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taxlist, a package for structuring taxonomic lists and related information #233
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Thanks for your submission @kamapu, we're discussing and will get back to you soon. |
👋 again @kamapu, it's a bit of a tricky situation and we're going to need more information about your package before making a decision. The general question is: how would an R user with a taxonomy problem at hand know how to choose one of the two packages? Your answer could be a table as in this pre-submission inquiry or a decision tree. I know it's a bit of work that might not even warrant onboarding, but it'd be something useful to have in the docs of your package (and of Thanks for your patience! |
👋 @kamapu! Any update or answer on the above? Thank you! |
👋 @kamapu! Any update or answer on the above? Thank you! |
Dear @maelle, there are not really updates on this issue. At the moment I am for a longer period in the field (Kenya). Though, it will be difficult for me to really document differences between Now my question is: Can I submit two packages as a bulk in ROpenSci or should I leave Best regards! |
One (pre-)submission by package is best. Have a productive time in the field! |
Dear @maelle: I went through most of the functions in the manual of Basically both mentioned packages fulfil similar tasks but use different approaches, Contributions of taxlistFurther aspects are probably not implemented in
Features in DevelopmentAdditional features in development, which may not be yet included in
Final RemarksI hope the previous comments properly support |
Thanks for looking through the docs/code @kamapu! Here are some thoughts:
Yep,
There is no such feature explicitly and we dont have plans for one at the moment
I have no plans to support import or export of specific file formats in |
thanks @kamapu for the reply - we're discussing now |
@sckott These are great news! I will put some effort to produce the required functions though I may require the support of @zachary-foster. |
👋 @kamapu! I think it'd be great to add the conversion functions before the onboarding process. I'll put this submission on hold, but in the meantime, feel free to ask any questions. |
OK, I hope, there is no hurry (I'm already busy with the closure of 2018). You may not wander, if I use the gap between Christmas and New Year for it 😧 |
No problem, I might ping you once in a while but that's fine. Please do join the Slack as soon as you want (I sent you an invite). |
👋 @kamapu! Happy New Year! Any update? |
@maelle Happy New Year! I though, the day will come: I had no time but ways thinking about every day. Now I'll start the discussion with @zachary-foster |
The discussion can be followed here |
Thank you @kamapu for the update! Before assigning reviewers, we still need the package to have a test suite, with test coverage reporting of at least 75%. |
Dear @noamross Do you mean, I should follow this instructions? |
@maelle "unsolved issues" actually mean, it is not depending on me anymore... |
Before I get to this again, just want to clarify - do the unresolved issues refer to the UTF-8 strings in the example data set? Or something else? |
In general I consider as unresolved:
Of course, I can still receive and try suggestions. |
Hi @kamapu,
Something that is not checked by default by Hope this could be useful. |
Dear all, sorry for annoying you with the issue of encodings. While I am sort of developing a pathological aversion for this aspect of programming, for people dealing with taxonomy (including myself), the use of names and their authorities is quite crucial in the management of information, thus considered in The possible solutions explored until now, just to get rid of a note, are not satisfying me in a 100%. Now I have a request for you: The next is a block of code including the outputs in my console (I'm working in Linux with UTF-8 locale). My question is: Do you get the exact output as in my case? library(stringi)
library(taxlist)
Names <- Easplist@taxonNames$AuthorName[c(5299, 5021, 5019)]
Names
#> [1] "Borsch, Kai Müll. & Eb.Fisch." "Ruiz & Pav."
#> [3] "Ség."
stri_enc_mark(Names)
#> [1] "UTF-8" "ASCII" "UTF-8"
iconv(Names, "utf8", "ascii")
#> [1] NA "Ruiz & Pav." NA
stri_enc_toascii(Names)
#> [1] "Borsch, Kai M\032ll. & Eb.Fisch." "Ruiz & Pav."
#> [3] "S\032g."
stri_trans_general(Names, "latin-ascii")
#> [1] "Borsch, Kai Mull. & Eb.Fisch." "Ruiz & Pav."
#> [3] "Seg." See also this discussion. |
For reference link to Discourse thread https://discuss.ropensci.org/t/note-on-utf-8-strings-by-goodpractice-gp/2165 |
@kamapu regarding your last question, I do get the exact same output as you do. Furthermore, |
Review round 2: I'm generally fine with the new form of the package. I just have some minor comments at this point. Unresolved issues
Rest of the response
|
My apologies for the delay in responding to these new revisions and response. I have itemized them below mostly for my own mental organization (they match the structure of @kamapu 's response, I can keep track of what I have checked). Note/caveat: I normally run all the checks on two different operating systems to provide better coverage in my ran everything on my other computer. This time I did my entire initial review on a Windows OS and am now checking everything again on my Mac. This could be a "good" thing because I've covered more ground, but IMO it's also suboptimal because some of the changes I've seen could potentially be caused by different software/packages instead of changes to the package. I think this is mostly the case with the LaTeX issues, but wanted to include the disclaimer. Statement of needThis edit is great and satisfies my question(s) about the context and uses for the package. Community guidelinesNewly added contributing guidelines look good. Good practices checklistUTF-8 string issuesIt looks like this one is still being hashed out to some extent... I hope you find a good resolution for it. It sounds from the ropensci.org post like maybe this will remain an issue for people with a setup that doesn't have a font that renders the non-ascii characters. Maybe a note in the vignette about whether/how this would affect functionality would be good, or better yet a custom check or error message upon install... I am sure other package developers will have this issue so you're doing a service to the community by trying to figure it out! LaTeX issueThis one is my fault; I normally run all the checks on two different operating systems to provide better coverage in my ran everything on my other computer. No LaTeX errors in Automated tests
Help files
Thanks - let me know if you have questions/comments about any of the above. |
👋 @kamapu, would you soon be able to respond the reviewers' new comments? Thank you. |
Sorry for the break (many duties and a new family member arrived). I'm ready to go! |
Response to Reviews in Round 2Dear @maelle @mcsiple @levisc8 I will than refer to the comments of reviewers at round 2. Response to @levisc8Unresolved Issues
Rest
Response to @mcsipleTwo comments to this review, otherwise I agree with the rest.
|
Yes, it looks good to me. Thank you @kamapu , @levisc8 and @maelle (and
congratulations from me too!)
…On Thu, Sep 17, 2020 at 12:02 AM Maëlle Salmon ***@***.***> wrote:
Thanks @kamapu <https://github.com/kamapu> and congrats again on the new
family member!
@mcsiple <https://github.com/mcsiple> @levisc8
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Approved! Thanks @kamapu for submitting and @mcsiple @levisc8 for your reviews! 😸 To-dos:
Should you want to acknowledge your reviewers in your package DESCRIPTION, you can do so by making them Welcome aboard! We'd love to host a post about your package - either a short introduction to it with an example for a technical audience or a longer post with some narrative about its development or something you learned, and an example of its use for a broader readership. If you are interested, consult the blog guide, and tag @stefaniebutland in your reply. She will get in touch about timing and can answer any questions. We've put together an online book 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. |
🥳 🥳 🥳 |
Please ping me once you've transferred the repo so that I might give you admin rights back, and feel free to ask me any question. |
Transfer to ropensci
|
@maelle I just transferred the repository to ROpenSci and tried to respond to all bullet points accordingly. |
@kamapu I gave you admin rights again. I am not sure I follow your question. Where are those images now? What docs/ropensci deploys is a pkgdown website. I see images in https://docs.ropensci.org/taxlist/, what is missing? |
@maelle |
Oh, yes!
|
Awesome! Let me plug two blog posts of mine 😁 In any case I think I can close this issue but feel free to ask questions here / in the forum / etc. Thanks all again! |
Thanks to everyone, also from my side. |
Summary
The
taxlist
package structures taxonomic information into S4 objects and implements methods for the manipulation of contained information.Such objects may or may not contain information on synonymy, taxonomic ranks, parent-child relations, taxon views (references used to establish relation between taxon usage names and taxon concepts), and taxon (functional) traits.
https://github.com/kamapu/taxlist
Reproducibility, because this package makes taxonomic information available in a quasi-standard format and tests inconsistencies on the content of taxonomic lists.
In general to taxonomists and biodiversity scientists, in particular to vegetation ecologists (
taxlist
objects are implemented in the package vegtable).yours differ or meet our criteria for best-in-category?
While its functionality may overlap the package taxa, the package
taxlist
attempts to be flexible in the degree of completeness of data (incompleteness is very frequent in vegetation-plot databases), it is meant to be integrated in objects containing diversity information (as in the mentioned packagevegtable
) and to import data from local storage (spreadsheets, Turboveg data sets and even PostgreSQL tables by using vegtable2).Requirements
Confirm each of the following by checking the box. This package:
Publication options
paper.md
matching JOSS's requirements with a high-level description in the package root or ininst/
.Detail
Does
R CMD check
(ordevtools::check()
) succeed? Paste and describe any errors or warnings:Does the package conform to rOpenSci packaging guidelines? Please describe any exceptions:
If this is a resubmission following rejection, please explain the change in circumstances:
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:
@arendsee
@zachary-foster
@sckott
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