[PRE REVIEW]: DVMDOSTEM: a terrestrial ecosystem model designed to represent arctic, boreal and permafrost ecosystem dynamics #7136

editorialbot · 2024-08-22T20:36:11Z

Submitting author: @tobeycarman (Tobey Carman)
Repository: https://github.com/uaf-arctic-eco-modeling/dvm-dos-tem
Branch with paper.md (empty if default branch): joss-paper-2
Version: v0.8.1
Editor: @mengqi-z
Reviewers: Pending
Managing EiC: Kristen Thyng

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/de6adf41412b7028d7be0a2064ea78cf"><img src="https://joss.theoj.org/papers/de6adf41412b7028d7be0a2064ea78cf/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/de6adf41412b7028d7be0a2064ea78cf/status.svg)](https://joss.theoj.org/papers/de6adf41412b7028d7be0a2064ea78cf)

Author instructions

Thanks for submitting your paper to JOSS @tobeycarman. Currently, there isn't a JOSS editor assigned to your paper.

@tobeycarman if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

@editorialbot commands

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

editorialbot · 2024-08-22T20:36:12Z

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

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

@editorialbot commands

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

@editorialbot generate pdf

editorialbot · 2024-08-22T20:36:32Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.28 s (945.7 files/s, 329801.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C++                             45           4659           4328          19754
Python                          61           5869           7099          12768
C/C++ Header                    57           1302            685           3499
reStructuredText                26           1412           1736           2882
Markdown                        13            506              0           1623
Jupyter Notebook                12              0          18877           1047
Bourne Shell                    32            387            556            845
TeX                              1              0              0            326
Julia                            2             51            139            234
CSV                              2              0              0            228
Dockerfile                       1             40            137            182
JavaScript                       2              8             40            181
YAML                             4             60            152            141
make                             2             22             15            130
diff                             1              2              6             44
JSON                             1              0              0             27
DOS Batch                        1              8              1             26
CSS                              1              3              3             24
-------------------------------------------------------------------------------
SUM:                           264          14329          33774          43961
-------------------------------------------------------------------------------

Commit count by author:

  2213	Tobey Carman
   545	Ruth Rutter
    83	Tobey B. Carman
    58	Heather Greaves
    54	Elchin
    40	Colin Tucker
    31	Helene Genet
    18	dependabot[bot]
    17	tobey
    15	Aiza Kabeer
    12	El
    11	benjamin-maglio
     9	Jana Canary
     9	vbriones
     7	Elchin Jafarov
     6	Hannah Mevenkamp
     6	amullen01
     5	Fengming Yuan
     5	bmaglio
     4	rarutter
     3	Heather E Greaves
     2	Alec Bennett
     2	Dogukan Teber
     2	Shawn P. Serbin
     2	colin tucker
     1	Christina Schaedel
     1	Doğukan Teber
     1	Joshua Rady
     1	Mark Lara
     1	Tobey
     1	Yuan

editorialbot · 2024-08-22T20:36:32Z

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

✅ OK DOIs

- 10.1088/1748-9326/ad50ed is OK
- 10.1002/eap.2499 is OK
- 10.1890/08-0806.1 is OK
- 10.1111/gcb.12392 is OK
- 10.1002/eap.1641 is OK
- 10.1088/1748-9326/8/4/045016 is OK
- 10.5194/bg-11-6573-2014 is OK
- 10.5194/bg-11-6573-2014 is OK
- 10.1088/1748-9326/8/3/035030 is OK
- 10.1111/j.1365-2486.2009.02051.x is OK
- 10.1073/pnas.1103910108 is OK
- 10.52381/ICOP2024.190.1 is OK
- 10.1029/92GB00219 is OK
- 10.1002/eap.1768 is OK
- 10.2307/1941899 is OK
- 10.1038/s43247-022-00498-3 is OK
- 10.1109/38.56302 is OK
- 10.1038/s41558-023-01909-9 is OK
- 10.1146/annurev-environ-012220-011847 is OK
- 10.1038/nature14338 is OK
- 10.1146/annurev-environ-012220-011847 is OK
- 10.1038/nature14338 is OK
- 10.1038/s43017-021-00240-1 is OK
- 10.1029/2010JG001302 is OK
- 10.1029/2008JG000841 is OK
- 10.1029/2001jd001244 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: NetCDF Climate and Forecast (CF) Metadata Conventi...
- No DOI given, and none found for title: Estimation of above- and below-ground ecosystem pa...
- No DOI given, and none found for title: Docker: lightweight Linux containers for consisten...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot · 2024-08-22T20:36:36Z

Paper file info:

📄 Wordcount for paper.md is 2444

✅ The paper includes a Statement of need section

editorialbot · 2024-08-22T20:36:38Z

License info:

✅ License found: MIT License (Valid open source OSI approved license)

editorialbot · 2024-08-22T20:37:34Z

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

editorialbot · 2024-08-22T20:38:14Z

Five most similar historical JOSS papers:

growR: R Implementation of the Vegetation Model ModVege
Submitting author: @kuadrat
Handling editor: @mikemahoney218 (Active)
Reviewers: @shubhamjain15, @RobLBaker
Similarity score: 0.6375

Enhanced software and platform for the Town Energy Balance (TEB) model
Submitting author: @dmey
Handling editor: @mjsottile (Retired)
Reviewers: @ethan-nelson, @jayten
Similarity score: 0.6159

WDPM: the Wetland DEM Ponding Model
Submitting author: @KevinShook
Handling editor: @kbarnhart (Retired)
Reviewers: @r-barnes, @awickert, @KCallaghan
Similarity score: 0.6130

MetSim: A Python package for estimation and disaggregation of meteorological data
Submitting author: @arbennett
Handling editor: @sjpfenninger (Retired)
Reviewers: @Chilipp, @dsryberg
Similarity score: 0.6122

pyDeltaRCM: a flexible numerical delta model
Submitting author: @amoodie
Handling editor: @kbarnhart (Retired)
Reviewers: @zsylvester, @jhnienhuis, @salterg
Similarity score: 0.6067

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

kthyng · 2024-08-22T21:11:48Z

Hi @tobeycarman and thanks for your submission! I am looking for some specific items to make sure your submission fits our requirements at a high level (not at the more detailed review level) before moving on to finding an editor or putting this on our waitlist if no relevant editors are available. I'll comment over time as I have a chance to go through them:

OSI-approved license
Installation instructions
Documentation exists at all
Tests of some sort
Check paper (make sure compiles, read through, check for length 250-1000 words)
Substantial scholarly effort
Clear research application

In the meantime, please take a look at the comments above ⬆️ from the editorialbot to address any DOI, license, or paper issues if you're able (there may not be any), or suggest reviewers. For reviewers, please suggest 5 reviewers from the database listed above or your own (non-conflicted) extended network. Their github handles are most useful to receive but please don't use "@" to reference them since it will prematurely ping them.

tobeycarman · 2024-08-23T21:56:49Z

@kthyng Thanks! re: the above issues:

license, looks OK
install instructions, see QuickStart in the README, (requires some comfort with Docker); much more info in the User Guide, see especially the Dev Info section and the Basic Model Setup and Run
Documentation - never complete, but see the User Guide
Tests of some sort - never complete, but see the section in the User Guide about testing and deployment
Check paper - we are over the recommended word count, but feel it is justified given the size of the project. I was able to compile the paper but was not able to get the ORCID icons to work for all the authors.
Substantial scholarly effort - see 30 year history.
Clear research application - see "statement of need" in paper

One note - I just discovered an issue with Git LFS which we have been using to manage testing data. I will try to address this ASAP, but if you or any other editors run into issues with cloning or pulling from the repo, please let me know.

tobeycarman · 2024-08-26T22:41:44Z

@kthyng, see below for list of 5 possible reviewers, selected from the database:

r-barnes C/C++, Javascript, Julia, Python, R, SQL Geoscience Ecology Evolutionary Biology High-performance computing Computer science
kdorheim C/C++, Python, R Climate Biology Ecology
kdm9 Bash/Shell, C/C++, Javascript, LaTeX, Python, R bioinformatics, genomics, plant science, ecology
JoanyMarino LaTeX, Python, R ecology, mathematical modelling, dynamical systems, data quality analisys, initial data analysis
david-yannick Python, R Environmental science, ecology, statistics, biogeochemistry, ecophysiology, micrometeorology

kthyng · 2024-08-28T21:28:15Z

@tobeycarman Some questions/comments:

are there installation instructions that do not rely on docker? While docker images may get users up and running, another part of JOSS software is that users would want to contribute to your software, and they will need to be able to develop which will usually mean build the software not using docker images.
Reviewers will most likely comment on empty sections in your comments and ask you to fill these in. Now is a good time to do this.
It looks like you did a lot of updates in 2022 — publishing with JOSS is a great reason to update to present day!
Indeed this is a large code base, but I disagree that that justifies an overly long paper. Please shorten it and aim for 1000 words. You can move extra material to your docs if it isn't already there.

tobeycarman · 2024-08-29T16:48:08Z

@kthyng,

re: Docker, we don't actively maintain install instructions without Docker. We found that using Docker images and containers to standardize the development environments dramatically improved the development process.
re: Empty sections in the comments, I am not sure what you are referring to?
re: Word count, I will look into reducing it. We would gladly accept feedback on which sections reviewers find to be less relevant.

editorialbot · 2024-08-29T21:22:29Z

My name is now @editorialbot

editorialbot · 2024-08-29T21:22:51Z

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

@editorialbot commands

tobeycarman · 2024-08-29T21:23:08Z

@editorialbot commands

editorialbot · 2024-08-29T21:23:12Z

Hello @tobeycarman, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

# Check the references of the paper for missing DOIs
@editorialbot check references

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

tobeycarman · 2024-08-29T21:26:49Z

@editorialbot generate pdf

editorialbot · 2024-08-29T21:27:33Z

⚠️ An error happened when generating the pdf.

tobeycarman · 2024-09-10T20:58:32Z

@editorialbot generate pdf

editorialbot · 2024-09-10T20:59:09Z

⚠️ An error happened when generating the pdf.

kthyng · 2024-09-11T17:41:03Z

@tobeycarman

Docker, we don't actively maintain install instructions without Docker. We found that using Docker images and containers to standardize the development environments dramatically improved the development process.

I won't block this from review based on this but this may come up again.

Empty sections in the comments, I am not sure what you are referring to?

I see I wrote comment but I meant your docs. As an example, lots of this page says "write this".

Word count, I will look into reducing it. We would gladly accept feedback on which sections reviewers find to be less relevant.

Please, follow this: https://joss.readthedocs.io/en/latest/paper.html#what-should-my-paper-contain. Information that is not in the paper can be in your docs. You probably want sections Summary, Statement of Need, maybe one more section, and Acknowledgments, maybe a figure or two. The goal is to explain the software at a high level to a general audience initially, then give just enough information at the next level for someone to know if they want more information, comparing with the relevant other packages.

kthyng · 2024-10-02T15:20:51Z

@tobeycarman What is your status?

kthyng · 2024-10-28T17:23:28Z

@tobeycarman Are you planning to follow up in this issue?

tobeycarman · 2024-10-29T19:27:57Z

@kthyng I haven't forgotten. Just back from some leave time and will be working on this. Your feedback/this issue prompted some re-organization and, as suggested, documentation writing that we will commit in addition to updates to the paper.

kthyng · 2024-10-29T19:38:48Z

Ok no problem. I am going to add the "paused" label to this for organization on my end.

tobeycarman · 2024-11-18T18:45:51Z

@editorialbot generate pdf

editorialbot · 2024-11-18T18:47:46Z

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

editorialbot · 2024-11-18T18:48:34Z

Five most similar historical JOSS papers:

OpenSCM Two Layer Model: A Python implementation of the two-layer climate model
Submitting author: @znicholls
Handling editor: @leouieda (Retired)
Reviewers: @sadielbartholomew, @ashiklom
Similarity score: 0.6774

pyDeltaRCM: a flexible numerical delta model
Submitting author: @amoodie
Handling editor: @kbarnhart (Retired)
Reviewers: @zsylvester, @jhnienhuis, @salterg
Similarity score: 0.6759

Enhanced software and platform for the Town Energy Balance (TEB) model
Submitting author: @dmey
Handling editor: @mjsottile (Retired)
Reviewers: @ethan-nelson, @jayten
Similarity score: 0.6681

mosartwmpy: A Python implementation of the MOSART-WM coupled hydrologic routing and water management model
Submitting author: @thurber
Handling editor: @kthyng (Active)
Reviewers: @JannisHoch, @cheginit
Similarity score: 0.6631

growR: R Implementation of the Vegetation Model ModVege
Submitting author: @kuadrat
Handling editor: @mikemahoney218 (Active)
Reviewers: @shubhamjain15, @RobLBaker
Similarity score: 0.6625

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

tobeycarman · 2024-11-20T21:23:51Z

@editorialbot generate pdf

editorialbot · 2024-11-20T21:25:18Z

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

editorialbot · 2024-11-20T21:26:01Z

Five most similar historical JOSS papers:

OpenSCM Two Layer Model: A Python implementation of the two-layer climate model
Submitting author: @znicholls
Handling editor: @leouieda (Retired)
Reviewers: @sadielbartholomew, @ashiklom
Similarity score: 0.6822

pyDeltaRCM: a flexible numerical delta model
Submitting author: @amoodie
Handling editor: @kbarnhart (Retired)
Reviewers: @zsylvester, @jhnienhuis, @salterg
Similarity score: 0.6797

Enhanced software and platform for the Town Energy Balance (TEB) model
Submitting author: @dmey
Handling editor: @mjsottile (Retired)
Reviewers: @ethan-nelson, @jayten
Similarity score: 0.6742

growR: R Implementation of the Vegetation Model ModVege
Submitting author: @kuadrat
Handling editor: @mikemahoney218 (Active)
Reviewers: @shubhamjain15, @RobLBaker
Similarity score: 0.6718

mosartwmpy: A Python implementation of the MOSART-WM coupled hydrologic routing and water management model
Submitting author: @thurber
Handling editor: @kthyng (Active)
Reviewers: @JannisHoch, @cheginit
Similarity score: 0.6655

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

tobeycarman · 2024-12-04T22:27:01Z

@kthyng I think we are ready to move this forward again. I cut a new release of DVMDOSTEM yesterday and published the documentation which has updated information that we ported from the original JOSS draft. And the paper is compiling, see above ☝️. It would be great to get the status "in review" as there are some folks who would like something to cite for some upcoming AGU presentations.

editorialbot · 2024-12-05T06:16:39Z

📄 Preprint file created: Find it here in the Artifacts list 📄

kthyng · 2024-12-09T21:52:15Z

@editorialbot set v0.8.1 as version

editorialbot · 2024-12-09T21:52:18Z

Done! version is now v0.8.1

kthyng · 2024-12-09T21:56:32Z

@tobeycarman Looks like some great changes! I see a few "write this" sections in your docs that would be great to address before reviewers get to them but I won't hold up review based on them. This will be going to the waitlist until a relevant editor has capacity so you'll probably have some time to work on this. (https://uaf-arctic-eco-modeling.github.io/dvm-dos-tem/SA_UQ.html, https://uaf-arctic-eco-modeling.github.io/dvm-dos-tem/examples_and_tutorials/example_experiment_0.html#plot-soil-temperatures).

kthyng · 2024-12-09T21:56:42Z

@editorialbot check repository

editorialbot · 2024-12-09T21:58:25Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.26 s (1005.3 files/s, 303705.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C++                             45           4762           4354          20204
Python                          58           5331           6885          12649
C/C++ Header                    57           1312            685           3533
reStructuredText                28           1480           1832           2967
Markdown                        13            480              0           1491
Bourne Shell                    31            377            531            819
Jupyter Notebook                 9              0           5327            756
TeX                              2              1              0            719
Julia                            2             57            139            243
Dockerfile                       1             40            137            182
YAML                             5             62            159            164
make                             2             22             15            130
CSV                              1              0              0            118
JavaScript                       1              8             40             91
diff                             1              2              6             44
JSON                             1              0              0             27
DOS Batch                        1              8              1             26
CSS                              1              3              3             24
-------------------------------------------------------------------------------
SUM:                           259          13945          20114          44187
-------------------------------------------------------------------------------

Commit count by author:

  2254	Tobey Carman
   565	Ruth Rutter
    83	Tobey B. Carman
    58	Heather Greaves
    54	Elchin
    40	Colin Tucker
    31	Helene Genet
    18	dependabot[bot]
    17	tobey
    16	benjamin-maglio
    15	Aiza Kabeer
    12	El
    10	Dogukan Teber
     9	Jana Canary
     9	vbriones
     7	Elchin Jafarov
     6	Hannah Mevenkamp
     6	amullen01
     5	Fengming Yuan
     5	bmaglio
     4	rarutter
     3	Heather E Greaves
     2	Alec Bennett
     2	Shawn P. Serbin
     2	colin tucker
     1	Christina Schaedel
     1	Doğukan Teber
     1	Joshua Rady
     1	Mark Lara
     1	Tobey
     1	Yuan

editorialbot · 2024-12-09T21:58:32Z

Paper file info:

📄 Wordcount for paper.md is 1131

✅ The paper includes a Statement of need section

editorialbot · 2024-12-09T21:58:34Z

License info:

✅ License found: MIT License (Valid open source OSI approved license)

kthyng · 2024-12-09T21:59:57Z

Please check the capitalization in your references. You can preserve capitalization by placing {} around characters/words in your .bib file. (e.g. "alaska")

We have a backlog of submissions so I will add this to our waitlist. Thanks for your patience.

tobeycarman · 2024-12-09T23:21:52Z

re: capitalization on references, fixed in dvm-dos-tem PR#761. Note that this will not be reflected in the published documentation until the next version release.

kthyng · 2024-12-10T16:42:48Z

@mengqi-z Can you edit this submission?

kthyng · 2024-12-10T16:42:55Z

@editorialbot invite @mengqi-z as editor

editorialbot · 2024-12-10T16:42:58Z

Invitation to edit this submission sent!

mengqi-z · 2024-12-16T16:00:29Z

@kthyng, apologies for the delay - I was traveling last week. I’d be happy to edit this submission.

mengqi-z · 2024-12-16T16:01:05Z

@editorialbot assign me as editor

editorialbot · 2024-12-16T16:01:09Z

Assigned! @mengqi-z is now the editor

mengqi-z · 2024-12-16T17:20:59Z

👋 @r-barnes @kdorheim @kdm9 - Would any of you be available to review a submission for JOSS? JOSS uses a checklist-driven review process, which you can find here: https://joss.readthedocs.io/en/latest/review_criteria.html

editorialbot added pre-review Track: 6 (ESE) Earth Sciences and Ecology labels Aug 22, 2024

kthyng added the paused label Oct 29, 2024

kthyng added waitlisted Submissions in the JOSS backlog due to reduced service mode. and removed paused labels Dec 9, 2024

editorialbot assigned mengqi-z Dec 16, 2024

[PRE REVIEW]: DVMDOSTEM: a terrestrial ecosystem model designed to represent arctic, boreal and permafrost ecosystem dynamics #7136

[PRE REVIEW]: DVMDOSTEM: a terrestrial ecosystem model designed to represent arctic, boreal and permafrost ecosystem dynamics #7136

Comments

editorialbot commented Aug 22, 2024 • edited Loading

Status

editorialbot commented Aug 22, 2024

editorialbot commented Aug 22, 2024

editorialbot commented Aug 22, 2024

editorialbot commented Aug 22, 2024

editorialbot commented Aug 22, 2024

editorialbot commented Aug 22, 2024

editorialbot commented Aug 22, 2024

kthyng commented Aug 22, 2024 • edited Loading

tobeycarman commented Aug 23, 2024

tobeycarman commented Aug 26, 2024

kthyng commented Aug 28, 2024 • edited Loading

tobeycarman commented Aug 29, 2024

editorialbot commented Aug 29, 2024

editorialbot commented Aug 29, 2024

tobeycarman commented Aug 29, 2024

editorialbot commented Aug 29, 2024

tobeycarman commented Aug 29, 2024

editorialbot commented Aug 29, 2024

tobeycarman commented Sep 10, 2024

editorialbot commented Sep 10, 2024

kthyng commented Sep 11, 2024

kthyng commented Oct 2, 2024

kthyng commented Oct 28, 2024

tobeycarman commented Oct 29, 2024

kthyng commented Oct 29, 2024

tobeycarman commented Nov 18, 2024

editorialbot commented Nov 18, 2024

editorialbot commented Nov 18, 2024

tobeycarman commented Nov 20, 2024

editorialbot commented Nov 20, 2024

editorialbot commented Nov 20, 2024

tobeycarman commented Dec 4, 2024 • edited Loading

editorialbot commented Dec 5, 2024

kthyng commented Dec 9, 2024

editorialbot commented Dec 9, 2024

kthyng commented Dec 9, 2024

kthyng commented Dec 9, 2024

editorialbot commented Dec 9, 2024

editorialbot commented Dec 9, 2024

editorialbot commented Dec 9, 2024

kthyng commented Dec 9, 2024

tobeycarman commented Dec 9, 2024

kthyng commented Dec 10, 2024

kthyng commented Dec 10, 2024

editorialbot commented Dec 10, 2024

mengqi-z commented Dec 16, 2024

mengqi-z commented Dec 16, 2024

editorialbot commented Dec 16, 2024

mengqi-z commented Dec 16, 2024

editorialbot commented Aug 22, 2024 •

edited

Loading

kthyng commented Aug 22, 2024 •

edited

Loading

kthyng commented Aug 28, 2024 •

edited

Loading

tobeycarman commented Dec 4, 2024 •

edited

Loading