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

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

This vignette documents how `dabestr` is able to generate estimation plots for experiments with repeated-measures designs. `dabestr` allows for the calculation and plotting of effect sizes for:

- Comparing each group to a shared control (control vs. group i; `baseline`)
- Comparing each measurement to the one directly preceding it (group i vs group i+1; `sequential`)

This is an improved version of paired data plotting in previous versions, which only supported computations involving one test group and one control group.

To use these features, you can simply declare the argument `paired = "sequential"` or `paired = "baseline"` correspondingly while running `load()`. You must also pass a column in the dataset that indicates the identity of each observation, using the `id_col` keyword.

```{r setup, warning = FALSE, message = FALSE}
library(dabestr)
```

## Create dataset for demo
```{r}
set.seed(12345) # Fix the seed so the results are replicable.
# pop_size = 10000 # Size of each population.
N <- 20 # The number of samples taken from each population

# Create samples
c1 <- rnorm(N, mean = 3, sd = 0.4)
c2 <- rnorm(N, mean = 3.5, sd = 0.75)
c3 <- rnorm(N, mean = 3.25, sd = 0.4)

t1 <- rnorm(N, mean = 3.5, sd = 0.5)
t2 <- rnorm(N, mean = 2.5, sd = 0.6)
t3 <- rnorm(N, mean = 3, sd = 0.75)
t4 <- rnorm(N, mean = 3.5, sd = 0.75)
t5 <- rnorm(N, mean = 3.25, sd = 0.4)
t6 <- rnorm(N, mean = 3.25, sd = 0.4)

# Add a `gender` column for coloring the data.
gender <- c(rep("Male", N / 2), rep("Female", N / 2))

# Add an `id` column for paired data plotting.
id <- 1:N

# Combine samples and gender into a DataFrame.
df <- tibble::tibble(
  `Control 1` = c1, `Control 2` = c2, `Control 3` = c3,
  `Test 1` = t1, `Test 2` = t2, `Test 3` = t3, `Test 4` = t4, `Test 5` = t5, `Test 6` = t6,
  Gender = gender, ID = id
)

df <- df %>%
  tidyr::gather(key = Group, value = Measurement, -ID, -Gender)
```

## Loading Data
```{r}
two_groups_paired_sequential <- load(df,
  x = Group, y = Measurement,
  idx = c("Control 1", "Test 1"),
  paired = "sequential", id_col = ID
)

print(two_groups_paired_sequential)
```

```{r}
two_groups_paired_baseline <- load(df,
  x = Group, y = Measurement,
  idx = c("Control 1", "Test 1"),
  paired = "baseline", id_col = ID
)

print(two_groups_paired_baseline)
```

When only 2 paired data groups are involved, assigning either "baseline" or "sequential" to `paired` will give you the same numerical results. 
```{r}
two_groups_paired_sequential.mean_diff <- mean_diff(two_groups_paired_sequential)
two_groups_paired_baseline.mean_diff <- mean_diff(two_groups_paired_baseline)
```

```{r}
print(two_groups_paired_sequential.mean_diff)
```

```{r}
print(two_groups_paired_baseline.mean_diff)
```

For paired data, we use [slopegraphs](https://www.edwardtufte.com/bboard/q-and-a-fetch-msg?msg_id=0003nk) (another innovation from Edward Tufte) to connect paired observations. Both Gardner-Altman and Cumming plots support this.

```{r}
dabest_plot(two_groups_paired_sequential.mean_diff,
  raw_marker_size = 0.5, raw_marker_alpha = 0.3
)
```

```{r, eval = FALSE}
dabest_plot(two_groups_paired_sequential.mean_diff,
  float_contrast = FALSE,
  raw_marker_size = 0.5, raw_marker_alpha = 0.3,
  contrast_ylim = c(-0.3, 1.3)
)
```

```{r, echo = FALSE}
pp_plot <- dabest_plot(two_groups_paired_sequential.mean_diff,
  float_contrast = FALSE,
  raw_marker_size = 0.5, raw_marker_alpha = 0.3,
  contrast_ylim = c(-0.3, 1.3)
)

cowplot::plot_grid(
  plotlist = list(NULL, pp_plot, NULL),
  nrow = 1,
  ncol = 3,
  rel_widths = c(2.5, 5, 2.5)
)
```

```{r}
dabest_plot(two_groups_paired_baseline.mean_diff,
  raw_marker_size = 0.5, raw_marker_alpha = 0.3
)
```

```{r, eval = FALSE}
dabest_plot(two_groups_paired_baseline.mean_diff,
  float_contrast = FALSE,
  raw_marker_size = 0.5, raw_marker_alpha = 0.3,
  contrast_ylim = c(-0.3, 1.3)
)
```

```{r, echo = FALSE}
pp_plot <- dabest_plot(two_groups_paired_baseline.mean_diff,
  float_contrast = FALSE,
  raw_marker_size = 0.5, raw_marker_alpha = 0.3,
  contrast_ylim = c(-0.3, 1.3)
)

cowplot::plot_grid(
  plotlist = list(NULL, pp_plot, NULL),
  nrow = 1,
  ncol = 3,
  rel_widths = c(2.5, 5, 2.5)
)
```

You can also create repeated-measures plots with multiple test groups. In this case, declaring `paired` to be "sequential" or "baseline" will generate the same slopegraph, reflecting the repeated-measures experimental design, but different contrast plots, to show the "sequential" or "baseline" comparison:

```{r}
sequential_repeated_measures.mean_diff <- load(df,
  x = Group, y = Measurement,
  idx = c(
    "Control 1", "Test 1",
    "Test 2", "Test 3"
  ),
  paired = "sequential", id_col = ID
) %>%
  mean_diff()

print(sequential_repeated_measures.mean_diff)
```

```{r}
dabest_plot(sequential_repeated_measures.mean_diff,
  raw_marker_size = 0.5, raw_marker_alpha = 0.3
)
```

```{r}
baseline_repeated_measures.mean_diff <- load(df,
  x = Group, y = Measurement,
  idx = c(
    "Control 1", "Test 1",
    "Test 2", "Test 3"
  ),
  paired = "baseline", id_col = ID
) %>%
  mean_diff()

print(baseline_repeated_measures.mean_diff)
```

```{r}
dabest_plot(baseline_repeated_measures.mean_diff,
  raw_marker_size = 0.5, raw_marker_alpha = 0.3
)
```

As with unpaired data, `dabestr` empowers you to perform complex visualizations and statistics for paired data as well.

```{r}
multi_baseline_repeated_measures.mean_diff <- load(df,
  x = Group, y = Measurement,
  idx = list(
    c(
      "Control 1", "Test 1",
      "Test 2", "Test 3"
    ),
    c(
      "Control 2", "Test 4",
      "Test 5", "Test 6"
    )
  ),
  paired = "baseline", id_col = ID
) %>%
  mean_diff()

dabest_plot(multi_baseline_repeated_measures.mean_diff,
  raw_marker_size = 0.5, raw_marker_alpha = 0.3
)
```
