species_profile: Generate the co-occurrence profile for a species

In fqar: Floristic Quality Assessment Tools for R

Generate the co-occurrence profile for a species

Description

species_profile() accepts a species and list of inventories like those generated by assessment_list_inventory() and returns the co-occurrence profile of that species. Repeated co-occurrences across multiple assessments are included in summary calculations but self co-occurrences are not.

Usage

species_profile(species, inventory_list, native = FALSE)

Arguments

species	The scientific name of the target plant species
inventory_list	A list of site inventories having the format of assessment_list_inventory()
native	Logical indicating whether only native co-occurrences should be considered.

Value

A data frame with 14 columns:

• target_species (character)

• target_species_c (numeric)

• cospecies_n (numeric)

• cospecies_native_n (numeric)

• cospecies_mean_c (numeric)

• cospecies_native_mean_c (numeric)

• cospecies_std_dev_c (numeric)

• cospecies_native_std_dev_c (numeric)

• percent_native (numeric)

• percent_nonnative (numeric)

• percent_native_low_c (numeric)

• percent_native_med_c (numeric)

• percent_native_high_c (numeric)

• discrepancy_c (numeric)

Examples

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


ontario <- download_assessment_list(database = 2)
ontario_invs <- assessment_list_inventory(ontario)
species_profile("Aster lateriflorus", ontario_invs)

fqar documentation built on June 22, 2025, 1:06 a.m.