General function to create a site model.
Usage
create_site_model(name, id, gamma_site_model = create_gamma_site_model(), ...)
Arguments
- name
the site model name. Valid names can be found in
get_site_model_names
- id
the IDs of the alignment (can be extracted from the FASTA filename using
get_alignment_id
)- gamma_site_model
a gamma site model, as created by create_gamma_site_model
- ...
specific site model parameters
Note
Prefer using the
named functions
create_gtr_site_model
,
create_hky_site_model
,,
create_jc69_site_model
,
and create_tn93_site_model
See also
See create_gtr_site_model
for more examples
with a GTR site model. See create_hky_site_model
for more examples with an HKY site model. See
create_jc69_site_model
for more examples with a JC69
site model. See create_tn93_site_model
for more
examples with a TN93 site model
Examples
if (is_on_ci()) {
check_empty_beautier_folder()
input_filename <- get_fasta_filename()
gtr_site_model <- create_gtr_site_model()
hk_site_model <- create_hky_site_model()
jc69_site_model <- create_jc69_site_model()
tn93_site_model <- create_tn93_site_model()
# Can use any site model
output_filename <- get_beautier_tempfilename()
create_beast2_input_file(
input_filename = input_filename,
output_filename = output_filename,
site_model = jc69_site_model
)
file.remove(output_filename)
remove_beautier_folder()
check_empty_beautier_folder()
}