[PRE REVIEW]: GaussianRandomFields.jl: A Julia package to generate and sample from Gaussian random fields

[editorialbot]

Submitting author: !--author-handle-->@PieterjanRobbe<!--end-author-handle-- (Pieterjan Robbe) Repository: https://github.com/PieterjanRobbe/GaussianRandomFields.jl Branch with paper.md (empty if default branch): joss Version: v2.2.2 Editor: !--editor-->@jbytecode<!--end-editor-- Reviewers: @ziyiyin97, @shahmoradi Managing EiC: Arfon Smith

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

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.04 s (1140.9 files/s, 211436.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           34            635            270           7218
Markdown                         6            200              0            532
YAML                             7              2             10            221
TeX                              1             14              0            125
TOML                             2              5              0             34
-------------------------------------------------------------------------------
SUM:                            50            856            280           8130
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 469

[editorialbot]

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

OK DOIs

- 10.1137/141000671 is OK
- 10.5194/gmd-15-3161-2022 is OK

MISSING DOIs

- 10.3390/a13050110 may be a valid DOI for title: p-refined multilevel quasi-Monte Carlo for Galerkin finite element methods with applications in civil engineering
- 10.1145/3240765.3240860 may be a valid DOI for title: Uncertainty quantification of electronic and photonic ICs with non-Gaussian correlated process variations
- 10.1016/j.jhydrol.2015.07.036 may be a valid DOI for title: Influence of conceptual model uncertainty on contaminant transport forecasting in braided river aquifers
- 10.1002/nla.2281 may be a valid DOI for title: Enhanced multi-index Monte Carlo by means of multiple semicoarsened multigrid for anisotropic diffusion problems
- 10.1155/asp/2006/31062 may be a valid DOI for title: Adaptive Markov random fields for example-based super-resolution of faces
- 10.1038/s41598-022-26898-1 may be a valid DOI for title: Physics-embedded inverse analysis with algorithmic differentiation for the earth’s subsurface

INVALID DOIs

- https://doi.org/10.5334/jors.431 is INVALID because of 'https://doi.org/' prefix

[editorialbot]

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

[arfon]

@editorialbot query scope

@PieterjanRobbe – due to the relatively small size of this code, the editors will now discuss if it meets the substantial scholarly effort criterion for review by JOSS. We should get back to you sometime next week. If you want to fix the DOIs (noting that @editorialbot's suggestions are not always right), you can, then use the following commands (one at a time, as the first line of a new comment) to regenerate the PDF and check the references.

@editorialbot generate pdf @editorialbot check references

Note to editors, the line count for this submission is a little misleading as there are a couple of large data files. The Julia in src is:

github.com/AlDanial/cloc v 1.96  T=0.02 s (1024.5 files/s, 114209.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           19            506            766            846
-------------------------------------------------------------------------------
SUM:                            19            506            766            846
-------------------------------------------------------------------------------

[editorialbot]

Submission flagged for editorial review.

[PieterjanRobbe]

@editorialbot generate pdf

[editorialbot]

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

[PieterjanRobbe]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1137/141000671 is OK
- 10.3390/a13050110 is OK
- 10.1046/j.1365-8711.2000.03086.x is OK
- 10.1145/3240765.3240860 is OK
- 10.5194/gmd-15-3161-2022 is OK
- 10.1016/j.jhydrol.2015.07.036 is OK
- 10.5334/jors.431 is OK
- 10.1002/nla.2281 is OK
- 10.1155/asp/2006/31062 is OK
- 10.1038/s41598-022-26898-1 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[PieterjanRobbe]

Hi @arfon, thanks for considering this submission! I've added the DOI's, and reference checking seems fine now.

[PieterjanRobbe]

Just pointing out that this package has been used in several independent research works, including:

• Pulsipher, J. L., Benjamin R. D., and Victor M. Z. "Random field optimization." Computers & Chemical Engineering 165 (2022): 107854. (link)
• Wu, H., Greer, S. Y., and 'Malley, D. "Physics-embedded inverse analysis with algorithmic differentiation for the earth’s subsurface." Scientific Reports 13.1 (2023): 718. (link)
• Wu, H., O'Malley, D., Golden, J. K., and Vesselinov, V. V. "Inverse analysis with variational autoencoders: A comparison of shallow and deep networks." Journal of Machine Learning for Modeling and Computing 3.2 (2022). (link)
• Schäfer, F., Katzfuss, M., and Owhadi, H. "Sparse Cholesky Factorization by Kullback-Leibler Minimization." SIAM Journal on scientific computing 43.3 (2021): A2019-A2046. (link)
• Belliveau, P., and Haber, E. "Parametric level-set inverse problems with stochastic background estimation." Inverse Problems 39.7 (2023): 075003. (link)
• Revell, C. K., Herrera, J. A., Lawless, C., Lu, Y., Kadler, K. E., Chang, J., and Jensen, O. E. "Modelling collagen fibril self-assembly from extracellular medium in embryonic tendon." (preprint) (link)
• Hang, H., Giusti, C., Ziegelmeier, L., & Henselman-Petrusek, G. "U-match factorization: sparse homological algebra, lazy cycle representatives, and dualities in persistent (co) homology." (preprint) (link)

as well as in our own work:

• Blondeel, P., Robbe, P., Van hoorickx, C., François, S., Lombaert, G., & Vandewalle, S. "p-refined multilevel quasi-Monte Carlo for Galerkin finite element methods with applications in civil engineering." Algorithms, 13.5 (2022): 110. (link)
• Robbe, P., Nuyens, D., and Vandewalle, S. "Enhanced multi‐index Monte Carlo by means of multiple semicoarsened multigrid for anisotropic diffusion problems." Numerical Linear Algebra with Applications 28.3 (2021): e2281. (link)
• Robbe, P., Nuyens, D., and Vandewalle, S. "A multi-index quasi-Monte Carlo algorithm for lognormal diffusion problems." SIAM Journal on Scientific Computing 39.5 (2017): S851-S872. (link)
• Robbe, P., Nuyens, D., and Vandewalle, S. "Recycling samples in the multigrid multilevel (quasi-) Monte Carlo method." SIAM Journal on Scientific Computing 41.5 (2019): S37-S60. (link)

[gkthiruvathukal]

@PieterjanRobbe Thanks for following up. We have determined that this submission is within scope. I will be assigning an editor as soon as I can. Thank you for your patience!

[jbytecode]

@editorialbot assign me as editor

[editorialbot]

Assigned! @jbytecode is now the editor

[jbytecode]

@PieterjanRobbe - Thank you for submitting your software to JOSS. I am the handling editor of this submission.

Do you have any suggestions for potential reviewers? You can search the list of people that have already agreed to review and may be suitable for this submission. Please do mention their usernames here without using the @ character (because we don't want to bother them).

Thank you in advance.

[PieterjanRobbe]

Hi @jbytecode, thank you so much for stepping in! A quick search on uncertainty quantification (an area of expertise where Gaussian random fields are commonly used) gives me the following suggestions:

• shahmoradi
• ziyiyin97
• salrm8
• georgiastuart
• AnjaliSandip/
• prmiles
• Himscipy

Let me know if you would need additional suggestions for potential reviewers. Thanks again!

[jbytecode]

👋👋👋 Dear @shahmoradi and Dear @ziyiyin97 👋👋👋

Would you be willing to assist in reviewing this submission for JOSS (Journal of Open Source Software)?

JOSS publishes articles about open source research software. The submission I'd like you to review is titled: "GaussianRandomFields.jl: A Julia package to generate and sample from Gaussian random fields". You can find more information at the top of this Github issue (https://github.com/openjournals/joss-reviews/issues/5537).

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. If you have any questions please let me know.

This is the pre-review issue. After setting at least 2 reviewers we will start the review process in a separate thread. In that thread, there will be 23 check items for each single reviewer.

Thank you in advance!

[ziyiyin97]

Yes I'd be happy to

[jbytecode]

@editorialbot add @ziyiyin97 as reviewer

@ziyiyin97 - Thank you for the quick response! After assigning the 2nd reviewer, I will start the review in a separate thread. I will introduce the instructions there.

[editorialbot]

@ziyiyin97 added to the reviewers list!

[shahmoradi]

Thank you for your invitation. Yes, I can help with this review.

[PieterjanRobbe]

Thank you both!

[jbytecode]

@editorialbot add @shahmoradi as reviewer

[editorialbot]

@shahmoradi added to the reviewers list!

[jbytecode]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/5595.