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reportRmd 0.1.4

New features

• new predsum() summarises binary prediction model performance (sensitivity, specificity, PPV, NPV, accuracy, AUC, AUC-PR, F1, Brier score) with Clopper-Pearson or bootstrap CIs; output presets “epi”, “data-science”, “all” or a custom set of statistics
• support for Firth-penalised logistic regression (logistf) models in rm_mvsum(), with penalised likelihood ratio global p-values and profile penalised likelihood CIs
• rm_uvsum() and rm_mvsum() now support clustered coxph models, reporting robust Wald tests
• rm_survsum() and rm_cifsum() now accept factor or character status variables; rm_cifsum() works when there are no censored observations
• rm_covsum() and rm_compactsum() Monte Carlo p-values and predsum() bootstrap CIs are now reproducible (B and seed arguments; RNG state is restored)
• VIF calculation now uses type = "predictor" in the presence of interactions

Minor improvements and fixes

• rm_mvsum(include_unadjusted = TRUE): fixed failures with coxph models, non-95% CIwidth, formulas stored in variables, dot formulas and transformed terms; continuous covariates and continuous:continuous interactions are no longer dropped from the unadjusted column; digits, CIwidth, whichp and showEvent are now passed to the univariate models
• rm_uvsum(): excluded covariates (dates, the response, single-value variables) are no longer fit; reflevel now works with ordered factors; removeInf is now applied
• rm_covsum() and rm_compactsum() now use expected rather than observed cell counts to choose the exact test, so the two functions agree; the grouping variable is dropped from covariates; non-numeric p-values (e.g. “excl”) are no longer adjusted
• rm_covsum(): fixed error with date variables on Windows
• ggkmcif2(): fixed curves being cut off when times was shorter than the data range; accepts US spelling of arguments; works with ggplot2 >= 3.4.0 (now the stated minimum)
• psthr() displays “Not Estimable” only when all values are NA
• fixed display of special characters in column headers
• fixed unescaped variable names in getVarLevels(), Global p-values being adjusted and double-formatted in bolded output, and a tidyselect deprecation warning for character column names
• consistent tidy evaluation (enquo) for variable selection
• vignette: corrected include_unadjusted section; new Prediction Metrics and Reproducibility sections
• expanded test suite

reportRmd 0.1.1

New features

• new more compact and flexible reporting function (rm_compactsum) that allows more control over each variable summarised and displays text summarising which tests and effect sizes were computed
• new function to apply variable labels to ggplots (replace_plot_labels)
• more comprehensive model summary function to allow plot extensions
• incorporated tidyselect into main summary functions
• support for tidycmprsk models
• ability to output to a scrolling table in HTML formats

Minor improvements and fixes

• fixes to special characters in HTML output
• removed ability to force Wald confidence intervals, confidence intervals now computed by the updated confint in base R
• rm_mvsum and rm_uvsum have been updated in the backend to enable easier extendibility to different model types
• bug fix in nestTable so variables order properly with repeat level names
• numerous bug fixes in formatting of tables, especially with duplicated variable and level names
• added automated testing of the proportional hazards assumption when reporting coxph models
• bug fix for computing global p-values in models with offset terms
• documentation updates

reportRmd 0.1.0

New features

• cumulative incidence can now be summarised by event type and time
• revised survival curves are now properly aligned and return ggplots
• variable labels are automatically displayed in summary tables
• forest plots now support poisson and negative binomial models
• options to globally set the number of digits for a report

Minor improvements and fixes

• updated excelCol to handle column ranges (ie A-Z, instead of A,B,C,…)
• updated mvsum to accept negative binomial models from MASS
• updated uvsum to fit negative binomial models
• differentiated univariate and multivariable estimates in forest plots with shapes
• added functionality to export tables in html and latex formats
• added functionality to summarise date variables
• previously the digit argument did not work for variables with more than one class, this has been fixed
• long data calls (as may be created with tidy statements) are now supported in summary functions
• table bolding for interaction terms is now consistent
• Total N, Number of Events now properly reported when interactions are present
• nestTable now works properly with two-column tables
• covTitle argument restored in rm_covsum

reportRmd 0.0.2

• Added functionality to include effect sizes in summary tables
• forestplot2 now works with geeglm objects

Bug fixes: - fixed bug where some p-values didn’t output after update to R 4.2.2 - special characters now better shown in tables - fixed bug so that NA are always shown as blank - fixed bug in nestTable so that variable indenting is consistent

reportRmd 0.0.1

• 5 October 2022 first CRAN release

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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