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EMODnet · Aug 12, 2024 · 45dc038 · 45dc038
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,4 +1,4 @@
-^EMODnetWFS\.Rproj$
+^emodnet.wfs\.Rproj$
 ^\.Rproj\.user$
 ^README\.Rmd$
 ^README\.md$
@@ -16,5 +16,5 @@
 ^Meta$
 ^attic$
 ^codemeta\.json$
-^vignettes/EMODnetWFS\.Rmd\.orig$
+^vignettes/emodnet.wfs\.Rmd\.orig$
 ^\.lintr$
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -1,6 +1,6 @@
-# Contributing to EMODnetWFS
+# Contributing to emodnet.wfs
 
-This outlines how to propose a change to EMODnetWFS. 
+This outlines how to propose a change to emodnet.wfs. 
 
 ## Fixing typos
 
@@ -16,7 +16,7 @@ If you’ve found a bug, please file an issue that illustrates the bug with a mi
 
 ### Pull request process
 
-*   Fork the package and clone onto your computer. If you haven't done this before, we recommend using `usethis::create_from_github("EMODnet/EMODnetWFS", fork = TRUE)`.
+*   Fork the package and clone onto your computer. If you haven't done this before, we recommend using `usethis::create_from_github("EMODnet/emodnet.wfs", fork = TRUE)`.
 
 *   Install all development dependencies with `pak::pak()`, and then make sure the package passes R CMD check by running `devtools::check()`. 
     If R CMD check doesn't pass cleanly, it's a good idea to ask for help before continuing. 

diff --git a/.github/workflows/Test-Services.yaml b/.github/workflows/Test-Services.yaml
@@ -68,6 +68,6 @@ jobs:
         run: |
           options(crayon.enabled = TRUE)
           install.packages(".", repos = NULL, type="source")
-          test_service <- lapply(EMODnetWFS::emodnet_wfs()$service_name, EMODnetWFS::emodnet_init_wfs_client);
+          test_service <- lapply(emodnet.wfs::emodnet_wfs()$service_name, emodnet.wfs::emodnet_init_wfs_client);
           testthat::test_that("All services work", {testthat::expect_equal(class(test_service), "list")})
         shell: Rscript {0}
diff --git a/NEWS.md b/NEWS.md
@@ -1,14 +1,14 @@
-# EMODnetWFS (development version)
+# emodnet.wfs (development version)
 
-* Added ability to pass vendor parameter to `EMODnetWFS::emodnet_get_layers()` queries (#88).
+* Added ability to pass vendor parameter to `emodnet.wfs::emodnet_get_layers()` queries (#88).
 * Added memoising (caching during each R session) of the functions getting services
  and layers information (#52).
 
-# EMODnetWFS 2.0.1
+# emodnet.wfs 2.0.1
 
 * Introduced better handling of server response errors.
 
-# EMODnetWFS 2.0.0
+# emodnet.wfs 2.0.0
 
 
 * NEW FEATURE: Added `ecql` filtering capability and ability to interrogate feature attribute (see relevant vignette).

diff --git a/R/emodnet.wfs-package.R b/R/emodnet.wfs-package.R
@@ -8,16 +8,16 @@
 NULL
 
 emodnetwfs_collaborators <- function() {
-  readLines(system.file("collaborators.txt", package = "EMODnetWFS"))
+  readLines(system.file("collaborators.txt", package = "emodnet.wfs"))
 }
 
 emodnetwfs_user_agent <- function() {
-  version <- as.character(utils::packageVersion("EMODnetWFS"))
+  version <- as.character(utils::packageVersion("emodnet.wfs"))
 
   if (nzchar(Sys.getenv("EMODNETWFS_CI"))) {
     return(
       sprintf(
-        "EMODnetWFS R package %s CI https://github.com/EMODnet/EMODnetWFS",
+        "emodnet.wfs R package %s CI https://github.com/EMODnet/emodnet.wfs",
         version
       )
     )
@@ -28,20 +28,20 @@ emodnetwfs_user_agent <- function() {
     gh_username %in% emodnetwfs_collaborators()) {
     return(
       sprintf(
-        "EMODnetWFS R package %s DEV https://github.com/EMODnet/EMODnetWFS",
+        "emodnet.wfs R package %s DEV https://github.com/EMODnet/emodnet.wfs",
         version
       )
     )
   }
 
   sprintf(
-    "EMODnetWFS R package %s https://github.com/EMODnet/EMODnetWFS",
+    "emodnet.wfs R package %s https://github.com/EMODnet/emodnet.wfs",
     version
   )
 }
 
 globalVariables(c("layer_name", "n"))
 
 release_bullets <- function() { # nocov start
-  c('update vignette with knitr::knit("vignettes/EMODnetWFS.Rmd.orig", output = "vignettes/EMODnetWFS.Rmd")') # nolint: line_length_linter
+  c('update vignette with knitr::knit("vignettes/emodnet.wfs.Rmd.orig", output = "vignettes/emodnet.wfs.Rmd")') # nolint: line_length_linter
 } # nocov end
diff --git a/R/emodnet_wfs.R b/R/emodnet_wfs.R
@@ -1,6 +1,6 @@
 .emodnet_wfs <- function() {
   utils::read.csv(
-    system.file("services.csv", package = "EMODnetWFS"),
+    system.file("services.csv", package = "emodnet.wfs"),
     stringsAsFactors = FALSE
   )
 }

diff --git a/R/layers.R b/R/layers.R
@@ -77,8 +77,8 @@
 #' `"biology_occurrence_data"` service),
 #' you might consider a combination of these ideas:
 #' - using [`outputFormat = "CSV"`](https://docs.geoserver.org/stable/en/user/services/wfs/reference.html#getfeature);
-#' - filtering using [`cql_filters`](https://emodnet.github.io/EMODnetWFS/articles/ecql_filtering.html) or
-#' [bounding boxes](https://emodnet.github.io/EMODnetWFS/articles/request-params.html#limit-spatial-extent-using-a-boundary-box)
+#' - filtering using [`cql_filters`](https://emodnet.github.io/emodnet.wfs/articles/ecql_filtering.html) or
+#' [bounding boxes](https://emodnet.github.io/emodnet.wfs/articles/request-params.html#limit-spatial-extent-using-a-boundary-box)
 #' (possibly splitting the area of interests into several requests);
 #' - Using [EMODnet's download toolbox](https://emodnet.ec.europa.eu/geoviewer/).
 # nolint end

diff --git a/R/ui.R b/R/ui.R
@@ -1,17 +1,17 @@
 cli_alert_success <- function(text, .envir = parent.frame()) {
-  if (!getOption("EMODnetWFS.quiet", FALSE)) {
+  if (!getOption("emodnet.wfs.quiet", FALSE)) {
     cli::cli_alert_success(text, .envir = .envir)
   }
 }
 
 cli_alert_info <- function(text, .envir = parent.frame()) {
-  if (!getOption("EMODnetWFS.quiet", FALSE)) {
+  if (!getOption("emodnet.wfs.quiet", FALSE)) {
     cli::cli_alert_info(text, .envir = .envir)
   }
 }
 
 cli_alert_danger <- function(text, .envir = parent.frame()) {
-  if (!getOption("EMODnetWFS.quiet", FALSE)) {
+  if (!getOption("emodnet.wfs.quiet", FALSE)) {
     cli::cli_alert_danger(text, .envir = .envir)
   }
 }
diff --git a/README.md b/README.md
@@ -460,22 +460,22 @@ To cite emodnet.wfs, please use the output from
 citation(package = "emodnet.wfs")
 #> To cite package 'emodnet.wfs' in publications use:
 #> 
-#>   Krystalli A, Fernández-Bejarano S, Salmon M (????). _EMODnetWFS:
+#>   Krystalli A, Fernández-Bejarano S, Salmon M (????). _emodnet.wfs:
 #>   Access EMODnet Web Feature Service data through R_. R package version
 #>   2.0.1.9001. Integrated data products created under the European
 #>   Marine Observation Data Network (EMODnet) Biology project
 #>   (EASME/EMFF/2017/1.3.1.2/02/SI2.789013), funded by the by the
 #>   European Union under Regulation (EU) No 508/2014 of the European
 #>   Parliament and of the Council of 15 May 2014 on the European Maritime
-#>   and Fisheries Fund, <https://github.com/EMODnet/EMODnetWFS>.
+#>   and Fisheries Fund, <https://github.com/EMODnet/emodnet.wfs>.
 #> 
 #> A BibTeX entry for LaTeX users is
 #> 
 #>   @Manual{,
-#>     title = {{EMODnetWFS}: Access EMODnet Web Feature Service data through R},
+#>     title = {{emodnet.wfs}: Access EMODnet Web Feature Service data through R},
 #>     author = {Anna Krystalli and Salvador Fernández-Bejarano and Maëlle Salmon},
 #>     note = {R package version 2.0.1.9001. Integrated data products created under the European Marine Observation Data Network (EMODnet) Biology project (EASME/EMFF/2017/1.3.1.2/02/SI2.789013), funded by the by the European Union under Regulation (EU) No 508/2014 of the European Parliament and of the Council of 15 May 2014 on the European Maritime and Fisheries Fund},
-#>     url = {https://github.com/EMODnet/EMODnetWFS},
+#>     url = {https://github.com/EMODnet/emodnet.wfs},
 #>   }
 ```
 

diff --git a/man/emodnet_get_layers.Rd b/man/emodnet_get_layers.Rd
diff --git a/pkgdown/_pkgdown.yml b/pkgdown/_pkgdown.yml
@@ -1,4 +1,4 @@
-url: "https://emodnet.github.io/EMODnetWFS/"
+url: "https://emodnet.github.io/emodnet.wfs/"
 
 home:
   title: Access EMODnet Web Feature Service data through R

diff --git a/tests/testthat.R b/tests/testthat.R
@@ -1,4 +1,4 @@
 library(testthat) # nolint: undesirable_function_linter
-library(EMODnetWFS) # nolint: undesirable_function_linter
+library(emodnet.wfs) # nolint: undesirable_function_linter
 
-test_check("EMODnetWFS")
+test_check("emodnet.wfs")
diff --git a/tests/testthat/_snaps/deprecate-service-version.md b/tests/testthat/_snaps/deprecate-service-version.md
@@ -4,6 +4,6 @@
       deprecate_msg_service_version("1.1", "blop")
     Condition
       Warning:
-      The `service_version` argument of `blop()` is deprecated as of EMODnetWFS 2.0.1.
+      The `service_version` argument of `blop()` is deprecated as of emodnet.wfs 2.0.1.
       i All calls are made with service version 2.0.0. For more control, consider using {ows4r} directly.
 
diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R
@@ -1 +1 @@
-pre_test_options <- options(EMODnetWFS.quiet = TRUE)# nolint: undesirable_function_linter
+pre_test_options <- options(emodnet.wfs.quiet = TRUE)# nolint: undesirable_function_linter
diff --git a/tests/testthat/test-ui.R b/tests/testthat/test-ui.R
@@ -1,20 +1,20 @@
 test_that("cli_alert_success() works", {
-  withr::local_options(EMODnetWFS.quiet = TRUE)
+  withr::local_options(emodnet.wfs.quiet = TRUE)
   expect_silent(cli_alert_success("hihihi"))
-  withr::local_options(EMODnetWFS.quiet = FALSE)
+  withr::local_options(emodnet.wfs.quiet = FALSE)
   expect_snapshot(cli_alert_success("hihihi"))
 })
 
 test_that("cli_alert_info() works", {
-  withr::local_options(EMODnetWFS.quiet = TRUE)
+  withr::local_options(emodnet.wfs.quiet = TRUE)
   expect_silent(cli_alert_info("hihihi"))
-  withr::local_options(EMODnetWFS.quiet = FALSE)
+  withr::local_options(emodnet.wfs.quiet = FALSE)
   expect_snapshot(cli_alert_info("hihihi"))
 })
 
 test_that("cli_alert_danger() works", {
-  withr::local_options(EMODnetWFS.quiet = TRUE)
+  withr::local_options(emodnet.wfs.quiet = TRUE)
   expect_silent(cli_alert_danger("hihihi"))
-  withr::local_options(EMODnetWFS.quiet = FALSE)
+  withr::local_options(emodnet.wfs.quiet = FALSE)
   expect_snapshot(cli_alert_danger("hihihi"))
 })
diff --git a/vignettes/articles/ecql_filtering.Rmd b/vignettes/articles/ecql_filtering.Rmd
@@ -10,7 +10,7 @@ knitr::opts_chunk$set(
 ```
 
 
-So far, we've demonstrated using `EMODnetWFS` to request complete layers.
+So far, we've demonstrated using emodnet.wfs to request complete layers.
 
 However, WFS services allows us to be selective with what features are returned from the EMODnet servers. 
 For example: using [CQL filters](https://docs.geoserver.org/stable/en/user/tutorials/cql/cql_tutorial.html), we can send a query including a filtering clause that will be executed on the server and return only the subset of the information we request. 
@@ -48,7 +48,7 @@ The examples provided here are only a small subset of filtering functionality av
 First, let's load the library and start a new WFS client with `emodnet_init_wfs_client`.
 
 ```{r setup}
-library(EMODnetWFS)
+library(emodnet.wfs)
 ```
 
 
@@ -327,6 +327,6 @@ unique(filter_sf3$country)
 
 ### Advanced use
 
-There is more that can accomplished by using the EMODnet WFS services than downloading data. The EMODnetWFS package is built on top of the [ows4R](https://github.com/eblondel/ows4R) library, meaning that all the functionalities of this package are available for EMODnetWFS. The ows4R returns a special type of R object called R6. You can learn more in Hadley Wickham's chapter on R6 Objects of the [Advance R book](https://adv-r.hadley.nz/r6.html).
+There is more that can accomplished by using the EMODnet WFS services than downloading data. The emodnet.wfs package is built on top of the [ows4R](https://github.com/eblondel/ows4R) library, meaning that all the functionalities of this package are available for emodnet.wfs. The ows4R returns a special type of R object called R6. You can learn more in Hadley Wickham's chapter on R6 Objects of the [Advance R book](https://adv-r.hadley.nz/r6.html).
 
 For instance: it is not efficient to read a large dataset into R just and later subset part of it. This requires longer waiting times and more bandwidth usage, and in very large datasets it would simply not be possible. For instance, all the occurrences data available through the EMODnet Biology portal are stored in [one table](https://www.emodnet-biology.eu/emodnet-data-format): These are approximately 30 millions rows! In this case, we suggest you access the EMODnet Biology occurrence data through the [download toolbox](https://www.emodnet-biology.eu/toolbox/) or the [eurobis R package](https://github.com/lifewatch/eurobis/) instead.
diff --git a/vignettes/articles/request-params.Rmd b/vignettes/articles/request-params.Rmd
@@ -18,10 +18,10 @@ knitr::opts_chunk$set(
 
 ## Initialise a WFS client
 
-Let's start by loading `EMODnetWFS` and initialising a WFS client to the `human_activities` WFS service.
+Let's start by loading emodnet.wfs and initialising a WFS client to the `human_activities` WFS service.
 
 ```{r setup}
-library(EMODnetWFS)
+library(emodnet.wfs)
 
 wfs <- emodnet_init_wfs_client("human_activities")
 ```
@@ -181,7 +181,7 @@ WFS vendor parameters are additonal, non-standard request parameters defined by
 
 The majority of EMODnet services are GeoServer WFS implementations which support a variety of vendor-specific WFS parameters.
 
-One of these are **`cql_filters`**. These are handled explicitly through the `EMODnetWFS` package through the `cql_filter` argument in `emodnet_get_layers()` and are documented in detail in `article("ecql_filtering")`.
+One of these are **`cql_filters`**. These are handled explicitly through the emodnet.wfs package through the `cql_filter` argument in `emodnet_get_layers()` and are documented in detail in `article("ecql_filtering")`.
 
 For additional vendor parameters available through GeoServer implementations please refer to the [WFS vendor parameters documentatio](https://docs.geoserver.org/latest/en/user/services/wfs/vendor.html)
 

diff --git a/vignettes/EMODnetWFS-unnamed-chunk-6-1.png → vignettes/emodnet.wfs-unnamed-chunk-6-1.png b/vignettes/EMODnetWFS-unnamed-chunk-6-1.png → vignettes/emodnet.wfs-unnamed-chunk-6-1.png
diff --git a/vignettes/EMODnetWFS-unnamed-chunk-9-1.png → vignettes/emodnet.wfs-unnamed-chunk-9-1.png b/vignettes/EMODnetWFS-unnamed-chunk-9-1.png → vignettes/emodnet.wfs-unnamed-chunk-9-1.png
diff --git a/vignettes/EMODnetWFS.Rmd → vignettes/emodnet.wfs.Rmd b/vignettes/EMODnetWFS.Rmd → vignettes/emodnet.wfs.Rmd
@@ -1,5 +1,5 @@
 ---
-title: "EMODnetWFS Case Study: Accessing and mapping EMODnet data"
+title: "emodnet.wfs Case Study: Accessing and mapping EMODnet data"
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{API details}
@@ -17,11 +17,11 @@ The package was designed to make EMODnet vector data layers easily accessible in
 ## Data Product
 ### Installation
 
-You can install the development version of `EMODnetWFS` from GitHub with:
+You can install the development version of emodnet.wfs from GitHub with:
 
 
 ``` r
-remotes::install_github("EMODnet/EMODnetWFS")
+pak::pak("EMODnet/emodnet.wfs")
 ```
 
 ### Explore the EMODnet WFS services with R
@@ -37,13 +37,13 @@ install.packages(c("sf", "dplyr", "mapview"))
 
 
 
-With the `EMODnetWFS` package, we can explore and combine the data served by the [EMODnet lots ](https://www.emodnet.eu/en/portals) through [OGC Web Feature Services](https://en.wikipedia.org/wiki/Web_Feature_Service) or WFS.
+With the emodnet.wfs package, we can explore and combine the data served by the [EMODnet lots ](https://www.emodnet.eu/en/portals) through [OGC Web Feature Services](https://en.wikipedia.org/wiki/Web_Feature_Service) or WFS.
 
 Imagine we are interested in seabed substrates. The first step is to choose what EMODnet lot can provide with these data. For that, we can check the services available with the `emodnet_wfs()` function.
 
 
 ``` r
-library(EMODnetWFS)
+library(emodnet.wfs)
 library(mapview)
 library(dplyr)
 library(sf)
@@ -148,7 +148,7 @@ emodnet_get_layer_info(
 
 
 
-We are now ready to read the layers into R with `emodnet_get_layers()`. EMODnetWFS reads the geometries as simple features (See `sf` package) transformed to [4326](https://epsg.io/4326) by default. Specifying another map projection is possible by passing a EPGS code or projection string with `emodnet_get_layers(crs = "your projection")`. The argument `reduce_layers = TRUE` stack all the layers in one single tibble. Default is FALSE and returns a list of sf objects, one per layer.
+We are now ready to read the layers into R with `emodnet_get_layers()`. emodnet.wfs reads the geometries as simple features (See `sf` package) transformed to [4326](https://epsg.io/4326) by default. Specifying another map projection is possible by passing a EPGS code or projection string with `emodnet_get_layers(crs = "your projection")`. The argument `reduce_layers = TRUE` stack all the layers in one single tibble. Default is FALSE and returns a list of sf objects, one per layer.
 
 
 ``` r
@@ -224,4 +224,4 @@ Tim Appelhans, Florian Detsch, Christoph Reudenbach and Stefan Woellauer (2020).
 
 Please cite this package as:
 
-Anna Krystalli (2020). EMODnetWFS: Access EMODnet Web Feature Service data through R. R package version 0.0.2. https://github.com/EMODnet/EMODnetWFS. Integrated data products created under the European Marine Observation Data Network (EMODnet) Biology project (EASME/EMFF/2017/1.3.1.2/02/SI2.789013), funded by the by the European Union under Regulation (EU) No 508/2014 of the European Parliament and of the Council of 15 May 2014 on the European Maritime and Fisheries Fund.
+Anna Krystalli (2020). emodnet.wfs: Access EMODnet Web Feature Service data through R. R package version 0.0.2. https://github.com/EMODnet/emodnet.wfs. Integrated data products created under the European Marine Observation Data Network (EMODnet) Biology project (EASME/EMFF/2017/1.3.1.2/02/SI2.789013), funded by the by the European Union under Regulation (EU) No 508/2014 of the European Parliament and of the Council of 15 May 2014 on the European Maritime and Fisheries Fund.
diff --git a/vignettes/EMODnetWFS.Rmd.orig → vignettes/emodnet.wfs.Rmd.orig b/vignettes/EMODnetWFS.Rmd.orig → vignettes/emodnet.wfs.Rmd.orig