search

openjournals / joss-reviews

Reviews for the Journal of Open Source Software
Creative Commons Zero v1.0 Universal
703 stars 36 forks source link

[REVIEW]: goFlux: A user-friendly way to calculate GHG fluxes yourself, regardless of user experience #6393

Closed editorialbot closed 5 months ago

editorialbot commented 6 months ago

Submitting author: !--author-handle-->@qepanna<!--end-author-handle-- (Karelle Rheault) Repository: https://github.com/Qepanna/goFlux Branch with paper.md (empty if default branch): Version: v0.1.0 Editor: !--editor-->@arfon<!--end-editor-- Reviewers: @Schuch666, @shubhamjain15, @hahsan1 Archive: 10.5281/zenodo.10908262

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/d760de0a609420569b011ed2df3d0b8c"><img src="https://joss.theoj.org/papers/d760de0a609420569b011ed2df3d0b8c/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/d760de0a609420569b011ed2df3d0b8c/status.svg)](https://joss.theoj.org/papers/d760de0a609420569b011ed2df3d0b8c)

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

@Schuch666 & @shubhamjain15 & @hahsan1, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

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

Checklists

📝 Checklist for @Schuch666

📝 Checklist for @shubhamjain15

📝 Checklist for @hahsan1

editorialbot commented 6 months ago

Hello humans, 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 commented 6 months ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.05 s (960.8 files/s, 254527.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               36            684           3839           3857
JSON                             1              0              0           2597
Markdown                         2            126              0            491
YAML                             5             41             14            196
TeX                              1              6              0             70
-------------------------------------------------------------------------------
SUM:                            45            857           3853           7211
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 6 months ago

Wordcount for paper.md is 796

editorialbot commented 6 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.2136/sssaj1981.03615995004500020017x is OK
- 10.1111/j.1365-2389.2010.01291.x is OK
- 10.1371/journal.pone.0200876 is OK
- 10.21105/joss.01751 is OK

MISSING DOIs

- None

INVALID DOIs

- None
editorialbot commented 6 months ago

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

arfon commented 6 months ago

@Schuch666, @shubhamjain15, @hahsan1 – This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above. Please create your checklist typing: 

@editorialbot generate my checklist

As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/6393 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

shubhamjain15 commented 6 months ago

Review checklist for @shubhamjain15

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Schuch666 commented 6 months ago

Review checklist for @Schuch666

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Schuch666 commented 6 months ago

Hi @Qepanna, You mention in the installation section that "must first install the package devtools", but the user can use another package that provide the same functionality such as the remotes package:

remotes::install_github('qepanna/goflux')

can you include a note that include remotes?

shubhamjain15 commented 6 months ago

Hi @Qepanna, Could you take a look at this error in the 'uCH4_import' and 'uN2O_import' functions. My guess is you need to remove the highlighted lines (attached image) in the code which may have been for testing purposes only. 

library(goFlux)
file.path <- system.file("extdata", "uCH4/uCH4.txt", package = "goFlux")
uCH4_imp <- uCH4_import(inputfile = file.path)
file.path <- system.file("extdata", "uN2O/uN2O.txt", package = "goFlux")
uN2O_imp <- uN2O_import(inputfile = file.path)

Warning: cannot open file 'inst/extdata/uCH4/uCH4.txt': No such file or directoryWarning: Error occurred in file uCH4.txt: Error in file(file, "rt"): cannot open the connection Warning: cannot open file 'inst/extdata/uN2O/uN2O.txt': No such file or directoryWarning: Error occurred in file uN2O.txt: Error in file(file, "rt"): cannot open the connection

import_error

shubhamjain15 commented 6 months ago

@Qepanna In the 'goFlux' function, the input dataframe allows for chamID to be used instead of UniqueID, but when I go to plot the results using flux.plot, it throws an error:

library(goFlux)
CO2_flux <- goFlux(LI8100_imp, "CO2dry_ppm")
CO2_flux_res <- best.flux(CO2_flux)
CO2_flux_plots <- flux.plot(CO2_flux_res, LI8100_imp, "CO2dry_ppm", shoulder=20,
                            plot.legend, plot.display, quality.check)

Error in flux.plot(CO2_flux_res, LI8100_imp, "CO2dry_ppm", shoulder = 20, : 'UniqueID' is required and was not found in 'dataframe'

The argument description for the flux.plot function says the same dataframe can be used for both goFlux and flux.plot. Would it be possible to allow chamID in flux.plot as well?

hahsan1 commented 6 months ago

Review checklist for @hahsan1

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Qepanna commented 6 months ago

Hi @Qepanna, You mention in the installation section that "must first install the package devtools", but the user can use another package that provide the same functionality such as the remotes package:

remotes::install_github('qepanna/goflux')

can you include a note that include remotes?

Hi @Schuch666, originally it was included that one could use the remotes packages, however I encounterd some errors using this package and I thought it would be best to avoid using it. Would you still recommend that I include the package remotes?

Qepanna commented 6 months ago

Hi @Qepanna, Could you take a look at this error in the 'uCH4_import' and 'uN2O_import' functions. My guess is you need to remove the highlighted lines (attached image) in the code which may have been for testing purposes only.

library(goFlux)
file.path <- system.file("extdata", "uCH4/uCH4.txt", package = "goFlux")
uCH4_imp <- uCH4_import(inputfile = file.path)
file.path <- system.file("extdata", "uN2O/uN2O.txt", package = "goFlux")
uN2O_imp <- uN2O_import(inputfile = file.path)

Warning: cannot open file 'inst/extdata/uCH4/uCH4.txt': No such file or directoryWarning: Error occurred in file uCH4.txt: Error in file(file, "rt"): cannot open the connection Warning: cannot open file 'inst/extdata/uN2O/uN2O.txt': No such file or directoryWarning: Error occurred in file uN2O.txt: Error in file(file, "rt"): cannot open the connection

import_error

Hi @shubhamjain15, thank you for pointing that out. I fixed these functions and they now seem to work.

Qepanna commented 6 months ago

@Qepanna In the 'goFlux' function, the input dataframe allows for chamID to be used instead of UniqueID, but when I go to plot the results using flux.plot, it throws an error:

library(goFlux)
CO2_flux <- goFlux(LI8100_imp, "CO2dry_ppm")
CO2_flux_res <- best.flux(CO2_flux)
CO2_flux_plots <- flux.plot(CO2_flux_res, LI8100_imp, "CO2dry_ppm", shoulder=20,
                            plot.legend, plot.display, quality.check)

Error in flux.plot(CO2_flux_res, LI8100_imp, "CO2dry_ppm", shoulder = 20, : 'UniqueID' is required and was not found in 'dataframe'

The argument description for the flux.plot function says the same dataframe can be used for both goFlux and flux.plot. Would it be possible to allow chamID in flux.plot as well?

Hi @shubhamjain15, this is a very good point. I added the option to the flux.plot function to use chamID instead of UniqueID.

shubhamjain15 commented 6 months ago

Thanks @Qepanna, it works for me. Another quick question - While loading the "DX4015.TXT" file, it only loads the first 14 rows upto time - 08:20:35. However, in the txt file, I do see more rows that go upto 08:30:44. Is there any specific reason why those rows were not read or excluded by the import function?

library(goFlux)
file.path <- system.file("extdata", "DX4015/DX4015.TXT", package = "goFlux")
DX4015_imp <- DX4015_import(inputfile = file.path)
print(nrow(DX4015_imp))

[1] 14

Schuch666 commented 6 months ago

Hi @Qepanna, You mention in the installation section that "must first install the package devtools", but the user can use another package that provide the same functionality such as the remotes package: remotes::install_github('qepanna/goflux') can you include a note that include remotes?

Hi @Schuch666, originally it was included that one could use the remotes packages, however I encounterd some errors using this package and I thought it would be best to avoid using it. Would you still recommend that I include the package remotes?

Hello @Qepanna,

I did not have any issues installing using remotes (for me I use remotes for R installations that don't need all the developing tools from devtools because remotes is lighter), but it is up to you to include or not instructions to use remotes (If users still need to avoid remotes to install your package). But instead of "must first install devtools" in the installation instructions should be something less restrictive.

PS: is possible that the issue with your package / remotes is already fixed because both packages may have several updates

Schuch666 commented 6 months ago

Dear all, there is my general comments:

In general the documentation is very good, and the documentation (specially the website) has god additional technical content.

I found some small errors running some of the "import raw data into R" examples but the last version of the package was this errors already fixed.

And a few questions/suggestions:

  1. In the paper/documentation there is "identify measurements", can you include more information (identification of the instrument? identification of start/end of measures? variables that are measured? other flags?)
  2. For the visualization part (https://qepanna.quarto.pub/goflux/flux2pdf.html), there is a part that change the timezone of R environment, I recommend to include as a tip instead of the example.
  3. Can an option to save the window or disable the auto-close of the click.peak function? This plot can be useful (https://github.com/Qepanna/goFlux/issues/2#issue-2176867056)
  4. In the goFlux webpage (https://qepanna.quarto.pub/goflux/goFlux.html), there is a data(LGR_manID) that need to be included in the example.
  5. I have a recommendation to the goFlux functiuon: if the function is called without an argument gastype, can be included a menu to choose the variable or a print message with the variable names (or maybe a print of the variables that can be used and an error if this is part of the desing). (https://github.com/Qepanna/goFlux/issues/1#issue-2176863327)
  6. What is the difference of goFlux and best.flux? Is the first one always combines LM and HM and the second one use some criteria and calculate the flux using LM or HM depending of the results? There is any diagnostic output to inform the user more about the best method or how the output was calculated (some variables on the output, a message or some kind of log file)? (https://github.com/Qepanna/goFlux/issues/3#issue-2176870036)
  7. In the website (https://qepanna.quarto.pub/goflux/bestflux.html), there is a data(LGR_manID) that need to be included in the example.
  8. In the website (https://qepanna.quarto.pub/goflux/flux2pdf.html), part of the example is on different box (tip) and the how to calculate CO2_flux_res and CH4_flux_res is missing, this can be found in previous page but should be better include all steps
  9. On the website (https://qepanna.quarto.pub/goflux/import.html#mgga-gla131-series) the file used on the examples from UGGA and MGGA are the same, are they suppose to be the same (with identical format)?

I have included 3 issues with my suggestions on the issue page

Schuch666 commented 6 months ago

There is an inconsistency on the naming convention on the functions: You have function with the name best.flux (with a dot) flux2pdf (a number), goFlux (a capital letter), EGM5_import (using underline) and goFlux_nokmax (using an underline and a capital letter). I suggest that you rename these files to match with only one naming standard.

For the functions for specific instruments: some cases the names are not very informative to the user for LI7820_imp (this is a dataset from LI7820 instrument), and for other cases change the order LI7820_import to import_LI7820 make more sense in the organization of the documentation and help to write the code (but this is up to you to change or not).

hahsan1 commented 6 months ago

I have successfully installed the package and tested out various functions in the documentation. The documentation is very thorough and detailed. It may be helpful to have a separate bare bones "Example" section where it runs through each step (e.g., import, goFlux, best.flux, plotting) for just a single data set. The documentation currently has a fair bit of methodology/equations that could potentially be an Appendix.

Qepanna commented 5 months ago

Thanks @Qepanna, it works for me. Another quick question - While loading the "DX4015.TXT" file, it only loads the first 14 rows upto time - 08:20:35. However, in the txt file, I do see more rows that go upto 08:30:44. Is there any specific reason why those rows were not read or excluded by the import function?

library(goFlux)
file.path <- system.file("extdata", "DX4015/DX4015.TXT", package = "goFlux")
DX4015_imp <- DX4015_import(inputfile = file.path)
print(nrow(DX4015_imp))

[1] 14

Hi @shubhamjain15, thank you for pointing that out. It was part of all import functions that negative values should be removed. However, there was a mistake and 0 values were also removed. I now modified all import function to keep 0 values.

Qepanna commented 5 months ago

Hi @Qepanna, You mention in the installation section that "must first install the package devtools", but the user can use another package that provide the same functionality such as the remotes package: remotes::install_github('qepanna/goflux') can you include a note that include remotes?

Hi @Schuch666, originally it was included that one could use the remotes packages, however I encounterd some errors using this package and I thought it would be best to avoid using it. Would you still recommend that I include the package remotes?

Hello @Qepanna,

I did not have any issues installing using remotes (for me I use remotes for R installations that don't need all the developing tools from devtools because remotes is lighter), but it is up to you to include or not instructions to use remotes (If users still need to avoid remotes to install your package). But instead of "must first install devtools" in the installation instructions should be something less restrictive.

PS: is possible that the issue with your package / remotes is already fixed because both packages may have several updates

I included that both packages can be used and I just found out that the issue can arise with either packages. The issue concerns the API rate limit. There is a troubleshoot section about that in the README file and the webpage. However, it anoys me that users are required to create a GitHub account to avoid that problem. Do you know if there is any way to avoid this issue altogether?

Qepanna commented 5 months ago

Dear all, there is my general comments:

In general the documentation is very good, and the documentation (specially the website) has god additional technical content.

I found some small errors running some of the "import raw data into R" examples but the last version of the package was this errors already fixed.

And a few questions/suggestions:

  1. In the paper/documentation there is "identify measurements", can you include more information (identification of the instrument? identification of start/end of measures? variables that are measured? other flags?)
  2. For the visualization part (https://qepanna.quarto.pub/goflux/flux2pdf.html), there is a part that change the timezone of R environment, I recommend to include as a tip instead of the example.
  3. Can an option to save the window or disable the auto-close of the click.peak function? This plot can be useful (Suggestion: keep the plots from click.peak Qepanna/goFlux#2 (comment))
  4. In the goFlux webpage (https://qepanna.quarto.pub/goflux/goFlux.html), there is a data(LGR_manID) that need to be included in the example.
  5. I have a recommendation to the goFlux functiuon: if the function is called without an argument gastype, can be included a menu to choose the variable or a print message with the variable names (or maybe a print of the variables that can be used and an error if this is part of the desing). (sugestion: goFlux without gastype Qepanna/goFlux#1 (comment))
  6. What is the difference of goFlux and best.flux? Is the first one always combines LM and HM and the second one use some criteria and calculate the flux using LM or HM depending of the results? There is any diagnostic output to inform the user more about the best method or how the output was calculated (some variables on the output, a message or some kind of log file)? (Diagnostic output from goFlux function Qepanna/goFlux#3 (comment))
  7. In the website (https://qepanna.quarto.pub/goflux/bestflux.html), there is a data(LGR_manID) that need to be included in the example.
  8. In the website (https://qepanna.quarto.pub/goflux/flux2pdf.html), part of the example is on different box (tip) and the how to calculate CO2_flux_res and CH4_flux_res is missing, this can be found in previous page but should be better include all steps
  9. On the website (https://qepanna.quarto.pub/goflux/import.html#mgga-gla131-series) the file used on the examples from UGGA and MGGA are the same, are they suppose to be the same (with identical format)?

I have included 3 issues with my suggestions on the issue page

Dear @Schuch666, thank you for all your suggestions. I have modified the related functions and the webpage accordingly for the most part. Here are my detailed answers to your comments. I also copied those answers on the corresponding issues you oppened.

  1. I do not understand the comment. This step is already clearly identified as coming after the import, therefore I cannot add anything about “identification of the instrument”. On the webpage, there is an extensive demonstration about the “identification of start/end of measures”. For the other two suggestions, I don’t understand what you mean. Could you give specific examples of modifications in the text where it would improve the clarity?
  2. If you meant instead the demonstration on the page https://qepanna.quarto.pub/goflux/manualID.html, I moved that part to a Tip Callout.
  3. I see two options for saving these plots: Either create a new function that will make plots from the output of click.peak, OR if save.plot = TRUE in click.peak, the output of click.peak is now a list of two objects: one data frame and one list of plots. The first option requires a bit more effort, but, from a “user-friendly” point of view, it can help users avoid making mistakes. On the other hand, these plots are not that useful to keep, since the function flux.plot will essentially return the same plot, but with additional content from the output of goFlux and best.flux. What do you think is best?
  4. I added data(LGR_manID) to the example.
  5. I changed the error message for goFlux if gastype = NULL. Now, if no argument is provided to gastype, an error message is returned: 
    Error in goFlux(LGR_manID, gastype = NULL) : 
'gastype' must be one of the following: 'CO2dry_ppm', 'CH4dry_ppb', 'COdry_ppb', 'N2Odry_ppb', 'NH3dry_ppb' or 'H2O_ppm'
  6. The function goFlux calculates both LM and HM. The function best.flux adds diagnostic columns and the best.flux column, which is the selection between LM and HM. In the description of the best.flux function (?best.flux), under #Value, it says: “A data.frame identical to the input flux.result (output from goFlux) with the additional columns HM.diagnose, LM.diagnose, best.flux, model and quality.check. For each criteria selected, an additional column is also added to specify the limits used for those criteria (e.g. RMSE.lim, p.val.lim, etc.)” In the description of the function, it is well detailed how each criterion is evaluated and how the diagnostic is printed in these columns. For example, for the criteria g.limit, it says in the description: “The g.limit indicates a threshold for the g.factor, which is the ratio between a non-linear flux estimate and a linear flux estimate. With the best.flux function, one can choose a limit at which the HM model is deemed to overestimate f0. Recommended thresholds for the g-factor are <4 for a flexible threshold, <2 for a medium threshold, or <1.25 for a more conservative threshold. The default threshold is g.limit = 2. If the g-factor is above the specified threshold, the best flux estimate will switch to LM instead of HM and give a warning in the columns quality.check and HM.diagnose.” All of these details are also mentionned on the webpage. I believe the output from best.flux and the description of the function as they already are fit with the suggestion you gave and no action is required.
  7. I added data(LGR_manID) to the example.
  8. The tips boxes were rearranged after the example so that it is easier to follow and copy-paste errors should be easily avoided. In addition, all steps of the calculations for each gas were included.
  9. Yes, it is normal that they are the same. These two instruments return the same file format. That is also why the function is the same for these two instruments. However, I thought it would be best to make two examples because their precisions are different (argument prec in the function).
shubhamjain15 commented 5 months ago

Thanks @Qepanna. Great work! @arfon I have completed my checklist and do not have any further comments or issues with this submission. Thanks for inviting me for this review.

arfon commented 5 months ago

Looks like we're close to wrapping up here. Thanks for the timely reviews folks ⚡

@Schuch666 – I can see that there are a few items left unchecked in your review checklist – are you still awaiting changes from the author on these matters or do you believe your feedback has been incorporated and these can now be checked off?

Schuch666 commented 5 months ago

Dear all,

@Qepanna

  1. This comment is specific to the paper summary "2. identify measurements", replace for "define the start and end points of each measurement and assign a UniqueID", identify measurements is not self explanatory.

For 2-9 everything is fine.

About the issue with remotes and API rate limit, I'm not sure, can you create a issue with the steps to reproduce the error and tag me?

I don't have a reply about the inconsistency / non-explanatory names used on the package and I'm including this as a suggestion on the issue session of the package repository.

Thank you

Schuch666 commented 5 months ago

@arfon for my part the only remaining issue is my comment 1

Qepanna commented 5 months ago

There is an inconsistency on the naming convention on the functions: You have function with the name best.flux (with a dot) flux2pdf (a number), goFlux (a capital letter), EGM5_import (using underline) and goFlux_nokmax (using an underline and a capital letter). I suggest that you rename these files to match with only one naming standard.

For the functions for specific instruments: some cases the names are not very informative to the user for LI7820_imp (this is a dataset from LI7820 instrument), and for other cases change the order LI7820_import to import_LI7820 make more sense in the organization of the documentation and help to write the code (but this is up to you to change or not).

Dear @Schuch666, I answered this comment in the issue you opened.

Qepanna commented 5 months ago

I have successfully installed the package and tested out various functions in the documentation. The documentation is very thorough and detailed. It may be helpful to have a separate bare bones "Example" section where it runs through each step (e.g., import, goFlux, best.flux, plotting) for just a single data set. The documentation currently has a fair bit of methodology/equations that could potentially be an Appendix.

Dear @hahsan1, I agree that an overall example is necessary. I had planned to make downloadable scripts for each pathway. Could you open an issue with your suggestion?

Qepanna commented 5 months ago
  1. define the start and end points of each measurement and assign a UniqueID

Dear @Schuch666, I corrected the paper with your suggestion.

Qepanna commented 5 months ago

Dear all,

@Qepanna

  1. This comment is specific to the paper summary "2. identify measurements", replace for "define the start and end points of each measurement and assign a UniqueID", identify measurements is not self explanatory.

For 2-9 everything is fine.

About the issue with remotes and API rate limit, I'm not sure, can you create a issue with the steps to reproduce the error and tag me?

I don't have a reply about the inconsistency / non-explanatory names used on the package and I'm including this as a suggestion on the issue session of the package repository.

Thank you

Dear @Schuch666, I created an issue regarding the API rate limit and answered the other two comments.

Qepanna commented 5 months ago

Looks like we're close to wrapping up here. Thanks for the timely reviews folks ⚡

@Schuch666 – I can see that there are a few items left unchecked in your review checklist – are you still awaiting changes from the author on these matters or do you believe your feedback has been incorporated and these can now be checked off?

Dear, @arfon, I am only missing two comments to answer:

hahsan1 commented 5 months ago

I have posted an issue highlighting the suggestion to add a standalone example in the documentation. I have no further comments to add. Great work on the package!

Qepanna commented 5 months ago

@arfon @Schuch666 @shubhamjain15 @hahsan1 Hi everyone, thank you for the fast review process and the great suggestions! I answered all comments and believe that the package is ready.

arfon commented 5 months ago

OK, thanks for the great discussion here and the iterative improvements throughout the review!

@Qepanna – looks like we're very close to being done here. I will circle back here next week, but in the meantime, please give your own paper a final read to check for any potential typos etc.

After that, could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

arfon commented 5 months ago

@editorialbot generate pdf

editorialbot commented 5 months ago

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

Qepanna commented 5 months ago

I made some modifications and I found that the mention "* These authors contributed equally" should be removed.

Qepanna commented 5 months ago

@editorialbot generate pdf

editorialbot commented 5 months ago

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

Qepanna commented 5 months ago

OK, thanks for the great discussion here and the iterative improvements throughout the review!

@Qepanna – looks like we're very close to being done here. I will circle back here next week, but in the meantime, please give your own paper a final read to check for any potential typos etc.

After that, could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

  • The title of the archive is the same as the JOSS paper title
  • That the authors of the archive are the same as the JOSS paper authors
  • I can then move forward with accepting the submission.

Hi @arfon, here is the DOI from Zenodo: https://zenodo.org/doi/10.5281/zenodo.10908262

arfon commented 5 months ago

@editorialbot set 10.5281/zenodo.10908262 as archive

editorialbot commented 5 months ago

Done! archive is now 10.5281/zenodo.10908262

arfon commented 5 months ago

@editorialbot generate pdf

editorialbot commented 5 months ago

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

arfon commented 5 months ago

@editorialbot recommend-accept

editorialbot commented 5 months ago 
Attempting dry run of processing paper acceptance...
editorialbot commented 5 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.2136/sssaj1981.03615995004500020017x is OK
- 10.1111/j.1365-2389.2010.01291.x is OK
- 10.1371/journal.pone.0200876 is OK
- 10.21105/joss.01751 is OK

MISSING DOIs

- No DOI given, and none found for title: flux: Flux Rate Calculation from Dynamic Closed Ch...
- No DOI given, and none found for title: gasfluxes: Greenhouse Gas Flux Calculation from Ch...

INVALID DOIs

- None
editorialbot commented 5 months ago

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

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/5207, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Qepanna commented 5 months ago

@arfon - Looks all good to me!