General function to create a clock model

create_clock_model(name, id, ...)

Arguments

name

the clock model name. Valid names can be found in get_clock_model_names

id

a clock model's ID

...

specific clock model parameters

Value

a valid clock model

Note

Prefer using the named function create_rln_clock_model and create_strict_clock_model

See also

An alignment ID can be extracted from its FASTA filename using get_alignment_id. For more examples about creating a relaxed log-normal clock model, see create_rln_clock_model. For more examples about creating a strict clock model, see create_strict_clock_model.

Author

Richèl J.C. Bilderbeek

Examples

rln_clock_model <- create_rln_clock_model()

beast2_input_file <- get_beautier_tempfilename()
create_beast2_input_file(
  get_fasta_filename(),
  beast2_input_file,
  clock_model = rln_clock_model
)
file.remove(beast2_input_file)
#> [1] TRUE

strict_clock_model <- create_strict_clock_model()

beast2_input_file <- get_beautier_tempfilename()
create_beast2_input_file(
  get_fasta_filename(),
  beast2_input_file,
  clock_model = strict_clock_model
)
file.remove(beast2_input_file)
#> [1] TRUE