Package index • BarnebyLives

Workflow functions

User facing functions for carrying out the BL workflow

associate_dropper(): remove collection from associated species
associates_spell_check(): Format associated species, and spell check them internally
author_check(): Check spelling of botanical author abbreviations
autofill_checker(): Search for accidental auto-increments from spreadsheet autofills
coords2sf(): create an sf object row by row to reflect different datum
date2text(): take mdy format date and make it written herbarium label format
date_parser(): create herbarium format dates for specimens
directions_grabber(): Have Google maps help you write directions to a site
dms2dd(): this function parses coordinates from DMS to decimal degrees
family_spell_check(): check that family is spelledcorrectly.
format_database_import(): Export a spreadsheet for mass upload to an herbariums database
geodata_writer(): write out spatial data for collections to Google Earth or QGIS
label_writer(): write herbarium labels to pdf
map_maker(): Make a quick county dot map to display the location of the collection
physical_grabber(): gather physical characteristics of the site
political_grabber(): gather political site information
powNAce(): Easily compare POW column to input columns
powo_searcher(): query plants of the world online for taxonomic information
site_writer(): gather distance and azimuth from site to center of town
spell_check(): check that genera and specific epithets are spelled (almost) correctly
split_scientificName(): split out a scientific input column to pieces

Preparing data to run BL

Data prep functions

data_download(): Download the data required to establish a BL instance
data_setup(): Set up the downloaded data for a BarnebyLives instance
TaxUnpack(): a function to subset the WCVP data set to an area of focus
check_data_setup_outputs(): Check whether expected output files from data_setup() exist
tileSelector(): Determine which raster tiles to download for topographic variables

Data

collection_examples: Collection examples for a shipping manifest
database_templates: database_templates
google_towns: This is a reproduced and slightly curated list of populated places.
herbaria_info: herbaria_info
project_examples: project_examples
shipping_examples: shipping_examples
names_vec: 10 random plant names from taxize
wcvp_update(): install or update World Vascular Plants Checklist

Label formatting functions

functions used while labels are being generated

associates_writer(): do or don't write the associated plant species
collection_writer(): format collector info and codes
escape_latex(): escape characters for use with LaTeX rendering
species_font(): ensure proper italicization of a associated species
writer(): write values and collapse NAs
writer_fide(): do or don't write determination information

Some internals

functions used internally

all_authors(): retrieve author results for autonyms
directions_overview(): return a quick route summary from googleway::google_directions
format_degree(): ASCII compliant degree symbol
get_google_directions(): identify a populated place near a collection and get directions from there
notFound(): notify user if an entry had any results not found in POWO
mason(): a wrapper around terra::makeTiles for setting the domain of a project
result_grabber(): collect the results of a successful powo search
specificDirections(): Import Google directions to a site
try_again(): try to download from Kew again, with just the binomial
writer2(): write values and collapse NAs