Add travel history to a PMO's specimens

Appends one travel_out_six_month (TravelInfo) record per row of traveler_info to the matching specimen. Column names default to the schema field names, so the produced records are schema-shaped; non-default column names are used verbatim as keys.

Usage

pmo_update_specimen_with_traveler_info(
  pmo,
  traveler_info,
  specimen_name_col = "specimen_name",
  travel_country_col = "travel_country",
  travel_start_col = "travel_start_date",
  travel_end_col = "travel_end_date",
  bed_net_usage_col = NULL,
  geo_admin1_col = NULL,
  geo_admin2_col = NULL,
  geo_admin3_col = NULL,
  lat_lon_col = NULL,
  replace_current_traveler_info = FALSE
)

Arguments

pmo

A PortableMicrohaplotypeObject or parsed PMO list.

traveler_info

A data.frame of travel records.

specimen_name_col

Column matching specimens in the PMO.

travel_country_col, travel_start_col, travel_end_col

Required travel columns; the start/end values must be YYYY-MM or YYYY-MM-DD.

bed_net_usage_col, geo_admin1_col, geo_admin2_col, geo_admin3_col, lat_lon_col

Optional travel columns.

replace_current_traveler_info

If TRUE, clear any existing travel records on matched specimens before appending.

Value

The updated PMO as a raw nested list.

Examples

p <- read_pmo(
  system.file("extdata", "example_full_pmo.json.gz", package = "pmotoolsr"))
travel <- data.frame(
  specimen_name = pmo_get_specimen_names(p)[1],
  travel_country = "Kenya", travel_start_date = "2018-01",
  travel_end_date = "2018-02")
updated <- pmo_update_specimen_with_traveler_info(p, travel)