README.md

In Daphnisd/REMODBio: EMODnet Biology data download package

REMODBio

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.

Installation

Installing REMODBio requires the devtools and 'imis' packages:

install.packages("devtools")
devtools::install_github("EMODnet/imis")
devtools::install_github("Daphnisd/REMODBio")
library("REMODBio")

Usage:

• 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)

Output:

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

Disclaimer

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:

• If any individual data source of EurOBIS constitutes a significant proportion of the downloaded and used records (e.g. more than 10% of the data is derived from a single source), the individual data source should also be cited.
• If any individual data source of EurOBIS constitutes a substantial proportion of the downloaded and used records (e.g. more than 25% of the data is derived from a single source or the data is essential to arrive at the conclusion of the analysis), the manager or custodian of this data set should be contacted.
• In any case, it may be useful to contact the data custodian directly. The data custodian might have additional data available that may strengthen the analysis or he/she might be able to provide additional helpful information that may not be apparent from the provided metadata.
• The data may not be redistributed without the permission of the appropriate data owners. If data are extracted from the EMODnet Data Portal for redistribution, please contact us at [e-mail].

Daphnisd/REMODBio documentation built on May 22, 2019, 2:43 p.m.