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Setup EpiTrax object with configuration and disease lists

setup_epitrax.Rd

setup_epitrax initializes an EpiTrax object with configuration and report disease lists. It is a convenience function that combines get_epitrax, epitrax_set_config_from_file, and epitrax_add_report_diseases.

Usage

setup_epitrax(
  epitrax_file = NULL,
  disease_list_files = NULL,
  config_list = NULL,
  config_file = NULL
)

Arguments

epitrax_file

Optional path to the EpiTrax data file. Data file should be a CSV. If omitted, the user will be prompted to choose a file interactively.

disease_list_files

Optional list containing filepaths to internal and public report disease lists. If omitted, the default lists will be used and a warning will be thrown.

config_list, config_file

Configuration options may be specified as a list or as a path to a YAML config file, respectively. Only one can be specified at a time. If both are specified, the function will return an error. If both are omitted, the default config values will be used.

Value

An EpiTrax object with configuration and report diseases set.

Examples

data_file <- system.file("sample_data/sample_epitrax_data.csv",
                         package = "epitraxr")
disease_lists <- list(
  internal = system.file("tinytest/test_files/disease_lists/internal_list.csv",
                         package = "epitraxr"),
  public = system.file("tinytest/test_files/disease_lists/public_list.csv",
                       package = "epitraxr")
)

epitrax <- setup_epitrax(
  epitrax_file = data_file,
  disease_list_files = disease_lists
)