Write reports from EpiTrax object to Excel files

epitrax_write_xlsxs writes the internal and public reports from an EpiTrax object to Excel files in the specified filesystem. Combines all internal reports into one Excel file with separate sheets for each report. Likewise with public reports.

Usage

epitrax_write_xlsxs(epitrax, fsys)

Arguments

epitrax

Object of class epitrax.

fsys

Filesystem list containing paths for internal and public reports.

Value

The original EpiTrax object, unchanged.

Examples

fsys <- list(
  internal = file.path(tempdir(), "internal_reports"),
  public = file.path(tempdir(), "public_reports"),
  settings = file.path(tempdir(), "report_settings")
)
fsys <- setup_filesystem(fsys)

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_preport_ytd_rates() |>
 epitrax_write_xlsxs(fsys = fsys)
#> 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'