Skip to content
Examples how to use the babette R package
Branch: master
Clone or download

Latest commit

Fetching latest commit…
Cannot retrieve the latest commit at this time.

Files

Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
pics
.gitignore
LICENSE
README.md

README.md

babette_examples

Examples how to use the babette R package.

For all examples, do load babette:

library(babette)

All examples use the BEAST2 Primates.nex alignment file and convert it to a FASTA file first.

Example #0: install and self-test

See install.md for the installation instructions.

See babette example 0: self-test for the code.

Example #1: all default

Using all default settings, only specify a DNA alignment.

Example #1: all default

See babette example 1: all default

Example #2: fixed crown age

The way to do so, is to date the node of the most recent common ancestor of all taxa:

Example #2: using a MRCA to specify a crown age

See babette example 2: fixed crown age

Example #3: JC69 site model

Example #3: JC69 site model

See babette example 3: JC69 site model

Example #4: Relaxed clock log normal

Example #4: Relaxed clock log normal

See babette example 4: Relaxed clock log normal

Example #5: Birth-Death tree prior

Example #5: Birth-Death tree prior

See babette example 5: Birth-Death tree prior

Example #6: Yule tree prior with a normally distributed birth rate

Example #6: Yule tree prior with a normally distributed birth rate

See babette example 6: Yule tree prior with a normally distributed birth rate

Thanks to Yacine Ben Chehida for this use case

Example #7: HKY site model with a non-zero proportion of invariants

Example #7: HKY site model with a non-zero proportion of invariants

See babette example 7: HKY site model with a non-zero proportion of invariants

Thanks to Yacine Ben Chehida for this use case

Example #8: Strict clock with a known clock rate

Example #8: Strict clock with a known clock rate

See babette example 8: Strict clock with a known clock rate

Thanks to Paul van Els and Yacine Ben Chehida for this use case.

Example #9: sample from prior

Picture needed here

See babette example 9: sample from prior

You can’t perform that action at this time.