This vignette provides information on how to use the
FossilSimShiny
application to perform simple tasks.
Let’s dive right in.
Once you have installed the FossilSimShiny
package,
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
inside RStudio's
browser, you can instead use:
Fig. 1. FossilSimShiny main screen.
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
Fig. 3. Generating a tree from set parameters.
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.
Once you have a phylogenetic tree, you can generate
it’s taxonomy.
Fig. 5. Clicking the taxonomy tab.
Inside you can set different parameters:
Probability of symmetric speciation
Rate of anagenesis
Fig. 6. Simulating a taxonomy with the default parameters.
Once you have a phylogenetic tree, you can
immediately simulate fossil records.
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:
Fig. 8. Generating fossil records for our tree using a uniform distribution.
.png
Fig. 9. Going back to the taxonomy view to save it as an image.
Fig. 10. Saving our taxonomy as an image.
Your plot should get saved as a .png
to your
/downloads
folder.
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).
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.