Get both internal and public disease lists

get_report_disease_lists is a convenience function that combines get_internal_disease_list and get_public_disease_list.

Usage

get_report_disease_lists(internal_list_fp, public_list_fp, default_diseases)

Arguments

internal_list_fp

Filepath. Path to internal disease list CSV file.

public_list_fp

Filepath. Path to public disease list CSV file.

default_diseases

String vector. List of default diseases to use if either file doesn't exist.

Value

A list with two elements:

• internal: Dataframe with EpiTrax_name column

• public: Dataframe with EpiTrax_name and Public_name columns

Examples

# Using default lists (when files don't exist)
default_list <- c("Measles", "Chickenpox")
disease_lists <- get_report_disease_lists("", "", default_list)
#> Warning: You have not provided a disease list for internal reports.
#>  - The program will default to using only the diseases found in the input dataset.
#>  - If you would like to use a different list, please include a file with a column named
#> 
#> 	'EpiTrax_name'
#> Warning: You have not provided a disease list for public reports.
#>  - The program will default to using only the diseases found in the input dataset.
#>  - If you would like to use a different list, please include a file with columns named
#> 
#> 	'EpiTrax_name' and 'Public_name'

# Using disease list files
i_file <- system.file("tinytest/test_files/disease_lists/internal_list.csv",
                       package = "epitraxr")
p_file <- system.file("tinytest/test_files/disease_lists/public_list.csv",
                       package = "epitraxr")
disease_lists <- get_report_disease_lists(
  internal_list_fp = i_file,
  public_list_fp = p_file,
  default_diseases = default_list
)