Compute site impact indicator

Usage

site_impact(
  cube,
  impact_data = NULL,
  col_category = NULL,
  col_species = NULL,
  col_mechanism = NULL,
  trans = 1,
  type = NULL
)

Arguments

cube: The data cube of class sim_cube or processed_cube from b3gbi::process_cube()
impact_data: The dataframe of species impact which contains columns of category, species and mechanism.
col_category: The name of the column containing the impact categories. The first two letters each categories must be an EICAT short names (e.g "MC - Minimal concern")
col_species: The name of the column containing species names
col_mechanism: The name of the column containing mechanisms of impact
trans: Numeric. The type of transformation to convert the EICAT categories to numerical values. 1 converts ("MC", "MN", "MO", "MR", "MV") to (0,1,2,3,4) 2 converts ("MC", "MN", "MO", "MR", "MV") to (1,2,3,4,5) and 3 converts ("MC", "MN", "MO", "MR", "MV") to (1,10,100,1000,10000)
type: The type indicators based on the aggregation of within and across species in a site. The type can be precautionary, precautionary cumulative, mean, mean cumulative or cumulative.

Value

The dataframe of impact indicator per sites (class site_impact)

Examples

# define cube for taxa
acacia_cube <- taxa_cube(
  taxa = taxa_Acacia,
  region = southAfrica_sf,
  res = 0.25,
  first_year = 2010
)

siteImpact <- site_impact(
  cube = acacia_cube,
  impact_data = eicat_acacia,
  col_category = "impact_category",
  col_species = "scientific_name",
  col_mechanism = "impact_mechanism",
  trans = 1,
  type = "precautionary cumulative"
)