The goal of plantr is to provide a simple R wrapper around the USDA PLANTS Database API, allowing users to easily download data on plant species as a part of their regular workflow.
Installation
You can install the development version of plantr with:
remotes::install_github("mikemahoney218/plantr")Usage
plantr is a little seedling of a package at the moment, without much in the way of higher-order functions. With that said, the main workhorse of the package is already implemented as ptr_search, letting you search the PLANTS Database directly from R. Searching the basic API (which returns data on plant names and USDA symbols) is as simple as:
library(plantr)
ptr_search(common_name = "balsam fir")
#> synonym_plants accepted_plant.symbol accepted_plant.scientific_name
#> 1 NULL ABBAP Abies balsamea var. phanerolepis
#> 2 NULL ABBAB Abies balsamea var. balsamea
#> 3 NULL ABBA Abies balsamea
#> accepted_plant.common_name
#> 1 balsam fir
#> 2 balsam fir
#> 3 balsam firThe full API may also be searched by setting basic to FALSE. Note that this example uses a single USDA plant symbol in order to speed up processing time:
ptr_search(symbol = "ABBAB", basic = FALSE)
#> synonyms accepted.symbol
#> 1 PIBA3, Pinus balsamea ABBAB
#> accepted.nativity
#> 1 Canada, Lower 48 States, Saint Pierre and Miquelon, N, N, N
#> accepted.scientific_name accepted.state_noxious_status
#> 1 Abies balsamea var. balsamea NULL
#> accepted.federal_noxious_status accepted.plants_invasive_status
#> 1 NULL NULL
#> accepted.state_te_status accepted.federal_te_status
#> 1 NULL NULL
#> accepted.regional_wetland_indicator_status accepted.common_name
#> 1 NULL balsam fir
#> accepted.growth_habits accepted.durations accepted.classification.kingdom
#> 1 Tree, TR Perennial, PR Plantae
#> accepted.classification.subkingdom accepted.classification.superdivision
#> 1 Tracheobionta Spermatophyta
#> accepted.classification.division accepted.classification.subclass
#> 1 Coniferophyta NA
#> accepted.classification.order accepted.classification.genus
#> 1 Pinales Abies
#> accepted.classification.species accepted.classification.variety
#> 1 balsamea balsamea
#> accepted.classification.plant_class
#> 1 Pinopsida
#> accepted.distribution.states
#> 1 01, 03, 04, 24, NF, 10, 33, 39, 50, 27, 09, 55, 18, 51, 23, 54, 26, 25, 08, 09, 19, 44, 36, 11, 07, LB, 42, 005, 061, 031, 001, 135, 071, 021, 115, 003, 111, 041, 087, 045, 017, 059, 029, 077, 163, 057, 169, 075, 007, 035, 065, 137, Becker, Itasca, Cook, Aitkin, Roseau, Koochiching, Cass, Pine, Anoka, Otter Tail, Douglas, Mahnomen, Fillmore, Carlton, Isanti, Clearwater, Lake of the Woods, Washington, Hubbard, Winona, Lake, Beltrami, Crow Wing, Kanabec, St. Louis, 035, 075, 115, 051, 123, 013, 125, 017, 019, 061, 073, 107, 031, 078, 131, 003, 091, 005, 021, 007, 099, 029, 071, 037, 001, 009, 069, 129, 113, 083, 121, 097, 141, 117, 085, 067, 109, 033, 119, 135, 041, Eau Claire, Marinette, Shawano, Iron, Vernon, Burnett, Vilas, Chippewa, Clark, Kewaunee, Marathon, Rusk, Douglas, Menominee, Washington, Ashland, Pepin, Barron, Columbia, Bayfield, Price, Door, Manitowoc, Florence, Adams, Brown, Lincoln, Washburn, Sawyer, Oconto, Trempealeau, Portage, Wood, Sheboygan, Oneida, Langlade, St. Croix, Dunn, Taylor, Waupaca, Forest, 047, 069, 065, 109, 029, 063, 011, 143, 073, 089, 019, 153, 137, 071, 031, 041, 033, 097, 003, 131, 039, 103, 055, 051, 053, 043, 013, 129, 135, 083, 001, 035, 095, 133, 007, 061, 119, 105, Emmet, Iosco, Ingham, Menominee, Charlevoix, Huron, Arenac, Roscommon, Isabella, Leelanau, Benzie, Schoolcraft, Otsego, Iron, Cheboygan, Delta, Chippewa, Mackinac, Alger, Ontonagon, Crawford, Marquette, Grand Traverse, Gladwin, Gogebic, Dickinson, Baraga, Ogemaw, Oscoda, Keweenaw, Alcona, Clare, Luce, Osceola, Alpena, Houghton, Montmorency, Mason, 027, 001, 015, 017, 011, 003, Worcester, Barnstable, Hampshire, Middlesex, Franklin, Berkshire, 003, 009, 013, 011, 005, Hartford, New Haven, Tolland, New London, Litchfield, 007, Providence, 049, 123, 115, 083, 031, 089, 077, 067, 025, 019, 033, 043, 013, 109, 065, 041, 015, 009, 121, 101, 095, 045, 053, 081, 029, 111, 105, 039, Lewis, Yates, Washington, Rensselaer, Essex, St. Lawrence, Otsego, Onondaga, Delaware, Clinton, Franklin, Herkimer, Chautauqua, Tompkins, Oneida, Hamilton, Chemung, Cattaraugus, Wyoming, Steuben, Schoharie, Jefferson, Madison, Queens, Erie, Ulster, Sullivan, Greene, 117, 069, 081, 105, 123, 027, 089, 115, 107, 113, 061, 127, 035, 131, 103, Tioga, Lackawanna, Lycoming, Potter, Warren, Centre, Monroe, Susquehanna, Schuylkill, Sullivan, Huntingdon, Wayne, Clinton, Wyoming, PikePlease note that plantr is still in an experimental phase, and breaking changes may happen to any function as development continues.
