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README.Rmd
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---
output: github_document
df_print: "tibble"
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
options(verbose = FALSE)
```
# Download data from EurOBIS using the LifeWatch/EMODnet-Biology Web Feature Services
<!-- badges: start -->
[](http://lifewatch.be)
[](https://lifecycle.r-lib.org/articles/stages.html#experimental)
[](https://github.com/lifewatch/eurobis/actions/workflows/R-CMD-check.yaml)
<!-- badges: end -->
The `eurobis` R package allows you to download data from EurOBIS.
You can query on:
- **Dataset**: provide the Integrated Marine Information System ([IMIS](https://www.vliz.be/en/integrated-marine-information-system)) unique identifier for datasets [DasID](https://www.vliz.be/imis?page=webservices).
- **Taxon**: use a scientific name (e.g. the sea turtle _Caretta caretta_) or a [WoRMS AphiaID](https://www.marinespecies.org/about.php#what_is_aphia) (e.g. [137205](https://www.marinespecies.org/aphia.php?p=taxdetails&id=137205))
- **Traits**: get all occurrences that are benthos. Or zooplankton. Or both. Powered by [WoRMS](https://www.marinespecies.org/).
- **Time**: just give start and end dates.
- **Geographically**: it allows to query on more than 300 records from the [Marine Regions Gazetteer](https://marineregions.org/gazetteer.php) by giving the [MRGID](https://marineregions.org/mrgid.php). Or just pass the area of your interest as a polygon written in as [Well Known Text](https://en.wikipedia.org/wiki/Well-known_text_representation_of_geometry)
- Other important classifications as [IUCN Red List](https://www.iucnredlist.org/en), [MSDF Indicators](https://msfd.eu/knowseas/guidelines/3-INDICATORS-Guideline.pdf) or [Habitats Directive](https://ec.europa.eu/environment/nature/conservation/species/habitats_dir_en.htm) and [CITES](https://cites.org/eng/app/index.php) Annexes.
Or create your own selection using the [EMODnet Biology toolbox](http://www.emodnet-biology.eu/toolbox). Just copy the webservice URL and paste in R.
## Installation
You can install the development version from GitHub with `devtools`:
```{r install, eval=FALSE}
devtools::install_github("lifewatch/eurobis")
```
## Get occurrences
Use the `eurobis_occurrences()` family of functions to query data.
A basic example is:
```{r occurrences_get}
library(eurobis)
# Get one single dataset
eurobis_occurrences_basic(dasid = 8045)
```
For detailed information run:
```{r occurrences, eval=FALSE}
help(eurobis_occurrences)
```
## Query by traits
Use the `functional_group` argument:
```{r func_groups, eval = FALSE}
# Get one single dataset
eurobis_occurrences_basic(dasid = 8045, functional_groups = "angiosperms")
```
See the full list of queriable traits in the exported dataset `species_traits`:
```{r traits}
species_traits
```
## Query by location
You can also filter by location, either using the Marine Regions Gazetteer Identifier (MRGID) or passing any polygon as Well Known Text.
```{r mrgid, eval = FALSE}
eurobis_occurrences_basic(mrgid = 5688, geometry = "POLYGON ((-9.099426 40.33016, -9.099426 40.9788, -8.366089 40.9788, -8.366089 40.33016, -9.099426 40.33016))")
```
To help drawing the area of your interest, you can use `eurobis_map_draw()`. You can draw here a polygon interactively:
```{r draw, eval = FALSE}
selected_area <- eurobis_map_draw()
#> POLYGON ((-9.099426 40.33016, -9.099426 40.9788, -8.366089 40.9788, -8.366089 40.33016, -9.099426 40.33016))
eurobis_occurrences_full(geometry = selected_area)
```
To help choosing the MRGID from Marine Regions, see the list of queriable regions and their MRGIDs with the family of functions `eurobis_map_regions_*`: these will open a leaflet map including the layers, read via Web Map Services (WMS).
```{r map2, eval = FALSE}
# MEOW Ecoregions
eurobis_map_regions_ecoregions()
# Exclusive Economic Zones (EEZ)
eurobis_map_regions_eez()
# International Hydrographic Office areas (IHO)
eurobis_map_regions_iho()
# Marine Regions intersection of EEZ and IHO. Named as Marine Region in eurobis_list_regions()
eurobis_map_regions_eez_iho()
# EMODnet-Biology Reporting Areas
eurobis_map_regions_reportingareas()
```
See the manual with:
```{r map3, eval = FALSE}
help(eurobis_map_regions)
```
Note that passing both an MRGID and a geometry does not restrict to the selected area within the MRGID record, but adds both data fetched from the selected data and the MRGID record.
## Why an EurOBIS R package? Didn't exist an OBIS package already?
Yes, you could also use the [OBIS R package](https://github.com/iobis/robis) `robis`. The main advantage of the `eurobis` R package is the functionality to query on species traits.
## 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 [email protected].
[](http://www.lifewatch.be/)