emodnet.wcs

Access EMODnet Web Coverage Service data through R

https://github.com/emodnet/emodnet.wcs

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 (17.9%) to scientific vocabulary

Keywords

biology dataproducts emodnet geospatial marine-data r-package raster-data wcs

Last synced: 6 months ago · JSON representation

Repository

Access EMODnet Web Coverage Service data through R

Basic Info

Host: GitHub
Owner: EMODnet
License: other
Language: R
Default Branch: main
Homepage: https://emodnet.github.io/emodnet.wcs
Size: 2.86 MB

Statistics

Stars: 7
Watchers: 2
Forks: 1
Open Issues: 15
Releases: 0

Topics

biology dataproducts emodnet geospatial marine-data r-package raster-data wcs

Created over 3 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog Contributing License Code of conduct Codemeta

README.Rmd

---
output: github_document
---



```{r setup, include=FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# emodnet.wcs



[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental) [![CRAN status](https://www.r-pkg.org/badges/version/emodnet.wcs)](https://CRAN.R-project.org/package=emodnet.wcs) [![R-CMD-check](https://github.com/EMODnet/emodnet.wcs/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/EMODnet/emodnet.wcs/actions/workflows/R-CMD-check.yaml) [![Codecov test coverage](https://codecov.io/gh/EMODnet/emodnet.wcs/branch/main/graph/badge.svg)](https://app.codecov.io/gh/EMODnet/emodnet.wcs?branch=master)
[![Codecov test coverage](https://codecov.io/gh/EMODnet/emodnet.wcs/graph/badge.svg)](https://app.codecov.io/gh/EMODnet/emodnet.wcs)
[![R-CMD-check](https://github.com/EMODnet/emodnet.wcs/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/EMODnet/emodnet.wcs/actions/workflows/R-CMD-check.yaml)


The goal of emodnet.wcs is to allow interrogation of and access to EMODnet geographic raster data in R though the [EMODnet Web Coverage Services](https://github.com/EMODnet/Web-Service-Documentation#web-coverage-service-wcs).
See below for available Services.
This package was developed by Sheffield University as part of EMODnet Biology WP4.

[Web Coverage services (WCS)](https://www.ogc.org/standards/wcs)is a standard created by the OGC that refers to the receiving of geospatial information as 'coverages': digital geospatial information representing space-varying phenomena.
One can think of it as Web Feature Service (WFS) for raster data.
It gets the 'source code' of the map, but in this case it's not raw vectors but raw imagery.

An important distinction must be made between WCS and Web Map Service (WMS).
They are similar, and can return similar formats, but a WCS is able to return more information, including valuable metadata and more formats.
It additionally allows more precise queries, potentially against multi-dimensional backend formats.

## Installation

You can install the development version of emodnet.wcs from GitHub with:

```r
# install.packages("pak")
pak::pak("EMODnet/emodnet.wcs")
```

Load the library

```{r load-lib}
library(emodnet.wcs)
```

If you want to avoid reading messages from emodnet.wcs such as "WCS client created successfully", 
set the `"emodnet.wcs.quiet"` option to `TRUE`.

```r
options("emodnet.wcs.quiet" = TRUE)
```

## Available services

All available services are contained in the tibble returned by `emdn_wcs()`.

```{r services, echo=FALSE}

knitr::kable(emdn_wcs())
```

To explore available services in your R session use:

```r
View(emdn_wcs())
```

## Create Service Client

Create new WCS Client.
Specify the service using the`service` argument.

```{r wcs-init}
wcs <- emdn_init_wcs_client(service = "biology")
```

## Get metadata about a WCS service and available coverages

Get service level and a subset of coverage level metadata, compiled for easy review by supplying a `WCSClient` object to `emdn_get_wcs_info`.

```{r wcs-info}
emdn_get_wcs_info(wcs)
```

Info can also be extracted using a service name instead of a `WCSClient` object.

```{r wcs-info-name}
emdn_get_wcs_info(service = "biology")
```

Get more detailed coverage metadata about specific coverage.

```{r wcs-info-coverage}
emdn_get_coverage_info(
  wcs,
  coverage_ids = "Emodnetbio__aca_spp_19582016_L1"
)
```

> **Note**
> 
> To minimize the number of requests sent to webservices, these functions use [`memoise`](https://memoise.r-lib.org/) to cache results inside the active R session.
> To clear the cache, re-start R or run `memoise::forget(emdn_get_wcs_info)`/`memoise::forget(emdn_get_coverage_info)`

The package also offers a number of functions for extracting individual metadata in more usable forms. e.g.

```{r}
emdn_get_coverage_ids(wcs)
```

For more details, please refer to the [Getting metadata about Services \& Coverages](https://emodnet.github.io/emodnet.wcs/articles/metadata.html) article in the `emodnet.wcs` online documentation.

## Downloading Coverages

The package also provides a function to download full or subsets of coverages from emodnet.wcs services.

The following example downloads a spatial subset of a coverage using a bounding box.

```{r}
cov <- emdn_get_coverage(
  wcs,
  coverage_id = "Emodnetbio__aca_spp_19582016_L1",
  bbox = c(xmin = 0, ymin = 40, xmax = 5, ymax = 45),
  nil_values_as_na = TRUE
)

cov
```

```{r}
terra::plot(cov)
```

For more details on downloading coverages, please refer to the [Download Coverages](https://emodnet.github.io/emodnet.wcs/articles/coverages.html) article in the `emodnet.wcs` online documentation.

```{r, include=FALSE}
fs::dir_ls(type = "file", glob = "*.tif") |>
  fs::file_delete()
```

## Citation

To cite emodnet.wcs, please use the output from `citation(package = "emodnet.wcs")`.

```{r}
citation(package = "emodnet.wcs")
```

## Code of Conduct

Please note that the emodnet.wcs project is released with a [Contributor Code of Conduct](https://emodnet.github.io/emodnet.wcs/CODE_OF_CONDUCT.html).
By contributing to this project, you agree to abide by its terms.

Owner

Name: EMODnet
Login: EMODnet
Kind: organization
Email: info@emodnet.eu
Location: Belgium

Website: https://emodnet.ec.europa.eu
Twitter: EMODnet
Repositories: 19
Profile: https://github.com/EMODnet

Your gateway to marine data in Europe

CodeMeta (codemeta.json)

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GitHub Events

Total

Issues event: 22
Delete event: 2
Issue comment event: 36
Push event: 34
Pull request review event: 11
Pull request review comment event: 11
Pull request event: 10
Fork event: 1
Create event: 7

Last Year

Issues event: 22
Delete event: 2
Issue comment event: 36
Push event: 34
Pull request review event: 11
Pull request review comment event: 11
Pull request event: 10
Fork event: 1
Create event: 7

Committers

Last synced: 6 months ago

All Time

Total Commits: 256
Total Committers: 2
Avg Commits per committer: 128.0
Development Distribution Score (DDS): 0.258

Past Year

Commits: 65
Committers: 1
Avg Commits per committer: 65.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Anna Krystalli	a**i@g**m	190
Maëlle Salmon	m**n@y**e	66

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 54
Total pull requests: 22
Average time to close issues: about 2 months
Average time to close pull requests: 1 day
Total issue authors: 5
Total pull request authors: 2
Average comments per issue: 0.94
Average comments per pull request: 0.0
Merged pull requests: 21
Bot issues: 5
Bot pull requests: 0

Past Year

Issues: 15
Pull requests: 8
Average time to close issues: about 2 months
Average time to close pull requests: 2 days
Issue authors: 2
Pull request authors: 1
Average comments per issue: 1.27
Average comments per pull request: 0.0
Merged pull requests: 7
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

annakrystalli (32)
maelle (15)
github-actions[bot] (5)
pnogas67 (1)
pepijn-devries (1)

Pull Request Authors

annakrystalli (13)
maelle (9)

Top Labels

Issue Labels

bug (8) documentation (6) enhancement (5) tests (2) ows4R (1) emodnet-servers (1)

Pull Request Labels

Dependencies

DESCRIPTION cran

R >= 4.1 depends
ows4R >= 0.3 depends
checkmate * imports
curl * imports
glue * imports
httr * imports
memoise * imports
purrr * imports
rlang * imports
sf * imports
tibble * imports
usethis * imports
covr * suggests
httptest * suggests
testthat >= 3.0.0 suggests
webmockr * suggests
withr * suggests

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r-lib/actions/pr-push v1 composite
r-lib/actions/setup-r v1 composite
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ecosyste.ms

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Open Source Science

emodnet.wcs

Science Score: 26.0%

Keywords

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Basic Info

Statistics

Topics

Metadata Files

README.Rmd

Owner

CodeMeta (codemeta.json)

GitHub Events

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