[PRE REVIEW]: PhaseTypeR: an R package for phase-type distributions in population genetics

[editorialbot]

Submitting author: !--author-handle-->@rivasiker<!--end-author-handle-- (Iker Rivas-González) Repository: https://github.com/rivasiker/PhaseTypeR Branch with paper.md (empty if default branch): joss-paper Version: v1.0.4 Editor: !--editor-->@majensen<!--end-editor-- Reviewers: @tkchafin, @nhejazi Managing EiC: Kevin M. Moerman

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.10 s (1093.5 files/s, 225127.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
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HTML                            41           2137            480          11061
R                               31            587           1083           1807
Rmd                              4            670            977            910
Markdown                        13            216              0            771
CSS                              4             99             49            431
JavaScript                       5             68             39            290
TeX                              3             27              0            278
YAML                             6             31              6            206
SVG                              1              0              1             11
-------------------------------------------------------------------------------
SUM:                           108           3835           2635          15765
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 2396

[editorialbot]

Failed to discover a valid open source license

[editorialbot]

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

[editorialbot]

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

OK DOIs

- 10.18637/jss.v025.i07 is OK
- 10.1017/jpr.2019.60 is OK

MISSING DOIs

- 10.1111/sjos.12505 may be a valid DOI for title: Fitting inhomogeneous phase-type distributions to data: the univariate and the multivariate case
- 10.1007/978-3-319-22264-6_7 may be a valid DOI for title: mapfit: An R-Based Tool for PH/MAP Parameter Estimation
- 10.1007/978-1-4757-6285-3 may be a valid DOI for title: Probability models for DNA sequence evolution
- 10.1093/schbul/syp004 may be a valid DOI for title: Coalescent Theory: An Introduction
- 10.1006/tpbi.1995.1025 may be a valid DOI for title: Statistical properties of segregating sites
- 10.4171/ecr/17-1/8 may be a valid DOI for title: Genealogies and inference for populations with highly skewed offspring distributions
- 10.1017/jpr.2021.79 may be a valid DOI for title: The shape of a seed bank tree
- 10.1101/2021.08.23.457399 may be a valid DOI for title: Rates of convergence in the two-island and isolation-with-migration models

INVALID DOIs

- https://doi.org/10.1016/j.tpb.2019.02.001 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.15807/jorsj.59.72 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1007/s00285-021-01689-w is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1534/genetics.114.173898 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1006/tpbi.1997.1307 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/0304-4149(82)90011-4 is INVALID because of 'https://doi.org/' prefix

[rivasiker]

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[rivasiker]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1007/978-1-4939-7049-0 is OK
- 10.1016/j.tpb.2019.02.001 is OK
- 10.18637/jss.v025.i07 is OK
- 10.1111/sjos.12505 is OK
- 10.1017/jpr.2019.60 is OK
- 10.15807/jorsj.59.72 is OK
- 10.1007/978-3-319-22264-6_7 is OK
- 10.1007/s00285-021-01689-w is OK
- 10.1007/978-0-387-78168-6 is OK
- 10.1093/schbul/syp004 is OK
- 10.1534/genetics.114.173898 is OK
- 10.1006/tpbi.1997.1307 is OK
- 10.1016/0304-4149(82)90011-4 is OK
- 10.1006/tpbi.1995.1025 is OK
- 10.4171/ECR/17-1/8 is OK
- 10.1017/jpr.2021.79 is OK
- 10.1016/j.tpb.2022.08.001 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[rivasiker]

@editorialbot check repository

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.12 s (921.4 files/s, 189777.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            41           2137            480          11061
R                               31            587           1083           1807
Rmd                              4            670            977            910
Markdown                        13            216              0            771
CSS                              4             99             49            431
JavaScript                       5             68             39            290
TeX                              3             27              0            287
YAML                             6             31              6            206
SVG                              1              0              1             11
-------------------------------------------------------------------------------
SUM:                           108           3835           2635          15774
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 2396

[rivasiker]

@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:

[rivasiker]

List of potential reviewers based on their preferred topics:

• ethanbass
• dwinter
• mtomasini
• rachelss
• esteinig
• bvreede
• xin-huang

[Kevin-Mattheus-Moerman]

@rivasiker thanks for this submission. I will be looking for a handling editor. Unfortunately all editors in this domain are currently busy handling many other submissions. Hence I have waitlisted this submission at the moment. We will assign an editor once one becomes available. Thanks for your patience.

[Kevin-Mattheus-Moerman]

@editorialbot invite @majensen as editor

[editorialbot]

Invitation to edit this submission sent!

[Kevin-Mattheus-Moerman]

@majensen do you think you could handle this work as editor? (if so can you remove the waitlisted label and assign yourself). Thanks

[majensen]

@editorialbot assign me as editor

[editorialbot]

Assigned! @majensen is now the editor

[Kevin-Mattheus-Moerman]

@majensen thanks for editing this one. Are you able to start recruiting reviewers for this submission?

[majensen]

@Kevin-Mattheus-Moerman @rivasiker so sorry about the delay. I will begin now!

[majensen]

Hi @ethanbass -- would you be able to review this work in JOSS? We could use your expertise in this area. Thanks for your consideration! --@majensen

[majensen]

Hello @dwinter - do you have time and willingness to review this work for JOSS? I appreciate your previous review, and we would be grateful for your expertise. Thanks for considering --@majensen

[ethanbass]

Hi @ethanbass -- would you be able to review this work in JOSS? We could use your expertise in this area. Thanks for your consideration! --@majensen

Thank you for thinking of me. I feel I may not be so qualified to review this submission. I am not really a popgen person and I feel that some of this may be over my head.

[dwinter]

Hi @majensen . Sincere apologies, this seems like a cool problem and program but my availability to review it now is very limited between work and finally taking an extended break from work over the Southern Summer. I don't think I would be able to start a review until February at the very earliest I'm sorry.

[majensen]

@dwinter not a problem - I appreciate your consideration!

[majensen]

Thanks for considering @ethanbass - will keep you on the list for next time.

[majensen]

Hi @tkchafin - would you be willing and available to review this work for JOSS? I could use your expertise in population genetics. Thanks for your consideration --@majensen

[majensen]

Hello @nhejazi - would you be willing and available to review this work for JOSS? Based on your recent paper I believe you could help us out here. Thanks for your consideration --@majensen

[tkchafin]

Yes I can review, but with the holidays and personal leave I am taking it would take longer than usual (end of January at the earliest, more likely early February)

[majensen]

Thanks @tkchafin that would be fine. I appreciate your support!

[majensen]

@editorialbot add @tkchafin as reviewer

[editorialbot]

@tkchafin added to the reviewers list!

[majensen]

@editorialbot remind me in 3 weeks

[editorialbot]

Reminder set for @majensen in 3 weeks

[nhejazi]

Hi @majensen -- Sure, I can help with reviewing this

[majensen]

Hi @cboettig - would you be willing to review this work for JOSS? I believe you might fit in the intersection of the technical and biological aspects of this paper. Thanks for considering! --@majensen

[majensen]

@nhejazi -Thanks very much! I will add you to the reviewers.

[majensen]

@editorialbot add @nhejazi as reviewer

[editorialbot]

@nhejazi added to the reviewers list!

[cboettig]

apologies, I'm over-committed right now!

[majensen]

Thanks @cboettig - will catch you next time

[majensen]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/5054.

[majensen]

@rivasiker @tkchafin @nhejazi - we'll go ahead and start at #5054. @tkchafin I will ping you towards the end of Jan. Thanks!