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Attempting PDF compilation. Reticulating splines etc...

👉 Check article proof 📄 👈

@jsgalan - please carry out your review in this issue by updating the checklist above and giving feedback in this issue. The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

Any questions/concerns please let me know.

Hi all,

I am sorry for my belated response. Here are my initial review comments:

-Please make sure to explain the acronyms, are TGXnet and Nofima Companies?
-In the reference from Martens and Naes, please check the title "Principal component regression in NIR analysis: Viewpoints, background details and selection of components", and add the DOI accordingly, check site

Best

@jsgalan thank you very much your first comments and for taking on the reviewer job.

1. I have updated the reference. Thank you for bringing my attention to this. I also inserted DOI's and ISBN where those were missing.
2. TGXnet is a (coding) company in Norway and Nofima is a food research institute in Norway. Where and how would you like me to insert this information? In paper.md in the affiliation part?

I will make @whedon produce a new pdf with the updated references. I will ask @whedon to generate another pdf once I got your feedback regarding point 2.

best

@whedon generate pdf

Attempting PDF compilation. Reticulating splines etc...

PDF failed to compile for issue #980 with the following error:

% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed

0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 14 0 14 0 0 192 0 --:--:-- --:--:-- --:--:-- 194
Error reading bibliography ./paper.bib (line 7, column 3):
unexpected "i"
expecting space, ",", white space or "}"
Error running filter pandoc-citeproc:
Filter returned error status 1
Looks like we failed to compile the PDF

@whedon generate pdf

Attempting PDF compilation. Reticulating splines etc...

👉 Check article proof 📄 👈

@whedon generate pdf

Attempting PDF compilation. Reticulating splines etc...

👉 Check article proof 📄 👈

👋 @jsgalan - do you think you might be able to complete your review in the next two weeks?

Hi all,

I overall think is a great package that will simplify a few routinely task done (by us) chemometricians.

ISSUES ABOUT THE SOFTWARE PACKAGE

i have successfully installed both packages hoggorm and hoggormplot.

which is good, but still I have a few suggestions to be made:

• add the examples to the package itself, both as .py and .ipynb
• separate each example type via a folder and put each examples under a suitable and explanatory filename. For instance in the Partial Least Squares Regression example there are 3 examples:

1. Partial Least Squares regression in sensometrics
2. Partial Least Squares Regression in spectroscopy
3. Partial Least Squares regression with air pollution data

The notebooks are great for teaching purposes in the webpage, but it still need to be in code with a proper documentation.

• I see there is a 'tests' foldre in the package, please explain the usage of this examples in the main documentation

• Please Specify in the documentation the matplotlib and numpy version used to compile the package. For instance, I am using Matplotlib 2.2.0 and numy 1.15.0, and have issues with closing the figures for no apparent reason.

• In the issue of plots, could you add an example where 2 plots are in the same figure(), i am not sure if i should use subplot from matplotlib or a specific command in your package.

• I will be happy to see working PLS2, RV, RV2 and SMI examples.

ISSUES ABOUT THE PAPER AND SUBMISSION

• I am unsure the license is following an OSI license type (https://opensource.org/licenses/alphabetical)

• In the article itself i think it should be addressed more clearly the issues that this softwares solves. It is evident to me as a chemometrician familiar with the methods, but in my experience not many fields relate to the use of PSLR as their methods of data summarization and explanation.

• I see you guys are using NIPALS algorithm please add the appropriate citation for the algorithm (as reference please check: http://www.vias.org/tmdatanaleng/dd_nipals_algo.html)

• Add more information about how and when to see special matrix correlation coefficients RV, RV2 and SMI.

• There is a typo in the main hoggorm page ( https://github.com/olivertomic/hoggorm) it reads matrix corrlation coefficients RV, RV2 and SMI where it should be "correlation".

Best

Hi @jsgalan! Thanks a lot for your effort and providing feedback on the package. I will try to implement all requirements as quickly as possible and get back to you once I am done.

best wishes

👋 @olivertomic - how are you getting along making your changes?

Hi @arfon. Thanks for getting in touch. I have been extremely busy with teaching, but I will pick up the work this week and hope to have everything finished within a week or two.

Hi @olivertomic, I will be happy to check those changes !

Best

Thank you @jsgalan. We have started working with your comments and will come back as soon as we are ready.

best wishes
Oliver

I see that no progress has been made on this submission since the reviewer comments from Nov 10, 2018. At this point, I will add the "paused" label.

@olivertomic — Please ping @openjournals/joss-eics when you're have made your enhancements and would like us to take a new look.

Dear @labarba - Thank you for your notice. We have made some progress, like adding some examples in Jupyter Notebooks (as requested by @jsgalan ), but admittedly the process has been painfully slow due to various reasons. We will ping @openjournals/joss-eics once we are done. Thank you again.

👋 @olivertomic - are you still planning to make these changes, or should we withdraw the paper, with the idea that you can resubmit it later?

Dear @danielskatz . Yes, we are still planning on making these changes. I am finally done teaching this semester and plan to finish this up by end of June. I hope this time frame is still OK.

In my opinion, yes, if this is a firm commitment, but I will also defer to @arfon as the editor of the submission.

Dear @danielskatz . Yes, we are still planning on making these changes. I am finally done teaching this semester and plan to finish this up by end of June. I hope this time frame is still OK.

👍 this sounds OK to me.

Thanks a lot @danielskatz and @arfon. A firm commitment it is. End of June.