specleanr (version 1.0.0)

getdata: Download species records from online database.

Description

Download species records from online database.

Usage

getdata(
  data,
  colsp = NULL,
  extent = NULL,
  db = c("gbif", "vertnet", "inat"),
  gbiflim = 50000,
  vertlim = 1000,
  inatlim = 3000,
  verbose = FALSE,
  warn = FALSE,
  pct = 80,
  sn = FALSE,
  ...
)

Value

Lists of species records from online databases

Arguments

data

dataframe, list, vector, string. data to retrieve records from online databases (GBIF, VertNET, and iNaturalist).

colsp

string. A variable of species names. Provided if data is a data frame, so not required for lists and vector.

extent

vector or sf. Bounding box to limit the download of records within a particular area. Otherwise all records from the GBIF will be downloaded. These can be provided in two forms, either a shapefile (sf) class accepted or provide a list of named xmin, ymin, xmax, and ymax in this particular order.

db

vector. The different databases allowed including 'gbif', 'vertnet', and 'inat'.

gbiflim

integer. Limits on the records from the Global Biodiversity Information Platform

vertlim

integer. Limits on the records from VertNET.

inatlim

integer. Limits on the records from iNaturalist database.

verbose

logical. TRUE if detailed messages should be indicated and FALSE if download messages are not needed. Default TRUE.

warn

logical. To indicate if warning messages should be shown. Default FALSE.

pct

numeric. The percentage similarity used to assign a relatively similar name from FishBase if the exact match is absent. Default 90 The higher the values, the higher percentage similarity are considered to replace a species name that is cheeked from Fishbase.

sn

logical. Whether to consider synonyms. Default FALSE so accepted names will be considered from FishBase database.

...

More function for species data download can be used. See rgbif::occ_data for more information, rinat::get_inat_obs, and rvertnet::searchbyterm.

Details

Note always check the validity of the species name with standard database FishBase or World Register of Marine Species. If the records are more than 50000 in GBIF, and extent can be provide to limit the download.

Examples

if (FALSE) {

gbdata <- getdata(data = 'Gymnocephalus baloni', gbiflim = 100, inatlim = 100, vertlim = 100)

#Get for two species
sp_records <- getdata(data=c('Gymnocephalus baloni', 'Hucho hucho'),
                            gbiflim = 100,
                            inatlim = 100,
                            vertlim = 100)
#for only two databases
sp_records_2db <- getdata(data=c('Gymnocephalus baloni', 'Hucho hucho'),
                           db= c('gbif','inat'),
                            gbiflim = 100,
                            inatlim = 100,
                            vertlim = 100)

}