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eurobis

Loads data from EurOBIS into R and query on taxon, location and more

https://github.com/lifewatch/eurobis

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (16.4%) to scientific vocabulary

Keywords

dataset emodnet-biology jerico-relevant lifewatch r rstats
Last synced: 9 months ago · JSON representation

Repository

Loads data from EurOBIS into R and query on taxon, location and more

Basic Info
Statistics
  • Stars: 1
  • Watchers: 5
  • Forks: 0
  • Open Issues: 9
  • Releases: 0
Topics
dataset emodnet-biology jerico-relevant lifewatch r rstats
Created about 7 years ago · Last pushed over 1 year ago
Metadata Files
Readme License Codemeta

README.Rmd 

---
output: github_document
df_print: "tibble"
---



```{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


[![Funding](https://img.shields.io/static/v1?label=powered+by&message=lifewatch.be&labelColor=1a4e8a&color=f15922)](http://lifewatch.be)
[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
[![R-CMD-check](https://github.com/lifewatch/eurobis/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/lifewatch/eurobis/actions/workflows/R-CMD-check.yaml)



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 bio@emodnet.eu.

[![LifeWatch.be](https://raw.githubusercontent.com/lifewatch/eurobis/master/fig/LifeWatch_banner_test.PNG)](http://www.lifewatch.be/)

Owner

  • Name: LifeWatch.be
  • Login: lifewatch
  • Kind: organization
  • Email: info@lifewatch.be
  • Location: Belgium

CodeMeta (codemeta.json) 

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GitHub Events

Total
  • Push event: 3
Last Year
  • Push event: 3

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 130
  • Total Committers: 7
  • Avg Commits per committer: 18.571
  • Development Distribution Score (DDS): 0.492
Past Year
  • Commits: 6
  • Committers: 1
  • Avg Commits per committer: 6.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Daphnis De Pooter D****d@v****e 66
salvafern s****z@v****e 42
LennertSchepers 6****s 16
Ruben Perez r****p@v****e 2
salvafern 5****n 2
bart-v b****v@v****e 1
rubenpp7 4****7 1
Committer Domains (Top 20 + Academic)
vliz.be: 4

Issues and Pull Requests

Last synced: over 2 years ago

All Time
  • Total issues: 26
  • Total pull requests: 3
  • Average time to close issues: 6 months
  • Average time to close pull requests: about 6 hours
  • Total issue authors: 5
  • Total pull request authors: 1
  • Average comments per issue: 1.92
  • Average comments per pull request: 0.0
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 6
  • Pull requests: 0
  • Average time to close issues: 6 days
  • Average time to close pull requests: N/A
  • Issue authors: 2
  • Pull request authors: 0
  • Average comments per issue: 3.5
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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Top Authors
Issue Authors
  • salvafern (14)
  • maelle (4)
  • johannow (4)
  • LennertSchepers (3)
  • bakeevdias (1)
Pull Request Authors
  • rubenpp7 (3)
Top Labels
Issue Labels
enhancement (8) bug (4) question (2)
Pull Request Labels

Dependencies

DESCRIPTION cran
  • R >= 2.10 depends
  • assertthat * imports
  • checkmate * imports
  • cli * imports
  • curl * imports
  • glue * imports
  • httr2 * imports
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  • leaflet.extras2 * imports
  • magrittr * imports
  • mapedit * imports
  • methods * imports
  • ows4R >= 0.3 imports
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  • sf * imports
  • shiny * imports
  • tibble * imports
  • utils * imports
  • wk * imports
  • worrms * imports
  • dplyr * suggests
  • mapview * suggests
  • testthat >= 3.0.0 suggests