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

```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
library(DescrTab2)
library(tidyverse)
options(print_format="html")
```


# Introduction
In this document, we compare various DescrTab2 tests and descriptive statistics
with their SAS equivalents.

These comparisons are not automated. The user may check if the results presented
within this document are according to the users preferences.


The datasets used in these comparisons are taken mostly from the `?help` pages
of the underlying test functions used within `DescrTab2`. For the SAS
comparisons, these datasets are then written to `.csv` format and read into SAS
with help of the `?foreign` package.

The origin of these datasets is described in the respective sections.

# A note about the layout

This document is created by including in the .html SAS output. Unfortunately, this has ugly side effects for the formatting of this document, but everything should still be readable.


# Wilcoxon one-sample signed-rank test

Dataset origin: `?wilcox.test` (accessed on R-version 4.0.3).


```{r wilcox.test 1 sample, results='asis'}

x <- c(1.83,  0.50,  1.62,  2.48, 1.68, 1.88, 1.55, 3.06, 1.30)
y <- c(0.878, 0.647, 0.598, 2.05, 1.06, 1.29, 1.06, 3.14, 1.29)
dat_wilcox.test_1_sample <- tibble(diff = x-y)

descr(dat_wilcox.test_1_sample, test_options = c(nonparametric=TRUE))
```


```{r wilcox.test 1 sample SAS, results='asis', echo=FALSE}
URS_ID <- "wilcox.test_1_sample"
sas_html <- here::here(
    "vignettes",
    "validation_report",
    URS_ID,
    paste0(URS_ID, "_example_", 1, ".html")
  )

if(file.exists(sas_html)){
  shiny::includeHTML(sas_html)
}
```


# Mann-Whitney U test
Dataset origin: `?wilcox.test` (accessed on R-version 4.0.3).

```{r wilcox.test 2 sample, results='asis'}

x <- c(0.80, 0.83, 1.89, 1.04, 1.45, 1.38, 1.91, 1.64, 0.73, 1.46)
y <- c(1.15, 0.88, 0.90, 0.74, 1.21)
group <- c(rep("Trt", length(x)), rep("Ctrl", length(y)))
dat_wilcox.test_2_sample <- tibble(var=c(x,y), group=group)

descr(dat_wilcox.test_2_sample, "group", test_options = c(nonparametric=TRUE))
```


```{r wilcox.test 2 sample SAS, results='asis', echo=FALSE}
URS_ID <- "wilcox.test_2_sample"
sas_html <- here::here(
    "vignettes",
    "validation_report",
    URS_ID,
    paste0(URS_ID, "_example_", 1, ".html")
  )

if(file.exists(sas_html)){
  shiny::includeHTML(sas_html)
}
```

# Kruskal-Wallis one-way ANOVA

Dataset origin: `?kruskal.test` (accessed on R-version 4.0.3).


```{r kruskal.test, results='asis'}

x <- c(2.9, 3.0, 2.5, 2.6, 3.2) # normal subjects
y <- c(3.8, 2.7, 4.0, 2.4)      # with obstructive airway disease
z <- c(2.8, 3.4, 3.7, 2.2, 2.0) # with asbestosis
group <- c(rep("Trt", length(x)), rep("Ctrl", length(y)), rep("Placebo", length(z)))
dat_kruskal.test <- tibble(var=c(x,y,z), group=group)

descr(dat_kruskal.test, "group", test_options = c(nonparametric=TRUE)) 
```


```{r kruskal.test SAS, echo=FALSE, results='asis'}
URS_ID <- "kruskal.test"
sas_html <- here::here(
    "vignettes",
    "validation_report",
    URS_ID,
    paste0(URS_ID, "_example_", 1, ".html")
  )


if(file.exists(sas_html)){
  shiny::includeHTML(sas_html)
}
```


# Friedman test

Dataset origin: `?friedman.test` (accessed on R-version 4.0.3).

```{r friedman.test, results='asis'}

RoundingTimes <-
matrix(c(5.40, 5.50, 5.55,
         5.85, 5.70, 5.75,
         5.20, 5.60, 5.50,
         5.55, 5.50, 5.40,
         5.90, 5.85, 5.70,
         5.45, 5.55, 5.60,
         5.40, 5.40, 5.35,
         5.45, 5.50, 5.35,
         5.25, 5.15, 5.00,
         5.85, 5.80, 5.70,
         5.25, 5.20, 5.10,
         5.65, 5.55, 5.45,
         5.60, 5.35, 5.45,
         5.05, 5.00, 4.95,
         5.50, 5.50, 5.40,
         5.45, 5.55, 5.50,
         5.55, 5.55, 5.35,
         5.45, 5.50, 5.55,
         5.50, 5.45, 5.25,
         5.65, 5.60, 5.40,
         5.70, 5.65, 5.55,
         6.30, 6.30, 6.25),
       nrow = 22,
       byrow = TRUE,
       dimnames = list(1 : 22,
                       c("Round Out", "Narrow Angle", "Wide Angle")))

idx <- rep(1:22, 3)
dat <- tibble(var = c(RoundingTimes[,1], RoundingTimes[,2], RoundingTimes[,3]),
              group = c(rep("Round Out", 22), rep("Narrow Angle", 22), rep("Wide Angle", 22)))


descr(dat, "group", test_options = list(nonparametric=TRUE, indices=idx, paired=TRUE))

```

```{r friedman.test SAS, echo=FALSE, results='asis'}
URS_ID <- "friedman.test"
sas_html <- here::here(
    "vignettes",
    "validation_report",
    URS_ID,
    paste0(URS_ID, "_example_", 1, ".html")
  )


if(file.exists(sas_html)){
  shiny::includeHTML(sas_html)
}
```

# Cochrans Q test

Dataset origin: This is a replicate of the dataset from the [SAS documentation
of the Cochrane Q test from proc freq](https://documentation.sas.com/?cdcId=pgmsascdc&cdcVersion=9.4_3.4&docsetId=statug&docsetTarget=statug_freq_examples10.htm&locale=en).

```{r CochranQTest, results='asis'}

d.frm <- DescTools::Untable(xtabs(c(6,2,2,6,16,4,4,6) ~ ., 
    expand.grid(rep(list(c("F","U")), times=3))), 
    colnames = LETTERS[1:3])

# rearrange to long shape    
d.long <- reshape(d.frm, varying=1:3, times=names(d.frm)[c(1:3)], 
                  v.names="resp", direction="long")
idx <- d.long$id
dat <- d.long[, 1:2] %>% mutate(time=as.character(time), resp=as.character(resp))

descr(dat, "time", test_options = list(indices=idx, paired=TRUE))

```

```{r CochranQTest SAS, echo=FALSE, results='asis'}
URS_ID <- "CochraneQTest"
sas_html <- here::here(
    "vignettes",
    "validation_report",
    URS_ID,
    paste0(URS_ID, "_example_", 1, ".html")
  )


if(file.exists(sas_html)){
  shiny::includeHTML(sas_html)
}
```

# McNemars test

Dataset origin: `?mcnemar.test` (accessed on R-version 4.0.3).
Note that this dataset is not explicitly defined in `?mcnemar.test`.
It is constructed to reflect the cross table defined there.

```{r mcnemar.test, results='asis'}
dat <- tibble::tibble(var = c(rep("Approve", 794), rep("Approve", 150), rep("Disapprove", 86), rep("Disapprove", 570),
                      rep("Approve", 794), rep("Disapprove", 150), rep("Approve", 86), rep("Disapprove", 570)),
              group= c(rep("first", 1600), rep("second",1600)))
              
descr(dat, "group", test_options = list(paired=TRUE, indices=c(1:1600, 1:1600)))
descr(dat, "group", test_options = list(paired=TRUE, exact=TRUE, indices=c(1:1600, 1:1600)))

dat <-
  tibble::tibble(x = c(
    rep("Approve", 794),
    rep("Approve", 150),
    rep("Disapprove", 86),
    rep("Disapprove", 570)
  ),
  y = c(
    rep("Approve", 794),
    rep("Disapprove", 150),
    rep("Approve", 86),
    rep("Disapprove", 570)
  ))


```
```{r mcnemar.test2}
mcnemar.test(dat$x, dat$y, correct = FALSE)
```


```{r mcnemar.test SAS, echo=FALSE, results='asis'}
URS_ID <- "mcnemar.test"
sas_html <- here::here(
    "vignettes",
    "validation_report",
    URS_ID,
    paste0(URS_ID, "_example_", 1, ".html")
  )


if(file.exists(sas_html)){
  shiny::includeHTML(sas_html)
}
```

# Chi-squared test

Dataset origin: "Gender-Party dataset":`?chisq.test` (accessed on R-version 4.0.3).
"a-b dataset": selfmade.

```{r chisq.test1, results='asis'}

dat <- tibble(gender=c(rep("F",sum(c(762, 327, 468)) ), rep("M", sum( c(484, 239, 477)))),
              party=c(rep("Democrat", 762), rep("Independent", 327), rep("Republican", 468),
                      rep("Democrat", 484), rep("Independent", 239), rep("Republican", 477)))
              
descr(dat, "gender")
descr(dat)
```

```{r chisq.test2}
chisq.test(dat$gender, dat$party)
chisq.test(table(dat$gender))
chisq.test(table(dat$party))
```

```{r chisq.test3, results='asis'}
dat <- tibble(
  
  a = factor(c(0,
               0,
               1,
               1,
               0,
               0,
               0,
               0,
               0,
               0,
               1)),
  b = factor(c(1,
               1,
               1,
               1,
               1,
               1,
               1,
               0,
               0,
               1,
               0))

)
descr(dat, "b")
```


```{r chisq.test SAS, echo=FALSE, results='asis'}
URS_ID <- "chisq.test"
sas_html <- here::here(
    "vignettes",
    "validation_report",
    URS_ID,
    paste0(URS_ID, "_example_", 1, ".html")
  )


if(file.exists(sas_html)){
  shiny::includeHTML(sas_html)
}
```


# t-test

Dataset origin: `?t.test`, which references `?sleep`
(accessed on R-version 4.0.3).

```{r t.test, results='asis'}

dat <- sleep[, c("extra", "group")]
              

descr(dat[, "extra"]) 
descr(dat, "group")
descr(dat, "group", test_options = list(paired=TRUE, indices=rep(1:10, 2)))

```


```{r t.test SAS, echo=FALSE, results='asis'}
URS_ID <- "t.test"
sas_html <- here::here(
    "vignettes",
    "validation_report",
    URS_ID,
    paste0(URS_ID, "_example_", 1, ".html")
  )


if(file.exists(sas_html)){
  shiny::includeHTML(sas_html)
}
```


# F-test

Dataset origin: Modified version of `?datasets::npk`. `npk` is used in `?aov`
(accessed on R-version 4.0.3).

```{r aov, results='asis'}

dat <- data.frame(
  y = npk$yield,
  P = ordered(gl(3, 24)),
  N = ordered(gl(3, 1, 24))
)
              
descr(dat[, c("y", "P")], "P") 
descr(dat[, c("y", "N")], "N") 

```


```{r aov SAS, echo=FALSE, results='asis'}
URS_ID <- "aov"
sas_html <- here::here(
    "vignettes",
    "validation_report",
    URS_ID,
    paste0(URS_ID, "_example_", 1, ".html")
  )


if(file.exists(sas_html)){
  shiny::includeHTML(sas_html)
}
```

# Mixed model ANOVA
Dataset origin: Modified version of `?nlme::Orthodont`. `Orthodont` is used in
`?lme` (accessed on R-version 4.0.3).

```{r mixed, results='asis'}

dat <- nlme::Orthodont
dat2 <- nlme::Orthodont[1:64,]
dat2$Sex <- "Divers"
dat2$distance <- dat2$distance + c(rep(0.1*c(1,4,3,2), 10), 0.1*rep(c(0.4,2,1.5, 2.3), 6) )
dat2$Subject <- str_replace_all(dat2$Subject, "M", "D")
dat <- bind_rows(dat, dat2)
dat <- as_tibble(dat)


descr(dat[, c("Sex", "distance")], "Sex", test_options = list(paired=TRUE, indices=dat$Subject))

```


```{r mixed SAS, echo=FALSE, results='asis'}
URS_ID <- "mixed"
sas_html <- here::here(
    "vignettes",
    "validation_report",
    URS_ID,
    paste0(URS_ID, "_example_", 1, ".html")
  )


if(file.exists(sas_html)){
  shiny::includeHTML(sas_html)
}
```

# Boschloos test
Dataset origin: selfmade.


DescrTab2 uses the exact2x2::boschloo with option `tsmethod=central`  to calculate p-values. There is no comparison for this option readily available.
```{r boschloo1, results='asis'}
dat <- tibble(gender=factor(c("M", "M", "M", "M", "M", "M", "F", "F", "F", "F", "F")),
              party=factor(c("A", "A", "B", "B", "B", "B", "A", "A", "A", "B", "B")))
descr(dat, "gender", test_options = c(exact=TRUE))
```

```{r boschloo2}
exact2x2::boschloo(3, 5, 2, 6, tsmethod="central")
```

However, we can compare the exact2x2::boschloo with `tsmethod=minlike` to `Exact::exact.test`:

```{r boschloo3}
exact2x2::boschloo(3, 5, 2, 6, tsmethod="minlike")
Exact::exact.test(table(dat), method="boschloo", to.plot = FALSE)
```


