symbiota: Retrieve records from the Symbiota portals

In rSymbiota: Interface to 'Symbiota' Portals for Accessing Multi-Organismal Biodiversity Data

Description

Retrieve records from the Symbiota portals

Usage

symbiota(taxon = "Amanita muscaria", db = "mycoportal", country = "",
  state = "", county = "", locality = "", elevation_from = "",
  elevation_to = "", host = "", taxon_type = 1, north_lat = "",
  south_lat = "", west_lon = "", east_lon = "", point_lat = "",
  point_lon = "", radius = "", collector = "", collector_num = "",
  coll_date1 = "", coll_date2 = "", syns = TRUE, verbose = FALSE,
  screenshot = FALSE, port = 4445L, browserName = "chrome",
  remoteServerAddr = "localhost", wait = 4, max_attempts = 5)

Arguments

taxon	character string specifying the taxon name (e.g., species name, family name or higher taxon)
db	portal name, for an overview see portals
country	character string specifying country, e.g., "USA"
state	character string specifying state, e.g., "Massachusetts"
county	character string specifying county, e.g., "Worcester"
locality	character string specifying locality, e.g., "Harvard Forest"
elevation_from	character string, meter, e.g., "1000"
elevation_to	character string, meter
host	character string specifying host species, e.g., "Betula alba"
taxon_type	integer, one of 1 to 5 representing "Family or Scientific Name", "Scientific Name only", "Family Only", "Higher Taxonomy", Common Name"
north_lat	character string, coordinate e.g., "45"
south_lat	character string, coordinate
west_lon	character string, coordinate, e.g., "-72"
east_lon	character string, coordinate
point_lat	character string, coordinate
point_lon	character string, coordinate
radius	character string, km, e.g., "50"
collector	character string specifying collector name
collector_num	character string specifying collector number
coll_date1	character string specifying collection data from, e.g., "19 August 1926"
coll_date2	character string specifying collection data from, e.g., "19 August 2018"
syns	logical, if TRUE synonyms from MycoBank and IndexFungorum are searched
verbose	logical
screenshot	logical, whether screenshot of results should be displayed in Viewer
port	default is 4445L
browserName	character string specifying the browser to use, recommended: "chrome"
remoteServerAddr	default is "localhost
wait	numberic specifying the seconds to wait for website to load, recommended 2 for good internet connections; higher otherwise. It would be good to first look up the number of pages for a species and to compare it with the function output to see whether loading times are sufficient.
max_attempts	maximum number of tries in case of internet instability or lost connection

Details

Interface to the web databases of the Symbiota portals. Symbiota is an open source content management system for curating specimen- and observation-based biodiversity data. Currently ca. 40 portals are avaiable: Consortium of North American Lichen Herbaria, Arctic Lichen Flora, Consortium of North American Bryophyte Herbaria, Frullania Collaborative Research Network, Macroalgal Consortium Herbarium Portal, MyCoPortal, Smithsonian Tropical Research Institute Portal (STRI), Aquatic Invasives, Aquatic Invasives, Aquatic Invasives, Consortium of Midwest Herbaria, SEINet, Intermountain Region Herbaria Network (IRHN), SouthEast Regional Network of Expertise and Collections (SERNEC), North American Network of Small Herbaria, Northern Great Plains Herbaria, Consortium of Northeastern Herbaria (CNH), Madrean Archipelago Biodiversity Assessment (MABA), Madrean Archipelago Biodiversity Assessment (MABA) - Fauna, Herbario Virtual Austral Americano, CoTRAM – Cooperative Taxonomic Resource for Amer. Myrtaceae, InvertEBase Data Portal, Symbiota Collections of Arthropods Network (SCAN), Lepidoptera of North America Network (LepNet), Neotropical Entomology, Neotropical Flora, Monarch (California Academy of Sciences), The Lundell Plant Diversity Portal, Virtual Flora of Wisconsin, Red de Herbarios del Noroeste de México, University of Colorado Herbarium, The Open Herbarium, Consortium of Pacific Herbaria, Minnesota Biodiversity Atlas, Documenting Ethnobiology in Mexico and Central America, OpenZooMuseum, Mid-Atlantic Herbaria Consortium, Channel Islands Biodiversity Information System, Consortium of Small Vertebrate Collections (CSVColl), The University of New Hampshire Collection of Insects and Other Arthropods. For an overview and URLs see portals. The function currently searches all collections, because the package is meant for large-scale access.

Value

x an object of class records with the following components:

nr.records	A numeric giving the number of records retrieved
citation	A character string with the recommended citation from the website
query	A list of the user arguments used
records	A data.frame with the query records results (accessible via 'at' symbol)
db	A character string specifying the database

Author(s)

Franz-Sebastian Krah

References

http://symbiota.org/docs/

Gries, C., Gilbert, E. E., and Franz, N. M. (2014). Symbiota–a virtual platform for creating voucher-based biodiversity information communities. Biodiversity Data Journal, (2).

Examples

## Not run: 
## Download Amanita muscaria observations and plot visualize data
spec.dist <- symbiota(taxon = "Helvella", db = "mycoportal", wait = 3)
# for all available portals and examples see vignette
## increase wait if your internet is slow (in general fast internet is recommended)

# This is how the records table can be accessed:
recordsTable(spec.dist)

## However, for the other functions of the package, the output of 'symbiota'
## can be directly forwarded, for example:

plot_distmap(x = spec.dist, mapdatabase = "world", interactive = FALSE,
gazetter = TRUE)
plot_distmap(x = spec.dist, mapdatabase = "usa", interactive = FALSE)
plot_distmap(x = spec.dist, mapdatabase = "world", interactive = TRUE)
plot_datamap(x = spec.dist, mapdatabase = "state", index = "rec")
plot_recordstreemap(x = spec.dist, log = FALSE)

## End(Not run)

rSymbiota documentation built on July 7, 2019, 5:02 p.m.