Clean lab data — clean_lab_data • sirfunctions

Main lab data cleaning function. Automatically detects whether the dataset came from WHO or the regional office.

Usage

clean_lab_data(
  lab_data,
  start_date,
  end_date,
  afp_data = NULL,
  ctry_name = NULL,
  lab_locs_path = NULL,
  use_edav = TRUE
)

Arguments

lab_data: tibble Lab dataset.
start_date: str Start date of analysis.
end_date: str End date of analysis.
afp_data: tibble AFP linelist. Either ctry.data$afp.all.2 or raw.data$afp.
ctry_name: str or list Name or a list of countries. Defaults to NULL.
lab_locs_path: str Location of testing lab locations. Default is NULL. Will download from EDAV, if necessary.
use_edav: logical Whether to obtain data from EDAV. Defaults to TRUE.

Value

tibble Cleaned lab data.

Examples

if (FALSE) { # \dontrun{
lab_path <- "C:/Users/abc1/lab_data_who.csv"
ctry.data <- init_dr("algeria", lab_data_path = lab_path)
ctry.data$lab_data <- clean_lab_data(ctry.data, "2021-01-01", "2023-12-31")

# Not using the desk review pipeline
raw.data <- get_all_polio_data()
ctry.data <- extract_country_data("algeria", raw.data)
ctry.data$lab_data <- read_csv(lab_path)
ctry.data$lab_data <- clean_lab_data(
  ctry.data$lab.data, "2021-01-01", "2023-12-31",
  ctry.data$afp.all.2, "algeria"
)
} # }