Skip to contents

Compute species impact indicator

Source: R/species_impact.R
compute_impact_per_species.Rd

Combines occurrences cube and impact data using the given method (e.g., mean) to compute the impact indicator per species.

Usage

compute_impact_per_species(
  cube,
  impact_data = NULL,
  method = NULL,
  trans = 1,
  col_category = NULL,
  col_species = NULL,
  col_mechanism = 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 impact_category, scientific_name and impact_mechanism.

method

The method of computing the indicator. The method used in the aggregation of within impact of species. The method can be

  • "max":The maximum method assigns a species the maximum impact across all records of the species. It is best for precautionary approaches. Also, the assumption is that the management of the highest impact can cover for the lower impact caused by a species and can be the best when there is low confidence in the multiple impacts of species of interest. However, the maximum method can overestimate the impact of a species especially when the highest impact requires specific or rare conditions and many lower impacts were recorded.

  • "mean": assigns a species the mean impact of all the species impact. This method computes the expected impact of the species considering all species impact without differentiating between impacts. This method is adequate when there are many impact records per species.

  • "max_mech": Assigns a species the summation of the maximum impact per mechanism. The assumption is that species with many mechanisms of impact have a higher potential to cause impact.

trans

Numeric: 1 (default), 2 or 3. The method of transformation to convert the EICAT categories c("MC", "MN", "MO", "MR", "MV") to numerical values:

  • 1: converts the categories to c(0, 1, 2, 3, 4)

  • 2: converts the categories to to c(1, 2, 3, 4, 5)

  • 3: converts the categories to to c(1, 10, 100, 1000, 10000)

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.

Value

A dataframe of impact indicator per species (class species_impact).

See also

Other Indicator function: compute_impact_indicator(), compute_impact_per_site()

Examples

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

speciesImpact <- compute_impact_per_species(
  cube = acacia_cube,
  impact_data = eicat_acacia,
  method = "mean",
  trans = 1
)