The khsmisc package

The khsmisc package provides a set of custom functions for epidemiology research. For a package that loads core libraries that fit well with this approach (e.g., tidyverse), see the khsverse package.

Installation

The khsmisc package can be installed or updated from GitHub. A CRAN submission is not planned. If the remotes library is missing, install it first (install.packages("remotes")).

Install or update the khsmisc package:

remotes::install_github("stopsack/khsmisc")

Functions for Epidemiology Research

  • Data handling: varlist() for variable list/dataset inventory, Stata style; write_csv_safely(), save_safely(), saveRDS_safely(), and pdf_safely() to export CSV files, R objects, or PDFs without overwriting existing files; and make_exclusions() to perform sequential exclusions when generating an analytical dataset.
  • Functions for vectors: scale_to_range() to scale a vector to a given range; Mode() to obtain the most common value; and roundp() to round and format p-values.
  • Estimation functions: estimate_rmtl() for restricted mean time lost and its difference.
  • Functions for descriptive tables: tabulate_rowcol() for categorical variables; tsummary() for continuous variables.
  • Functions for figures: stripplot() for box/whiskers plots overlaid with a dot plot of all data points; corrmat() for correlation matrices; exclusion_flowchart() for a flowchart with consequences of exclusion criteria; brickchart() for plotting proportions while showing individual observations.
  • Others: R Markdown template, available via File > New File > R Markdown > From Template.

Note The functions

  • table1() for formatted descriptive tables via gtsummary,
  • table2() for stratified result tables,
  • mygt() for formatting/printing tables as a ‘gt’ object, and
  • estimation functions rates(), scoreci(), and survdiff_ci()

have been merged into functionality now available in the rifttable package and are being maintained there.

An analysis example: TCGA BLCA

  • The “Get Started” vignette described an sample analysis workflow using the khsmisc package and TCGA BLCA.