Closed jabiologo closed 2 years ago
melvidoni
commented
3 years ago Hello @jabiologo, thanks for the submission.
Before we consider the package, we would like you to elaborate on the overlap of rWind with other packages. Please, edit your post and be as thorough as possible. Please let me know once it is done.
melvidoni
commented
3 years ago Hello @jabiologo , please extend the explanation as requested so we can move forward.
jabiologo
commented
3 years ago Hi @melvidoni , sorry about the delay. Please, find the edited post above and let me know any questions you have. Thanks in advance.
melvidoni
commented
3 years ago Thank you for the corrections. @maurolepore will be the Handling Editor.
maurolepore
commented
3 years ago Hi @jabiologo! It's my pleasure to edit your submission. I'm about to start editor checks. You'll here back from me within the next couple of days.
maurolepore
commented
3 years ago @jabiologo, here are the editor checks. Please respond to the comments prefixed with "(ml##)" and consider the other comments optional for now. Once you address the prefixed comments I'll start looking for reviewers.
Documentation > README
Automated checks:
spelling::spell_check_package() finds a number of potentially misspelled
words. Please check them then run spelling::update_wordlist().goodpractice::gp() finds a number of issues. Please try to address or
justify them in the particular context of this package.The file .travis.yml suggests the continuous integration service that rWind uses is Travis. We recommend moving away from Travis and instead using GitHub actions.
The file .travis.yml suggests the package is tested only on a single platform. If applicable, consider testing with the three main platforms.
(ml05) The file .travis.yml suggests the package is tested only with R-release. We require that rOpenSci packages are tested against the latest, previous and development versions of R to ensure both backwards and forwards compatibility with base R.
Consider running an automated code-styler such as usethis::use_tidy_style().
This standard makes the code more readable for reviewers and contributors.
I expected a single .Rproj file but instead I see two:
# bash
ls -l *.Rproj$ -rwxrwxr-x 1 rstudio rstudio 356 Mar 13 08:29 rWind1.Rproj
$ -rw-rw-r-- 1 rstudio rstudio 343 Mar 13 20:34 rWind.RprojDESCRIPTION
urlchecker::urlcheck() finds problematic URLs. You may fix them with
urlchecker::url_update().
Consider running usethis::use_tidy_description() to organize DESCRIPTION in
a standard way and facilitate review.
These fields are not included when running
usethis::create_package(). Are they necessary? The field
"Packaged" seems outdated; for maintainability consider removing
it.
-NeedsCompilation: no
-Packaged: 2016-11-24 11:37:02 UTC; javi
-Repository: noneusethis::create_package() the value of LazyData is
lowercase true not uppercase TRUE. Please check it's the
same or better use the true to stick to usethis default.Consider using the convention by which every exported function f() should
have two corresponding files named "R/f.R" and "tests/testthat/test-f.R". This
convention plays well with development tools from the usethis package (e.g.
use_r() and use_test()) and the testthat package (as test failures report
the name of the problematic test-file).
Consider using rmarkdown syntax in roxygen documentation. You may enable it
with usethis::use_roxygen_md(). This makes roxygen documentation easier to
maintain and read.
Reviewers: TBC
Due date: TBC
maurolepore
commented
3 years ago Hello @jabiologo, How are things going? Do you need more time or help?
jabiologo
commented
3 years ago Hi @maurolepore thanks for contacting. My colleague Klaus already did some changes:
-> remove travisCI, fix 1 url
-> add github actions for checks
-> remove redundant file
-> fix some spelling mistakes
-> clean up DESCRIPTION file
-> bug fix
-> add test againbut I was too busy with some deadlines and I'd need more time to finish some more things and respond the comments. Could I have one more week? Thanks in advance.
maurolepore
commented
3 years ago Sure. I mostly wanted to touch base to ensure you have the resources you need. You seem to be in good track but let me know otherwise.
maurolepore
commented
3 years ago Hi @jabiologo, are you still good to address this issues soon or do you prefer to put the submission on hold until you are ready?
jabiologo
commented
3 years ago Hi @maurolepore, sorry for the delay and thanks for your constructive commentaries. We addressed the most of the suggestion you made, please find below a detailed list with some responses:
(ml01) rWind currently works with just two databases, one for wind data and other for sea currents data, one of the URLs was duplicated since it referred to the same database. We have corrected this.
(ml02) We have added more detailed description of the package as well as the reference to the peer reviewed published paper about rWind for more information.
. We have added one simple example from the vignette into the README file.
. We have added some statements about differences and improvements over other packages.
. We have removed the “License” section
(ml03) Spell check has been conducted and word list has been updated (ml04) goodpractice::gc() has been run. It suggested two main issues: only 41% of our code is currently tested. Current time availability doesn’t allow us to afford new test… The other main issue was related to too long code lines. Those lines are the URLs used by rWind to connect to different data bases to download wind and sea currents data, so we consider it makes sense to maintain as they are. . Travis file has been removed and GitHub actions are now used . The package tests are now conducted in Windows, iOS and Linux (ml05) GitHub actions are now used to test the package . use_tidy_style() done and updated . rWind1.Rproj has been removed
. urlchecker::url_update() has been run. It reports an issue related to https://www.ncdc.noaa.gov/data-access/model-data/model-datasets/global-forcast-system-gfs. However, we think it is due to the way the original server is managing the query for this URL. . usethis issues have been addressed . snake_case issue: rWind is already in wide use, the paper has been cited at least 19 times in other peer reviewed papers and many blog post and tweets have been cited. In any case, we can consider in a near future to make something similar as the package igraph, in which they maintain both, original and snake_case functions. Could this work for you? . We’ll consider the "R/f.R" and "tests/testthat/test-f.R" structure in near future. . usethis::use_roxygen_md() done
Thanks again for your work.
maurolepore
commented
3 years ago @jabiologo,
Thanks for addressing most of my most pressing concerns.
(ml04) ... only 41% of our code is currently tested. Current time availability doesn’t allow us to afford new test.
Our guide states that Test coverage below 75% will likely require additional tests or explanation before being sent for review. Although test coverage near 100% is a poor predictor of high-quality code, low test coverage is a good predictor of poor quality code (Unit testing principles, practices, and patterns).
Increasing test coverage might not be too time consuming and will likely pay off. If appropriate you may exclude specific chunks of code with an explanatory comment. And if you haven't seen them yet, check rOpenSci's resources on testing R packages, and let me know if you get stuck.
I totally understand you are busy. It happens and you should not worry. Would you like to give it a go or prefer to hold?
(The hold has no impact other than freeing me to help review other packages)
jabiologo
commented
3 years ago Hi @maurolepore
Thanks very much for your nice comments. I was talking with my friend and we think it would be a good idea to hold the submission to free you to help with other packages. In the meanwhile we could address the testing issue. What would be the procedure to restart the submission?
Thanks in advance, best
maurolepore
commented
3 years ago Thanks @jabiologo. Whenever you are ready, add a comment here saying so. Then I'll remove the holding label and start searching for reviewers. "The holding status will be revisited every 3 months, and after one year the issue will be closed".
maurolepore
commented
3 years ago Hi @jabiologo, it's about the time when we should review the "holding" status. Shall we keep it?
--
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
maurolepore
commented
3 years ago Hi @jabiologo, it's time to remind you that this package continues on hold. Let me know whenever you're ready to proceed with the review. Else I'll touch base again around Jan 30, 2022, and if the hold continues I'll close this issue on April 30, 2022.
--
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
maurolepore
commented
2 years ago Hi @jabiologo, it's time to remind you that this package continues on hold. Let me know whenever you're ready to proceed with the review. Else I'll close this issue on April 30, 2022.
--
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
maurolepore
commented
2 years ago Hi @jabiologo, I'm closing this issue now because it's been on hold for more than 1 year.
--
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
Submitting Author Name: Javier Fernández López Submitting Author Github Handle: !--author1-->@jabiologo<!--end-author1-- Other Package Authors Github handles: (comma separated, delete if none) @KlausVigo, @PabloRL, Yurena Arjona Repository: https://github.com/jabiologo/rWind Version submitted: 1.1.6 Editor: @maurolepore Reviewers: TBD
Archive: TBD
Version accepted: TBD
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): rWind contain tools for downloading, editing and transforming wind and sea current data from several sources. It also allows to use wind and sea currents data to compute the minimum cost path taking into account flow speed and direction to perform connectivity analysis.
Who is the target audience and what are scientific applications of this package?
Researchers interested in wind and sea currents data, specially focused in anisotropic connectivity analyses.
Are there other R packages that accomplish the same thing? If so, how does yours differ or meet our criteria for best-in-category? There are several packages to download and manage wind and sea currents data, but rWind allows to transform them in a easy way into a raster format and to compute connectivity cost analysis among different locations. rWind currently works with just two databases: wind data from Global Forecast System (GFS) of the USA's National Weather Service (NWS) (NOAA/NCEP Global Forecast System (GFS) Atmospheric Model; https://www.ncdc.noaa.gov/data-access/model-data/model-datasets/global-forcast-system-gfs), and ocean currents data from Ocean Surface Current Analyses Real-time (OSCAR) (https://coastwatch.pfeg.noaa.gov/erddap/info/jplOscar_LonPM180/index.html). rWind is specially designed for non physicists/meteorologists to provide an easy interface to download, manage and include wind data specially (but not only) in biological analyses (landscape genetics, dispersion, migration, etc.). After the data download, rWind provide easy utilities to transform raw data (U and V vector components from wind and ocean currents) in flow direction and speed or to compute time series averages of this data. After that, users can use rWind to transform those data into raster layers to be managed with raster packages or other Geographic Information System. With this raster layers, rWind can be used to compute wind/ocean currents mediated cost analysis between locations. rWind applies by default the formula described in Felicisimo et al. 2008, but other cost computations can be provided by the user in the flow.dispersion function. Thus, rWind provides a complete framework from time series data download, aggregate, manage and cost computation in a simple way for the users. It was published as a Software Note in the journal Ecography in 2019 (Fernández‐López & Schliep 2019) and it has been cited in at least 16 papers till now (https://scholar.google.es/scholar?oi=bibs&hl=es&cites=8441515588044324558).
There are other packages that covers data download and data managing that could overlap with rWind. However, rWind is specially focused to offer to the users a straightforward workflow from data download to cost analysis between locations. Some identified packages that cover partially the same utilities as rWind are:
rnoaa: Client for many 'NOAA' data sources including the 'NCDC' climate 'API', with functions foreach of the 'API' 'endpoints': data, data categories, data sets, data types,locations, location categories, and stations. This package allows the access of a huge NOAA data sources, but is not focused in transform data into raster format, nor in cost analyses. In addition, the high amount of data sources makes not easy for a non specialized user to decide what data base should be used for each analyses. It has not "official" vignettes at https://cran.r-project.org/web/packages/rnoaa/index.html
RNCEP: This package, similarly as the previous one, contains functions to retrieve, organize, and visualize weather data from the NCEP/NCAR Reanalysis, and NCEP/DOE Reanalysis II datasets. As the precious one, it is focused into obtain, manage (aggregate, etc) and visualize a huge amount of weather data. Visualization (NCEP.vis.area) are plot-based, non raster layers, and conversion among formats is not addressed in the package. Cost analyses are not implemented. It has not "official" vignettes at https://cran.r-project.org/web/packages/RNCEP/index.html. Kemp et al (2012)
weathercran: This package is developed to search for and download multiple months/years of historical weather data from Environment and Climate Change Canada (ECCC) website. Data bases are different to those used by rWind and data managing and cost analysis computations are not covered in this package. It has many "official" vignettes at https://cran.r-project.org/web/packages/weathercan/index.html.
In short, rWind is focused to fill the gap between wind and ocean currents data adquisition/managing and cost analysis among locations. It provides a straightforward framework to accomplish all these processes in a single R package.
References Felicísimo, Á. M., Muñoz, J., & González-Solis, J. (2008). Ocean surface winds drive dynamics of transoceanic aerial movements. PLoS One, 3(8), e2928. Fernández‐López, J., & Schliep, K. (2019). rWind: download, edit and include wind data in ecological and evolutionary analysis. Ecography, 42(4). https://onlinelibrary.wiley.com/doi/full/10.1111/ecog.03730 https://doi.org/10.1111/ecog.03730 Kemp, M. U., Emiel van Loon, E., Shamoun‐Baranes, J., & Bouten, W. (2012). RNCEP: global weather and climate data at your fingertips. Methods in Ecology and Evolution, 3(1), 65-70. https://besjournals.onlinelibrary.wiley.com/doi/10.1111/j.2041-210X.2011.00138.x
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