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Import data for TreePPL program

Source: R/data.R
tp_data.Rd

Prepare data input for tp_run().

Usage

tp_data(data_input, data_file_name = "tmp_data_file", dir = tp_tempdir())

Arguments

data_input

One of the following options:

  • A named list (or structured list) containing TreePPL data, OR

  • The full path of a multiple sequence alignment in fasta (.fasta, .fas) or nexus (.nexus, .nex) format, OR

  • For test data, a string with the name of a model supported by treepplr (see tp_model_library()).

data_file_name

An optional name for the file created. Ignored if data_input is the name of a model from the TreePPL library.

dir

The directory where you want to save the data file in JSON format. Default is base::tempdir(). Ignored if data_input is the name of a model from the TreePPL library.

Value

The path for the data file that will be used by tp_run().

Details

data_input: The name of each list element has to match the name of a model input, which is defined in the TreePPL model code.

Examples

if (FALSE) { # \dontrun{
# Example using a model name supported by TreePPL
input <- tp_data("tree_inference")
input

# Example using an internal FASTA file (same input data as before, but in fasta format)
fasta_file <- system.file("extdata", "tree_inference.fasta", package = "treepplr")
input <- tp_data(fasta_file)
input
} # }