---
title: "Examples"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Examples}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

```{r}
library(UniExactFunTest)
```


```{r test, include=FALSE, eval=TRUE}
xs <- 
  list(
    matrix(c(
      0, 5,
      5, 0
    ), nrow=2, byrow=TRUE),
    matrix(c(
      0, 5,
      3, 5
    ), nrow=2, byrow=TRUE),
    matrix(c(
      0, 5,
      12, 3
    ), nrow=2, byrow=TRUE)
  )

for(x in xs) {
  print(knitr::kable(x))
  UEFT(x)
  UEFT(t(x))

}
```

## Ice cream and food-borne disease

Data source: Stephanie Glen. "Contingency Table: What is it used for?" From StatisticsHowTo.com: Elementary Statistics for the rest of us! https://www.statisticshowto.com/what-is-a-contingency-table/

```{r ice cream}
x <- matrix(c(
  13, 32,
  17, 23
), nrow=2, byrow=TRUE,
dimnames = list(
  c("Ice cream eaten", "No ice cream"),
  c("Cases", "Controls")
))
knitr::kable(x)
UEFT(x)
UEFT(t(x))

```

## AIDS and sexual preference

Data source: Stephanie Glen. "Contingency Table: What is it used for?" From StatisticsHowTo.com: Elementary Statistics for the rest of us! https://www.statisticshowto.com/what-is-a-contingency-table/

```{r AIDS}
x <- matrix(
  c(4,2,3,3,16,2), nrow=2, ncol=3, byrow=TRUE,
  dimnames=list(
              c("AIDS: yes", "AIDS: no"),
              c("Males", "Females", "Both")
))
knitr::kable(x)
UEFT(x)
UEFT(t(x))
```

## Cancer therapy

Data source: Mendenhall, W. M., Million, R. R., Sharkey, D. E., & Cassisi, N. J. (1984). Stage T3 squamous cell carcinoma of the glottic larynx treated with surgery and/or radiation therapy. International journal of radiation oncology, biology, physics, 10(3), 357–363. https://doi.org/10.1016/0360-3016(84)90054-3

```{r Mendenhall et al. 1984}
x <- matrix(c(
  21, 2,
  15, 3
), nrow=2, byrow=TRUE,
dimnames = list(
  c("Surgery", "Radiation therapy"),
  c("Cancer controlled", "Cancer not controlled")
))
knitr::kable(x)
UEFT(x)
UEFT(t(x))
```


## Sex and handedness

Data source: https://en.wikipedia.org/wiki/Contingency_table

```{r sex-handedness}
x <- matrix(c(
  43, 9,
  44, 4
), nrow=2, byrow=TRUE,
dimnames = list(
  c("Male", "Female"),
  c("Right-handed", "Left-handed")
))
knitr::kable(x)
UEFT(x)
UEFT(t(x))
```