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Write XML files for a disease to a directory

write_disease_dir.Rd

This function creates a directory structure for a specified disease and generates XML files for relative risks from risk factors and other diseases, as well as for disease prevalences, incidences, excess mortalities, and disability data. The directories and XML files are named and organized according to the input lists provided for each category. The function only creates files for provided arguments and leaves other files as they are.

Usage

write_disease_dir(
  disease_name,
  risk_factor_list,
  diseases_list,
  prevalences_list,
  incidences_list,
  excess_mortalities_list,
  disability_list
)

Arguments

disease_name

A character string representing the name of the disease. A directory will be created with this name if it does not already exist.

risk_factor_list

A named list where each element is a list containing two components: 'data' (the risk factor data) and 'type' (the type of risk factor). XML files will be generated for each risk factor.

diseases_list

A named list where each element is a list containing disease data under the key 'data'. XML files will be generated for relative risks from other diseases.

prevalences_list

A named list where each element is a list containing prevalence data under the key 'data'. XML files will be generated for each prevalence.

incidences_list

A named list where each element is a list containing incidence data under the key 'data'. XML files will be generated for each incidence.

excess_mortalities_list

A named list where each element is a list containing three components: 'unit_type' (the unit of the data), 'parameter_type' (the type of parameter), and 'data' (the excess mortality data). XML files will be generated for each excess mortality.

disability_list

A named list where each element is a list containing disability data under the key 'data'. XML files will be generated for each disability dataset.

Value

Returns TRUE if the directory structure and XML files were created successfully.

Details

The function creates a directory named after the disease and subdirectories for: containing:

  • Relative_Risks_From_Risk_Factor

  • Relative_Risks_From_Diseases

  • Prevalences

  • Incidences

  • Excess_Mortalities

  • Disabilities

For each category, the function generates XML files based on the data provided in the corresponding input list. Each XML file is saved in the appropriate subdirectory.

The risk factor 'type' can be 'continuous', 'continuous4p', 'categorical', 'categorical4p', 'compound', or 'compound4p'. The excess mortality 'parameter_type' can be 'Acutely Fatal' or 'Cured Fraction'.

See also

create_population_dir

Examples

if (FALSE) { # \dontrun{
# A list element corresponds to a risk factor (e.g., smoking)
risk_factors <- list("smoking" = list(data = data.frame(...), type = "categorical"))

# A list element corresponds to another disease (e.g., diabetes)
diseases <- list("diabetes" = list(data = data.frame(...)))

# A list element corresponds to a population (e.g., Netherlands)
prevalences <- list("NL" = list(data = data.frame(...)))
incidences <- list("NL" = list(data = data.frame(...)))
mortalities <- list("NL" = list(
  unit_type = "Rate",
  parameter_type = "Acutely Fatal",
  data = data.frame(...)
))
disabilities <- list("NL" = list(data = data.frame(...)))

create_disease_dir(
  "stroke", risk_factors, diseases, prevalences,
  incidences, mortalities, disabilities
)
} # }