dot-parse_file_paths: Internal function for parsing file paths

In familiar: End-to-End Automated Machine Learning and Model Evaluation

Internal function for parsing file paths

Description

Internal function for parsing file paths

Usage

.parse_file_paths(
  config = NULL,
  project_dir = waiver(),
  experiment_dir = waiver(),
  data_file = waiver(),
  verbose = TRUE,
  ...
)

Arguments

config	A list of settings, e.g. from an xml file.
project_dir	(optional) Path to the project directory. familiar checks if the directory indicated by experiment_dir and data files in data_file are relative to the project_dir.
experiment_dir	(recommended) Path to the directory where all intermediate and final results produced by familiar are written to. The experiment_dir can be a path relative to project_dir or an absolute path. In case no project directory is provided and the experiment directory is not on an absolute path, a directory will be created in the temporary R directory indicated by tempdir(). This directory is deleted after closing the R session or once data analysis has finished. All information will be lost afterwards. Hence, it is recommended to provide either experiment_dir as an absolute path, or provide both project_dir and experiment_dir.
data_file	(optional) Path to files containing data that should be analysed. The paths can be relative to project_dir or absolute paths. An error will be raised if the file cannot be found. The following types of data are supported. csv files containing column headers on the first row, and samples per row. csv files are read using data.table::fread. rds files that contain a data.table or data.frame object. rds files are imported using base::readRDS. RData files that contain a single data.table or data.frame object. RData files are imported using base::load. All data are expected in wide format, with sample information organised row-wise. More than one data file can be provided. familiar will try to combine data files based on column names and identifier columns. Alternatively, data can be provided using the data argument. These data are expected to be data.frame or data.table objects or paths to data files. The latter are handled in the same way as file paths provided to data_file.
verbose	Sets verbosity.
...	Unused arguments

Value

List of paths to important directories and files.

familiar documentation built on Sept. 30, 2024, 9:18 a.m.