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