Create annual counts internal report from an EpiTrax object
epitrax_ireport_annual_counts.Rdepitrax_ireport_annual_counts generates an internal report of annual
counts for each disease in the EpiTrax object data.
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(
epitrax_file = data_file,
config_file = config_file,
disease_list_files = disease_lists
) |>
epitrax_ireport_annual_counts()
#> 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'
epitrax$internal_reports$annual_counts
#> disease 2019 2020 2021 2022 2023 2024
#> 1 COVID-19 1014 1627 2398 1855 908 1191
#> 2 Chickenpox 218 318 263 234 249 292
#> 3 Influenza 625 1733 1889 2289 1664 1466
#> 4 Measles 211 326 292 414 586 304
#> 5 Syphilis 278 356 439 398 577 269