'get_report_diseases_internal' reads the internal list from a given CSV file or uses the default diseases, if the file doesn't exist.
Value
A dataframe containing the diseases to include in the internal report and possibly the disease groupings.
Details
The provided internal disease list file must contain at least a column named
EpiTrax_name which contains EpiTrax disease names to include in the 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_internal("", 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'
# Using a disease list file
list_file <- system.file("sample_data/sample_disease_list.csv",
package = "epitraxr")
disease_list <- get_report_diseases_internal(list_file, default_list)