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aquamapsdata - Curated Data From AquaMaps.Org #421

Closed mskyttner closed 2 years ago

mskyttner commented 3 years ago

Submitting Author Name: Markus Skyttner Submitting Author Github Handle: !--author1-->@mskyttner<!--end-author1-- Repository: https://github.com/raquamaps/aquamapsdata Version submitted: 0.1.6 Editor: @maurolepore Reviewers: TBD

Archive: TBD Version accepted: TBD --- - Paste the full DESCRIPTION file inside a code block below: ``` Package: aquamapsdata Type: Package Title: Curated Data From AquaMaps.Org Date: 2020-11-21 Version: 0.1.6 Authors@R: c( person("Markus", "Skyttner", email = "markus.skyttner@nrm.se", role = c("aut", "cre")), person("Christina", "Garilao", role = c("ctb"))) Maintainer: Markus Skyttner Description: This package provides access to curated data from aquamaps.org published in 2020. It does not embed the data statically into the package, instead it attempts to download an SQLite database from a remote location. It has a function called download_db() which retrieves the data published by aquamaps.org as an SQLite database. It also has functions for accessing the data. The data is expected to be updated on the remote location approximately once per year. License: file LICENSE URL: https://github.com/raquamaps/aquamapsdata BugReports: https://github.com/raquamaps/aquamapsdata/issues Encoding: UTF-8 LazyData: true RoxygenNote: 7.1.1 Imports: dplyr, dbplyr, RSQLite, R.utils, magrittr, stringi, purrr, DBI, RMySQL, duckdb, leaflet, rappdirs, raster, stringr, rlang, readr, rcrypt, sp, curl Suggests: knitr, httr, readxl, rmarkdown, xml2, DT, tidyr, testthat, covr Depends: R (>= 3.0) VignetteBuilder: knitr Roxygen: list(markdown = TRUE) SystemRequirements: rgdal ``` ## Scope - Please indicate which category or categories from our [package fit policies](https://ropensci.github.io/dev_guide/policies.html#package-categories) this package falls under: (Please check an appropriate box below. If you are unsure, we suggest you make a pre-submission inquiry.): - [x] data retrieval - [ ] data extraction - [ ] data munging - [ ] data deposition - [ ] workflow automation - [ ] version control - [ ] citation management and bibliometrics - [ ] scientific software wrappers - [ ] field and lab reproducibility tools - [ ] database software bindings - [x] geospatial data - [ ] text analysis - Explain how and why the package falls under these categories (briefly, 1-2 sentences): AquaMaps generates standardized computer-generated and fairly reliable large scale predictions of marine and freshwater species. The package provides functions for primarily accessing (and secondarily managing) curated data from aquamaps.org. It does not embed the data statically into the package itself; instead a function allows for a download of a compressed archive from archive.org, containing the full dataset in a single around 10+ GB large SQLite database file (close to 2 GB when compressed). - Who is the target audience and what are scientific applications of this package? The primary target audience is researchers studying ecology for aquatic species such as fish populations, when doing studies in ecology (federal agencies, academic researchers, industry users). Another audience consists of the people at aquamaps.org that manage the data. They have needs for workflows that allow them to expose the data using an R package and therefore need some functions to assist with converting and syncing data, making an extract (by minifying/slicing the data) and in general getting it in shape for being used in the package (including uploading data to archive.org, with approximately yearly frequency). - Are there other R packages that accomplish the same thing? If so, how does yours differ or meet [our criteria for best-in-category](https://ropensci.github.io/dev_guide/policies.html#overlap)? I haven't found any, but in the last couple of years I have looked mostly in a narrow fashion with regards to packages that provide data specifically from aquamaps.org. If widening the scope, the rfishbase and taxizedb packages are partly overlapping since these packages too provide for example for retrieving taxonomic information about aquatic species, but they're have a different scope or focus, since aquamapsdata is focused on providing spatial raster data for native habitats as predicted by the aquamaps algorithm. - (If applicable) Does your package comply with our [guidance around _Ethics, Data Privacy and Human Subjects Research_](https://devguide.ropensci.org/policies.html#ethics-data-privacy-and-human-subjects-research)? N/A - If you made a pre-submission enquiry, please paste the link to the corresponding issue, forum post, or other discussion, or @tag the editor you contacted. ## Technical checks Confirm each of the following by checking the box. - [x] I have read the [guide for authors](https://devguide.ropensci.org/guide-for-authors.html) and [rOpenSci packaging guide](https://devguide.ropensci.org/building.html). This package: - [x] does not violate the Terms of Service of any service it interacts with. - [x] has a CRAN and OSI accepted license. - [x] contains a [README with instructions for installing the development version](https://ropensci.github.io/dev_guide/building.html#readme). - [x] includes [documentation with examples for all functions, created with roxygen2](https://ropensci.github.io/dev_guide/building.html#documentation). - [x] contains a vignette with examples of its essential functions and uses. - [x] has a [test suite](https://ropensci.github.io/dev_guide/building.html#testing). - [x] has [continuous integration](https://ropensci.github.io/dev_guide/ci.html), including reporting of test coverage using services such as Travis CI, Coveralls and/or CodeCov. ## Publication options - [x] 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](http://besjournals.onlinelibrary.wiley.com/hub/journal/10.1111/(ISSN)2041-210X/)? If so:
MEE Options - [ ] The package is novel and will be of interest to the broad readership of the journal. - [ ] The manuscript describing the package is no longer than 3000 words. - [ ] You intend to archive the code for the package in a long-term repository which meets the requirements of the journal (see [MEE's Policy on Publishing Code](http://besjournals.onlinelibrary.wiley.com/hub/journal/10.1111/(ISSN)2041-210X/journal-resources/policy-on-publishing-code.html)) - (*Scope: Do consider MEE's [Aims and Scope](http://besjournals.onlinelibrary.wiley.com/hub/journal/10.1111/(ISSN)2041-210X/aims-and-scope/read-full-aims-and-scope.html) for your manuscript. We make no guarantee that your manuscript will be within MEE scope.*) - (*Although not required, we strongly recommend having a full manuscript prepared when you submit here.*) - (*Please do not submit your package separately to Methods in Ecology and Evolution*)
## Code of conduct - [x] I agree to abide by [rOpenSci's Code of Conduct](https://ropensci.github.io/dev_guide/policies.html#code-of-conduct) during the review process and in maintaining my package should it be accepted.
melvidoni commented 3 years ago

Hello @mskyttner, thanks for the submission. Before proceeding, the Editors have some questions for you.

  1. We are not sure whether this package helps access data or distributes data. There is the impression the authors pre-prepared some dataset from the website they mention.

  2. Are there no other more dynamic ways to get the data? Especially as in the future their prepared dataset might get stale.

  3. Also, some editors had troubles accessing aquamaps.org, as they got a security alert. Can you double-check that the provided link is correct?

mskyttner commented 3 years ago

Hello @melvidoni,

  1. Data for curated aquamaps as exposed by https://www.aquamaps.org is stored in a mysql database that powers that website, some more background about the data can be found here. The aquamapsdata R package is a little bit like taxizedb in the sense that it takes almost all data in this database and makes it accessible from R to researchers, but it does not access the mysql database directly, instead it uses a compressed archive variant in SQLite format that gets downloaded from archive.org. So yes, it does help with accessing the data. But there is also a set of functions in the package to support distribution ("data management") that can be used by aquamaps staff themselves to generate this archive, ie for converting the whole mysql database into a SQLite database (with indexes and full text search capabilities) and to push a compressed archive to archive.org. So yes, it helps with distributing the data, too. These functions for "data management/distribution" is what is pulling down the test coverage stats. To summarize: yes, there are functions in the package for these different audiences - for data access (researchers, consumers of the data) and for distributing the data (aquamaps staff and their workflows as producers of the data). Can you clarify "There is the impression the authors pre-prepared some dataset from the website they mention.", which authors and website are you referring to? Some more info on the data scope is available here: https://raquamaps.github.io/aquamapsdata/articles/intro.html#scope
  2. One could web scrape the aquamaps.org website. As in the archived https://github.com/ropensci-archive/zissou R package. But my understanding is that the aquamaps.org staff doesn't encourage that. There is no API yet, as far as I know.
  3. Thanks for bringing this up, I checked https://www.ssllabs.com/ssltest/analyze.html?d=www.aquamaps.org and that seems to be OK, so it looks like I could change those links to https://www.aquamaps.org, but before doing that I'll first check with the aquamaps.org staff if they can also add aquamaps.org as a valid SNI name (it seems to resolve with a warning if skipping the www part, with the message "This server could not prove that it is aquamaps.org; its security certificate is from www.fishbase.de"; possibly this is a configuration that can be adjusted).
melvidoni commented 3 years ago

Thank you for the detailed response @mskyttner. Could you please clarify who updates the "compressed archive variant in SQLite format that gets downloaded from archive.org" and how often it is done?

mskyttner commented 3 years ago

Yes @melvidoni, this is done by AquaMaps staff using the "data management" functions in the package and scripts like those in data-raw, a workflow which they have requested I developed support for in the package, in order to be able to do those updates more frequently, when data is changed or appended at the source. Historically the update frequency has been sporadic, with yearly updates being the goal. I have developed the package on basis of input from the AquaMaps team and will ask the staff there what their planned update frequency is and report back here going forward. Also, the database structure in the export / data distribution is "cleaned up" with regards to field names, scope/filters in order to be able to distribute the relevant data using a new more easily automatable workflow. I believe API support for delivering more up-to-date data has been discussed at AquaMaps but I'm not fully aware of the current plans for that.

melvidoni commented 3 years ago

Thanks for the clarifications. @maurolepore will be the Handling Editor. He will be performing the editors' checks soon.

maurolepore commented 3 years ago

@mskyttner thanks for your submission! It's my pleasure to be the handling editor.

Here are my editor checks (guidelines). I'll start exploring potential reviewers but I would like to assign them only after you meet or justify against my requests (see section "Requests" below). This is to ensure the reviewers focus in the most interesting aspects of your work, and ultimately to help you maximize the quality of your package. Let me know when you are ready.

I also added a section "Observations". This is to support my requests and to guide you in finding a solution or argument against my requests.

Please let me know if you have any question or concern.

Key editor checks

Editor comments

Requests

FIT AND OVERLAP

INSTALLATION

INTEGRITY

METADATA

TESTS

CI

STYLE

Observations

FIT AND OVERLAP

INSTALLATION

install(dependencies = TRUE, build_vignettes = TRUE)

Error: package or namespace load failed for ‘rcrypt’:
 .onLoad failed in loadNamespace() for 'rcrypt', details:
  call: fun(libname, pkgname)
  error: Please install GPG first or check if GPG can be run from the command line.
      The rcrypt package is just an interface to GPG. See https://gnupg.org/ for
      installation guidelines.

INTEGRITY

Error in .doLoadActions(where, attach) : 
  error in load action .__A__.1 for package raster: loadModule(module = "spmod", what = TRUE, env = ns, loadNow = TRUE): Unable to load module "spmod": package ‘codetools’ was installed before R 4.0.0: please re-install it
Calls: <Anonymous> ... asNamespace -> loadNamespace -> <Anonymous> -> .doLoadActions
Execution halted
Details ``` r devtools::check() #> Updating aquamapsdata documentation #> Loading aquamapsdata #> #> _. _. _. ._ _ _. ._ _ _| _. _|_ _. #> (_| (_| |_| (_| | | | (_| |_) _> (_| (_| |_ (_| #> | | #> Writing NAMESPACE #> Writing NAMESPACE #> ── Building ──────────────────────────────────────────────────── aquamapsdata ── #> Setting env vars: #> ● CFLAGS : -Wall -pedantic #> ● CXXFLAGS : -Wall -pedantic #> ● CXX11FLAGS: -Wall -pedantic #> ──────────────────────────────────────────────────────────────────────────────── #> checking for file ‘/home/mauro/git/aquamapsdata/DESCRIPTION’ ... ✓ checking for file ‘/home/mauro/git/aquamapsdata/DESCRIPTION’ #> ─ preparing ‘aquamapsdata’: #> checking DESCRIPTION meta-information ... ✓ checking DESCRIPTION meta-information #> ─ checking for LF line-endings in source and make files and shell scripts #> ─ checking for empty or unneeded directories #> ─ building ‘aquamapsdata_0.1.6.tar.gz’ #> #> ── Checking ──────────────────────────────────────────────────── aquamapsdata ── #> Setting env vars: #> ● _R_CHECK_CRAN_INCOMING_USE_ASPELL_: TRUE #> ● _R_CHECK_CRAN_INCOMING_REMOTE_ : FALSE #> ● _R_CHECK_CRAN_INCOMING_ : FALSE #> ● _R_CHECK_FORCE_SUGGESTS_ : FALSE #> ● NOT_CRAN : true #> ── R CMD check ───────────────────────────────────────────────────────────────── #> * using log directory ‘/tmp/Rtmp23ztZ6/aquamapsdata.Rcheck’ #> * using R version 4.0.3 (2020-10-10) #> * using platform: x86_64-pc-linux-gnu (64-bit) #> * using session charset: UTF-8 #> * using options ‘--no-manual --as-cran’ #> * checking for file ‘aquamapsdata/DESCRIPTION’ ... OK #> * checking extension type ... Package #> * this is package ‘aquamapsdata’ version ‘0.1.6’ #> * package encoding: UTF-8 #> * checking package namespace information ... OK #> * checking package dependencies ... OK #> * checking if this is a source package ... OK #> * checking if there is a namespace ... OK #> * checking for executable files ... OK #> * checking for hidden files and directories ... OK #> * checking for portable file names ... OK #> * checking for sufficient/correct file permissions ... OK #> * checking serialization versions ... OK #> * checking whether package ‘aquamapsdata’ can be installed ... ERROR #> Installation failed. #> See ‘/tmp/Rtmp23ztZ6/aquamapsdata.Rcheck/00install.out’ for details. #> * DONE #> #> Status: 1 ERROR #> See #> ‘/tmp/Rtmp23ztZ6/aquamapsdata.Rcheck/00check.log’ #> for details. #> ── R CMD check results ───────────────────────────────── aquamapsdata 0.1.6 ──── #> Duration: 28.4s #> #> > checking whether package ‘aquamapsdata’ can be installed ... ERROR #> See below... #> #> ── Install failure ───────────────────────────────────────────────────────────── #> #> * installing *source* package ‘aquamapsdata’ ... #> ** using staged installation #> ** R #> ** data #> *** moving datasets to lazyload DB #> ** exec #> ** inst #> ** byte-compile and prepare package for lazy loading #> Error in .doLoadActions(where, attach) : #> error in load action .__A__.1 for package raster: loadModule(module = "spmod", what = TRUE, env = ns, loadNow = TRUE): Unable to load module "spmod": package ‘codetools’ was installed before R 4.0.0: please re-install it #> Calls: ... asNamespace -> loadNamespace -> -> .doLoadActions #> Execution halted #> ERROR: lazy loading failed for package ‘aquamapsdata’ #> * removing ‘/tmp/Rtmp23ztZ6/aquamapsdata.Rcheck/aquamapsdata’ #> #> 1 error x | 0 warnings ✓ | 0 notes ✓ #> Error: R CMD check found ERRORs ``` 
devtools::test()
#> Loading aquamapsdata
#> 
#>   _.  _.      _. ._ _   _. ._   _  _|  _. _|_  _.
#>  (_| (_| |_| (_| | | | (_| |_) _> (_| (_|  |_ (_|
#>        |                   |
#> Testing aquamapsdata
#> ✓ |  OK F W S | Context
#> ⠏ |   0       | csquare                                                         ⠏ |   0       | Csquare Conversions                                             ✓ |  12       | Csquare Conversions
#> ⠏ |   0       | name_search                                                     ⠏ |   0       | Name Search                                                     ⠧ |   8       | Name Search                                                     ✓ |   9       | Name Search [0.1 s]
#> 
#> ══ Results ═════════════════════════════════════════════════════════════════════
#> Duration: 0.2 s
#> 
#> [ FAIL 0 | WARN 0 | SKIP 0 | PASS 21 ]
Details ``` r goodpractice::gp() #> Preparing: covr #> Preparing: cyclocomp #> Warning in MYPREPS[[prep]](state, quiet = quiet): Prep step for cyclomatic #> complexity failed. #> Preparing: description #> Preparing: lintr #> Preparing: namespace #> Preparing: rcmdcheck #> Warning in MYPREPS[[prep]](state, quiet = quiet): Prep step for rcmdcheck #> failed. #> ── GP aquamapsdata ───────────────────────────────────────────────────────────── #> #> It is good practice to #> #> ✖ write unit tests for all functions, and all package code in #> general. 25% of code lines are covered by test cases. #> #> R/aquamapsdata-package.R:89:NA #> R/aquamapsdata-package.R:90:NA #> R/aquamapsdata-package.R:91:NA #> R/aquamapsdata-package.R:92:NA #> R/aquamapsdata-package.R:93:NA #> ... and 427 more lines #> #> ✖ omit "Date" in DESCRIPTION. It is not required and it gets invalid #> quite often. A build date will be added to the package when you #> perform `R CMD build` on it. #> ✖ avoid long code lines, it is bad for readability. Also, many people #> prefer editor windows that are about 80 characters wide. Try make #> your lines shorter than 80 characters #> #> R/spatial.R:57:1 #> R/spatial.R:70:1 #> R/spatial.R:83:1 #> #> ✖ avoid sapply(), it is not type safe. It might return a vector, or a #> list, depending on the input data. Consider using vapply() instead. #> #> R/csquare.R:129:11 #> R/csquare.R:130:11 #> R/csquare.R:131:11 #> #> ✖ not import packages as a whole, as this can cause name clashes #> between the imported packages. Instead, import only the specific #> functions you need. #> ──────────────────────────────────────────────────────────────────────────────── ```

METADATA

> urlchecker::url_check()
! Warning: README.md:84:19 Moved
Unported License](http://creativecommons.org/licenses/by-nc/3.0/):
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                  https://creativecommons.org/licenses/by-nc/3.0/
x Error: README.md:32:2 Error: SSL: no alternative certificate subject name matches target host name 'aquamaps.org'
<https://aquamaps.org>, but the `aquamapsdata` package offers an a
 ^~~~~~~~~~~~~~~~~~~~
x Error: README.md:71:43 Error: SSL: no alternative certificate subject name matches target host name 'aquamaps.org'
`aquamapsdata` provides data output from <https://aquamaps.org>; when
                                          ^~~~~~~~~~~~~~~~~~~~
x Error: man/am_meta.Rd:18:7 Error: SSL: no alternative certificate subject name matches target host name 'aquamaps.org'
\href{https://aquamaps.org/}{AquaMaps}
      ^~~~~~~~~~~~~~~~~~~~~

SPELLCHECK

Details ``` r spelling::spell_check_package() #> DESCRIPTION does not contain 'Language' field. Defaulting to 'en-US'. #> WORD FOUND IN #> AGPL README.md:129 #> README.Rmd:103 #> alf intro.Rmd:154 #> amd NEWS.md:46 #> aquamaps aquamapsdata-package.Rd:8 #> con_am.Rd:18 #> db_minify.Rd:5 #> description:1,3 #> README.md:69,84 #> README.Rmd:75,81 #> intro.Rmd:146 #> AquaMaps am_citation.Rd:16,18,23,24 #> am_meta.Rd:18,28,41,47,52 #> am_search_exact.Rd:36 #> db_minify.Rd:17 #> title:1 #> README.md:28,81,88,93,100,114 #> README.Rmd:41,81,85,88,92,98 #> intro.Rmd:12,231,233,235,237,239 #> AquaMaps’ intro.Rmd:231 #> aquamapsdata’ README.md:130 #> aquamapsdb am_use_offline_db.Rd:12 #> aquamapsdata-package.Rd:12 #> au csquare_from_dd.Rd:22 #> csquare_to_dd.Rd:17 #> Barile README.md:81 #> README.Rmd:81 #> bathydemersal am_search_exact.Rd:66 #> bathypelagic am_search_exact.Rd:66 #> biologie am_citation.Rd:32 #> README.md:107 #> README.Rmd:94 #> Bluespotted intro.Rmd:98 #> Caranx intro.Rmd:131 #> Catalogue am_search_exact.Rd:37 #> catalogueoflife am_search_exact.Rd:37 #> cells’ intro.Rmd:231 #> chunkwise intro.Rmd:294 #> cmar csquare_from_dd.Rd:22 #> csquare_to_dd.Rd:17 #> CMD NEWS.md:10 #> README.md:5 #> README.Rmd:9 #> Codecov README.md:10 #> README.Rmd:11 #> csiro csquare_from_dd.Rd:22 #> csquare_to_dd.Rd:17 #> csq csquare_from_dd.Rd:22 #> csquare_to_dd.Rd:17 #> csquare csquare_from_dd.Rd:5,21 #> csquare_to_dd.Rd:5,10,16 #> csquarecode NEWS.md:22 #> CsquareCode am_csc_from_extent.Rd:19,22 #> intro.Rmd:178,208,210 #> CsquareCodes am_species_in_csc.Rd:10,16 #> am_species_per_csc.Rd:10 #> csquares csquare_from_dd.Rd:22 #> csquare_to_dd.Rd:17 #> csv NEWS.md:42 #> datadir intro.Rmd:259 #> de am_citation.Rd:31,32 #> README.md:107 #> README.Rmd:94 #> degress csquare_from_dd.Rd:14 #> DepthPrefMin am_search_exact.Rd:71 #> dplyr aquamapsdata-package.Rd:14 #> duckdb con_am.Rd:10 #> default_db.Rd:10 #> eval NEWS.md:16 #> extdata am_use_offline_db.Rd:5,12 #> con_am.Rd:10 #> default_db.Rd:10,17 #> NEWS.md:32 #> faq csquare_from_dd.Rd:22 #> csquare_to_dd.Rd:17 #> FB am_search_exact.Rd:94 #> FC am_map_leaflet.Rd:19 #> fcn am_custom_query.Rd:14 #> Fis am_search_exact.Rd:38 #> FishBase am_search_exact.Rd:40,46,53,66,69,75,80,82,86,94 #> freiburg am_citation.Rd:32 #> README.md:107 #> README.Rmd:94 #> Froese am_citation.Rd:31 #> README.md:81,107 #> README.Rmd:81,94 #> intro.Rmd:239 #> fts am_search_fuzzy.Rd:11 #> FTS NEWS.md:28 #> intro.Rmd:302 #> GameFish am_search_exact.Rd:68 #> geomar am_citation.Rd:31 #> README.md:107 #> README.Rmd:94 #> github README.md:36,39 #> README.Rmd:45,47 #> gz NEWS.md:46 #> hcaf am_meta.Rd:38,50 #> NEWS.md:30 #> intro.Rmd:210,233 #> HCAF intro.Rmd:158 #> HSPEC am_meta.Rd:39 #> hspen am_meta.Rd:47 #> NEWS.md:30 #> intro.Rmd:190 #> HSPEN am_search_exact.Rd:72 #> intro.Rmd:192 #> htm csquare_from_dd.Rd:22 #> csquare_to_dd.Rd:17 #> http am_search_fuzzy.Rd:11 #> csquare_from_dd.Rd:22 #> csquare_to_dd.Rd:17 #> https aquamapsdata-package.Rd:12 #> ie am_species_per_csc.Rd:5 #> ile intro.Rmd:154 #> IPCC am_meta.Rd:54 #> IUCN am_meta.Rd:36 #> am_search_exact.Rd:88,90,92 #> Kaschner am_citation.Rd:32 #> README.md:81,107 #> README.Rmd:81,94 #> intro.Rmd:239 #> Kesner README.md:81 #> README.Rmd:81 #> LME intro.Rmd:210 #> LOICZID which_cells_in_raster.Rd:5,19 #> loiczids which_cells_in_raster.Rd:16 #> lon csquare_to_dd.Rd:13 #> md am_citation.Rd:10 #> intro.Rmd:120 #> minified am_use_offline_db.Rd:12 #> db_minify_path.Rd:5,10 #> default_db.Rd:17 #> intro.Rmd:12 #> Minify db_minify.Rd:5 #> mysql con_am.Rd:10 #> db_sync.Rd:35 #> default_db.Rd:10 #> NonCommercial README.md:90 #> README.Rmd:86 #> occ NEWS.md:30 #> occuring am_species_in_csc.Rd:5 #> intro.Rmd:178 #> occurrencecells am_meta.Rd:56 #> pkgdown NEWS.md:12 #> pre con_am.Rd:17 #> NEWS.md:44 #> programmatically README.md:31 #> README.Rmd:43 #> Rainer am_citation.Rd:31 #> README.md:107 #> README.Rmd:94 #> intro.Rmd:239 #> RCP am_meta.Rd:54,55 #> intro.Rmd:235 #> Rees README.md:81 #> README.Rmd:81 #> rfroese am_citation.Rd:31 #> README.md:107 #> README.Rmd:94 #> Rius README.md:81 #> README.Rmd:81 #> Rmarkdown intro.Rmd:120 #> ROpenSci README.md:135 #> README.Rmd:106 #> RSQLite NEWS.md:16 #> README.md:63 #> README.Rmd:71 #> Salmo NEWS.md:16 #> SeaLifeBase am_search_exact.Rd:40,46,53,66,75,83,86,94 #> Segschneider README.md:81 #> README.Rmd:81 #> SLB am_search_exact.Rd:94 #> species’environmental intro.Rmd:190 #> SpeciesID am_species_per_csc.Rd:15 #> speciesoccursum am_meta.Rd:32 #> sql am_custom_query.Rd:14 #> sqlite am_custom_query.Rd:12 #> am_db_sqlite.Rd:5,13 #> am_search_fuzzy.Rd:11 #> con_am.Rd:10,11 #> db_minify_path.Rd:5,10 #> default_db.Rd:10,17 #> NEWS.md:42 #> stringi NEWS.md:24 #> stringr NEWS.md:24 #> tibble am_csc_from_extent.Rd:19 #> am_search_exact.Rd:97 #> am_search_fuzzy.Rd:14 #> tidyverse README.md:135 #> README.Rmd:106 #> intro.Rmd:42 #> traumatogenic am_search_exact.Rd:74 #> travis NEWS.md:38 #> trevally intro.Rmd:98 #> trutta NEWS.md:16 #> Unported README.md:90 #> README.Rmd:86 #> uthority intro.Rmd:154 #> venonous am_search_exact.Rd:75 #> WGS am_csc_from_extent.Rd:10,12,14,16 #> rasterize_coords.Rd:18 #> which_cells_in_raster.Rd:10 #> www am_search_exact.Rd:37 #> am_search_fuzzy.Rd:11 #> csquare_from_dd.Rd:22 #> csquare_to_dd.Rd:17 #> README.md:84 #> README.Rmd:81 #> xmax am_csc_from_extent.Rd:12 #> xmin am_csc_from_extent.Rd:10 #> ymax am_csc_from_extent.Rd:16 #> ymin am_csc_from_extent.Rd:14 #> yml NEWS.md:38 ```

TESTS

In some files test coverage is far under 80%.

covr::package_coverage()
#> aquamapsdata Coverage: 25.90%
#> R/aquamapsdata-package.R: 0.00%
#> R/download.R: 0.00%
#> R/spatial.R: 0.00%
#> R/db.R: 5.17%
#> R/data.R: 30.10%
#> R/csquare.R: 97.92%
#> R/zzz.R: 100.00%

CI

STYLE

> styler::style_pkg()
Styling  20  files:
 R/aquamapsdata-package.R          ℹ 
 R/csquare.R                       ℹ 
 R/data.R                          ℹ 
 R/db.R                            ℹ 
 R/download.R                      ℹ 
 R/pipe.R                          ✓ 
 R/spatial.R                       ℹ 
 R/utils.R                         ℹ 
 R/zzz.R                           ℹ 
 tests/testthat.R                  ✓ 
 tests/testthat/test_csquare.R     ℹ 
 tests/testthat/test_name_search.R ℹ 
 data-raw/am_meta.R                ℹ 
 data-raw/am_minify_db.R           ℹ 
 data-raw/am_search_boilerplate.R  ℹ 
 data-raw/am_slice_db.R            ℹ 
 data-raw/am_upload_ia.R           ! 
 data-raw/convert_csvs_to_db.R     ℹ 
 data-raw/head_hundred.R           ℹ 
 data-raw/onboarding_dev.R         ℹ 
────────────────────────────────────────
Status  Count   Legend 
✓   2   File unchanged.
ℹ   17  File changed.
x   1   Styling threw an error.
────────────────────────────────────────
Please review the changes carefully!
Warning message:
When processing data-raw/am_upload_ia.R: <text>:1:8: unexpected '{'
1: dontrun{
           ^

@mskyttner, could you please add the rOpenSci under review badge to your README?

You may use rodev::use_review_badge(), rodev::use_review_badge(<issue_number>). Badge URL is https://badges.ropensci.org/<issue_id>_status.svg.

Full link should be:

[![](https://badges.ropensci.org/<issue_id>_status.svg)](https://github.com/ropensci/software-review/issues/<issue_id>)

--

Reviewers:
Due date:

mskyttner commented 3 years ago

Thanks @maurolepore for the feedback! I'm breaking those requests/items up into steps/issues now and will ping back once ready.

maurolepore commented 3 years ago

Hi @mskyttner, just checking how you are going. What would be your estimated time to address the items I mentioned above? There is no rush. I only ask to see if in the meantime I can help with other submissions.

mskyttner commented 3 years ago

Hi @maurolepore thanks for checking up on me, I have been off for a while due to some health issues with my elderly parents but getting back now. I have about half of the editor check issues raised adressed (I think) here https://github.com/raquamaps/aquamapsdata/pull/32 but probably need another week to work through the CI / test coverage / style. I tried to use a rocker/geospatial base image rather than rocker/tidyverse base in the CI setup due to some issues with rgdal installation etc, still struggling a bit with getting that sorted out for all the platforms and versions of R etc. Will try to look more in depth at links with examples how this can be set up ^^.

maurolepore commented 3 years ago

Thanks for letting me know. I'm sorry to hear that. I'll apply the "holding" label and try help elsewhere. Let me know when you are ready.

maurolepore commented 3 years ago

@mskyttner, just touching base. Are you okay staying on hold?

maurolepore commented 3 years ago

@mskyttner I really hope you and your family are well. I realize I touched base a bit too early. The first revision of the 'holding' label will formally be on May 22.

The holding status will be revisited every 3 months, and after one year the issue will be closed. --https://devdevguide.netlify.app/policies.html#policiesreviewprocess

maurolepore commented 3 years ago

Hi @mskyttner, it's about the time when we should review the "holding" status. Shall we keep it or are you ready to resume work on this submission?

--

The author can choose to have their submission put on hold (editor applies the holding label). The holding status will be revisited every 3 months, and after one year the issue will be closed. -- -- https://devdevguide.netlify.app/policies.html#policiesreviewprocess

emilyriederer commented 2 years ago

Hi @mskyttner ! We are doing a sweep of stale review issues. Since this review has been open and inactive for so long, much may have changed including author, editor, and reviewer bandwidth and ever-evolving rOpenSci best practices. As such, I'm closing this issue. If you still have interest and capacity, we would welcome you to open a new submission issue!