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Calculate stool collection timeliness using only AFP data (DRAFT)

f.timely.01.Rd

[Deprecated]

Creates a table for timeliness by geographic unit including the number of timely stool samples for each interval and percent timeliness. Currently, the function will only work on ctry.data (output of extract_country_data()).

Usage

f.timely.01(
  afp.data,
  admin.data,
  start.date,
  end.date,
  spatial.scale,
  intervals.manual = F
)

Arguments

afp.data

tibble AFP data which includes GUID at a given spatial scale formated as adm(0,1,2)guid, onset date as date.

admin.data

tibble Full list of country administrative units by a given spatial scale including year, adm(0,1,2)guid, and ctry/prov/dist as appropriate.

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".

spatial.scale

str Spatial scale to group analysis by. Valid values are: -"prov" Province level.

  • "dist" District level.

  • "ctry" Country level.

intervals.manual

logical Should user input their own timeliness interval requirements? Default is FALSE. This is only required if timeliness column such as noti.7d.on, inv.2d.noti are not already calculated. This draft function will currently fail if this parameter is set to TRUE.

Value

tibble A summary table of timeliness of stool collection.

Details

This function is no longer maintained as it is not used in any of the analytic pipelines. An equivalent function is generate_int_data(), which expands and simplifies this function by also being able to take lab data to calculate lab timeliness intervals.

Examples

if (FALSE) { # \dontrun{
raw.data <- get_all_polio_data()
ctry.data <- extract_country_data("algeria", raw.data)
stool.summary <- f.timely.01(
  ctry.data$afp.all.2, ctry.data$ctry.pop,
  lubridate::as_date("2021-01-01"),
  lubridate::as_date("2023-12-31"),
  "ctry"
)
} # }