peregrine must use new babette interface

richelbilderbeek commented 4 years ago

In the old days, one would write:

bbt_run(
  beast2_options(
    output_log_filename = "out.log",
    output_trees_filenames = "out.trees
)

These two files, however, have been an inherent part of a beautier MCMC object.

Nowadays one writes:

bbt_run(
  inference_model = create_mcmc(
    tracelog = create_tracelog(
      filename = "out.log"
    ),
    treelog = create_treelog(
      filenames = "out.trees
    )
  )
)

Make peregrine use the new interface.

richelbilderbeek commented 4 years ago

I hope @Giappo will help me with this one...

Giappo commented 4 years ago

Hi @richelbilderbeek ,

There is one thing I do not understand. I just updated babette calling:

devtools::install_github("ropensci/babette")

If I call the help from "bbt_run" I obtain this:

bbt_run(fasta_filename, tipdates_filename = NA, site_model = beautier::create_jc69_site_model(), clock_model = beautier::create_strict_clock_model(), tree_prior = beautier::create_yule_tree_prior(), mrca_prior = NA, mcmc = beautier::create_mcmc(), beast2_input_filename = beastier::create_temp_input_filename(), rng_seed = 1, beast2_output_state_filename = beastier::create_temp_output_state_filename(), beast2_path = beastier::get_default_beast2_path(), overwrite = TRUE, verbose = FALSE, beast2_output_log_filename = "deprecated", beast2_output_trees_filenames = "deprecated", beast2_working_dir = "deprecated", fasta_filenames = "deprecated", site_models = "deprecated", clock_models = "deprecated", tree_priors = "deprecated", mrca_priors = "deprecated", posterior_crown_age = "deprecated", cleanup = "deprecated")

As you can see there is no "inference_model" section. So how can I use the new one?

richelbilderbeek commented 4 years ago

The new one is called bbt_run_from_model :+1:

Enjoy!

richelbilderbeek commented 4 years ago

AFAICS: Well done @Giappo!

Closing the Issue :+1:

richelbilderbeek / pirouette

peregrine must use new babette interface #351