How to use the ‘FossilSimShiny’ app: a
basic guide of the main functionalities
This vignette provides information on how to use the
FossilSimShiny application to perform simple tasks.
Launching the app
Let’s dive right in.
Once you have installed the
Simply use the command:
This should launch the application in your preferred browser.
If you are using
RStudio and you want to launch the app
RStudio's browser, you can instead use:
Fig. 1. FossilSimShiny main screen.
Generating a tree
To generate a tree, start by opening the tree tab by clicking on the
Fig. 2. Clicking the tree tab.
A new menu should appear. Inside this menu, you can set different tree
Once you are happy with the parameters you have set, press the
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
string inside the designated text box
Fig. 4. Importing a premade tree.Newick string
Since the app uses the
ape::read.tree() function from the
ape package. Look
for more information on how to format your trees.
Once you have a phylogenetic tree, you can generate
Note: if do not have a tree generated, go back to Phylogenetic Tree.
Open the taxonomy menu by clicking on the taxonomy
Fig. 5. Clicking the taxonomy tab.
Inside you can set different parameters:
When everything is set, press the simulate taxonomy
Fig. 6. Simulating a taxonomy with the default
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
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