Setup EpiTrax object with configuration and disease lists

setup_epitrax initializes an EpiTrax object with configuration and report disease lists. It is a convenience function that combines create_epitrax_from_file(), epitrax_set_config_from_file(), and epitrax_set_report_diseases().

Usage

setup_epitrax(
  filepath = NULL,
  num_yrs = 5,
  disease_list_files = NULL,
  config_list = NULL,
  config_file = NULL
)

Arguments

filepath

Optional filepath. EpiTrax data file should be a CSV. If this parameter is NULL, the user will be prompted to choose a file interactively.

num_yrs

Integer. Number of years of data to keep. Defaults to 5.

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 given.

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.

See also

create_epitrax_from_file(), epitrax_set_config_from_file(), epitrax_set_config_from_list(), and epitrax_set_report_diseases() which this function wraps.

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(
  filepath = data_file,
  disease_list_files = disease_lists
)