Create grouped disease statistics report from an EpiTrax object — epitrax_report_grouped

epitrax_report_grouped_stats generates a comprehensive report with current and historical statistics for diseases organized by group. The report includes monthly counts/rates, historical averages and medians, year-to-date counts, and trend analysis. It can be run for either internal or public reports.

Usage

epitrax_report_grouped_stats(epitrax, is.public = FALSE)

Arguments

epitrax: Object of class epitrax.
is.public: Logical indicating whether to generate a public report using the public disease list. If FALSE (default), generates an internal report using the internal disease list.

Value

Updated EpiTrax object with grouped statistics report added to either the internal_reports or public_reports field, depending on the is.public parameter.

Examples

data_file <- system.file("sample_data/sample_epitrax_data.csv",
                         package = "epitraxr")
config_file <- system.file("tinytest/test_files/configs/good_config.yaml",
                           package = "epitraxr")
disease_lists <- list(
  internal = "use_defaults",
  public = "use_defaults"
)

epitrax <- setup_epitrax(
  filepath = data_file,
  config_file = config_file,
  disease_list_files = disease_lists
) |>
 epitrax_report_grouped_stats()
#> 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'
#> Warning: The parameter 'diseases' should contain a 'Group_name' column. Since, no groups were provided, all diseases will be 'Uncategorized'.

names(epitrax$internal_reports)
#> [1] "grouped_stats_2019-2024"