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robis

R client for the OBIS API

https://github.com/iobis/robis

Science Score: 36.0%

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    Scientific vocabulary similarity
    Low similarity (14.0%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

R client for the OBIS API

Basic Info
Statistics
  • Stars: 44
  • Watchers: 10
  • Forks: 13
  • Open Issues: 21
  • Releases: 8
Created over 10 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog License

README.md

robis: an R client for the OBIS API

DOI

robis is an R package that allows accessing data from the Ocean Biodiversity Information System (OBIS) directly from R. OBIS is a global open-access data and information clearing-house on marine biodiversity for science, conservation and sustainable development.

With robis users can:

  • Download data from OBIS
  • Create a checklist of taxa that met a set of filters
  • Download measurements and facts associated with occurrences
  • Create maps from occurrences (including leaflet maps)

Installation

robis is available from CRAN.

```R

CRAN

install.packages("robis")

latest development version

remotes::install_github("iobis/robis") ```

Getting started

The main functions of the robis package are occurrences and checklist. You can easily download data for one species using:

R records <- occurrence(scientificname = "Abra sibogai")

Then you can plot the occurrences with:

R map_leaflet(records)

Or you can create a ggplot map using:

R map_ggplot(records)

With the function checklist it's possible to obtain a checklist of all taxa in OBIS that met a certain filter. For example, here we obtain all species from the family "Tellinidae"

R taxa <- checklist(scientificname = "Tellinidae")

See the Getting started vignette for more details on how to download data according to filters and how to extract measurements or facts from occurrence data using the function measurements.

Spatial Filtering

There are a variety of ways to add a spatial filter to your query:

  1. Filter by geography using areaid filters.

OBIS provides polygon filters for about 800 areas of interest, like the Southern Ocean or the Bay of Bengal. These can be viewed via the area function. The corresponding id values can be used in the areaid parameter of the occurrence and checklist functions.

  1. Filter with Well-Known Text (WKT) strings.

Both the occurrence and checklist functions allow spatial filtering with Well-Known Text (WK) strings, via the geometry parameter. Following this example from the OBIS Manual, here is an example of how to obtain a checklist of Mollusc species in a certain area:

mollcheck<-checklist(scientificname="Mollusca", geometry = "POLYGON ((2.3 51.8, 2.3 51.6, 2.6 51.6, 2.6 51.8, 2.3 51.8))")

If you're unsure how to construct WKT, robis includes the function get_geometry, which provides an interactive tool to draw shapes and return WKT than can be plugged into queries.

To use it, run: wkt <- get_geometry(). This will open up the tool in the Viewer of RStudio. You can zoom, pan, and use the shapes to draw on the map. Once you are satisfied with what you've drawn, click the 'Done' button in the bottom right hand corner, and it will assign the WKT to the object wkt. If you aren't happy with what you've drawn, you can click the trashcan icon to clear the shape from the tool.

How to use OBIS data

OBIS holds a large collection of biodiversity information, with more than 100 million presence records and almost 200 measurements and facts. This information is powering research in areas like taxonomy, phylogeny and ecology, and is being used as an important tool in conservation and management. You can learn more about OBIS with the OBIS manual. You can also explore some of our use cases or the many publications that applied OBIS data.

obistools package

There is a companion package, obistools, available from GitHub: github.com/iobis/obistools

obistools provide several tools for cleaning data downloaded from OBIS, like:

  • Checking points on land
  • Checking depths
  • Checking dates

Owner

  • Name: OBIS
  • Login: iobis
  • Kind: organization
  • Email: p.provoost@unesco.org
  • Location: Belgium

Ocean Biodiversity Information System

GitHub Events

Total
  • Issues event: 10
  • Watch event: 6
  • Issue comment event: 17
  • Push event: 3
  • Pull request review event: 1
  • Pull request event: 1
  • Fork event: 1
Last Year
  • Issues event: 10
  • Watch event: 6
  • Issue comment event: 17
  • Push event: 3
  • Pull request review event: 1
  • Pull request event: 1
  • Fork event: 1

Committers

Last synced: 10 months ago

All Time
  • Total Commits: 214
  • Total Committers: 6
  • Avg Commits per committer: 35.667
  • Development Distribution Score (DDS): 0.266
Past Year
  • Commits: 10
  • Committers: 2
  • Avg Commits per committer: 5.0
  • Development Distribution Score (DDS): 0.1
Top Committers
Name Email Commits
Pieter Provoost p****t@g****m 157
Samuel Bosch m****l@s****m 44
sformel s****e@f****m 9
silasprincipe 5****e 2
Ben Best b****t 1
ironholds i****s@g****m 1
Committer Domains (Top 20 + Academic)
formeldataservices.com: 1 samuelbosch.com: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 85
  • Total pull requests: 9
  • Average time to close issues: over 1 year
  • Average time to close pull requests: 3 months
  • Total issue authors: 28
  • Total pull request authors: 6
  • Average comments per issue: 1.38
  • Average comments per pull request: 2.0
  • Merged pull requests: 8
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 3
  • Average time to close issues: N/A
  • Average time to close pull requests: 9 days
  • Issue authors: 1
  • Pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 4.67
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • pieterprovoost (34)
  • samuelbosch (8)
  • ekleins (7)
  • sckott (4)
  • wardappeltans (3)
  • haniehsaeedi (2)
  • sformel (2)
  • goldsoundz80 (2)
  • tomjwebb (2)
  • jebyrnes (2)
  • 7yl4r (2)
  • miriamgrace (1)
  • sformel-usgs (1)
  • diodon (1)
  • Enchufa2 (1)
Pull Request Authors
  • sformel (4)
  • samuelbosch (2)
  • bbest (1)
  • roliveros-ramos (1)
  • Ironholds (1)
  • silasprincipe (1)
Top Labels
Issue Labels
bug (14) enhancement (6) documentation (4) feature (3) invalid (2) question (1)
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads:
    • cran 792 last-month
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 9
    (may contain duplicates)
  • Total versions: 21
  • Total maintainers: 1
cran.r-project.org: robis

Ocean Biodiversity Information System (OBIS) Client

  • Versions: 11
  • Dependent Packages: 0
  • Dependent Repositories: 6
  • Downloads: 792 Last month
Rankings
Forks count: 6.3%
Stargazers count: 9.6%
Dependent repos count: 12.1%
Average: 14.7%
Downloads: 17.5%
Dependent packages count: 27.9%
Maintainers (1)
pieterprovoost@gmail.com
Last synced: 10 months ago
conda-forge.org: r-robis
  • Versions: 10
  • Dependent Packages: 0
  • Dependent Repositories: 3
Rankings
Dependent repos count: 17.9%
Average: 40.3%
Forks count: 44.8%
Stargazers count: 46.9%
Dependent packages count: 51.5%
Last synced: 10 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.1.3 depends
  • curl * imports
  • data.table * imports
  • dplyr * imports
  • ggplot2 * imports
  • glue * imports
  • httpcache * imports
  • httr * imports
  • jsonlite * imports
  • leaflet * imports
  • mapedit * imports
  • purrr * imports
  • rlang * imports
  • sf * imports
  • stringr * imports
  • tibble * imports
  • tidyr * imports
  • tidyselect * imports
  • xml2 * imports
  • knitr * suggests
  • rmarkdown * suggests
  • spelling * suggests
  • testthat * suggests