Creates the 'run' section of a BEAST2 XML parameter file, without being indented.

create_beast2_input_run(
  input_filename,
  inference_model = beautier::create_inference_model()
)

Arguments

input_filename

A FASTA filename. Use get_fasta_filename to obtain a testing FASTA filename.

inference_model

a Bayesian phylogenetic inference model. An inference model is the complete model setup in which a site model, clock model, tree prior and more are specified. Use create_inference_model to create an inference model. Use check_inference_model to check if an inference model is valid. Use rename_inference_model_filenames to rename the files in an inference model.

Value

lines of XML text

Details

The run tag has these elements:


   <run[...]>
       <state[...]>
       [...]
       </state>
       <init[...]>
       [...]
       </init>
       <distribution[...]>
       [...]
       </distribution>
       [operator ids]
       [loggers]
    </run>

See also

Use create_beast2_input_state to create the XML text of the state tag. Use create_beast2_input_init to create the XML text of the init tag. Use create_beast2_input_distr to create the XML text of the distribution tag. Use create_beast2_input_operators to create the XML text of the [operator ids] section. Use create_loggers_xml to create the XML text of the [loggers] part.

Author

Richèl J.C. Bilderbeek