---
title: "pairPropTest"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{pairPropTest}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  digits = 2
)
library(coreStatsNMR)
library(dplyr)
library(tidyr)

set.seed(1234)
iris_wtd <- iris %>%
  mutate(rand_bin = as.character(sample(1:3, nrow(iris), replace = TRUE)),
         weight = sample(1:3, nrow(.), replace = TRUE),
         index = row_number(.)) 
```

`pairPropTest` is a function for comparing a set of proportion pairs for statistically significant differences.

## Sample data

`pairPropTest` applied to the `iris` dataset, after glancing at the first few rows of data.

```{r iris}
head(iris_wtd) %>% 
    knitr::kable()

pairPropTest(iris_wtd, "index", "rand_bin", "Species") %>%
  head(8) %>% 
  knitr::kable(digits = 2)

## Get underlying counts
pairPropTest(iris_wtd, "index", "rand_bin", "Species",
             counts = TRUE) %>%
  head(8) %>% 
  knitr::kable(digits = 2)
```

## Weighted tests

The package also supports weighted testing, using the `wtd.chi.sq()` function from the `weights` package.

```{r iris_wtd}
wtdPairPropTest(iris_wtd, "index", "rand_bin", "Species", "weight") %>%
  head(8) %>% 
  knitr::kable(digits = 2)

## Get underlying counts
wtdPairPropTest(iris_wtd, "index", "rand_bin", "Species", "weight",
                counts = TRUE) %>%
  head(8) %>% 
  knitr::kable(digits = 2)

## Use unadjusted p-values
wtdPairPropTest(iris_wtd, "index", "rand_bin", "Species", "weight",
                p.adjust.method = "none") %>%
  head(8) %>% 
  knitr::kable(digits = 2)
```