Get the public disease list — get_report_diseases

'get_report_diseases_public' reads the public list from a given CSV file or uses the default diseases if the file doesn't exist.

Usage

get_report_diseases_public(filepath, defaults)

Arguments

filepath: Filepath. Public disease list CSV file.
defaults: String vector. List of default diseases to use if the above file doesn't exist.

Value

A dataframe containing the diseases to include in the public report and the name to use for each disease in the public report. It may also contain the disease groupings.

Details

The provided public disease list file must contain two columns named EpiTrax_name and Public_name which map EpiTrax disease names to a public-facing name for the public report. The file can optionally contain a column named Group_name, which maps the diseases in EpiTrax_name to a disease group. This is only used for reports that include disease groupings.

See the example file here: system.file("sample_data/sample_disease_list.csv", package = "epitraxr")

Examples

# Using default list (when file doesn't exist)
default_list <- c("Measles", "Chickenpox")
disease_list <- get_report_diseases_public("", default_list)
#> 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 a disease list file
list_file <- system.file("sample_data/sample_disease_list.csv",
                        package = "epitraxr")
disease_list <- get_report_diseases_public(list_file, default_list)