Virus detection in ES sites

Generates a dot plot for viral detections across ES sites, with SIA dates overlaid.

Usage

generate_es_site_det(
  sia.data,
  es.data,
  es_start_date = (lubridate::as_date(es_end_date) - lubridate::years(1)),
  es_end_date = end_date,
  output_path = Sys.getenv("DR_FIGURE_PATH"),
  vaccine_types = NULL,
  detection_types = NULL,
  ctry.data = lifecycle::deprecated(),
  es.data.long = lifecycle::deprecated()
)

Arguments

sia.data

tibble SIA surveillance data.

es.data

Environmental surveillance data, cleaned using clean_es_data() or a cleaned ctry.data$es.

es_start_date

str Start date of analysis. By default, it is one year from the end date.

es_end_date

str End date of analysis.

output_path

str Local path to output the figure to.

vaccine_types

list A named list with colors assigned names corresponding to vaccine types. By default, it will use a prefilled list inside the function. However, the function will alert for missing vaccine types and the user must pass another list appended by that vaccine type.

detection_types

list A named list with colors assigned names corresponding to viral detection type. By default, it will use a prefilled list inside the function. However, the function will alert for missing detection types and the user must pass another list appended by that vaccine type.

ctry.data

Please pass the SIA data directly to sia.data instead of a list containing it.

es.data.long

Please pass cleaned ES data instead.

Value

ggplot A dot plot of viral detections per ES sites and SIA campaigns.

Examples

if (FALSE) { # \dontrun{
ctry.data <- init_dr("algeria")
es.data <- clean_es_data(ctry.data$es)
generate_es_site_det(ctry.data, es.data)
} # }