doc/examples.md

In richelbilderbeek/raket: What If Speciation Takes Time?

Examples

For all examples, do load babette:

library(babette)

All examples read the alignment from a FASTA file (usually my_fasta.fas) and create a BEAST2 input file called my_beast.xml.

Example #1: all default

Using all default settings, only specify a DNA alignment.

posterior <- run_beast2(
  "test_output_0.fas"
)

All other parameters are set to their defaults, as in BEAUti.

Example #2: fixed crown age

Using all default settings, only specify a DNA alignment.

[No screenshot, as this cannot be done in BEAUti yet]

posterior <- run_beast2(
  "my_fasta.fas",
  posterior_crown_age = 15
)

Example #3: JC69 site model

posterior <- run_beast2(
  "my_alignment.fas",
  site_models = create_jc69_site_model()
)

Example #4: Relaxed clock log normal

```{r example_4} posterior <- run_beast2( "my_alignment.fas", clock_models = create_rln_clock_model() )

## Example #5: Birth-Death tree prior

![Example #5: Birth-Death tree prior](bd_2_4.png)

```{r example_5}
posterior <- run_beast2(
  "my_alignment.fas",
  tree_priors = create_bd_tree_prior() 
)

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

```{r example_6} posterior <- run_beast2( "my_alignment.fas", tree_priors = create_yule_tree_prior( birth_rate_distr = create_normal_distr() ) )

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](hky_prop_invariant_0_5_2_4.png)

```{r example_7}
posterior <- run_beast2(
  "my_alignment.fas",
  site_models = create_hky_site_model(
    gamma_site_model = create_gamma_site_model(prop_invariant = 0.5)
  )
)

Thanks to Yacine Ben Chehida for this use case

Example #8: Strict clock with a known clock rate

```{r example_8} posterior <- run_beast2( "my_alignment.fas", clock_models = create_strict_clock_model( clock_rate_param = create_clock_rate_param(value = 0.5)) )

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

## Example #9: Two alignments

![Example 9: Two alignments](anthus_2_4.png)

```{r example_9}
posterior <- run_beast2(
  c("anthus_aco.fas", "anthus_nd2.fas")
)

Thanks to Paul van Els for this use case and supplying these FASTA files.

Example #10: Two alignments, different site models

{r example_10} babette::posterior <- run_beast2( c("anthus_aco.fas", "anthus_nd2.fas"), site_models = list( create_hky_site_model(), create_tn93_site_model() ) )

Since v1.12 this it is supported to have two alignments with different site models, clock models and tree priors.

Thanks to Paul van Els for this use case.

richelbilderbeek/raket documentation built on Dec. 31, 2019, 7:41 p.m.