emodnet.wfs: Access EMODnet Web Feature Service data through R #653
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Checks for emodnet.wfs (v2.0.2.9000)git hash: 5b516d4c
Package License: MIT + file LICENSE 1. Package DependenciesDetails of Package Dependency Usage (click to open)
The table below tallies all function calls to all packages ('ncalls'), both internal (r-base + recommended, along with the package itself), and external (imported and suggested packages). 'NA' values indicate packages to which no identified calls to R functions could be found. Note that these results are generated by an automated code-tagging system which may not be entirely accurate.
Click below for tallies of functions used in each package. Locations of each call within this package may be generated locally by running 's <- pkgstats::pkgstats(<path/to/repo>)', and examining the 'external_calls' table. emodnet.wfsnamespace_layer_names (4), emodnetwfs_user_agent (3), get_abstract_null (2), get_layer_default_crs (2), get_layer_format (2), get_layer_metadata (2), get_service_name (2), guess_layer_format (2), check_layer_crs (1), check_service_name (1), check_wfs (1), checkmate_crs (1), cli_alert_danger (1), cli_alert_info (1), cli_alert_success (1), deprecate_msg_service_version (1), emodnet_get_all_wfs_info (1), emodnet_get_layers (1), emodnet_init_wfs_client (1), emodnetwfs_collaborators (1), ews_get_layer (1), get_layer_bbox (1), get_service_url (1), layer_attribute_descriptions (1), layer_attributes_get_names (1) basec (7), attributes (2), capabilities (2), format (2), parent.frame (2), strsplit (2), as.character (1), length (1), paste (1), pretty (1), regmatches (1), sum (1), suppressWarnings (1), try (1), version (1) magrittr%>% (14) purrrmap_chr (11), map (1), map2 (1) graphicstext (2), title (2) checkmateassert_character (3) memoisememoise (3) dplyrmutate (1) sfst_crs (1) statsdf (1) tibbletibble (1) utilspackageVersion (1) whoamigh_username (1) NOTE: Some imported packages appear to have no associated function calls; please ensure with author that these 'Imports' are listed appropriately. 2. Statistical PropertiesThis package features some noteworthy statistical properties which may need to be clarified by a handling editor prior to progressing. Details of statistical properties (click to open)
The package has:
Statistical properties of package structure as distributional percentiles in relation to all current CRAN packages
All parameters are explained as tooltips in the locally-rendered HTML version of this report generated by the The final measure (
2a. Network visualisationClick to see the interactive network visualisation of calls between objects in package 3.
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| id | name | conclusion | sha | run_number | date |
|---|---|---|---|---|---|
| 10668665094 | Commands | skipped | 77ed52 | 314 | 2024-09-02 |
| 10668583391 | lint-changed-files | success | 643dd5 | 13 | 2024-09-02 |
| 10678310116 | pages build and deployment | success | 7b12c0 | 56 | 2024-09-03 |
| 10678239121 | pkgcheck | success | 5b516d | 123 | 2024-09-03 |
| 10678239120 | pkgdown | success | 5b516d | 319 | 2024-09-03 |
| 10678239122 | R-CMD-check | success | 5b516d | 1210 | 2024-09-03 |
| 10678239118 | test-coverage.yaml | success | 5b516d | 293 | 2024-09-03 |
| 10674669352 | Test-Services | success | 77ed52 | 533 | 2024-09-03 |
| 10674607777 | test-without-fixtures | success | 77ed52 | 387 | 2024-09-03 |
3b. goodpractice results
R CMD check with rcmdcheck
rcmdcheck found no errors, warnings, or notes
Test coverage with covr
Package coverage: 93.31
Cyclocomplexity with cyclocomp
No functions have cyclocomplexity >= 15
Static code analyses with lintr
lintr found no issues with this package!
Package Versions
| package | version |
|---|---|
| pkgstats | 0.1.6.17 |
| pkgcheck | 0.1.2.58 |
Editor-in-Chief Instructions:
This package is in top shape and may be passed on to a handling editor
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Hi @maelle, I've got a NOTE when I run checks on your package with the documentation. ─ checking Rd files ... [0s/0s] NOTE
checkRd: (-3) emodnet_get_layers.Rd:40-41: Lost braces
40 | \item{character string or character vector of length 1.
| ^
checkRd: (-3) emodnet_get_layers.Rd:42-44: Lost braces
42 | \item{character vector of length equal to the length of layers.
| ^
checkRd: (-3) emodnet_get_layers.Rd:45-48: Lost braces
45 | \item{named character vector. Each filter will be applied to the layerAlso, the tests seem to take quite a while to run. Locally I edited the DESCRIPTION file to include Could you check on the NOTE and see if you can fix it and I'll assign an editor in the meantime? |
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@ropensci-review-bot assign @jhollist as editor |
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Assigned! @jhollist is now the editor |
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Thanks @adamhsparks! What exactly do you mean by running checks on the package with the documentation? I changed the markup for those items but would like to re-run the checks as you did to ensure I did fix the problem. I have added that field to DESCRIPTION, so the tests run faster now, thank you! |
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@maelle, sorry, that was worded poorly or missing a comma. It was just |
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@ropensci-review-bot assign @MargaretSiple-NOAA as editor |
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Assigned! @MargaretSiple-NOAA is now the editor |
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@ropensci-review-bot seeking reviewers |
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Please add this badge to the README of your package repository: [](https://github.com/ropensci/software-review/issues/653)Furthermore, if your package does not have a NEWS.md file yet, please create one to capture the changes made during the review process. See https://devguide.ropensci.org/releasing.html#news |
Editor checks:
Editor commentsGreat documentation and package setup. Thank you for being thorough! A couple very minor notes:
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@ropensci-review-bot add @robitalec to reviewers |
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@robitalec added to the reviewers list. Review due date is 2024-10-14. Thanks @robitalec for accepting to review! Please refer to our reviewer guide. rOpenSci’s community is our best asset. We aim for reviews to be open, non-adversarial, and focused on improving software quality. Be respectful and kind! See our reviewers guide and code of conduct for more. |
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@robitalec: If you haven't done so, please fill this form for us to update our reviewers records. |
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@ropensci-review-bot add @LizHareDogs to reviewers |
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@LizHareDogs added to the reviewers list. Review due date is 2024-10-17. Thanks @LizHareDogs for accepting to review! Please refer to our reviewer guide. rOpenSci’s community is our best asset. We aim for reviews to be open, non-adversarial, and focused on improving software quality. Be respectful and kind! See our reviewers guide and code of conduct for more. |
ropensci-review-bot
added
3/reviewer(s)-assigned
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labels
Checks for emodnet.wfs (v2.0.2.9000)git hash: d98df335
Package License: MIT + file LICENSE 1. Package DependenciesDetails of Package Dependency Usage (click to open)
The table below tallies all function calls to all packages ('ncalls'), both internal (r-base + recommended, along with the package itself), and external (imported and suggested packages). 'NA' values indicate packages to which no identified calls to R functions could be found. Note that these results are generated by an automated code-tagging system which may not be entirely accurate.
Click below for tallies of functions used in each package. Locations of each call within this package may be generated locally by running 's <- pkgstats::pkgstats(<path/to/repo>)', and examining the 'external_calls' table. emodnet.wfsnamespace_layer_names (4), emodnetwfs_user_agent (3), get_abstract_null (2), get_layer_default_crs (2), get_layer_format (2), get_layer_metadata (2), get_service_name (2), guess_layer_format (2), check_layer_crs (1), check_service_name (1), check_wfs (1), checkmate_crs (1), cli_alert_danger (1), cli_alert_info (1), cli_alert_success (1), deprecate_msg_service_version (1), emodnet_get_all_wfs_info (1), emodnet_get_layers (1), emodnet_init_wfs_client (1), emodnetwfs_collaborators (1), ews_get_layer (1), get_layer_bbox (1), get_service_url (1), layer_attribute_descriptions (1), layer_attributes_get_names (1) basec (7), attributes (2), capabilities (2), format (2), parent.frame (2), strsplit (2), as.character (1), length (1), paste (1), pretty (1), regmatches (1), sum (1), suppressWarnings (1), try (1), version (1) magrittr%>% (14) purrrmap_chr (11), map (1), map2 (1) graphicstext (2), title (2) checkmateassert_character (3) memoisememoise (3) dplyrmutate (1) sfst_crs (1) statsdf (1) tibbletibble (1) utilspackageVersion (1) whoamigh_username (1) NOTE: Some imported packages appear to have no associated function calls; please ensure with author that these 'Imports' are listed appropriately. 2. Statistical PropertiesThis package features some noteworthy statistical properties which may need to be clarified by a handling editor prior to progressing. Details of statistical properties (click to open)
The package has:
Statistical properties of package structure as distributional percentiles in relation to all current CRAN packages
All parameters are explained as tooltips in the locally-rendered HTML version of this report generated by the The final measure (
2a. Network visualisationClick to see the interactive network visualisation of calls between objects in package 3.
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| id | name | conclusion | sha | run_number | date |
|---|---|---|---|---|---|
| 11227084499 | R-CMD-check | success | d98df3 | 1220 | 2024-10-08 |
| 11319160507 | Test-Services | success | d98df3 | 574 | 2024-10-14 |
| 11319086114 | test-without-fixtures | success | d98df3 | 428 | 2024-10-14 |
3b. goodpractice results
R CMD check with rcmdcheck
rcmdcheck found no errors, warnings, or notes
Test coverage with covr
Package coverage: 93.31
Cyclocomplexity with cyclocomp
No functions have cyclocomplexity >= 15
Static code analyses with lintr
lintr found no issues with this package!
Package Versions
| package | version |
|---|---|
| pkgstats | 0.1.6.19 |
| pkgcheck | 0.1.2.61 |
Editor-in-Chief Instructions:
This package is in top shape and may be passed on to a handling editor
Package ReviewPlease check off boxes as applicable, and elaborate in comments below. Your review is not limited to these topics, as described in the reviewer guide
DocumentationThe package includes all the following forms of documentation:
Functionality
Estimated hours spent reviewing: 4.5
Review CommentsThanks to the authors of emodnet.wfs for submitting this well presented package. It was a pleasure to explore the available data from this source that I was not previously familiar with. emodnet.wfs checked lots of boxes in terms of packaging guide and what I would expect as a new user including:
On my local machine, R CMD check returned 0 errors/warnings/notes and goodpractice checks looked good. My four main comments are related to: 1) function naming, 2) function documentation, 3) introductory vignette, and 4) returned objects. Function namingGiven the purpose of the emodenet.wfs package is to provide access to emodnet data through R, it is understandable and expected that the names are inherited from the broader EMODnet documentation. Looking at the NAMESPACE, I see:
and a variety of operators/modifiers including “get_”, “get_all”, “_info”, “client”, “descriptions”, “get_names”, “summarise”, “tbl”. My suggestion is to consider renaming functions to provide a more intuitive scheme for users. I understand this requires deprecating old functions, future breaking changes, etc - generally a fair amount of work. But I think it's important that function names are intuitive for users and follow a coherent scheme. My suggestions are to first remove all instances of “emodnet” since that is implied by the package name. Next, focuse on maybe three families of functions: “wfs_”, “layer_”, “attribute_”. Then reduce the length of function names and clarify the operation or expected output by including one or two specific operators. For instance, just by reading the function names, what might a user expect the differences are between “emodnet_wfs” and “emodnet_init_wfs_client”? Or for example, is there a risk that layer_attribute_* and layer_attributes_* provides a frustrating user experience if they miss this difference in pluralization? My related suggestion is to consider including a dictionary of this scheme somewhere in the README or introductory vignette. I am not sure exactly where/if this already exists in the broader EMODnet documentation but I think a description of each family of functions wfs/layer/attributes would be useful for new users getting started with the package. Function documentationThe documentation for this package is not extensively detailed. For example, the description sections for R functions are missing except for 1 function (emodnet_get_layers). I would suggest including a paragraph to describe each exported function so the user sees more than the title and list of parameters when they first open the help pages. I would also suggest including the name of the function in the parameters when an argument for a function is the output from another function, eg. in R/info.R: @param wfs …, from emodnet_init_wfs_client. Introductory vignetteI appreciated the suggestion from @MargaretSiple-NOAA but I think one step further for renaming the introductory vignette is to highlight that it is the introductory vignette with something like “getting started” or “introduction to” etc. At the moment, the introductory vignette on the pkgdown site is nestled between the other two vignettes making it unclear which vignette a user should start with. The word “lot” is used a couple of times but it is unclear what this word refers to with respect to emodnet.wfs functions (wfs/layers/attributes). Consider using {knitr} tables or similar functions to tidy up the printing of outputs. This chunk feels like a pretty non-introductory chunk of code. Not sure if it's required or could be simplified. There is an error related to mapview/webshot in the pkgdown/rendered vignette: # Transform to Polygon geometry type from Multisurface
if (unique(st_geometry_type(habitats_directive_layers)) == "MULTISURFACE") {
habitats_directive_layers <- habitats_directive_layers %>%
st_cast(to = "GEOMETRYCOLLECTION") %>%
st_collection_extract(type = "POLYGON")
}
# Visualize
map <- mapview(habitats_directive_layers, zcol = "habitat_description", burst = TRUE)
map
#> Error in loadNamespace(name): there is no package called 'webshot'Returned objectsThe argument "reduce_layers" could use more explanation. The documentation suggests reducing layers will be attempted, but what is an example of reasons which reducing might fail? Why does a single layer return a list? I think it's intuitive to match the names of multiple layers requested to a named list but wouldn't a user specifying a single layer expect an sf object to be directly returned? > result <- emodnet_get_layers(
+ service = "biology",
+ layers = "mediseh_zostera_m_pnt"
+ )
✔ WFS client created successfully
ℹ Service: "https://geo.vliz.be/geoserver/Emodnetbio/wfs"
ℹ Version: "2.0.0"
> class(result)
[1] "list"Minor commentsGiven the overlap in authorship, if the authors are aware of how EMODnetWCS differs from emodnet.wfs or what the roadmap looks like for EMODnetWCS, it might be useful to include it in the README under other web services. Are these also additional tools to reference there? Could you add more precision to how "these three ways to access EMODnet complement each other"? Codecov badge present in README twice, pointing to the root and tree/main, giving different code coverage percentages. The authors could use Are there any rate limits/rules for the API? If so, could these be mentioned in the README and vignettes? The skimr package is listed in the Suggests only to be used once in the ECQL filtering vignette. Is it a necessary dependency? I find reading through the vignette that the single skimr line returns an unexpected/different/confusing output to the previous outputs. Some broken links detected with {urlchecker}. > urlchecker::url_check()
! Warning: vignettes/emodnet.wfs.Rmd:199:100 Moved
Blondel, Emmanuel. (2020, May 27). ows4R: R Interface to OGC Web-Services (Version 0.1-5). Zenodo. http://doi.org/10.5281/zenodo.3860330
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
https://doi.org/10.5281/zenodo.3860330
✖ Error: README.md:67:70 400: Bad Request
| geology_sea_floor_bedrock | <https://drive.emodnet-geology.eu/geoserver/bgr/wfs> |
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
✖ Error: README.md:69:70 400: Bad Request
| geology_submerged_landscapes | <https://drive.emodnet-geology.eu/geoserver/bgs/wfs> |
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
✖ Error: README.md:66:70 400: Bad Request
| geology_marine_minerals | <https://drive.emodnet-geology.eu/geoserver/gsi/wfs> |
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
✖ Error: README.md:68:70 400: Bad Request
| geology_seabed_substrate_maps | <https://drive.emodnet-geology.eu/geoserver/gtk/wfs> |
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
✖ Error: README.md:65:70 400: Bad Request
| geology_events_and_probabilities | <https://drive.emodnet-geology.eu/geoserver/ispra/wfs> |
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
✖ Error: README.md:64:70 400: Bad Request
| geology_coastal_behavior | <https://drive.emodnet-geology.eu/geoserver/tno/wfs> |
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
! Warning: README.md:26:11 Moved
Services](https://emodnet.ec.europa.eu/en/data). [Web Feature services
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
https://emodnet.ec.europa.eu/en/data-0
✖ Error: README.md:59:70 400: Bad Request
| biology_occurrence_data | <https://geo.vliz.be/geoserver/Dataportal/wfs> |
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
✖ Error: README.md:58:70 400: Bad Request
| biology | <https://geo.vliz.be/geoserver/Emodnetbio/wfs> |
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
✖ Error: README.md:90:16 400: Bad Request
#> ℹ Service: "https://geo.vliz.be/geoserver/Emodnetbio/wfs"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
✖ Error: README.md:95:17 400: Bad Request
#> ....|-- url: https://geo.vliz.be/geoserver/Emodnetbio/wfs
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
✖ Error: README.md:107:16 400: Bad Request
#> ℹ Service: "https://geo.vliz.be/geoserver/Emodnetbio/wfs"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
✖ Error: README.md:271:16 400: Bad Request
#> ℹ Service: "https://geo.vliz.be/geoserver/Emodnetbio/wfs"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
✖ Error: README.md:339:16 400: Bad Request
#> ℹ Service: "https://geo.vliz.be/geoserver/Emodnetbio/wfs"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
✖ Error: README.md:62:70 400: Bad Request
| chemistry_contaminants | <https://geoserver.hcmr.gr/geoserver/EMODNET_SHARED/wfs> |
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
✖ Error: README.md:57:70 400: Bad Request
| bathymetry | <https://ows.emodnet-bathymetry.eu/wfs> |
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
✖ Error: README.md:70:70 400: Bad Request
| human_activities | <https://ows.emodnet-humanactivities.eu/wfs> |
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
✖ Error: README.md:73:70 400: Bad Request
| seabed_habitats_individual_habitat_map_and_model_datasets | <https://ows.emodnet-seabedhabitats.eu/geoserver/emodnet_open_maplibrary/wfs> |
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
✖ Error: README.md:72:70 400: Bad Request
| seabed_habitats_general_datasets_and_products | <https://ows.emodnet-seabedhabitats.eu/geoserver/emodnet_open/wfs> |
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
✖ Error: vignettes/emodnet.wfs.Rmd:29:338 404: Not Found
For this tutorial we will make use of the `sf`, `dplyr` and `mapview` packages. The simple features `sf` package is a well known standard for dealing with geospatial vector data. The package `dplyr` is a strong library for data manipulation. This package also loads `magrittr`'s pipe operator `%>%` (you could also use the [base pipe](https://r4ds.hadley.nz/workflow-pipes.html)), which allows to write pipelines in R. To visualize geometries, `mapview` will create quick interactive maps.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
! Warning: vignettes/emodnet.wfs.Rmd:40:97 Moved
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.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
https://emodnet.ec.europa.eu/en/emodnet-themes |
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Thank you for this insightful review @robitalec!! 🙏 |
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Thank you @robitalec ! |
Package ReviewPlease check off boxes as applicable, and elaborate in comments below. Your review is not limited to these topics, as described in the reviewer guide
DocumentationThe package includes all the following forms of documentation:
Functionality
Estimated hours spent reviewing: 25
Review CommentsI am reviewing as part of the Champions program. My mentor is François Michonneau (@fmichonneau) and I have credited him with some of the suggestions below. Line numbers mentioned below are in the unrendered files. README.mdReadthroughFrom the perspective of someone who has not worked with this kind of data, it would be helpful if the introduction (which starts at line 21) could provide a little more context. What is geographic Line 26 line 78 line 184 Line 313 Following instructions on Mac OS using Emacs, Emacs SPeaks StatisticsLine 78 Otherwise, sample commands work as expected. VignetteAll the commands in the vignette work for me. Line 24 has the heading "data product." The meaning of this isn't clear to me. Will this be instructions on how to access a data product or how to create a data product? Line 109 has this command: I am able to run this command, which opens a browser. I can't check the map with the screen reader, but the text on the screen seems appropriate. In the rendered vignette at devtoolsNo problems with:
check() and test() find no problems. pkgcheckI am unable to do this locally on my Mac. Here's the error: This is apparently known because the ropensci-review-botEverything here checks ou, including pkgcheck, which ccouldn't be run locally. Coverage is 93, which is great. Locally-built website/emodnet.wfs/docs/index.htmlThis is a detailed and well-organized introduction to the {emodnet.wfs} functions. Additional, less technical context would help new users orient themselves to working with this type of data.
What does CRS stand for? What is the purpose of the transformation? /emodnet.wfs/docs/articles/ecql_filtering.htmlLine numbers in corresponding .Rmd file The paragraph at line 332 recommends using an alternative R package (eurobis) for large data sets. Using request parameters to limit query resultsI was unable to confirm the map from but I did get links for zooming in and out and what sounded like a legend. line 180 Help pagesIt's super helpful that the help pages are crosslinked, so the reader can put the function in it's context in the workflow It would be helpful to have more context again about vocabulary like "layers." "features". The effect of In Are these different variables measured at common observation times? For function The Value section of the help page for CodeThe authors have much more experience with package development than I do, and the code looked great to me.
The list of services and URLs is provided as a .csv file with the package. SummaryCongratulations to the authors on a great package that will be appreciated by researchers who will be able to easily access this complex data. Thank you for this opportunity to study good code, learn a couple of new tips, and explore a package in a more broad way than I usually do in my work. |
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Thank you for this thorough review @LizHareDogs ! |
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@ropensci-review-bot submit review #653 (comment) time 4.5 |
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Logged review for robitalec (hours: 4.5) |
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@ropensci-review-bot submit review #653 (comment) time 25 |
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Logged review for LizHareDogs (hours: 25) |
ropensci-review-bot
added
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Hi @LizHareDogs I apologize for not replying to this in the review thread. I could have sworn I wrote you something, but I can't find it! We do not have an official way here to provide credit as a reviewer aside from tagging them in the review thread (which you have done!), but another editor suggested that outside credit like a LinkedIn recommendation is also an appropriate way to record the work they put into mentoring you, and can also be helpful for them when future employers are looking at mentoring experience. I liked this blog post because it has concrete guidelines. OK, now I am back to reading both of your reviews :) |
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Hi @maelle - both reviews are in and have insightful comments; thank you both for that. The documentation suggestions from both reviewers will improve the accessibility of the package, especially for new users. I have just a couple small notes on naming conventions/documentation:
It is looking good so far and I will pass it off to you to address the reviewers' comments! ⚡ |
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Thank you all for such helpful feedback!! I'm just back from vacation, and will work on the suggestions ASAP (this week or next). Thank you!! Regarding acknowledging all reviewers, we can list @fmichonneau along with @robitalec and @LizHareDogs in DESCRIPTION with the "rev" role. |
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@LizHareDogs Sorry about the error you're seeing with |
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@maelle, @salvafern, @annakrystalli: please post your response with Here's the author guide for response. https://devguide.ropensci.org/authors-guide.html |
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👋 here! @annakrystalli, @salvafern and I are actively working on the package. We're meeting today, but still have a few things to cross off the list. Thank you for your understanding. 🙏 |
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@MargaretSiple-NOAA It will take us a few more weeks to finish work on the package as the three of us are juggling other projects, but we have a plan. Should we put this issue on hold? |
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@maelle Yes, no problem! I will tell the bot. |
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@ropensci-review-bot put on hold |
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Submission on hold! |
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Thanks a lot to the reviewers @robitalec, @LizHareDogs, @fmichonneau and to the editor @MargaretSiple-NOAA for extremely useful feedback. We listed all reviewers in the Response to @robitalec's reviewFunction naming
We’ve decided to keep the current naming that we had chosen to align with the OGC standards. We’ve made many improvements to the documentation (README including heading titles, vignettes, manual pages) to ensure (hopefully!) the package becomes more user-friendly. Function documentation
We have improved all manual pages, in particular we have made sure the titles of functions are more user-facing (with words like data sources, datasets, variables instead of web services, layers, attributes) with the description using the more specific words. We also improved the titles of sections on the pkgdown reference page. EMODnet/emodnet.wfs#177 Introductory vignette
We changed the title and position of the vignette in the navbar
We have rephrase the uses of “EMODnet lot” to “EMODnet thematic lot”. We have explained how EMODnet is organized in 7 thematic lots in the README.md and get started vignette. We have also added a new column to the emodnet_wfs() tibble
We show data.frames as tibbles in https://emodnet.github.io/emodnet.wfs/articles/emodnet.wfs.html
We have simplified the code by requesting instead the data as geojson, and explained the reasoning for it. This is a known feature / issue of OGC services and we linked to sources explaining the feature.
We fixed this bug. Returned objects
We have renamed the argument to “simplify” to align it with base R functions, and we have clarified in the manual that it only works if column names are the same. Minor comments
We have made the section about other packages more extensive: https://emodnet.github.io/emodnet.wfs/#unlock-the-full-potential-of-the-emodnet-web-services-access-raster-and-gridded-datasets
We have added the sentence “The use of the EMODnet Web Feature Services is not subjet to rate limiting at the moment.” to the README.
We ended up removing the line using skimr.
We fixed the links in a few commits. Urlchecker now finds no broken link. ## Response to @LizHareDogs's review README.mdReadthrough
We've added context and pre-requisites to the README.
We fixed the typo.
We replace the code with the sentence “To explore available services you can use
We added the definition in two vignettes.
We added the context to the README in https://emodnet.github.io/emodnet.wfs/index.html#pre-requisites Following instructions on Mac OS using Emacs, Emacs SPeaks Statistics
We have removed the exclusive mention of Vignette
We removed the confusing heading. “Data product” is an internal phrase for EMODnet team members, irrelevant for users of the package.
We have fixed the bug that lead to this chunk not working (we had not registered the Locally-built website/emodnet.wfs/docs/index.html
We have improved the manual pages, README, vignettes to ensure all terms like “layers” are accompanied by more beginner-friendly explanations. We have listed pre-requisites and resources in the README. /emodnet.wfs/docs/articles/ecql_filtering.html
We fixed the typo.
We have improved the filtering vignette with an explanation of why to use eurobis. Using request parameters to limit query results
We fixed the typo. Help pages
We have improved help pages. In particular the reference index now features “easier” terms near the official terms: https://emodnet.github.io/emodnet.wfs/reference/index.html
We have renamed the parameter to
In short: no. The only thing in common between the data available through this package is that they are in vector format, hence they can be points, lines, polygons etc. Depending on the dataset (layer) you are looking at, there might be a variable (attribute) that specifies time, but not all datasets (layer) will have a time dimension. In any case, when a time dimension is specified, EMODnet follows the ISO 8601 standard. Except if you are looking at multidimensional gridded data in a CF / COARDS compliant netcdf file, typically in ERDDAP, which the Unix Time format, normally as “days since January 1, 1970".
We have improved context in the README and headers of manual pages. Example: https://emodnet.github.io/emodnet.wfs/reference/emodnet_get_wfs_info.html
We have added cross-references between manual pages of functions that help examine attributes, and we have made sure there are evaluated examples in the pkgdown manual pages. Code
We agree that it is a limitation, but before making a new service available to users of the package we would like to test it. Conclusion (for now 😸 )Thanks again to the reviewers and editor, we feel our package already became much stronger as a result of the feedback we received. |
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@ropensci-review-bot submit response #653 (comment) |
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Logged author response! |
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@MargaretSiple-NOAA could we please remove the holding label, since we've submitted our response? Thank you! |
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@maelle Yes! Sorry! One sec. |
Submitting Author Name: Maëlle Salmon
Submitting Author Github Handle: @maelle
Other Package Authors Github handles: (comma separated, delete if none) @salvafern, @annakrystalli
Repository: https://github.com/EMODnet/emodnet.wfs/
Version submitted: 2.0.2
Submission type: Standard
Editor: @MargaretSiple-NOAA
Reviewers: @robitalec, @LizHareDogs
Archive: TBD
Version accepted: TBD
Language: en
Scope
Please indicate which category or categories from our package fit policies this package falls under: (Please check an appropriate box below. If you are unsure, we suggest you make a pre-submission inquiry.):
Explain how and why the package falls under these categories (briefly, 1-2 sentences):
The package allow interrogation of and access to EMODnet’s, European Marine Observation and Data Network, geographic vector data.
The target audience of the package are EMODnet users that might need programmatic access to EMODnet's geographic vector data.
The package allows to include EMODnet vector data into scientific pipelines without needing to manually explore and download data from the EMODnet Geographic Viewer.
The data covers seven disciplinary themes (bathymetry, geology, physics, chemistry, biology, seabed habitats and human activities).
No, to our knowledge emodnet.wfs is the only package that provides access to EMODnet data in R though the EMODnet Web Feature
Services.
The emodnet.wfs package was developed in collaboration with other EMODnet members.
There are in total three ways to access EMODnet data that complement each other and which we documented in emodnet.wfs README:
Some EMODnet data are also published in an ERDDAP server. One can access these data in R using the rOpenSci rerddap R package.
This package emodnet.wfs uses Web Feature Services, hence it is limited to getting vector data. EMODnet also hosts raster data that can be accessed via Web Coverage Services (WCS). The R package EMODnetWCS makes these data available in R. We intend to also submit the latter to software review at one point (and we intend to rename it).
(If applicable) Does your package comply with our guidance around Ethics, Data Privacy and Human Subjects Research?
N/A
If you made a pre-submission inquiry, please paste the link to the corresponding issue, forum post, or other discussion, or tag the editor you contacted.
Explain reasons for any
pkgcheckitems which your package is unable to pass.Technical checks
Confirm each of the following by checking the box.
This package:
Publication options
Do you intend for this package to go on CRAN?
Do you intend for this package to go on Bioconductor?
Do you wish to submit an Applications Article about your package to Methods in Ecology and Evolution? If so:
MEE Options
Code of conduct
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