How to use the 'FossilSimShiny' app: a basic guide of the main functionalities

In FossilSimShiny: Shiny Application for 'FossilSim'

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

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)

\

knitr::include_graphics("images/main-menu.png")
cap = "**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.\ \

knitr::include_graphics("images/main-menu-click-tree.png")
cap = "**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.\ \

knitr::include_graphics("images/tree-menu-click-sim.png")
cap = "**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.\ \

knitr::include_graphics("images/newick.png")
cap = "**Fig. 4**. Importing a premade tree.</br>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.\ \

knitr::include_graphics("images/main-menu-click-tax.png")
cap = "**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.\ \

knitr::include_graphics("images/tax-menu.png")
cap = "**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.\ \

knitr::include_graphics("images/main-menu-click-fos.png")
cap = "**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

\

knitr::include_graphics("images/fos-menu.png")
cap = "**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.\ \

knitr::include_graphics("images/going-back-tax.png")
cap = "**Fig. 9**. Going back to the taxonomy view to save it as an image."

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

knitr::include_graphics("images/saveas.png")
cap = "**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.\

FossilSimShiny documentation built on May 29, 2024, 10:22 a.m.