assessment_cooccurrences {fqar}

Generate a species co-occurrence matrix from assessment inventories

Description

assessment_coccurrences() accepts a list of species inventories downloaded from universalfqa.org and returns a complete listing of all co-occurrences. Repeated co-occurrences across multiple assessments are included, but self co-occurrences are not, allowing for meaningful summary statistics to be computed.

Usage

assessment_cooccurrences(inventory_list)

Arguments

inventory_list

A list of site inventories having the format of assessment_list_inventory()

Value

A data frame with 13 columns:

• target_species (character)

• target_species_c (numeric)

• target_species_nativity (character)

• target_species_n (numeric)

• cospecies_scientific_name (character)

• cospecies_family (character)

• cospecies_acronym (character)

• cospecies_nativity (character)

• cospecies_c (numeric)

• cospecies_w (numeric)

• cospecies_physiognomy (character)

• cospecies_duration (character)

• cospecies_common_name (character)

Examples

# assessment_cooccurrences is best used in combination with
# download_assessment_list() and assessment_list_inventory().


maine <- download_assessment_list(database = 56)
maine_invs <- assessment_list_inventory(maine)
maine_cooccurrences <- assessment_cooccurrences(maine_invs)