SRA functions

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)

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.