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Fix #162
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@maelle
maelle committed Jul 1, 2024
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2 changes: 1 addition & 1 deletion README.Rmd
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# EMODnetWFS: Access EMODnet Web Feature Service data through R

<!-- badges: start -->
[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html)
[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
[![R build status](https://github.com/EMODnet/EMODnetWFS/workflows/R-CMD-check/badge.svg)](https://github.com/EMODnet/EMODnetWFS/actions)
[![Codecov test coverage](https://codecov.io/gh/EMODnet/EMODnetWFS/branch/main/graph/badge.svg)](https://app.codecov.io/gh/EMODnet/EMODnetWFS/tree/main)
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41 changes: 30 additions & 11 deletions README.md
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<!-- badges: start -->

[![Lifecycle:
experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html)
[![Project Status: Active – The project has reached a stable, usable
state and is being actively
developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
[![R build
status](https://github.com/EMODnet/EMODnetWFS/workflows/R-CMD-check/badge.svg)](https://github.com/EMODnet/EMODnetWFS/actions)
[![Codecov test
Expand Down Expand Up @@ -53,6 +54,7 @@ All available services are contained in the tibble returned by
| biology_occurrence_data | <https://geo.vliz.be/geoserver/Dataportal/wfs> |
| chemistry_cdi_data_discovery_and_access_service | <https://geo-service.maris.nl/emodnet_chemistry/wfs> |
| chemistry_cdi_distribution_observations_per_category_and_region | <https://geo-service.maris.nl/emodnet_chemistry_p36/wfs> |
| chemistry_contaminants | <https://geoserver.hcmr.gr/geoserver/EMODNET_SHARED/wfs> |
| chemistry_marine_litter | <https://www.ifremer.fr/services/wfs/emodnet_chemistry2> |
| geology_coastal_behavior | <https://drive.emodnet-geology.eu/geoserver/tno/wfs> |
| geology_events_and_probabilities | <https://drive.emodnet-geology.eu/geoserver/ispra/wfs> |
Expand Down Expand Up @@ -82,6 +84,9 @@ wfs_bio <- emodnet_init_wfs_client(service = "biology")
#> ✔ WFS client created successfully
#> ℹ Service: "https://geo.vliz.be/geoserver/Emodnetbio/wfs"
#> ℹ Version: "2.0.0"
```

``` r

wfs_bio
#> <WFSClient>
Expand Down Expand Up @@ -376,23 +381,29 @@ library(rerddap)
#> Registered S3 method overwritten by 'hoardr':
#> method from
#> print.cache_info httr
```

``` r

erddap_url <- "https://erddap.emodnet.eu/erddap/"

rerddap::ed_datasets(url = erddap_url)
#> # A tibble: 8 × 16
#> griddap Subset tabledap Make.A.Graph wms files Title Summary FGDC ISO.19115
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 "" "http… https:/… https://erd… "" "" * Th… "This … "" ""
#> 2 "" "" https:/… https://erd… "" "htt… EMOD… "The d… "" ""
#> 3 "" "" https:/… https://erd… "" "htt… EMOD… "The d… "" ""
#> 4 "" "http… https:/… https://erd… "" "htt… EMOD… "The d… "htt… "https:/…
#> 5 "" "" https:/… https://erd… "" "htt… Pres… "The p… "htt… "https:/…
#> 6 "" "" https:/… https://erd… "" "" PSMS… "Perma… "" ""
#> 7 "" "" https:/… https://erd… "" "htt… PSMS… "Perma… "" ""
#> 8 "" "http… https:/… https://erd… "" "htt… TAO/… "This … "htt… "https:/…
#> 1 "" "/erd… /erddap… /erddap/tab… "" "" * Th… "This … "" ""
#> 2 "" "" /erddap… /erddap/tab… "" "/er… EMOD… "The d… "" ""
#> 3 "" "" /erddap… /erddap/tab… "" "/er… EMOD… "The d… "" ""
#> 4 "" "/erd… /erddap… /erddap/tab… "" "/er… EMOD… "The d… "/er… "/erddap…
#> 5 "" "" /erddap… /erddap/tab… "" "/er… Pres… "The p… "/er… "/erddap…
#> 6 "" "" /erddap… /erddap/tab… "" "" PSMS… "Perma… "" ""
#> 7 "" "" /erddap… /erddap/tab… "" "/er… PSMS… "Perma… "" ""
#> 8 "" "/erd… /erddap… /erddap/tab… "" "/er… TAO/… "This … "/er… "/erddap…
#> # ℹ 6 more variables: Info <chr>, Background.Info <chr>, RSS <chr>,
#> # Email <chr>, Institution <chr>, Dataset.ID <chr>
```

``` r

rerddap::ed_search(query = "vessel density", url = erddap_url)
#> # A tibble: 16 × 2
Expand All @@ -414,6 +425,9 @@ rerddap::ed_search(query = "vessel density", url = erddap_url)
#> 14 Vessel traffic density, 2019, Tanker EMODPACE_VD_10_Tan…
#> 15 Vessel traffic density, 2019, Tug and Towing EMODPACE_VD_07_Tug
#> 16 Vessel traffic density, 2019, Unknown EMODPACE_VD_12_Unk…
```

``` r

human_activities_data_info <- rerddap::info(datasetid = "humanactivities_9f8a_3389_f08a", url = erddap_url)
human_activities_data_info
Expand All @@ -427,9 +441,15 @@ human_activities_data_info
#> Variables:
#> vd:
#> Units: seconds
```

``` r

year_2020_gridded_data <- griddap(datasetx = human_activities_data_info, time = c("2020-03-18", "2020-03-19"))
#> info() output passed to x; setting base url to: https://erddap.emodnet.eu/erddap
```

``` r
head(year_2020_gridded_data$data)
#> x y time vd
#> 1 -622500 7034500 2020-04-01T00:00:00Z NA
Expand All @@ -456,7 +476,6 @@ To cite EMODnetWFS, please use the output from

``` r
citation(package = "EMODnetWFS")
#>
#> To cite package 'EMODnetWFS' in publications use:
#>
#> Krystalli A, Fernández-Bejarano S, Salmon M (????). _EMODnetWFS:
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