NEWS.md

In stopsack/khsmisc: Miscellaneous functions for epidemiology research

khsmisc 0.5.0

• Remove deprecated functions that have moved to the rifttable package:
• table2(): the core function of rifttable
• table1(): see rifttable::table1_design()
• scoreci(), survdiff_ci(), rates(): now internal functions available via rifttable
• mytab(): use khsmisc::tabulate_rowcol()
• mygt() is deprecated in favor of rifttable::rt_gt()
• Compatibility with forcats::fct_na_value_to_level() in {forcats} >= 1.0.0
• Add examples how to alternatively define make_exclusions() criteria
• Start reducing dependencies
• Make corrmat() font size more customizable

khsmisc 0.4.6

• table1() and table2() have been superseded by the more flexible and more lightweight {rifttable} package. They will remain available in this package for the near future as underlying packages permit.
• Keep table2() compatible with {dplyr} 1.1.0 (input type checks)

khsmisc 0.4.5

• Provide workaround for gt tables to allow knitting to github_document: mygt() and table1() now export directly to markdown, using knitr::kable(), eliminating the extraneous inline CSS. The tab_style() and tab_footnote() functions are wrappers that also accept on kable tables.
• Update RMarkdown template: here(), knit to github_document by default.
• brickchart(): add clip and flip options
• table2(): also pass confounders, trend to custom functions
• Required updated {gt}, {gtsummary}; remove dependencies {survminer}, {svglite}; add requirement for {knitr}, suggest the {here} package

khsmisc 0.4.4

• table2(): add option to suppress estimates if per-cell count lower than the design option nmin
• brickchart(): make proportion and counts per group available for labeling
• table1(): display one or more unstratified datasets

khsmisc 0.4.3

• table1():
• Add option to display multiple stratified datasets side-by-side
• Adapt to gtsummary's removal of global options to avoid warnings and format percentages to no decimal digits even at <10%
• table2():
• Add type = "irrrob", Poisson models with robust standard errors for ratios of continuous outcomes
• Suppress horizontal rules between results from type and type2
• Update vignette about ratio models for continuous outcomes
• Update "Getting started" vignette, using simulated data to avoid downloads

khsmisc 0.4.2

• make_exclusions(): return a list of observations filtered out (excluded)
• brickchart(): do not drop by or group categories without events
• New vignette about ratio of continuous outcomes with table2()

khsmisc 0.4.1

• table1() and table2() %>% mygt(): Remove horizontal border lines at the top of indented lines (parameter remove_border).
• mygt():
• Return raw HTML if knitting R Markdown to output: github_document.
• Format column labels.
• table2():
• Pass along indentation of labels to mygt() as an attribute instead of HTML.
• Improve handling of missing effect modifier strata, empty exposure strata, uniform binary exposures, logical effect modifiers, missing per-stratum estimates, and rounding of type = "time" and "events/time".
• New type = "range" (min-max).
• brickchart(): make compatible (without legend) with ggplot >= 3.3.4; make facets customizable.
• roundp(): format p as > 0.99 instead of 1.00.
• Update R Markdown template.

khsmisc 0.4.0

• make_exclusions(): New function for sequential exclusions to derive an analytical data set and prepare a flow chart for exclusion_flowchart().
• estimate_rmtl(): New function, reshaping code by Conner and Trinquart, that estimates restricted mean time lost, handling competing risks and weighting.
• survdiff_ci(): New function for differences in x-year survival/cumulative incidence.
• table2():
• Breaking change: In the design matrix, digits for rounding can no longer be provided as part of type. Use separate column digits if needed.
• Add unstratified, descriptive tables without an exposure variable, as well as showing overall and stratified estimates in one table.
• Allow for custom estimation functions (table2(custom = list(fun_a, fun_b))) that can be called via, e.g., type = "custom1".
• Add more predefined type options: medsurv median survival, medfu/maxfu median/maximum follow-up, surv/cuminc survival and cumulative incidence from Kaplan-Meier, rmtl restricted mean time lost, rmtdiff/survdiff/cumincdiff difference in RMTL/survival/cumulative incidence, mean (sd)/sd mean and standard deviation.
• If a regression model cannot provide estimates for a stratum, print --.
• Add argument risk_digits for rounding of risk/cumulative incidence.
• Fix type = "median (iqr)": do not remove missing values, like elsewhere.
• Add screenshots of formatted output to man/figures/.
• Require up-to-date gt, gtsummary dependencies.

khsmisc 0.3.6

• table1():
• Set rounding of column percentages for categorical (and binary) variables to 0 decimal digits by default.
• Add optional type parameter, passed along to gtsummary::tbl_summary().
• Update internal syntax and require gtsummary version >= 1.3.6.
• table2():
• Add optional type2 column to the design matrix to allow adding a second estimate per cell.
• Add prepare_md parameter and example for how to obtain a markdown-formatted label column (e.g., **bold** for a bold label).
• mygt(): add md option to get markdown formatting on selected columns through gt::fmt_markdown(columns = md)

khsmisc 0.3.5

• table2():
• Add trend to the design matrix to allow for estimating linear slopes for a continuously-coded exposure.
• Fix accidental handling of type = "irr" as an RR model with approach "i".

khsmisc 0.3.4

• brickchart(): Auto-generate color palette for an unlimited number of exposure categories. Expand examples.
• DESCRIPTION: Add Suggests: markdown to fix github-actions.
• table2(): For risk ratios and risk differences, allow passing on model fitting approach and number of bootstrap repeats.

khsmisc 0.3.3

• Change many examples after the ovarian dataset was removed from the survival package; use (lung) cancer instead.

khsmisc 0.3.2

• table2():
• Fix input check for outcome variable for type %in% c("fold", "or").
• Digits for rounding: Fix regular expression for parentheses.
• Add type = "cases/controls".
• Add type = "foldlog" for models of geometric means.
• Add type = "quantreg" for differences from quantile regression.
• Line breaks.
• brickchart(): New function for "brick charts"--proportions by category, where "bricks" display individual observations.

khsmisc 0.3.1

• table2(): Fix exposure category order if starting table with "blank" row.
• khsmisc_rmarkdown_template: custom RMarkdown template
• saveRDS_safely(): equivalent to save_safely() for single objects and .rds files
• geom_stepribbon(): ggplot aesthetic to highlight the difference between two Kaplan-Meier curves, corresponding to the difference in RMST

khsmisc 0.3.0

• Remove all packages loaded via Depends:. Instead, provide the khsverse package as an alternative package loader if desired. Remove readxl and magrittr dependencies altogether.
• DESCRIPTION: Add Remotes: to install risks package from Github
• table2(): Add left-truncated survival models, using time and time2 elements in the design matrix.
• Require readr >= 1.4.0 and change path = argument of write_csv_safely() to file =, as in save_safely() and pdf_savely().

khsmisc 0.2.6

• table2():
• Add type = "or" for logistic models.
• Fix "fold" (non-binary).
• Fix vector issue in use of digits_....
• Update vignette to make use of table2().

khsmisc 0.2.5

• table2():
• Generalize regression model fitting framework in one function.
• Add Poisson models and Gaussian models with log link.
• Add median/IQR to descriptive statistics.
• Reshape requesting digits for rounding: diff_digits, ratio_digits, and rate_digits are global parameters of table2() that can be overridden using type = "(estimand) (digits)" in each line.
• In joint models, use the reference categories of the exposure and effect modifier factors.

khsmisc 0.2.4

• exclusion_flowchart(): visualize exclusions from study with a flowchart via DiagrammeR::grViz().
• table2():
• For vectors that are not categorical, force exposure to be a factor and issue a warning, but do not abort.
• Allow for blank lines.
• Handle continuous outcomes variables with type = "diff" and type = "mean".

khsmisc 0.2.3

• table1(), table2(), tsummary(): improve input error handling
• table2(): allow grouping multiple strata of the effect modifier; add type = "outcomes (risk)"

khsmisc 0.2.2

• table2(): include estimates from risk ratio and risk difference models; input checks; allow for missing effect modifier, confounders; more descriptive statistics; more examples.
• scoreci(): new function for Wilson score confidence intervals for proportions.

khsmisc 0.2.1

• table2(): add alpha version.

khsmisc 0.2.0

• tabulate_rowcol(): replacement for mytab() (which remains available); it supports tidy evaluation.
• All other functions allow variable name arguments with tidy evaluation without introducing breaking changes. corrmat(), tsummary(), and table1() still use all variables in a dataset if none are selected but can now take variable names as an argument.
• Breaking change: corrmat() argument missing renamed to use to be consistent with the underlying stats::cor().
• rates(): new parameters risk_time to specify the time point at which cumulative incidence should be calculated, and by for stratification variables. If a dataset has already been grouped using dplyr::group_by(), grouping will be retained.

khsmisc 0.1.0

• First release for the khsmisc package.

stopsack/khsmisc documentation built on Sept. 22, 2023, 12:26 p.m.