rSymbiota (version 1.0.0)

symbiota: Retrieve records from the Symbiota portals

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

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

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 <U+2013> 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 M<U+00E9>xico, 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.

References

http://symbiota.org/docs/

Gries, C., Gilbert, E. E., and Franz, N. M. (2014). Symbiota<U+2013>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)
# }