[REVIEW]: helios: An R package to process heating and cooling degrees for GCAM #6033

editorialbot · 2023-11-08T08:05:22Z

Submitting author: @mengqi-z (Mengqi Zhao)
Repository: https://github.com/JGCRI/helios
Branch with paper.md (empty if default branch):
Version: v1.0.1
Editor: @hugoledoux
Reviewers: @RBhupi, @ibarraespinosa
Archive: 10.5281/zenodo.10658818

Status

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Markdown: [![status](https://joss.theoj.org/papers/d51874055341099eebba993947673207/status.svg)](https://joss.theoj.org/papers/d51874055341099eebba993947673207)

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

@RBhupi & @ibarraespinosa, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
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✨ 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 ✨

Checklists

📝 Checklist for @RBhupi

📝 Checklist for @ibarraespinosa

The text was updated successfully, but these errors were encountered:

editorialbot · 2023-11-08T08:05:24Z

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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editorialbot · 2023-11-08T08:05:28Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1038/s41467-021-21785-1 is OK
- 10.1016/j.eneco.2014.07.003 is OK
- 10.1016/j.esr.2019.100411 is OK
- 10.1038/s41560-021-00974-8 is OK
- 10.57931/1885756 is OK
- 10.5194/gmd-12-677-2019 is OK
- 10.5194/gmd-15-2533-2022 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-11-08T08:05:30Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.02 s (1296.8 files/s, 188705.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               15            595            722           1602
YAML                             6             35              4            209
Rmd                              2            217            366            191
Markdown                         5             47              0            151
TeX                              1              6              0             75
-------------------------------------------------------------------------------
SUM:                            29            900           1092           2228
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2023-11-08T08:05:32Z

Wordcount for paper.md is 839

editorialbot · 2023-11-08T08:06:58Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

RBhupi · 2023-11-10T23:24:46Z

Review checklist for @RBhupi

Conflict of interest

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/JGCRI/helios?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@mengqi-z) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

RBhupi · 2023-11-10T23:48:44Z

@mengqi-z I am trying a quick installation and having following dependency issue. Please, check.

> devtools::install_github("JGCRI/helios")
Downloading GitHub repo JGCRI/helios@HEAD
Downloading GitHub repo JGCRI/rmap@HEAD
Skipping 1 packages not available: jgcricolors
── R CMD build ────────────────────────────────────────────────────────────
✔  checking for file ‘/private/var/folders/8t/ld6_fkgd62q7qm1kqd0q_h5r0000gp/T/RtmpUItgiR/remotes1634f5abf84d5/JGCRI-rmap-2e357fa/DESCRIPTION’ ...
─  preparing ‘rmap’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
     NB: this package now depends on R (>= 3.5.0)
     WARNING: Added dependency on R >= 3.5.0 because serialized objects in
     serialize/load version 3 cannot be read in older versions of R.
     File(s) containing such objects:
       ‘rmap/data/allSubRegions.rda’ ‘rmap/data/exampleMapDataClass.rda’
       ‘rmap/data/exampleMapDataParam.rda’
       ‘rmap/data/example_gridData_GWPv4To2015.rda’
       ‘rmap/data/mapCountries.rda’ ‘rmap/data/mapCountriesUS52.rda’
       ‘rmap/data/mapGCAMBasins.rda’ ‘rmap/data/mapGCAMBasinsUS49.rda’
       ‘rmap/data/mapGCAMBasinsUS52.rda’ ‘rmap/data/mapGCAMLand.rda’
       ‘rmap/data/mapGCAMReg32.rda’ ‘rmap/data/mapGCAMReg32EU.rda’
       ‘rmap/data/mapGCAMReg32US52.rda’ ‘rmap/data/mapGCAMReg32Uruguay.rda’
       ‘rmap/data/mapHydroShed1.rda’ ‘rmap/data/mapHydroShed2.rda’
       ‘rmap/data/mapHydroShed3.rda’
       ‘rmap/data/mapIntersectGCAMBasin32RegUruguay.rda’
       ‘rmap/data/mapIntersectGCAMBasinCountry.rda’
       ‘rmap/data/mapIntersectGCAMBasinUS52.rda’
       ‘rmap/data/mapIntersectGCAMBasinUS52County.rda’
       ‘rmap/data/mapStates.rda’ ‘rmap/data/mapUS49.rda’
       ‘rmap/data/mapUS49County.rda’ ‘rmap/data/mapUS49HUC2.rda’
       ‘rmap/data/mapUS49HUC4.rda’ ‘rmap/data/mapUS52.rda’
       ‘rmap/data/mapUS52Compact.rda’ ‘rmap/data/mapUS52County.rda’
       ‘rmap/data/mapUS52CountyCompact.rda’ ‘rmap/data/mapUS52HUC2.rda’
       ‘rmap/data/mapUS52HUC4.rda’ ‘rmap/data/mapping_US49.rda’
       ‘rmap/data/mapping_US52.rda’ ‘rmap/data/mapping_country_gcam32.rda’
       ‘rmap/data/mapping_gcambasins.rda’
       ‘rmap/data/mapping_tethys_grid_basin_region_country.rda’
       ‘rmap/inst/extras/rmap_tethys_grid_basin_region_country.rds’
─  building ‘rmap_1.0.0.tar.gz’
   
ERROR: dependency ‘jgcricolors’ is not available for package ‘rmap’
* removing ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rmap’
Downloading GitHub repo JGCRI/rmap@HEAD
Skipping rmap, it is already being installed
── R CMD build ────────────────────────────────────────────────────────────
✔  checking for file ‘/private/var/folders/8t/ld6_fkgd62q7qm1kqd0q_h5r0000gp/T/RtmpUItgiR/remotes1634f26d99c71/JGCRI-helios-2bc630c/DESCRIPTION’ ...
─  preparing ‘helios’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
     NB: this package now depends on R (>= 3.5.0)
     WARNING: Added dependency on R >= 3.5.0 because serialized objects in
     serialize/load version 3 cannot be read in older versions of R.
     File(s) containing such objects:
       ‘helios/data/L244.HDDCDD_building.rda’
       ‘helios/data/L2441.HDDCDD_Fixed_gcamusa_seg.rda’
       ‘helios/data/example_cmip6_china_ncdf.rda’
       ‘helios/data/example_hdcd_monthly_usa.rda’
       ‘helios/data/example_hdcd_segment_usa.rda’
       ‘helios/data/example_pop_china_ncdf.rda’
       ‘helios/data/example_pop_usa_csv.rda’
       ‘helios/data/example_wrf_usa_ncdf.rda’ ‘helios/data/mapUS52.rda’
       ‘helios/data/noaa_hddcdd.rda’ ‘helios/data/segment_map_utc.rda’
       ‘helios/data/spatial_options.rda’
       ‘helios/inst/extras/noaa_hddcdd.RDS’
─  building ‘helios_1.0.0.tar.gz’
   
ERROR: dependency ‘rmap’ is not available for package ‘helios’
* removing ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/helios’
Warning messages:
1: In i.p(...) :
  installation of package ‘/var/folders/8t/ld6_fkgd62q7qm1kqd0q_h5r0000gp/T//RtmpUItgiR/file1634f53a9ea7e/rmap_1.0.0.tar.gz’ had non-zero exit status
2: In i.p(...) :
  installation of package ‘/var/folders/8t/ld6_fkgd62q7qm1kqd0q_h5r0000gp/T//RtmpUItgiR/file1634f77f716b/helios_1.0.0.tar.gz’ had non-zero exit status
>

mengqi-z · 2023-11-13T20:24:38Z

Hi @RBhupi , thank you for your feedback. This error is caused from one of helios dependencies called rmap. rmap has a dependency called jgcricolors that was removed from CRAN, which causes the installation issue. I updated the rmap so that it will install jgcricolors directly from its github. This should solve the problem you had. Could you please try again? Thank you!

ibarraespinosa · 2023-11-13T21:05:26Z

Hi @RBhupi, can you create an issue in @mengqi-z repo to communicate these issues please. Thanks!

hugoledoux · 2023-12-12T15:02:40Z

👋 @RBhupi and @ibarraespinosa I am just checking in to make sure you don't forget this review!

(although @ibarraespinosa did say no time before AGU, which is this week!)

RBhupi · 2023-12-13T02:10:09Z

@hugoledoux I have finished the review but the Reproducibility and Data sharing check-marks feel confusing. If I check-mark them, does that mean the paper has no original results and data?

hugoledoux · 2023-12-14T09:26:29Z

No! It just means that if there are claims of novelty for a method/algo you can as a reader reproduce them, but if not then just click it. Same for data, if all data necessary for you to test the package are available then you can click it.

ibarraespinosa · 2024-01-01T01:12:36Z

Review checklist for @ibarraespinosa

Conflict of interest

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/JGCRI/helios?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@mengqi-z) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

ibarraespinosa · 2024-01-01T01:24:40Z

@editorialbot generate pdf

editorialbot · 2024-01-01T01:26:11Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

mengqi-z · 2024-01-11T16:56:13Z

Hello all, just a quick update that I have addressed the comments from @ibarraespinosa in this issue JGCRI/helios#10. Please let me know if there are any further comments or questions. Thank you.

ibarraespinosa · 2024-02-05T05:54:10Z

@hugoledoux @RBhupi @mengqi-z @editorialbot Accepted

ibarraespinosa · 2024-02-05T05:54:18Z

@editorialbot generate pdf

editorialbot · 2024-02-05T05:55:22Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

mengqi-z · 2024-02-05T23:25:07Z

Hello @hugoledoux @ibarraespinosa @RBhupi,

Thank you all for reviewing 'helios' and providing valuable feedback. I believe I have addressed all the existing issues. Please let me know if there is anything else I need to do to complete the reviewing process. Thanks!

hugoledoux · 2024-02-12T11:20:33Z

@editorialbot generate pdf

editorialbot · 2024-02-12T11:21:42Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

hugoledoux · 2024-02-12T11:41:21Z

@mengqi-z I have proof-read the paper and made a PR with two small fixes: JGCRI/helios#17 Also, at l.34, the acronym "IAM" has never been introduced. Can you please fix those?

After this point could you:

Make a tagged release of your software, and list the version tag of the archived version here.
Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
Please list the DOI of the archived version here.

I can then move forward with recommending acceptance of the submission.

mengqi-z · 2024-02-14T17:26:51Z

Hi @hugoledoux,

Thank you. I have completed the steps following your instructions. Here is the latest release information:

The version tag of the archived version is v1.0.1
The reviewed helios is archived on Zenodo https://doi.org/10.5281/zenodo.10658818

Please let me know if you need anything else. Thank you.

hugoledoux · 2024-02-22T07:19:07Z

@editorialbot generate pdf

editorialbot · 2024-02-22T07:20:20Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

hugoledoux · 2024-02-22T07:24:43Z

@editorialbot set 10.5281/zenodo.10658818 as archive

editorialbot · 2024-02-22T07:24:45Z

Done! archive is now 10.5281/zenodo.10658818

hugoledoux · 2024-02-22T07:25:09Z

@editorialbot set v1.0.1 as version

editorialbot · 2024-02-22T07:25:11Z

Done! version is now v1.0.1

hugoledoux · 2024-02-22T07:25:15Z

@editorialbot recommend-accept

editorialbot · 2024-02-22T07:25:16Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-02-22T07:25:19Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1038/s41467-021-21785-1 is OK
- 10.1016/j.eneco.2014.07.003 is OK
- 10.1016/j.esr.2019.100411 is OK
- 10.1038/s41560-021-00974-8 is OK
- 10.57931/1885756 is OK
- 10.5194/gmd-12-677-2019 is OK
- 10.5194/gmd-15-2533-2022 is OK
- 10.1016/j.envsoft.2018.09.009 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2024-02-22T07:26:38Z

👋 @openjournals/ese-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#5035, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

hugoledoux · 2024-02-22T07:27:05Z

@mengqi-z thanks, sorry for small delay in processing this. One of our EiC will now take over and might ask for some more (minor) changes.

Thanks @ibarraespinosa and @RBhupi for the reviews! I hope you enjoyed it and are up for new JOSS reviews in the future.

kthyng · 2024-02-22T18:34:43Z

Check that version was updated
Check that software archive exists, has been input to JOSS, and title and author list look good
Check paper

kthyng · 2024-02-22T18:39:17Z

Ok looks good to me!

kthyng · 2024-02-22T18:39:24Z

@editorialbot accept

editorialbot · 2024-02-22T18:39:27Z

Doing it live! Attempting automated processing of paper acceptance...

editorialbot · 2024-02-22T18:45:57Z

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Zhao
  given-names: Mengqi
  orcid: "https://orcid.org/0000-0001-5385-2758"
- family-names: Khan
  given-names: Zarrar
  orcid: "https://orcid.org/0000-0002-8147-8553"
- family-names: Dorheim
  given-names: Kalyn
  orcid: "https://orcid.org/0000-0001-8093-8397"
- family-names: Vernon
  given-names: Chris
  orcid: "https://orcid.org/0000-0002-3406-6214"
doi: 10.5281/zenodo.10658818
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Zhao
    given-names: Mengqi
    orcid: "https://orcid.org/0000-0001-5385-2758"
  - family-names: Khan
    given-names: Zarrar
    orcid: "https://orcid.org/0000-0002-8147-8553"
  - family-names: Dorheim
    given-names: Kalyn
    orcid: "https://orcid.org/0000-0001-8093-8397"
  - family-names: Vernon
    given-names: Chris
    orcid: "https://orcid.org/0000-0002-3406-6214"
  date-published: 2024-02-22
  doi: 10.21105/joss.06033
  issn: 2475-9066
  issue: 94
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6033
  title: "helios: An R package to process heating and cooling degrees
    for GCAM"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06033"
  volume: 9
title: "helios: An R package to process heating and cooling degrees for
  GCAM"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

editorialbot · 2024-02-22T18:46:00Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-02-22T18:46:00Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.06033 joss-papers#5040
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06033
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kthyng · 2024-02-22T18:55:54Z

Congrats on your new publication @mengqi-z! Many thanks to editor @hugoledoux and reviewers @RBhupi and @ibarraespinosa for your time, hard work, and expertise!!

editorialbot · 2024-02-22T18:55:56Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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reStructuredText:
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mengqi-z · 2024-02-22T20:22:00Z

Thank you, everyone! @hugoledoux @RBhupi @ibarraespinosa @kthyng

editorialbot added R review TeX Track: 6 (ESE) Earth Sciences and Ecology waitlisted Submissions in the JOSS backlog due to reduced service mode. labels Nov 8, 2023

editorialbot assigned hugoledoux Nov 8, 2023

editorialbot mentioned this issue Nov 8, 2023

[PRE REVIEW]: helios: An R package to process heating and cooling degrees for GCAM #5722

Closed

This was referenced Dec 31, 2023

review for JOSS JGCRI/helios#9

Closed

review for joss JGCRI/helios#10

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editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Feb 22, 2024

editorialbot added accepted published Papers published in JOSS labels Feb 22, 2024

kthyng closed this as completed Feb 22, 2024

editorialbot mentioned this issue Sep 10, 2024

[PRE REVIEW]: cd2es: Converting climate data to energy system input data #7216

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editorialbot mentioned this issue Oct 22, 2024

[PRE REVIEW]: gaia: An R package to estimate crop yield responses to temperature and precipitation #7393

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[REVIEW]: helios: An R package to process heating and cooling degrees for GCAM #6033

[REVIEW]: helios: An R package to process heating and cooling degrees for GCAM #6033

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editorialbot commented Nov 8, 2023 • edited Loading

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RBhupi commented Nov 10, 2023 • edited Loading

Review checklist for @RBhupi

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RBhupi commented Nov 10, 2023

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ibarraespinosa commented Jan 1, 2024 • edited Loading

Review checklist for @ibarraespinosa

Conflict of interest

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Documentation

Software paper

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