234 scripts 7.6k downloads 53 mentions 29 exports 27 dependencies

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

TargetResultDate
Doc / VignettesOKNov 04 2024
R-4.5-winNOTENov 04 2024
R-4.5-linuxNOTENov 04 2024
R-4.4-winOKNov 04 2024
R-4.4-macOKNov 04 2024
R-4.3-winERRORNov 04 2024
R-4.3-macERRORNov 04 2024

Exports:acutci.meancoxphSeriesfixRegressionTablefollowupTableformatCIglmSerieslabelUnitslazyDateCodinglazyFactorCodingorgparseInteractionTermsplotConfidencepubformatpublishregressionTablespaghettiogramSpaghettiogramspecialFramesplinePlot.lrmstripessubgroupAnalysissummary.univariateTablesummary.utablesutabletable2x2UnitsunivariateTableutable

Dependencies:clicodetoolsdata.tablediagramdigestfuturefuture.applyglobalsKernSmoothlatticelavalistenvMASSMatrixmultcompmvtnormnumDerivparallellyprodlimprogressrRcppsandwichshapeSQUAREMsurvivalTH.datazoo

Readme and manuals

Help Manual

Help pageTopics
Publish packagePublish-package
Automatic selection and formatting of breaks in 'cut'acut
Compute mean values with confidence intervalsci.mean
Compute mean values with confidence intervalsci.mean.default
CiTable dataCiTable
Run a series of Cox regression modelscoxphSeries
Diabetes data of Dr John SchorlingDiabetes
Expand regression coefficient tablefixRegressionTable
Summary tables for a given followup time point.followupTable
Formatting confidence intervalsformatCI
Run a series of generalized linear regression analysesglmSeries
labelUnitslabelUnits
Efficient coding of date variableslazyDateCoding
Efficient coding of factor levelslazyFactorCoding
Wrapper function for publish with output format orgorg
Parse interaction termsparseInteractionTerms
Plot confidence intervalsplot.ci
Plotting regression coefficients with confidence limitsplot.regressionTable
plot.subgroupAnalysisplot.subgroupAnalysis
Plot confidence intervalsplotConfidence
Print confidence intervalsprint.ci
Printing univariate tablesprint.subgroupAnalysis
print results of 2x2 contingency table analysisprint.table2x2
Printing univariate tablesprint.univariateTable
Format numbers for publicationpubformat
Publishing tables and figurespublish
Tabulizing cause-specific hazard ratio from all causes with confidence limits and Wald test p-values.publish.CauseSpecificCox
Publish tables with confidence intervalspublish.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 formatpublish.matrix
Present logistic regression and Cox regression obtained with mitools::MIcombine based on smcfcs::smcfcs multiple imputation analysispublish.MIresult
Publishing results of riskRegressionpublish.riskRegression
Publish predictive accuracy resultspublish.Score
Format summary table of aov resultspublish.summary.aov
Alternative summary of survdiff resultspublish.survdiff
Regression tableregressionTable
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
SpaghettiogramSpaghettiogram spaghettiogram
Special framespecialFrame
Plot predictions of logistic regressionsplinePlot.lrm
Background and grid color control.stripes
Subgroup Analysis - Interactions and estimatessubgroupAnalysis
Summarize confidence intervalssummary.ci
Formatting regression tablesprint.summary.regressionTable summary.regressionTable
summary.subgroupAnalysissummary.subgroupAnalysis
Preparing univariate tables for publicationsummary.univariateTable summary.utable
Fast summary of a univariate tablesutable
2x2 table calculus for teachingtable2x2
trace datatrace
traceR datatraceR
Add units to data setUnits
Univariate tableunivariateTable utable