Timeliness of arrival at sequencing lab to sequencing results

Shows the timeliness of arrival in the sequencing lab to sequencing results. The target is 7 days for cases shipped for sequencing.

Usage

generate_lab_seqres_violin(
  lab_data,
  afp_data,
  start_date,
  end_date,
  priority_level = c("HIGH", "MEDIUM", "LOW (WATCHLIST)", "LOW"),
  who_region = NULL,
  rolling = TRUE,
  output_path = Sys.getenv("KPI_FIGURES"),
  y_max = NULL
)

Arguments

lab_data

tibble Global lab dataset.

afp_data

tibble AFP dataset.

start_date

str Start date of the analysis formatted as "YYYY-MM-DD".

end_date

str End date of the analysis formatted as "YYYY-MM-DD".

priority_level

list Priority levels to display. Defaults to c("HIGH", "MEDIUM", "LOW (WATCHLIST)", "LOW").

who_region

list Regions to display. Defaults to NULL, which shows all of the regions.

rolling

logical Using rolling periods or year-to-year? Defaults to TRUE.

output_path

str Where to output the figure to.

y_max

num Maximum value in the y-axis.

Value

ggplot A violin plot showing the timeliness of sequencing results.

Examples

if (FALSE) { # \dontrun{
raw_data <- get_all_polio_data()
lab_data <- edav_io("read", file_loc = get_constant("CLEANED_LAB_DATA"))
generate_lab_seqres_violin(lab_data, raw_data$afp,
                           "2021-01-01", "2023-12-31", getwd())
} # }