Create a parameter called clock_rate, as needed by create_strict_clock_model

create_clock_rate_param(value = "1.0", estimate = FALSE, id = NA)

Arguments

value

value of the parameter

estimate

TRUE if this parameter is to be estimated by BEAST2, FALSE otherwise

id

the parameter's ID

Value

a parameter called rate

Note

It cannot be estimated (as a hyper parameter) yet.

See also

the function create_param contains a list of all parameters that can be created

Author

Richèl J.C. Bilderbeek

Examples

clock_rate_param <- create_clock_rate_param(
  id = "anthus_aco", value = 1.0
)

# Use the parameter in a clock model
strict_clock_model <- create_strict_clock_model(
  clock_rate_param = clock_rate_param
)

# Use the distribution to create a BEAST2 input file
beast2_input_file <- get_beautier_tempfilename()
create_beast2_input_file(
  input_filename = get_fasta_filename(),
  beast2_input_file,
  clock_model = strict_clock_model
)
file.remove(beast2_input_file)
#> [1] TRUE