Awesome
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.
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:
See babette example 2: fixed crown age
Example #3: JC69 site model
See babette example 3: JC69 site model
Example #4: Relaxed clock log normal
See babette example 4: Relaxed clock log normal
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
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
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
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
Example #10: continue a run
- Video: YouTube download (.ogv)
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