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Impact categories

Source: R/impact_category.R
impact_cat.Rd

Aggregate species impact categories from impact data. Species are often reported to have multiple impact categories specific to different study locations and mechanisms through which they exert the impact. To get an estimate of a likely impact category which could apply more broadly, this function aggregate the multiple impact scores per species into one impact score per species.

Usage

impact_cat(
  impact_data,
  species_list,
  trans = 1,
  col_category = NULL,
  col_species = NULL,
  col_mechanism = NULL
)

Arguments

impact_data

The dataframe of species impact which contains columns of impact_category, scientific_name and impact_mechanism.

species_list

The vector of species' list to aggregate their impact categories.

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

The dataframe containing the aggregated species impact. max - maximum impact of a species. mean - mean impact of a species. max_mech - sum of maximum impact per categories of a species

See also

Other Prepare data: taxa_cube()

Examples

# define species list
species_list <- c(
  "Acacia adunca",
  "Acacia baileyana",
  "Acacia binervata",
  "Acacia crassiuscula",
  "Acacia cultriformis",
  "Acacia cyclops",
  "Acacia dealbata",
  "Acacia decurrens",
  "Acacia elata"
)

agg_impact <- impact_cat(
  impact_data = eicat_acacia,
  species_list = species_list,
  trans = 1
)