state_all_species_query: state_all_species_query

In usgs-bis/bad-neighbor-invasives: Bad Neighbor Analysis Package

Description

A BISON query/parsing function returning the number (abundance) of all species in a given state. The code does not return a full list of individual species, only the count. The code will lookup the state FIPS code if needed.

Usage

state_all_species_query(fips_list, taxon, state_name,
  get_buffer_fips = FALSE)

Arguments

fips_list	a single state two-digit FIPS code or a parenthetical group of FIPS codes. Pairs of state FIPS codes and surrounding states are pre-developed and stored in 'data/state_lookup.csv'. Note: the list includes the Distict of Columbia;
taxon	a string hierarchy_homonym_string in the form: "*\-179913\-*". Again, a predefined list is stored in: 'data/heirarchy_strings.csv'. The list of taxa is currently restricted to the best represented taxa in BISON.
state_name	a string name of the state to process.
get_buffer_fips	an optional flag to lookup the buffer states FIPS codes

Value

a tibble with the name of the state, the overall occurrence count for all species in the taxon, and a count of the number of species in the taxon in the state.

Examples

# find all birds ("*\-174371\-*") in Virginia
all_species <- state_all_species_query(fips_list = 51, taxon = "*\\-174371\\-*", state_name = "Virginia")

# same as above without knowing the fips
all_species <- state_all_species_query(taxon = "*\\-174371\\-*", state_name = "Virginia")

# run the above query for buffer states
all_species <- state_all_species_query(taxon = "*\\-174371\\-*", state_name = "Virginia", get_buffer_fips = TRUE)

usgs-bis/bad-neighbor-invasives documentation built on Sept. 26, 2019, 7:34 a.m.