mycoportal: Retrieve records from the MyCoPortal

In FranzKrah/rMyCoPortal: rMyCoPortal - An R package to interface with the Mycology Collections Portal

Description

Retrieve records from the MyCoPortal

Usage

mycoportal(taxon = "Amanita muscaria", country = "", state = "",
  county = "", locality = "", elevation_from = "",
  elevation_to = "", host = "", taxon_type = 1, collection = "all",
  north_lat = "", south_lat = "", west_lon = "", east_lon = "",
  point_lat = "", point_lon = "", radius = "", collector = "",
  collector_num = "", coll_date1 = "", coll_date2 = "",
  syns = TRUE, verbose = TRUE, screenshot = TRUE, port = 4445L,
  browserName = "chrome", remoteServerAddr = "localhost", wait = 2)

Arguments

taxon	character string specifying the taxon name (e.g., species name, family name or higher taxon). To query higher taxa, e.g. on order level, I recommend using mycoportal_hightax
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"
collection	either "all" or a vector or integers with number corresponding to collection. For a list of collections use function getCollections()
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	numeric 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.

Details

Interface to the web database MyCoPortal. Query records available by various user specifications.

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
db	A character string specifying the database (currently only MyCoPortal)

Author(s)

Franz-Sebastian Krah

References

http://mycoportal.org/portal/index.php

A. N. Miller and S. T. Bates The Mycology Collections Portal (MyCoPortal) (2017) Cryptogamie Mycologie, 37:15-36.

Examples

## Not run: 
## Download Amanita muscaria observations and plot visualize data
am.dist <- mycoportal(taxon = "Amanita muscaria")
plot_distmap(x = am.dist, mapdatabase = "world", interactive = FALSE)
plot_distmap(x = am.dist, mapdatabase = "state", interactive = FALSE)
plot_distmap(x = am.dist, mapdatabase = "world", interactive = TRUE)
plot_datamap(x = am.dist, mapdatabase = "world")
plot_recordstreemap(x = am.dist, log = FALSE)

## End(Not run)

FranzKrah/rMyCoPortal documentation built on May 14, 2019, 11:11 a.m.