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README.Rmd
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---
output: github_document
---
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[](https://github.com/FredHutch/VISCfunctions/actions)
[](https://app.codecov.io/gh/FredHutch/VISCfunctions)
[](https://opensource.org/licenses/MIT)
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```{r setup, include = FALSE}
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.
```{r eval=FALSE}
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](CONTRIBUTING.md) to learn more about how you can contribute to this package.