search

openjournals / joss-reviews

Reviews for the Journal of Open Source Software
Creative Commons Zero v1.0 Universal
721 stars 38 forks source link

[REVIEW]: ambrosia: An R package for calculating and analyzing food demand and in accordance with the Edmonds et al. food demand model #2890

Closed whedon closed 3 years ago

whedon commented 3 years ago

Submitting author: @kanishkan91 (Kanishka Narayan) Repository: https://github.com/JGCRI/ambrosia Version: v1.3.5 Editor: @dhhagan Reviewers: @tscheypidi, @jhollist Archive: 10.5281/zenodo.4628567

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/b1af4bb026f674b31d1175075607deef"><img src="https://joss.theoj.org/papers/b1af4bb026f674b31d1175075607deef/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/b1af4bb026f674b31d1175075607deef/status.svg)](https://joss.theoj.org/papers/b1af4bb026f674b31d1175075607deef)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@tscheypidi & @sahilseth, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @dhhagan know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Review checklist for @tscheypidi

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @jhollist

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 3 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @tscheypidi, @sahilseth it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

:star: Important :star:

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

  1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

watching

  1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

notifications

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf
whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1142/s2010007817500129 is OK
- 10.5334/jors.266 is OK
- 10.5194/gmd-8-939-2015 is OK
- 10.5334/jors.181 is OK
- 10.1201/9780203735268 is OK
- 10.1093/biomet/57.1.97 is OK
- 10.1093/comjnl/12.1.94 is OK
- 10.2307/1269576 is OK
- 10.4249/scholarpedia.2928 is OK

MISSING DOIs

- None

INVALID DOIs

- None
sahilseth commented 3 years ago

@dhhagan Could you please re-add me as a reviewer, I am seeing the following message: Sorry, we couldn't find that repository invitation. It is possible that the invitation was revoked or that you are not logged into the invited account.

kanishkan91 commented 3 years ago

@tscheypidi I have opened a branch and addressed the issue with the license. I will create a pull request and merge in once I address any other issues that you and other reviewers may find. Let me know what you think. Thanks!

tscheypidi commented 3 years ago

@kanishkan91 I found two discrepancies between author list of this submission and recorded contributions to the package for which I could not find a direct explanation myself:

kanishkan91 commented 3 years ago

@tscheypidi Thanks for the questions. Here are the responses,

If you would like, we can make the contributions of individual authors explicit in the paper. Let us know what you think. Thanks!

tscheypidi commented 3 years ago

Thanks for clarification. From my side it is sufficient to have it documented here in this issue.

dhhagan commented 3 years ago

@sahilseth was whedon able to solve your invite issue? Or do you still need me to re-invite you?

kanishkan91 commented 3 years ago

@tscheypidi We have addressed your comment regarding the installation instructions on the branch. We are working on documenting the parameters more clearly as you recommend. Will notify you once that change is done. Let us know what you think. Thanks again for these review comments!

whedon commented 3 years ago

:wave: @tscheypidi, please update us on how your review is going.

whedon commented 3 years ago

:wave: @sahilseth, please update us on how your review is going.

tscheypidi commented 3 years ago

I finished my first round of review and will get back to it when the authors had some chance to respond to the remaining issues.

kanishkan91 commented 3 years ago

@tscheypidi We are almost done addressing all your review comments (thanks much for those) and will do a new release today with the fixes.

@dhhagan @sahilseth Unless you have any comments at this point, we think we can do one release now and do another later addressing any review comments you might have. Do let us know if you are OK with this. Do let us know if we are missing anything important. Thank you!

kanishkan91 commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

dhhagan commented 3 years ago

@whedon remind @sahilseth in 1 day

whedon commented 3 years ago

Reminder set for @sahilseth in 1 day

kanishkan91 commented 3 years ago

@tscheypidi We have tried to address all of your review comments as a part of release v1.3.1 . I am summarizing our responses to each of the issues below for your convenience,

  1. We have removed the license restrictions as suggested and made sure that this is a BSD2 license.
  2. As suggested, we have recommended explicitly that the user build vignettes when loading the repository. Our instructions also indicate how the user can load the vignette directly.
  3. We have added explicit documentation on the 11 parameters used. These are documented in the documentation of the function vec2param() . We have added a table to the documentation that describes each parameter, its units and the acceptable range for the same and how we arrived at the range/how it is recommended that users arrive at the range (95% Joint confidence interval of the range of values generated during the parameter fitting exercise). In addition to this we have made some changes to vec2param() so that the user can either pass in a vector of nameless parameters or change individual parameters or load default parameters (value for each of these parameters is set at separate objects and then combined to a vector)
  4. We have incorporated your suggestions for the vignette. You will find that the vignette now contains documentation on what is being done in each section in detail. The code comments are also retained. This way, user can directly use the code or look into more in depth explanations as the case may be.
  5. We have taken out the reference in the readme (It made no sense). In its place we have included an explicit hyperlink to GCAM which achieves our desired objective.
  6. As suggested, we have added the contact information to the README.md
  7. Finally, on the shiny app, the app was intended for new users to experiment with parameter values. As you indicated, in its state it was usable only by experts. We have significantly overhauled the app. We have added documentation for the parameters, the results are also explained and we ended up taking out some technical results that can only be interpreted by experts. We would love to know if the improved app addresses your concerns.

Please do let us know what you think of all of the above. Let us know if we have missed anything important. Thanks once again for this tremendously useful review!

tscheypidi commented 3 years ago

@kanishkan91 Excellent work and thanks for putting so much effort into addressing my remarks. I particularly appreciate the extensions in vignette and app as well as the extended functionality of vec2param().

@dhhagan I am done with my review and all my concerns have been fully addressed by the authors.

whedon commented 3 years ago

:wave: @sahilseth, please update us on how your review is going.

kanishkan91 commented 3 years ago

@dhhagan @sahilseth Do let us know if you need anything with respect to this from our side. Thank you!

dhhagan commented 3 years ago

@kanishkan91 I will take a deeper look at this over the next 48 hours and get back to you.

dhhagan commented 3 years ago

@sahilseth Were you ever able to get access to the repository? I believe your review is the next/last step for this manuscript. Please update us on your progress once you get the chance. Thanks!

crvernon commented 3 years ago

Hi @dhhagan ! If we don't hear back from @sahilseth I found some other reviewers from recent JOSS publications that may be able to conduct the review. I'll not call them out here to ensure they are not tagged until you see fit, hence the quotes around their names: @trashbirdecology or @jkarreth

kanishkan91 commented 3 years ago

@dhhagan @sahilseth Hope you are doing well. Any updates related to this by chance? Please do let us know if you need anything from our side.Thanks!

dhhagan commented 3 years ago

Hey @kanishkan91 - sorry about the delay, the past few weeks have been...busy. I'll try finalizing a new reviewer in the next few days.

dhhagan commented 3 years ago

👋 @trashbirdecology - it seems like you would be a good fit to review this paper. Would be interested and have the time to do so?

trashbirdecology commented 3 years ago

I don’t have the capacity this month to do a timely review.

On Sat, Jan 30, 2021 at 10:05 AM David H Hagan notifications@github.com wrote:

👋 @trashbirdecology https://github.com/trashbirdecology - it seems like you would be a good fit to review this paper. Would be interested and have the time to do so?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/2890#issuecomment-770244687, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACL2TNM7VZY3NNOLXBUMUFTS4Q34DANCNFSM4UPS4SYA .

-- Sent from Gmail Mobile

dhhagan commented 3 years ago

@whedon list reviewers

whedon commented 3 years ago

Here's the current list of reviewers: https://bit.ly/joss-reviewers

dhhagan commented 3 years ago

:wave: Hi there, @rmflight @pboesu @molgor @ethanwhite @jhollist: do one of you have the time and interest to review this paper?

rmflight commented 3 years ago

Sorry @dhhagan , I don't think I have time to do this review.

molgor commented 3 years ago

Hi David, I’m reviewing a (JOSS) paper at the moment. I may have time in two weeks, if you haven’t found reviewers by then.

Cheers,

Juan

El 15/02/2021, a las 08:34, David H Hagan notifications@github.com escribió:

👋 Hi there, @rmflight https://github.com/rmflight @pboesu https://github.com/pboesu @molgor https://github.com/molgor @ethanwhite https://github.com/ethanwhite @jhollist https://github.com/jhollist: do one of you have the time and interest to review this paper?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/2890#issuecomment-779260848, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAKQ4VQNYN4S3N6YOQJHZELS7EWI3ANCNFSM4UPS4SYA.

pboesu commented 3 years ago

@dhhagan I'm unavailable until the end of March, I'm afraid.

ethanwhite commented 3 years ago

Already working on another JOSS review and can only handle one at a time at the moment.

jhollist commented 3 years ago

I can do this, but wouldn't be able to get to it until about the second week of March. If that is OK, then sign me up.

On Mon, Feb 15, 2021 at 9:34 AM David H Hagan notifications@github.com wrote:

👋 Hi there, @rmflight https://github.com/rmflight @pboesu https://github.com/pboesu @molgor https://github.com/molgor @ethanwhite https://github.com/ethanwhite @jhollist https://github.com/jhollist: do one of you have the time and interest to review this paper?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/2890#issuecomment-779260848, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABJPYSY6LWKJMIMNKOVNSKDS7EWI5ANCNFSM4UPS4SYA .

-- Jeffrey W. Hollister email: jeff.w.hollister@gmail.com cell: 401 556 4087 https://jwhollister.com

dhhagan commented 3 years ago

@jhollist That should work fine, seeing as we're already getting near the beginning of March. I'll add you as the second reviewer here. Let me know if you have any questions.

dhhagan commented 3 years ago

@whedon invite @jhollist as reviewer

whedon commented 3 years ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands
dhhagan commented 3 years ago

@whedon commands

whedon commented 3 years ago

Here are some things you can ask me to do:

# List all of Whedon's capabilities
@whedon commands

# Assign a GitHub user as the sole reviewer of this submission
@whedon assign @username as reviewer

# Add a GitHub user to the reviewers of this submission
@whedon add @username as reviewer

# Re-invite a reviewer (if they can't update checklists)
@whedon re-invite @username as reviewer

# Remove a GitHub user from the reviewers of this submission
@whedon remove @username as reviewer

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

# Change editorial assignment
@whedon assign @username as editor

# Set the software archive DOI at the top of the issue e.g.
@whedon set 10.0000/zenodo.00000 as archive

# Set the software version at the top of the issue e.g.
@whedon set v1.0.1 as version

# Open the review issue
@whedon start review

EDITORIAL TASKS

# All commands can be run on a non-default branch, to do this pass a custom 
# branch name by following the command with `from branch custom-branch-name`.
# For example:

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Remind an author or reviewer to return to a review after a
# certain period of time (supported units days and weeks)
@whedon remind @reviewer in 2 weeks

# Ask Whedon to do a dry run of accepting the paper and depositing with Crossref
@whedon accept

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

EiC TASKS

# Invite an editor to edit a submission (sending them an email)
@whedon invite @editor as editor

# Reject a paper
@whedon reject

# Withdraw a paper
@whedon withdraw

# Ask Whedon to actually accept the paper and deposit with Crossref
@whedon accept deposit=true
dhhagan commented 3 years ago

@whedon add @jhollist as reviewer

whedon commented 3 years ago

OK, @jhollist is now a reviewer

dhhagan commented 3 years ago

@whedon remove @sahilseth as reviewer

whedon commented 3 years ago

OK, @sahilseth is no longer a reviewer

dhhagan commented 3 years ago

@whedon re-invite @jhollist as reviewer

whedon commented 3 years ago

The reviewer already has a pending invite.

@jhollist please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

dhhagan commented 3 years ago

@whedon remind @jhollist in 1 week

whedon commented 3 years ago

Reminder set for @jhollist in 1 week