Interactive leaflet plotting for entry points — plot_entry_points

Helper function to plot riskintro's default risks using ggplot2.

Usage

plot_entry_points_interactive(dataset, scale, risk_col, ll = new_leaflet())

plot_animal_mobility_interactive(dataset, scale, risk_col, ll = new_leaflet())

plot_road_access_interactive(dataset, scale, risk_col, ll = new_leaflet())

plot_border_risk_interactive(dataset, scale, risk_col, ll = new_leaflet())

plot_epi_units_interactive(dataset, scale, risk_col, ll = new_leaflet())

plot_risk_table_interactive(dataset, scale, risk_col, ll = new_leaflet())

plot_risk(
  dataset,
  risk_name = NULL,
  risk_col = NULL,
  scale = NULL,
  interactive = FALSE
)

plot_entry_points(dataset, scale, risk_col)

plot_animal_mobility(dataset, scale, risk_col)

plot_road_access(dataset, scale, risk_col)

plot_border_risk(dataset, scale, risk_col)

plot_border_risk(dataset, scale, risk_col)

plot_epi_units(dataset, scale, risk_col)

plot_risk_table(dataset, scale, risk_col)

Arguments

dataset: risk table, generally the output of a
scale: the scale of risk_col, numeric vector of length 2, this is NULL by default and is inferred from attr(x, "scale").
risk_col: the risk column to represent in the visualisation, this is NULL by default and is inferred from attr(x, "risk_col").
ll: leaflet object to add layers to
risk_name: risk_name used to determine which plotting function to use, this is NULL by default and is inferred from attr(x, "table_name").
interactive: default to FALSE for ggplot2 visuals, TRUE returns interactive leaflet.

Value

leaflet map object

ggplot2 object with the appropriate visualisation if interactive is FALSE, otherwise, leaflet object

Examples

tunisia_raw <- sf::read_sf(system.file(
  package = "riskintrodata",
  "samples", "tunisia", "epi_units", "tunisia_adm2_raw.gpkg"
))

# Apply mapping to prepare colnames and validate dataset
tunisia <- apply_mapping(
  tunisia_raw,
  mapping = mapping_epi_units(
    eu_name = "NAME_2",
    geometry = "geom"
  ),
  validate = TRUE
)
#> ✔ All data in "epi_units" valided.

entry_points_fp <-
  system.file(
    package = "riskintrodata",
    "samples",
    "tunisia",
    "entry_points", "BORDER_CROSSING_POINTS.csv"
  )

entry_points <- readr::read_csv(entry_points_fp)
#> Rows: 110 Columns: 6
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr (4): NAME, TYPE, MODE, SOURCES
#> dbl (2): LONGITUDE_X, LATITUDE_Y
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

entry_points <- apply_mapping(
  dataset = entry_points,
  mapping = mapping_entry_points(
    point_name = "NAME",
    lng = "LONGITUDE_X",
    lat = "LATITUDE_Y",
    mode = "MODE",
    type = "TYPE",
    sources = "SOURCES"
  ),
  validate = TRUE
)
#> ✔ All data in "entry_points" valided.

ri_entry_points <- calc_entry_point_risk(
  entry_points = entry_points,
  epi_units = tunisia,
  emission_risk =
    calc_emission_risk(
      emission_risk_factors = riskintrodata::get_wahis_erf(
        disease = "Anthrax",
        species = "Cattle",
        animal_category = "Domestic"
      )
    )
) |>
  rescale_risk_scores()
#> ✔ All data in "emission_risk_factors" valided.
#> ✔ WAHIS emission risk factors dataset has 65 entries for `disease = Anthrax`, `species = Cattle`, and `animal_category = Domestic`.
#> Warning: ! There are missing emission risk scores for the following countries:
#> • BIH missing for 1 entry points.
#> • BRN missing for 1 entry points.
#> • DZA missing for 44 entry points.
#> • ESP missing for 1 entry points.
#> • FRA missing for 1 entry points.
#> • HUN missing for 2 entry points.
#> • ISR missing for 1 entry points.
#> • LBY missing for 12 entry points.
#> • MAR missing for 1 entry points.
#> • NOR missing for 1 entry points.
#> • PER missing for 1 entry points.
#> • PHL missing for 1 entry points.
#> • VNM missing for 1 entry points.
#> • ZAF missing for 1 entry points.
#> Create new entries in the emission risk factor table using `erf_row()`
#> (`?riskintrodata::erf_row()`).

plot_risk(ri_entry_points, interactive = FALSE)

plot_risk(ri_entry_points, interactive = TRUE)