Timely detection of AFP/ES samples

Generates a violin plot highlighting the median detection time of samples.

Usage

generate_timely_det_violin(
  raw_data,
  start_date,
  end_date,
  priority_level = c("HIGH", "MEDIUM", "LOW (WATCHLIST)", "LOW"),
  who_region = NULL,
  rolling = TRUE,
  risk_table = NULL,
  lab_locs = NULL,
  output_path = Sys.getenv("KPI_FIGURES"),
  y_max = NULL
)

Arguments

raw_data

list Global polio data. Output of get_all_polio_data()

start_date

str Analysis start date formatted as "YYYY-MM-DD".

end_date

str Analysis end date 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.

risk_table

tibble Priority level of each country. Defaults to NULL, which will download the information directly from EDAV.

lab_locs

tibble Summary of the sequencing capacities of labs. Output of get_lab_locs(). Defaults to NULL, which will download the information directly from EDAV.

output_path

str Where to output the figure to.

y_max

num The maximum y-axis value. Defaults to NULL, which will compute the y_max as the max value of days to notify hq.

Value

ggplot A violin plot showing timeliness of detection.

Examples

if (FALSE) { # \dontrun{
raw_data <- get_all_polio_data()
generate_timely_det_violin(raw_data, "2021-01-01", "2023-12-31")
} # }