CoordinateCleaner

[azizka]

Summary

• What does this package do? (explain in 50 words or less): Identify problematic records in large databases of biological and palaeontological collections, to improve data quality for analyses in biogeography, ecology and conservation.

• Paste the full DESCRIPTION file inside a code block below:

Package: CoordinateCleaner
Type: Package
Title: Automated Cleaning of Occurrence Records from Biological Collections
Version: 1.1-0
Date: 2018-04-08
Authors@R: c(person(given = "Alexander", family = "Zizka", email = "alexander.zizka@bioenv.gu.se",
                    role = c("aut", "cre")),
             person(given = "Daniele", family = "Silvestro", role = c("ctb")))
Description: Automated cleaning of geographic species occurrence records by automated flagging of problems common to biodiversity data from biological collections. Includes automated tests to easily flag (and exclude) records assigned to country or province centroid, the open ocean, the headquarters of the Global Biodiversity Information Facility, urban areas or the location of biodiversity institutions (museums, zoos, botanical gardens, universities). Furthermore identifies per species outlier coordinates, zero coordinates, identical latitude/longitude and invalid coordinates. Also implements an algorithm to identify data sets with a significant proportion of rounded coordinates. Especially suited for large data sets. See <https://github.com/azizka/CoordinateCleaner/wiki> for more details and tutorials.
License: GPL-3
Depends: R (>= 3.0.0), sp
Imports: geosphere, ggplot2, methods, raster, rgeos, rnaturalearth, stats
LazyData: true
RoxygenNote: 6.0.1
Suggests: testthat, covr

• URL for the package (the development repository, not a stylized html page): https://github.com/azizka/CoordinateCleaner

• Please indicate which category or categories from our package fit policies this package falls under *and why(? (e.g., data retrieval, reproducibility. If you are unsure, we suggest you make a pre-submission inquiry.):

• geospatial data, because the package deals with improving data quality of occurrence records of biological specimens

• reproducible research, because the package replaces potentially badly documented ad-hoc decisions from GUI GIS with clearly defined functions

• data munging, becasue the packages processes commonly used geospatial data (geographic coordinates)

•   Who is the target audience and what are scientific applications of this package? Anybody using geographic coordinates from biological collections on a large scale, thus mostly researchers in biogeography, (maco-)ecology, evolutionary biology and conservation practitioners

• Are there other R packages that accomplish the same thing? If so, how does yours differ or meet our criteria for best-in-category? Yes, scrubr, see this pre-submission enquiry: https://github.com/ropensci/onboarding/issues/199

•   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. https://github.com/ropensci/onboarding/issues/199, @sckott

Requirements

Confirm each of the following by checking the box. 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.
• [x] includes documentation with examples for all functions.
• [x] contains a vignette with examples of its essential functions and uses. The vignette is not part of the package. There are extensive tutorials (https://github.com/azizka/CoordinateCleaner/tree/master/Tutorials) and a wiki (https://github.com/azizka/CoordinateCleaner/wiki) on github
• [x] has a test suite.
• [x] has continuous integration, including reporting of test coverage, using services such as Travis CI, Coveralls and/or CodeCov.
• [x] I agree to abide by ROpenSci's Code of Conduct during the review process and in maintaining my package should it be accepted.

Publication options

• [x] Do you intend for this package to go on CRAN? it is on CRAN already https://cran.r-project.org/web/packages/CoordinateCleaner/index.html
• [ ] Do you wish to automatically submit to the Journal of Open Source Software? If so:
  • [ ] The package has an obvious research application according to JOSS's definition.
  • [ ] The package contains a paper.md matching JOSS's requirements with a high-level description in the package root or in inst/.
  • [ ] The package is deposited in a long-term repository with the DOI:
  • (Do not submit your package separately to JOSS)
• [x] Do you wish to submit an Applications Article about your package to Methods in Ecology and Evolution? If so:
  • [x] The package is novel and will be of interest to the broad readership of the journal.
  • [x] The manuscript describing the package is no longer than 3000 words.
  • [x] 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)
  • (Scope: Do consider MEE's Aims and Scope for your manuscript. We make no gaurantee that your manuscript willl 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) The manuscript is already submitted to MEE. It had to be submitted before April 1st.

Detail

• [x] Does R CMD check (or devtools::check()) succeed? Paste and describe any errors or warnings:

• [x] Does the package conform to rOpenSci packaging guidelines? Please describe any exceptions: Exceptions:

• NEWS file - there is one now, but only started with the latest version.

• Package name: Unfortunately, the name contains capital letters (CoordinateCleaner), but it is on CRAN already.

• _Function naming: Functions for individual tests are snakecase and pipe compatible, wrapper function around all tests are CamelCase.

• Documentation: not built with roxygen.

• If this is a resubmission following rejection, please explain the change in circumstances: Nope

• If possible, please provide recommendations of reviewers - those with experience with similar packages and/or likely users of your package - and their GitHub user names:

SaraVarela, sckott

[maelle]

Thanks @isteves! No, I just need to run the last checks which I'll do ASAP!

[maelle]

Approved! Thanks @azizka for submitting and @isteves @Pakillo for your reviews! 😺

To-dos:

• [ ] When mentioning the NEWS file in the README, add a link to the NEWS file so that it might be easier to find it.
• [ ] Transfer the repo to rOpenSci's "ropensci" GitHub organization under "Settings" in your repo. I have invited you to a team that should allow you to do so. You'll be made admin once you do.
• [ ] Add the rOpenSci footer to the bottom of your README " [![ropensci_footer](https://ropensci.org/public_images/ropensci_footer.png)](https://ropensci.org)"
• [ ] Fix any links in badges for CI and coverage to point to the ropensci URL. We no longer transfer Appveyor projects to ropensci Appveyor account so after transfer of your repo to rOpenSci's "ropensci" GitHub organization the badge should be [![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/ropensci/pkgname?branch=master&svg=true)](https://ci.appveyor.com/project/individualaccount/pkgname).
• [ ] We're starting to roll out software metadata files to all ropensci packages via the Codemeta initiative, see https://github.com/ropensci/codemetar/#codemetar for how to include it in your package, after installing the package - should be easy as running codemetar::write_codemeta() in the root of your package. Should you want to awknowledge your reviewers in your package DESCRIPTION, you can do so by making them "rev"-type contributors in the Authors@R field (with their consent). More info on this here.

Welcome aboard! We'd also love a blog post about your package, either a short-form intro to it (https://ropensci.org/tech-notes/) or long-form post with more narrative about its development. (https://ropensci.org/blog/). If you are interested, @stefaniebutland will be in touch about content and timing.

We've started putting together a gitbook with our best practice and tips, this chapter starts the 3d section that's about guidance for after onboarding. Please tell us what could be improved, the corresponding repo is here.

[azizka]

Hej,

great, thanks. Very exciting. I am teaching abroad with no opportunity to work on this the next two weeks, but will do this as soon as I come back!

Thanks again to all of you!

[azizka]

Hi, @isteves, @Pakillo, @maelle do you agree to be acknowledged as reviewers for the package? Please let me know here.

[azizka]

@maelle, after transferring ownership, how can I edit the short package description on the github page, since it links to the old pagedown, adress?

[maelle]

@azizka I've now made you admin of the repo again! I couldn't do that before transfer. Thanks for transferring! 😸

[stefaniebutland]

Hello @azizka. Congratulations on acceptance of CoordinateCleaner! Are you interested in writing a post for the rOpenSci blog, either a short-form intro to it (https://ropensci.org/tech-notes/) or long-form post with more narrative about its development (https://ropensci.org/blog/)?

This link will give you many examples of blog posts by authors of onboarded packages so you can get an idea of the style and length you prefer: https://ropensci.org/tags/onboarding/.

Here are some technical and editorial guidelines for contributing a post: https://github.com/ropensci/roweb2#contributing-a-blog-post.

Please let me know what you think.

[azizka]

Hi @stefaniebutland, yes I am interested in writing a blog post, but there is a manuscript for the package in review at MEE currently, I'd prefer to wait for a decision on that first. Cheers,

Alex

[stefaniebutland]

Sounds good @azizka. Would be nice to be able to note the publication in the post.

[azizka]

Hej @maelle,

almost done, the last thing is to migrate the badges. Where can I find help to migrate the travis-ci build and codecov badges properly, since they are not working at the moment.

Thanks!

[maelle]

@azizka weird, I have now activated the repo at https://travis-ci.org/ropensci/CoordinateCleaner (your badge points to travis-ci.com at the moment), let's see if that works.

[azizka]

OK, thanks. I switch to travis.org; let's see if it works once the first run is done. I fixed the codecov badge.

[azizka]

Alright, I think everything is working now. The latest version (2.0-2) is also on CRAN now. Is there anything else to do?

[maelle]

No, sorry, closing the issue now!

[stefaniebutland]

@azizka I see your manuscript is submitted to MEE. Wishing you a smooth process

[stefaniebutland]

@azizka, Scott Chamberlain who is the rOpenSci point person for the MEE collaboration told me that the coordinatecleaner paper will be published on 21 Feb - and MEE asked if we can coordinate blog post timing.

This would be great to bring more attention to your work if we can coordinate. Do you think you could have a draft post submitted by Thurs Feb 14 or Fri 15th this week? That would give me time to review and you to address any feedback.

(edited). Update - I understand that you're also working on a post for MEE. Our audiences are different, but we can discuss options for cross-posting if you don't want to write two posts.