An R package to get download from the EMODnet Biology WFS. This function allows you to download data using aphiaID, dasID or an geoserverURL you obtain through the EMODnet Biology toolbox http://www.emodnet-biology.eu/toolbox.
Installing REMODBio
requires the devtools
and 'imis' packages:
install.packages("devtools")
devtools::install_github("EMODnet/imis")
devtools::install_github("Daphnisd/REMODBio")
library("REMODBio")
getemodbiodata(dasid = "4662")
- download data from a single dataset. Use the dasid obtained through the http://www.emodnet-biology.eu/data-catalog (the id from the url) or use the function listemodnetdatasets()
to get an overview
getemodbiodata(aphiaid = "141433")
- download data from a single taxon (the child taxa will be included also). Use the id obtained through www.marinespecies.org
getemodbiodata(dasid = "1884", type ="basic")
- download data only for 8 essential columns (see http://www.emodnet-biology.eu/node/172#Basic)
getemodbiodata(mrgid=c("5670","3315")
- download data from a specific region using the mrgid from marineregions, or type View(IHOareas)
, View(EEZs)
, View(FAOareas)
to get an overview.
getemodbiodata(speciesgroup = "Angiosperms")
- download data from a functional group. Values are "Algae" , "Angiosperms", "Benthos", "Birds", "Fish", "Mammals", "phytoplankton", Reptiles", "zooplankton" (case sensitive - note phytoplankton and zooplankton are lower case)
getemodbiodata(dasid = c("1884","618", "5780" ), aphiaid = "2036", startyear = "1980", endyear = "2010")
getemodbiodata(geourl = "http://geo.vliz.be/geoserver/wfs/ows?service=WFS&version=1.1.0&request=GetFeature&typeName=Dataportal%3Aeurobis-obisenv&resultType=results&viewParams=where%3Adatasetid+IN+%285885%29%3Bcontext%3A0100&outputFormat=csv")
download data using the WFS urls optained through the EMODnet toolbox at http://www.emodnet-biology.eu/toolbox/en/download/occurrence/preview (- you make your selection and copi-paste the url behind the "get webservice url" button)
List with 3 data frames - data - downloaded records - meta - the descriptions of the terms - datasets - the titles, citations and licences of the datasets used in the download
If data are extracted from the EMODnet Biology for secondary analysis resulting in a publication, the appropriate source should be cited.
The downloaded data should be cited as: EMODnet Biology (yyyy) Fulll Occurrence Data and parameters downloaded from the EMODnet Biology Project (www.emodnet-biology.eu). Available online at www.emodnet-biology.eu/toolbox, consulted on yyyy-mm-dd.
Regarding the citation of the individual datasets, the following guidelines should be taken into account:
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