AMR/vignettes/freq.Rmd

---
title: "How to create frequency tables"
author: "Matthijs S. Berends"
date: '`r format(Sys.Date(), "%d %B %Y")`'
output: 
  rmarkdown::html_vignette:
    toc: true
    toc_depth: 3
vignette: >
  %\VignetteIndexEntry{How to create frequency tables}
  %\VignetteEncoding{UTF-8}
  %\VignetteEngine{knitr::rmarkdown}
editor_options: 
  chunk_output_type: console
---

```{r setup, include = FALSE, results = 'asis'}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#",
  results = 'asis',
  fig.width = 7.5,
  fig.height = 4.5
)
library(dplyr)
library(AMR)
```

## Introduction

Frequency tables (or frequency distributions) are summaries of the distribution of values in a sample. With the `freq()` function, you can create univariate frequency tables. Multiple variables will be pasted into one variable, so it forces a univariate distribution. We take the `septic_patients` dataset (included in this AMR package) as example.

## Frequencies of one variable

To only show and quickly review the content of one variable, you can just select this variable in various ways. Let's say we want to get the frequencies of the `gender` variable of the `septic_patients` dataset:
```{r, echo = TRUE}
# Any of these will work:
# freq(septic_patients$gender)
# freq(septic_patients[, "gender"])

# Using tidyverse:
# septic_patients$gender %>% freq()
# septic_patients[, "gender"] %>% freq()
# septic_patients %>% freq("gender")

# Probably the fastest and easiest:
septic_patients %>% freq(gender)  
```
This immediately shows the class of the variable, its length and availability (i.e. the amount of `NA`), the amount of unique values and (most importantly) that among septic patients men are more prevalent than women.

## Frequencies of more than one variable

Multiple variables will be pasted into one variable to review individual cases, keeping a univariate frequency table.

For illustration, we could add some more variables to the `septic_patients` dataset to learn about bacterial properties:
```{r, echo = TRUE, results = 'hide'}
my_patients <- septic_patients %>% left_join_microorganisms()
```
Now all variables of the `microorganisms` dataset have been joined to the `septic_patients` dataset. The `microorganisms` dataset consists of the following variables:
```{r, echo = TRUE, results = 'markup'}
colnames(microorganisms)
```

If we compare the dimensions between the old and new dataset, we can see that these `r ncol(my_patients) - ncol(septic_patients)` variables were added:
```{r, echo = TRUE, results = 'markup'}
dim(septic_patients)
dim(my_patients)
```

So now the `genus` and `species` variables are available. A frequency table of these combined variables can be created like this:
```{r, echo = TRUE}
my_patients %>%
  freq(genus, species, nmax = 15)
```

## Frequencies of numeric values

Frequency tables can be created of any input.

In case of numeric values (like integers, doubles, etc.) additional descriptive statistics will be calculated and shown into the header:

```{r, echo = TRUE}
# # get age distribution of unique patients
septic_patients %>% 
  distinct(patient_id, .keep_all = TRUE) %>% 
  freq(age, nmax = 5, header = TRUE)
```

So the following properties are determined, where `NA` values are always ignored:

* **Mean**

* **Standard deviation**

* **Coefficient of variation** (CV), the standard deviation divided by the mean

* **Mean absolute deviation** (MAD), the median of the absolute deviations from the median - a more robust statistic than the standard deviation

* **Five numbers of Tukey**, namely: the minimum, Q1, median, Q3 and maximum

* **Interquartile range** (IQR), the distance between Q1 and Q3

* **Coefficient of quartile variation** (CQV, sometimes called *coefficient of dispersion*), calculated as (Q3 - Q1) / (Q3 + Q1) using `quantile()` with `type = 6` as quantile algorithm to comply with SPSS standards

* **Outliers** (total count and unique count)

So for example, the above frequency table quickly shows the median age of patients being `r my_patients %>% distinct(patient_id, .keep_all = TRUE) %>% pull(age) %>% median(na.rm = TRUE)`.

## Frequencies of factors

To sort frequencies of factors on their levels instead of item count, use the `sort.count` parameter. 

`sort.count` is `TRUE` by default. Compare this default behaviour...

```{r, echo = TRUE}
septic_patients %>%
  freq(hospital_id)
```

... to this, where items are now sorted on factor levels:

```{r, echo = TRUE}
septic_patients %>%
  freq(hospital_id, sort.count = FALSE)
```

All classes will be printed into the header. Variables with the new `rsi` class of this AMR package are actually ordered factors and have three classes (look at `Class` in the header):

```{r, echo = TRUE}
septic_patients %>%
  freq(AMX, header = TRUE)
```

## Frequencies of dates

Frequencies of dates will show the oldest and newest date in the data, and the amount of days between them:

```{r, echo = TRUE}
septic_patients %>%
  freq(date, nmax = 5, header = TRUE)
```

## Assigning a frequency table to an object

A frequency table is actually a regular `data.frame`, with the exception that it contains an additional class.

```{r, echo = TRUE}
my_df <- septic_patients %>% freq(age)
class(my_df)
```

Because of this additional class, a frequency table prints like the examples above. But the object itself contains the complete table without a row limitation:

```{r, echo = TRUE}
dim(my_df)
```

## Additional parameters

### Parameter `na.rm`
With the `na.rm` parameter you can remove `NA` values from the frequency table (defaults to `TRUE`, but the number of `NA` values will always be shown into the header):

```{r, echo = TRUE}
septic_patients %>%
  freq(AMX, na.rm = FALSE)
```

### Parameter `row.names`
A frequency table shows row indices. To remove them, use `row.names = FALSE`:

```{r, echo = TRUE}
septic_patients %>%
  freq(hospital_id, row.names = FALSE)
```

### Parameter `markdown`
The `markdown` parameter is `TRUE` at default in non-interactive sessions, like in reports created with R Markdown. This will always print all rows, unless `nmax` is set. Without markdown (like in regular R), a frequency table would print like:

```{r, echo = TRUE, results = 'markup'}
septic_patients %>%
  freq(hospital_id, markdown = FALSE)
```