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Data Access and Management","monthly_downloads":700,"total_dependent_repos":9,"total_dependent_packages":0,"readme":"# robis: an R client for the OBIS API \u003ca href=\"https://github.com/iobis/robis\"\u003e\u003cimg src=\"man/figures/logo.png\" align=\"right\" height=\"139\" /\u003e\u003c/a\u003e\n\n[![DOI](https://zenodo.org/badge/47509713.svg)](https://zenodo.org/badge/latestdoi/47509713)\n\n__robis__ is an R package that allows accessing data from the Ocean Biodiversity Information System (OBIS) directly from R. 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You can easily download data for one species using:\n\n```R\nrecords \u003c- occurrence(scientificname = \"Abra sibogai\")\n```\n\nThen you can plot the occurrences with:\n\n```R\nmap_leaflet(records)\n```\n\nOr you can create a `ggplot` map using:\n\n```R\nmap_ggplot(records)\n```\n\n![](man/figures/map.png)\n\nWith 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\" \n\n```R\ntaxa \u003c- checklist(scientificname = \"Tellinidae\")\n```\n\nSee the [Getting started vignette](https://iobis.github.io/robis/articles/getting-started.html) 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`.\n\n#### Spatial Filtering\n\nThere are a variety of ways to add a spatial filter to your query:\n\n1. Filter by geography using `areaid` filters.\n\n\u003e OBIS provides polygon filters for about 800 areas of interest, like [the Southern Ocean](https://mapper.obis.org/?areaid=31907) or the [Bay of Bengal](https://mapper.obis.org/?areaid=34273). 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.\n\n2. Filter with Well-Known Text (WKT) strings.\n\n\u003e Both the `occurrence` and `checklist` functions allow spatial filtering with [Well-Known Text (WK)](https://en.wikipedia.org/wiki/Well-known_text_representation_of_geometry) strings, via the `geometry` parameter. Following this [example from the OBIS Manual](https://manual.obis.org/access.html#r-package), here is an example of how to obtain a checklist of Mollusc species in a certain area:\n\u003e\n\u003e `mollcheck\u003c-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))\")`\n\n\u003e 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.\n\n\u003e To use it, run: `wkt \u003c- 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.\n\n## How to use OBIS data\n\nOBIS 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](https://manual.obis.org/). You can also explore some of our [use cases](https://obis.org/usecases/) or the many [publications](https://obis.org/library/) that applied OBIS data.\n\n## obistools package\n\nThere is a companion package, __obistools__, available from GitHub: [github.com/iobis/obistools](https://github.com/iobis/obistools)\n\n__obistools__ provide several tools for cleaning data downloaded from OBIS, like:\n\n- Checking points on land\n- Checking depths\n- Checking dates\n","funding_links":[],"readme_doi_urls":[],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":[],"project_url":"https://ost.ecosyste.ms/api/v1/projects/20325","html_url":"https://ost.ecosyste.ms/projects/20325"}