VISCfunctions

The package provides functions for common tasks for creating statistical reports at Vaccine Immunology Statistical Center (VISC). The goal of VISCfunctions is to:

• provide standard statistical testing and estimating functions
• help format output for PDF and Word reports
• provide frequently used utility functions

for VISC statisticians and programmers at Fred Hutch.

Installation

The package is available on the Fred Hutch organization GitHub page.

remotes::install_github("FredHutch/VISCfunctions")

# Use the build_vignettes parameter to access the vignette
# (Note that this may auto-upgrade dependencies - this behavior can be controlled with the `upgrade` argument)
remotes::install_github("FredHutch/VISCfunctions", dependencies = TRUE, build_vignettes = TRUE)
vignette("Overview")

Overview

Below is an overview of the currently available functions in VISCfunctions.

Statistical testing and estimates

Compare two groups, return a p-value:

• two_sample_bin_test() for a Barnard, Fisher’s Exact, Chi-Square or McNemar test.
• two_samp_cont_test() for a t.test (paired or unpaired), Wilcox Rank-Sum, or Wilcox Signed-Rank test.
• cor_test() for a Spearman, Pearson, or Kendall correlation test.

Make all pairwise comparisons of a grouping variable (or any categorical variable), return descriptive statistics and p-values:

• pairwise_test_bin() for a Barnard, Fisher’s Exact, Chi-Square or McNemar test.
• pairwise_test_cont() for a t.test (paired or unpaired), Wilcox Rank-Sum, or Wilcox Signed-Rank test.
• cor_test_pairs() for a Spearman, Pearson, or Kendall correlation test.

Estimate binomial confidence intervals for a binary vector:

• binom_ci()

Formatting output

• paste_tbl_grp() to paste together information (usually descriptive statistics) from two groups.
• pretty_pvalues() to round and format p-values.
• stat_paste() to combine and format values, such as:
  • Mean (sd)
  • Median [min, max]
  • Estimate (SE of Estimate)
  • Estimate (95% CI Lower Bound, Upper Bound)
  • Estimate/Statistic (p value)
• escape() to protect control characters in a string for use in a latex table or caption
• collapse_group_row() as an alternative to kableExtra::collapse_rows() for long tables in latex

Survival and Magnitude Breadth

• create_step_curve() to create survival probabilities and generate a risk table
• mb_results() to create step curve info for magnitude breadth (MB) plots and AUC-MB

Utility functions

• round_away_0() is an alternative to the round() function to properly perform mathematical rounding.
• escape() is used to inserts a “\” in front of values, which is needed for Latex.
• get_full_name() looks up a username from Fred Hutch ID.
• get_session_info() creates a a data frame with session information.

Vignette

For more information, browse the vignette (browseVignettes("VISCfunctions")).

Contribute to this package

See our contibuting guide to learn more about how you can contribute to this package.