Map pest risk — map_risk • mappestRisk

This function produces a raster map where each pixel shows the number of months per year in which temperature is within a given set of bounds. If the input has several pairs of minimum and maximum temperatures (as produced by therm_suit_bounds()), the output raster has two layers: mean and standard deviation.

Usage

map_risk(
  t_vals = NULL,
  t_rast = NULL,
  region = NULL,
  res = 2.5,
  path = NULL,
  mask = TRUE,
  verbose = FALSE,
  plot = TRUE,
  interactive = FALSE
)

Arguments

t_vals: a data.frame or dplyr::tibble() as produced by therm_suit_bounds(). t_vals must contain results derived from a single model. It must contain at least one row of numeric values. Additionally, the minimum ("left") thermal boundary or tval_left must be lower than the maximum ("right") one, or tval_right for all rows. Nominative columns must be present in the input (i.e., model_name, suitability, pred_suit and iter).
t_rast: Optional 12-layer terra::SpatRaster() with monthly mean temperatures for the region of interest. If not provided, global WorldClim raster layers will be automatically (down)loaded using geodata::worldclim_global(), and cropped to region (if provided). Note that the download can be slow the first time you use the function in a new path. If you get a download error, consider running e.g options(timeout = 500) (or more).
region: Optional object specifying the region to map. Must overlap the extent of t_rast if both are provided. Can be a terra::SpatVector() polygon (obtained with terra::vect()); or an sf polygon, in which case it will be coerced with terra::vect()) to a terra::SpatVector(); or a character vector of country name(s) in English (see country_names), in which case climate maps will be downloaded for those countries; or a terra::SpatExtent() object (obtained with terra::ext()); or a numeric vector of length 4 specifying the region coordinates as follows: c(xmin, xmax, ymin, ymax). The latter two must be in the same CRS ast_rast if t_rast is provided, or in unprojected lon-lat coordinates (WGS84, EPSG:4326) otherwise. If NULL, the output maps will cover the entire t_rast if provided, or the entire world otherwise.
res: Argument to pass to geodata::worldclim_global() specifying the spatial resolution for the raster maps to download, if t_rast is not provided. The default is 2.5 arc-minutes. Beware that lower values (e.g., 0.5) may lead to extremely heavy data sets and large computation times.
path: Argument to pass to geodata::worldclim_global() (if t_rast is not provided) and/or to geodata::world() (if region is a vector of country names) specifying the folder path for the downloaded maps.
mask: Logical value to pass to terra::mask() specifying whether the output raster maps should be masked with the borders of the target 'region', if this is a polygon map or a vector of country names. The default is TRUE. If FALSE, the entire rectangular extent of 'region' will be used.
verbose: Logical value specifying whether to display messages about what the function is doing at possibly slow steps. The default is FALSE. Setting it to TRUE can be useful for checking progress when maps are large.
plot: Logical value specifying whether to plot the results in a map. Defaults to TRUE. Note that the function will always return a terra::SpatRaster() object even if plot = TRUE.
interactive: Logical value specifying whether the plotted map should be interactive (if plot=TRUE). The default is TRUE if the 'leaflet' package is installed.

Value

This function returns a terra::SpatRaster() with up to 2 layers: the (mean()) number of months with temperature within the species' thermal bounds; and (if t_vals has >1 rows) the standard deviation (stats::sd()) around that mean.

Examples

if (FALSE) { # interactive()
data("aphid")

fitted_tpcs <- fit_devmodels(temp = aphid$temperature,
                             dev_rate = aphid$rate_value,
                             model_name = "all")

plot_devmodels(temp = aphid$temperature,
               dev_rate = aphid$rate_value,
               fitted_parameters = fitted_tpcs,
               species = "Brachycaudus schwartzi",
               life_stage = "Nymphs")

# Obtain prediction TPCs with bootstraps for propagating uncertainty:
boot_tpcs <- predict_curves(temp = aphid$temperature,
                            dev_rate = aphid$rate_value,
                            fitted_parameters = fitted_tpcs,
                            model_name_2boot = c("lactin2", "briere2", "beta"),
                            propagate_uncertainty = TRUE,
                            n_boots_samples = 10)

print(boot_tpcs)

# Plot bootstrapped curves:

plot_uncertainties(temp = aphid$temperature,
                   dev_rate = aphid$rate_value,
                   bootstrap_tpcs = boot_tpcs,
                   species = "Brachycaudus schwartzi",
                   life_stage = "Nymphs")

# Calculate Q80 thermal bounds

boundaries <- therm_suit_bounds(preds_tbl = boot_tpcs,
                                model_name = "lactin2",
                                suitability_threshold = 80)
head(boundaries)

# Extract and Plot Risk maps

# if you don't have temperature rasters for your region:

risk_map_reunion <- map_risk(t_vals = boundaries,
                             path = tempdir(), # directory to download data
                             region = "Réunion",
                             mask = TRUE,
                             plot = TRUE,
                             interactive = FALSE,
                             verbose = TRUE)

# If you already have a raster of monthly average temperatures
# for your region of interest, you can use that as input for `t_rast`:
## first, load it
tavg_file <- system.file("extdata/tavg_reunion.tif", package = "mappestRisk")
tavg_rast <- terra::rast(tavg_file)

## then apply the function
risk_map_reunion <- map_risk(t_vals = boundaries,
                             t_rast = tavg_rast,
                             mask = TRUE,
                             path = tempdir(),
                             plot = TRUE,
                             interactive = FALSE,
                             verbose = TRUE)

# Using a spatial object for `region`
sobrarbe <- terra::vect(system.file("extdata/sobrarbe.gpkg",
                                   package = "mappestRisk"))

risk_map_sobrarbe <- map_risk(t_vals = boundaries,
                              region = sobrarbe,
                              path = tempdir(),
                              mask = TRUE,
                              plot = TRUE,
                              interactive = FALSE,
                              verbose = TRUE)
}