Author: Titouan Chambe
Date: 2024-04-29

# How to use the ‘FossilSimShiny’ app: a basic guide of the main functionalities

#### Titouan Chambe

#### 2024-04-29

This vignette provides information on how to use the `FossilSimShiny` application to perform simple tasks.

## Contents

- Launching the app
- Phylogenetic Tree
  - Generating a Tree
  - Importing a tree from Newick format
- Generating Taxonomy
- Simulating Fossils
- Saving your tree as a `.png`
- Last Words
- Additional Information

## Launching the app

Let’s dive right in.
Once you have installed the `FossilSimShiny` package,

    install.packages("FossilSimShiny")

Simply use the command:

    FossiSimShiny::launchFossilSimShiny()

This should launch the application in your preferred browser.
If you are using `RStudio` and you want to launch the app inside `RStudio's` browser, you can instead use:

    FossiSimShiny::launchFossilSimShiny(FALSE)

Fig. 1. FossilSimShiny main screen.

## Phylogenetic Tree

### Generating a tree

To generate a tree, start by opening the tree tab by clicking on the tree tab.

Fig. 2. Clicking the tree tab.

A new menu should appear. Inside this menu, you can set different tree parameters:

- Specialization rate

- Extinction rate

- Tip number

Once you are happy with the parameters you have set, press the simulate tree button to generate a tree.

Fig. 3. Generating a tree from set parameters.

### Importing a tree from Newick format

To use your own trees, simply tick the user tree check box and paste your `Newick` string inside the designated text box below.

Fig. 4. Importing a premade tree.Newick string used: `owls(((Strix_aluco:4.2,Asio_otus:4.2):3.1, Athene_noctua:7.3):6.3,Tyto_alba:13.5);`.

Since the app uses the `ape::read.tree()` function from the `ape` package. Look here for more information on how to format your trees.

## Generating Taxonomy

Once you have a phylogenetic tree, you can generate it’s taxonomy.

Note: if do not have a tree generated, go back to Phylogenetic Tree.
Open the taxonomy menu by clicking on the taxonomy tab.

Fig. 5. Clicking the taxonomy tab.

Inside you can set different parameters:

- Probability of symmetric speciation

- Rate of anagenesis

When everything is set, press the simulate taxonomy button.

Fig. 6. Simulating a taxonomy with the default parameters.

## Simulating Fossils

Once you have a phylogenetic tree, you can immediately simulate fossil records.

Note: if do not have a tree generated, go back to Phylogenetic Tree. Furthermore, if you wish to use a lineage-dependent model to simulate your fossils, it is recommended to generate the taxonomy first. Go to Generating Taxonomy.
First, click on the fossils tab.

Fig. 7. Clicking the fossils tab.

In the fossils tab, you must choose which model you would like to use to simulate your fossil records. Each one of them has their own peculiarities:

- Uniform
- Non-uniform
- Environment-dependent
- Lineage-dependent

Fig. 8. Generating fossil records for our tree using a uniform distribution.

## Saving your tree as a `.png`

Use the drop down in the top left corner of the app to select the plot that you would like to save.
As an example, let’s save a picture of our taxonomy.

Fig. 9. Going back to the taxonomy view to save it as an image.

Then, just press the save tree as image… button.

Fig. 10. Saving our taxonomy as an image.

Your plot should get saved as a `.png` to your `/downloads` folder.

## Last words

And voilà ! You know all the basics and can now generate your own trees, taxonomy and fossil records.
If you would like to dive a bit deeper into more advanced functionalities check out (COMING SOON).

## Additional information

All screenshots in this guide were taken on the Google Chrome browser using the built in `screenshot` command.
Dimensions: 1024x1024 75%, Output: 2048x2048, Resized to: 2048x2048.