---
title: "Plot rates through time"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Plot rates through time}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r set_options, include = FALSE}
knitr::opts_chunk$set(
  eval = FALSE, # Chunks of codes will not be evaluated by default
  collapse = TRUE,
  comment = "#>",
  fig.width = 7, fig.height = 5   # Set device size at rendering time (when plots are generated)
)
```

```{r setup, eval = TRUE, include = FALSE}
library(deepSTRAPP)

is_dev_version <- function (pkg = "deepSTRAPP")
{
  # # Check if ran on CRAN
  # not_cran <- identical(Sys.getenv("NOT_CRAN"), "true") # || interactive()

  # Version number check
  version <- tryCatch(as.character(utils::packageVersion(pkg)), error = function(e) "")
  dev_version <- grepl("\\.9000", version)

  # not_cran || dev_version
  
  return(dev_version)
}

```

```{r adjust_dpi_CRAN, include = FALSE, eval = !is_dev_version()}
knitr::opts_chunk$set(
  dpi = 50   # Lower DPI to save space
)
```
```{r adjust_dpi_dev, include = FALSE, eval = is_dev_version()}
knitr::opts_chunk$set(
  dpi = 72   # Default DPI for the dev version
)
```

<br>
This vignette presents the different options available to __plot rates through time__ following a deepSTRAPP workflow.

It is a nice and efficient way to provide illustrations and support the conclusions of the deepSTRAPP tests.

The plot can be performed on different types of data (i.e., continuous, binary, and multinomial). <br>
Below are examples with __continuous data__ (Example 1) and __categorical multinomial data__ (Example 2).

<br>

```{r plot_RTT_cont}
# ------ Example 1: Continuous trait data ------ #

#### Step 1: Prepare data ####

# Load results of a STRAPP test workflow run on continuous trait data
Ponerinae_deepSTRAPP_cont_old_calib_0_40 <- readRDS(system.file("extdata", 
    "Ponerinae_deepSTRAPP_cont_old_calib_0_40.rds", package = "deepSTRAPP"))
# This dataset is only available in development versions installed from GitHub.
# It is not available in CRAN versions.
# Use remotes::install_github(repo = "MaelDore/deepSTRAPP") to get the latest development version.

# Visualize trait data
hist(Ponerinae_deepSTRAPP_cont_old_calib_0_40$trait_data_df_over_time$trait_value)
# Visualize diversification rates data
hist(Ponerinae_deepSTRAPP_cont_old_calib_0_40$diversification_data_df_over_time$rates)

# Select a color scheme from lowest to highest values
color_scale = c("darkgreen", "limegreen", "orange", "red")

### Step 2: Plot RTT ####

# For continuous trait data, the trait data are divided into groups based on 'quantile_ranges'.
# They form groups of trait values used to visualize the existence of a correlation with rates.
# If groups with higher quartile ranges exhibit higher rates over time, and conversely, there is a positive correlation.
# If groups with higher quartile ranges exhibit lower rates over time, and conversely, there is a negative correlation.

## Generate default plot
plot_RTT_continuous <- plot_rates_through_time(
   deepSTRAPP_outputs = Ponerinae_deepSTRAPP_cont_old_calib_0_40,
   color_scale = color_scale)
   # PDF_file_path = "./plot_RTT_continuous.pdf")

# Here, we observed a negative correlation as quartiles of lower trait values are consistently
# associated with higher rates, and conversely.

## Adjust aesthetics of plot a posteriori
plot_RTT_continuous_adj <- plot_RTT_continuous$rates_TT_ggplot +
    # Change size and color of the title
    ggplot2::theme(plot.title = ggplot2::element_text(color = "red", size = 18))
print(plot_RTT_continuous_adj)

## Adjust quartile ranges

# You can define different trait quantile groups based on 'quantile_ranges'.
# The default is c(0, 0.25, 0.5, 0.75, 1.0) which yields four equivalent groups
# with each spanning 25% of the trait data.

# You can try a different option with for instance five groups:
plot_rates_through_time(
   deepSTRAPP_outputs = Ponerinae_deepSTRAPP_cont_old_calib_0_40,
   quantile_ranges = c(0, 0.20, 0.40, 0.60, 0.80, 1.0),
   color_scale = color_scale)
   # PDF_file_path = "./plot_RTT_continuous_5groups.pdf")

## Plot Confidence Intervals (CI)

# You can include confidence intervals on the plot.
# They are built from the BAMM posterior samples, which each yields different diversification rates,
# that can be plotted to show uncertainty in the evaluation.

# The function offers two types of CI (CI_type):
  # "fuzzy": draws a line for each posterior sample with high transparency to highlight 
           # redundancy across BAMM posterior samples.
  # "quantiles_rect": draws plain polygons whose range can be controlled with 'CI_quantiles'.
                    # By default, 95% CI are shown (CI_quantiles = 0.95).

# Plot "fuzzy" CI
plot_rates_through_time(
   deepSTRAPP_outputs = Ponerinae_deepSTRAPP_cont_old_calib_0_40,
   color_scale = color_scale,
   plot_CI = TRUE, # To add CI on the plot
   CI_type = "fuzzy") # Select type of CI

# Plot "quantiles_rect" CI
plot_rates_through_time(
   deepSTRAPP_outputs = Ponerinae_deepSTRAPP_cont_old_calib_0_40,
   color_scale = color_scale,
   plot_CI = TRUE, # To add CI on the plot
   CI_type = "quantiles_rect", # Select type of CI
   CI_quantiles = 0.9) # Adjust range of CI

# The lack of overlap between the two most extreme trait quantile groups tends to indicate
# that the correlation is significant. However, a proper STRAPP test is needed to confirm what is observed.

## Plot different types of rates

# deepSTRAPP also lets you plot different types of rates.
# Even if you carried out the analysis on "net_diversification" rates (as the default)
# you can still plot the evolution of "speciation" and "extinction" rates

# Plot "speciation" rates
plot_rates_through_time(
   deepSTRAPP_outputs = Ponerinae_deepSTRAPP_cont_old_calib_0_40,
   rate_type = "speciation",
   color_scale = color_scale,
   plot_CI = TRUE, # To add CI on the plot
   CI_type = "quantiles_rect", # Select type of CI
   CI_quantiles = 0.9) # Adjust range of CI

# Plot "extinction" rates
plot_rates_through_time(
   deepSTRAPP_outputs = Ponerinae_deepSTRAPP_cont_old_calib_0_40,
   rate_type = "extinction",
   color_scale = color_scale,
   plot_CI = TRUE, # To add CI on the plot
   CI_type = "quantiles_rect", # Select type of CI
   CI_quantiles = 0.9) # Adjust range of CI

```
```{r plot_RTT_cont_eval_dev, fig.width = 16, fig.height = 15, out.width = "100%", eval = is_dev_version(), echo = FALSE}
# Load results of a STRAPP test workflow run on continuous trait data
Ponerinae_deepSTRAPP_cont_old_calib_0_40 <- readRDS(system.file("extdata", 
    "Ponerinae_deepSTRAPP_cont_old_calib_0_40.rds", package = "deepSTRAPP"))

# Select a color scheme from lowest to highest values
color_scale = c("darkgreen", "limegreen", "orange", "red")

## Generate default plot
plot_RTT_continuous_1 <- plot_rates_through_time(
   deepSTRAPP_outputs = Ponerinae_deepSTRAPP_cont_old_calib_0_40,
   color_scale = color_scale, display_plot = FALSE, verbose = FALSE)
plot_RTT_continuous_1 <- plot_RTT_continuous_1$rates_TT_ggplot +
  ggplot2::ggtitle(label = "Default plot")

# Plot with five trait quantile groups
plot_RTT_continuous_2 <- plot_rates_through_time(
   deepSTRAPP_outputs = Ponerinae_deepSTRAPP_cont_old_calib_0_40,
   quantile_ranges = c(0, 0.20, 0.40, 0.60, 0.80, 1.0),
   color_scale = color_scale, display_plot = FALSE, verbose = FALSE)
plot_RTT_continuous_2 <- plot_RTT_continuous_2$rates_TT_ggplot +
  ggplot2::ggtitle(label = "Five groups")

# Plot "fuzzy" CI
plot_RTT_continuous_3 <- plot_rates_through_time(
   deepSTRAPP_outputs = Ponerinae_deepSTRAPP_cont_old_calib_0_40,
   color_scale = color_scale,
   plot_CI = TRUE, # To add CI on the plot
   CI_type = "fuzzy", # Select type of CI
   display_plot = FALSE, verbose = FALSE)
plot_RTT_continuous_3 <- plot_RTT_continuous_3$rates_TT_ggplot +
  ggplot2::ggtitle(label = "Fuzzy CI")

# Plot "quantiles_rect" CI
plot_RTT_continuous_4 <- plot_rates_through_time(
   deepSTRAPP_outputs = Ponerinae_deepSTRAPP_cont_old_calib_0_40,
   color_scale = color_scale,
   plot_CI = TRUE, # To add CI on the plot
   CI_type = "quantiles_rect", # Select type of CI
   CI_quantiles = 0.9, # Adjust range of CI
   display_plot = FALSE, verbose = FALSE)
plot_RTT_continuous_4 <- plot_RTT_continuous_4$rates_TT_ggplot +
  ggplot2::ggtitle(label = "Rectangular CI")

# Plot "speciation" rates
plot_RTT_continuous_5 <- plot_rates_through_time(
   deepSTRAPP_outputs = Ponerinae_deepSTRAPP_cont_old_calib_0_40,
   rate_type = "speciation",
   color_scale = color_scale,
   plot_CI = TRUE, # To add CI on the plot
   CI_type = "quantiles_rect", # Select type of CI
   CI_quantiles = 0.9, # Adjust range of CI
   display_plot = FALSE, verbose = FALSE)
plot_RTT_continuous_5 <- plot_RTT_continuous_5$rates_TT_ggplot +
  ggplot2::ggtitle(label = "Speciation rates")

# Plot "extinction" rates
plot_RTT_continuous_6 <- plot_rates_through_time(
   deepSTRAPP_outputs = Ponerinae_deepSTRAPP_cont_old_calib_0_40,
   rate_type = "extinction",
   color_scale = color_scale,
   plot_CI = TRUE, # To add CI on the plot
   CI_type = "quantiles_rect", # Select type of CI
   CI_quantiles = 0.9, # Adjust range of CI
   display_plot = FALSE, verbose = FALSE)
plot_RTT_continuous_6 <- plot_RTT_continuous_6$rates_TT_ggplot +
  ggplot2::ggtitle(label = "Extinction rates")

cowplot::plot_grid(plotlist = list(plot_RTT_continuous_1, plot_RTT_continuous_2,
                                   plot_RTT_continuous_3, plot_RTT_continuous_4,
                                   plot_RTT_continuous_5, plot_RTT_continuous_6),
                   ncol = 2, nrow = 3)

```
```{r plot_RTT_cont_eval_CRAN, eval = !is_dev_version(), echo = FALSE, out.width = "100%"}

# Plot pre-rendered graph
knitr::include_graphics("figures/5_Explore_plot_RTT_1_Example_continuous.PNG")

```

```{r plot_RTT_cat_3lvl}
# ------ Example 2: Categorical multinomial trait data ------ #

#### Step 1: Prepare data ####

# Load results of a STRAPP test workflow run on categorical (3-levels) trait data
Ponerinae_deepSTRAPP_cat_3lvl_old_calib_0_40 <- readRDS(system.file("extdata", 
    "Ponerinae_deepSTRAPP_cat_3lvl_old_calib_0_40.rds", package = "deepSTRAPP"))
# This dataset is only available in development versions installed from GitHub.
# It is not available in CRAN versions.
# Use remotes::install_github(repo = "MaelDore/deepSTRAPP") to get the latest development version.

# Visualize trait data
table(Ponerinae_deepSTRAPP_cat_3lvl_old_calib_0_40$trait_data_df_over_time$trait_value)
# Visualize diversification rates data
hist(Ponerinae_deepSTRAPP_cat_3lvl_old_calib_0_40$diversification_data_df_over_time$rates)

## Select color scheme for states
colors_per_states <- c("forestgreen", "sienna", "goldenrod")
names(colors_per_states) <- c("arboreal", "subterranean", "terricolous")

### Step 2: Plot RTT ####

# For categorical trait data, the trait data are states.
# We can directly plot the evolution of rates between states.
# In the case of multinomial data (with more than two states/ranges), 
# the function allows you to select the states you wish to plot, if not all.

## Generate default plot with all states
plot_rates_through_time(
   deepSTRAPP_outputs = Ponerinae_deepSTRAPP_cat_3lvl_old_calib_0_40,
   colors_per_levels = colors_per_states)
   # PDF_file_path = "./plot_RTT_categorical.pdf")

# Plot with "fuzzy" CI
plot_rates_through_time(
   deepSTRAPP_outputs = Ponerinae_deepSTRAPP_cat_3lvl_old_calib_0_40,
   colors_per_levels = colors_per_states,
   plot_CI = TRUE, 
   CI_type = "fuzzy")

# Plot with "quantiles_rect" CI
plot_rates_through_time(
   deepSTRAPP_outputs = Ponerinae_deepSTRAPP_cat_3lvl_old_calib_0_40,
   colors_per_levels = colors_per_states,
   plot_CI = TRUE, 
   CI_type = "quantiles_rect")

## Subset to plot only "arboreal" and "terricolous" states
plot_RTT_categorical <- plot_rates_through_time(
   deepSTRAPP_outputs = Ponerinae_deepSTRAPP_cat_3lvl_old_calib_0_40,
   select_trait_levels = c("arboreal", "terricolous"), # List the states to plot
   colors_per_levels = colors_per_states[c("arboreal", "terricolous")], # Subset colors
   plot_CI = TRUE, 
   CI_type = "quantiles_rect")

```
```{r plot_RTT_cat_3lvl_eval_dev, fig.width = 14, fig.height = 10, out.width = "100%", eval = is_dev_version(), echo = FALSE}
# Load results of a STRAPP test workflow run on continuous trait data
Ponerinae_deepSTRAPP_cat_3lvl_old_calib_0_40 <- readRDS(system.file("extdata", 
    "Ponerinae_deepSTRAPP_cat_3lvl_old_calib_0_40.rds", package = "deepSTRAPP"))

## Select color scheme for states
colors_per_states <- c("forestgreen", "sienna", "goldenrod")
names(colors_per_states) <- c("arboreal", "subterranean", "terricolous")

## Generate default plot
plot_RTT_categorical_1 <- plot_rates_through_time(
   deepSTRAPP_outputs = Ponerinae_deepSTRAPP_cat_3lvl_old_calib_0_40,
   colors_per_levels = colors_per_states,
   display_plot = FALSE, verbose = FALSE)
plot_RTT_categorical_1 <- plot_RTT_categorical_1$rates_TT_ggplot +
  ggplot2::ggtitle(label = "Default plot")

# Plot "fuzzy" CI
plot_RTT_categorical_2 <- plot_rates_through_time(
   deepSTRAPP_outputs = Ponerinae_deepSTRAPP_cat_3lvl_old_calib_0_40,
   colors_per_levels = colors_per_states,
   plot_CI = TRUE, 
   CI_type = "fuzzy",
   display_plot = FALSE, verbose = FALSE)
plot_RTT_categorical_2 <- plot_RTT_categorical_2$rates_TT_ggplot +
  ggplot2::ggtitle(label = "Fuzzy CI")

# Plot "quantiles_rect" CI
plot_RTT_categorical_3 <- plot_rates_through_time(
   deepSTRAPP_outputs = Ponerinae_deepSTRAPP_cat_3lvl_old_calib_0_40,
   colors_per_levels = colors_per_states,
   plot_CI = TRUE, 
   CI_type = "quantiles_rect",
   display_plot = FALSE, verbose = FALSE)
plot_RTT_categorical_3 <- plot_RTT_categorical_3$rates_TT_ggplot +
  ggplot2::ggtitle(label = "Rectangular CI")

## Subset to plot only "arboreal" and "terricolous" states
plot_RTT_categorical_4 <- plot_rates_through_time(
   deepSTRAPP_outputs = Ponerinae_deepSTRAPP_cat_3lvl_old_calib_0_40,
   select_trait_levels = c("arboreal", "terricolous"), # List the states to plot
   colors_per_levels = colors_per_states[c("arboreal", "terricolous")], # Subset colors
   plot_CI = TRUE, 
   CI_type = "quantiles_rect",
   display_plot = FALSE, verbose = FALSE)
plot_RTT_categorical_4 <- plot_RTT_categorical_4$rates_TT_ggplot +
  ggplot2::ggtitle(label = "Subset two states")

cowplot::plot_grid(plotlist = list(plot_RTT_categorical_1, plot_RTT_categorical_2,
                                   plot_RTT_categorical_3, plot_RTT_categorical_4),
                   ncol = 2, nrow = 2)

```
```{r plot_RTT_cat_3lvl_eval_CRAN, eval = !is_dev_version(), echo = FALSE, out.width = "100%"}

# Plot pre-rendered graph
knitr::include_graphics("figures/5_Explore_plot_RTT_2_Example_multinomial.PNG")

```