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Generate stool adequacy columns in the AFP dataset

generate_stool_data.Rd

The function adds the adequacy final column called adequacy.final and adequacy.final2 into the AFP linelist. The function borrows in part from f.stool.ad.01(), so that the adequacy final column generated can match with how the stool adequacy function treats bad or missing data and classify the adequacy final column. adequacy.final contains the original classification of the sample and adequacy.final2 contains the final classification according to how missing and bad data are treated.

Usage

generate_stool_data(
  afp.data,
  start_date,
  end_date,
  missing = "good",
  bad.data = "inadequate"
)

Arguments

afp.data

tibble AFP linelist. Either ctry.data$afp.all.2

start_date

str Start date of the analysis.

end_date

str End date of the analysis.

missing

str How to treat missing data. Valid values are: "good", "bad", "remove". Defaults to "good". When calculating the adequacy.final column:

  • "good" uses adequacy.03

  • "bad" uses adequacy.01

  • "exclude" uses adequacy.02

bad.data

str How to treat bad data. Valid values are:"remove", "inadequate". Defaults to "inadequate". "inadequate" treats samples with bad data as inadequate.

Value

tibble AFP linelist with stool adequacy columns.

Details

Unlike the stool adequacy function, this will not filter out NOT-AFP cases, as it is expected for other functions that use the output of this function to do the filtering. For example, generate_60_day_table_data().

See also

f.stool.ad.01()

Examples

if (FALSE) { # \dontrun{
raw.data <- get_all_polio_data(attach.spatial.data = FALSE)
stool.data <- generate_stool_data(raw.data$afp, "2021-01-01", "2023-12-31")
} # }