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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

Example #10: continue a run

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Examples how to use the babette R package

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