Function to calculate timeliness of detection

Calculates the overall timeliness of detection in AFP & ES POLIS data.

Usage

f.timely.detection.01(
  afp.data,
  es.data,
  ctryseq.data,
  start.date,
  end.date,
  rolling = F
)

Arguments

afp.data

tibble AFP data which includes classification of AFP cases with onset date and date of notification to HQ.

es.data

tibble ES data which includes classification of samples with collection date and date of notification to HQ.

ctryseq.data

tibble A table consisting of the following columns for each country:

• With sequencing capacity within or outside of the country

• Country (ADM0_NAME)

• Classification of AFP cases & ES samples

• Onset date of AFP cases and collection date of ES samples

• Date of notification to HQ (date.notification.to.hq)

This table is the output of get_lab_locs().

start.date

str Start date for evaluation with format "YYYY-MM-DD".

end.date

str End date for evaluation with format "YYYY-MM-DD".

rolling

logical Should timeliness be calculated in a rolling basis? Default FALSE.

Value

list A list with two tibbles with global and sub-global AFP / ES detection timeliness evaluation.

Examples

if (FALSE) { # \dontrun{

raw.data <- get_all_polio_data()
ctry.data <- extract_country_data("algeria", raw.data)
ctry.seq <- get_lab_locs()
global.summary <- f.timely.detection.01(
  raw.data$afp, raw.data$es, ctry.seq,
  "2021-01-01", "2023-12-31"
)
ctry.summary <- f.timely.detection.01(
  ctry.data$afp.all.2, ctry.data$es, ctry.seq,
  "2021-01-01", "2023-12-31"
)
} # }