rename_inference_model_filenames: Rename the filenames in an inference model

In beautier: 'BEAUti' from R

Rename the filenames in an inference model

Description

Rename the filenames in an inference model

Usage

rename_inference_model_filenames(inference_model, rename_fun)

Arguments

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.

rename_fun

a function to rename a filename, as can be checked by check_rename_fun. This function should have one argument, which will be a filename or NA. The function should return one filename (when passed one filename) or one NA (when passed one NA). Example rename functions are: get_remove_dir_fun get a function that removes the directory paths from the filenames, in effect turning these into local files get_replace_dir_fun get a function that replaces the directory paths from the filenames get_remove_hex_fun get a function that removes the hex string from filenames. For example, tracelog_82c1a522040.log becomes tracelog.log

Value

an inference model with the renamed filenames

Examples

check_empty_beautier_folder()

inference_model <- create_inference_model()
inference_model$mcmc$tracelog$filename <- "trace.log"
inference_model$mcmc$screenlog$filename <- "screen.log"
inference_model$mcmc$treelog$filename <- "tree.log"
inference_model$tipdates_filename <- "tipdates.csv"

# Nah, put the files in a folder
inference_model <- rename_inference_model_filenames(
  inference_model = inference_model,
  rename_fun = get_replace_dir_fun("/home/john")
)

# Nah, put the files in anoth folder
inference_model <- rename_inference_model_filenames(
  inference_model = inference_model,
  rename_fun = get_replace_dir_fun("/home/doe")
)

# Nah, store the files locally
rename_inference_model_filenames(
  inference_model = inference_model,
  rename_fun = get_remove_dir_fun()
)

check_empty_beautier_folder()

beautier documentation built on Nov. 2, 2023, 5:08 p.m.