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Generate a taxonomic hierarchy

Source: R/generate_taxonomy.R
generate_taxonomy.Rd

This function generates a random taxonomic hierarchy for a specified numbers of species, genera, families, orders, classes, phyla, and kingdoms. The output is a data frame with the hierarchical classification for each species.

Usage

generate_taxonomy(
  num_species,
  num_genera,
  num_families,
  num_orders = 1,
  num_classes = 1,
  num_phyla = 1,
  num_kingdoms = 1,
  seed = NA
)

Arguments

num_species

Number of species to generate, or a dataframe. With a dataframe, the function will create a species with taxonomic hierarchy for each row. The original columns of the dataframe will be retained in the output.

num_genera

Number of genera to generate.

num_families

Number of families to generate.

num_orders

Number of orders to generate. Defaults to 1.

num_classes

Number of classes to generate. Defaults to 1.

num_phyla

Number of phyla to generate. Defaults to 1.

num_kingdoms

Number of kingdoms to generate. Defaults to 1.

seed

A positive numeric value setting the seed for random number generation to ensure reproducibility. If NA (default), then set.seed() is not called at all. If not NA, then the random number generator state is reset (to the state before calling this function) upon exiting this function.

Value

A data frame with the taxonomic classification of each species. If num_species is a dataframe, the taxonomic classification is added to this input dataframe. The original columns of the dataframe will be retained in the output.

Details

The function works by randomly assigning species to genera, genera to families, families to orders, orders to classes, classes to phyla, and phyla to kingdoms. Sampling is done with replacement, allowing multiple lower-level taxa (e.g., species) to be assigned to the same higher-level taxon (e.g., genus).

See also

Other multispecies: map_add_coordinate_uncertainty(), map_filter_observations(), map_grid_designation(), map_sample_observations(), map_simulate_occurrences()

Examples

# 1. Create simple taxonomic hierarchy
generate_taxonomy(
  num_species = 5,
  num_genera = 3,
  num_families = 2,
  seed = 123)
#>    species species_key  genus  family  order  class  phylum  kingdom
#> 1 species1           1 genus3 family2 order1 class1 phylum1 kingdom1
#> 2 species2           2 genus3 family2 order1 class1 phylum1 kingdom1
#> 3 species3           3 genus3 family2 order1 class1 phylum1 kingdom1
#> 4 species4           4 genus2 family2 order1 class1 phylum1 kingdom1
#> 5 species5           5 genus3 family2 order1 class1 phylum1 kingdom1

# 2. Add taxonomic hierarchy to a dataframe
existing_df <- data.frame(
  count = c(1, 2, 5, 4, 8, 9, 3),
  det_prob = c(0.9, 0.9, 0.9, 0.8, 0.5, 0.2, 0.2)
  )

generate_taxonomy(
  num_species = existing_df,
  num_genera = 4,
  num_families = 2,
  seed = 125)
#>    species species_key  genus  family  order  class  phylum  kingdom count
#> 1 species1           1 genus2 family1 order1 class1 phylum1 kingdom1     1
#> 2 species2           2 genus2 family1 order1 class1 phylum1 kingdom1     2
#> 3 species3           3 genus3 family2 order1 class1 phylum1 kingdom1     5
#> 4 species4           4 genus4 family2 order1 class1 phylum1 kingdom1     4
#> 5 species5           5 genus4 family2 order1 class1 phylum1 kingdom1     8
#> 6 species6           6 genus3 family2 order1 class1 phylum1 kingdom1     9
#> 7 species7           7 genus1 family1 order1 class1 phylum1 kingdom1     3
#>   det_prob
#> 1      0.9
#> 2      0.9
#> 3      0.9
#> 4      0.8
#> 5      0.5
#> 6      0.2
#> 7      0.2