[REVIEW]: RivGraph: Automatic extraction and analysis of river and delta channel network topology

whedon commented 3 years ago

Submitting author: @jonschwenk (Jon Schwenk) Repository: https://github.com/jonschwenk/RivGraph Version: v0.4 Editor: @kbarnhart Reviewer: @eriknes, @leotrs Archive: 10.5281/zenodo.4591559

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Review checklist for @eriknes

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@jonschwenk) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @leotrs

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@jonschwenk) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

whedon commented 3 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @eriknes, @leotrs it looks like you're currently assigned to review this paper :tada:.

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whedon commented 3 years ago

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

whedon commented 3 years ago

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

OK DOIs

- 10.1016/0013-7952(93)90074-M is OK
- 10.1038/sdata.2017.191 is OK
- 10.1002/(SICI)1099-1646(199603)12:2/3<201::AID-RRR390>3.0.CO;2-A is OK
- 10.1007/s00285-016-1054-9 is OK
- 10.1111/j.1365-3156.2005.01428.x is OK
- 10.1016/j.jtbi.2012.12.007 is OK
- 10.1623/hysj.48.3.317.45290 is OK
- 10.1371/journal.pntd.0000940 is OK
- 10.1111/j.1467-8306.1972.tb00873.x is OK
- 10.5194/hess-19-2247-2015 is OK
- 10.1002/2016EF000485 is OK
- 10.1002/2016EF000485 is OK
- 10.1002/2016EF000485 is OK
- 10.5194/gmd-9-587-2016 is OK
- 10.1126/science.aat0636 is OK
- 10.1029/2006RG000197 is OK
- 10.3402/polar.v34.26891 is OK
- 10.1002/wrcr.20440 is OK
- 10.1002/9781119217886.ch13 is OK
- 10.1029/WR018i004p01184 is OK
- 10.1016/j.ocemod.2003.12.004 is OK
- 10.1111/jfr3.12187 is OK
- 10.2112/05-0573.1 is OK
- 10.1016/j.sste.2017.06.001 is OK
- 10.1007/s10750-016-2664-3 is OK
- 10.1016/j.jsames.2012.09.002 is OK
- 10.1007/s10584-014-1084-5 is OK
- 10.1179/136485906X105480 is OK
- 10.1007/s12517-015-2114-y is OK
- 10.1016/j.earscirev.2012.05.003 is OK
- 10.5194/gmd-8-2701-2015 is OK
- 10.5194/gmd-8-2701-2015 is OK
- 10.1002/2016GL068550 is OK
- 10.1061/(ASCE)HE.1943-5584.0001513 is OK
- 10.1073/pnas.1606119113 is OK
- 10.1126/science.345.6193.128 is OK
- 10.1126/science.1226337 is OK
- 10.4103/0971-5916.176632 is OK
- 10.1371/journal.pone.0138082 is OK
- 10.1038/474151a is OK
- 10.1111/j.1948-7134.2014.12068.x is OK
- 10.1179/136485908X252296 is OK
- 10.1002/2013JF002845 is OK
- 10.1179/136485906X105499 is OK
- 10.1111/j.1365-2915.2008.00720.x is OK
- 10.1016/S0169-555X(01)00092-7 is OK
- 10.1016/j.advwatres.2019.03.016 is OK
- 10.1002/2013WR013918 is OK
- 10.1002/2013WR013918 is OK
- 10.1175/JHM-D-14-0155.1 is OK
- 10.5194/hess-21-589-2017 is OK
- 10.1002/hyp.10398 is OK
- 10.1002/2017WR020471 is OK
- 10.5194/hess-22-709-2018 is OK
- 10.1002/2017WR020471 is OK
- 10.1038/ngeo1593 is OK
- 10.1029/2018GL081883 is OK
- 10.3934/mbe.2015009 is OK
- 10.1038/s41561-018-0262-x is OK
- 10.1038/nature06045 is OK
- 10.1007/978-3-642-12796-0_2 is OK
- 10.1016/0022-1694(92)90126-G is OK
- 10.1179/136485906X105507 is OK
- 10.1016/S0022-1694(03)00129-X is OK
- 10.1890/06-0562.1 is OK
- 10.1038/ngeo553 is OK
- 10.1038/ngeo1799 is OK
- 10.1093/infdis/jiw363 is OK
- 10.1002/esp.3290120205 is OK
- 10.1111/j.1751-8369.2009.00126.x is OK
- 10.1007/s13280-010-0109-1 is OK
- 10.1002/2015JG003131 is OK
- 10.4161/dish.25216 is OK
- 10.1038/nclimate2949 is OK
- 10.1029/2018EF001091 is OK
- 10.1088/0266-5611/30/11/114007 is OK
- 10.1155/2016/8180158 is OK
- 10.1002/(SICI)1096-9837(199712)22:12<1109::AID-ESP810>3.0.CO;2-O is OK
- 10.1111/j.1365-2915.2007.00667.x is OK
- DOI 10.3201/eid1405.071066 is OK
- 10.1073/pnas.1408184111 is OK
- 10.5194/gmd-12-677-2019 is OK
- 10.1073/pnas.1302089111 is OK
- 10.1073/pnas.1614303114 is OK
- 10.1016/j.pocean.2006.10.004 is OK
- 10.1175/JCLI-D-15-0775.1 is OK
- 10.1038/ngeo1582 is OK
- 10.1111/j.1365-3156.2008.02216.x is OK
- 10.1007/s12517-014-1594-5 is OK
- 10.1073/pnas.0606955103 is OK
- 10.1093/trstmh/tru189 is OK
- 10.1080/17513758.2012.733427 is OK
- 10.1038/337452a0 is OK
- 10.1002/2015WR017096 is OK
- 10.5194/hess-22-831-2018 is OK
- 10.1002/2017GL074873 is OK
- 10.1016/j.cageo.2011.08.011 is OK
- 10.1016/j.gloplacha.2014.01.011 is OK
- 10.1007/s10021-006-9013-8 is OK
- 10.1016/0037-0738(69)90010-4 is OK
- 10.5194/gmd-4-1051-2011 is OK
- 10.5194/acp-10-9689-2010 is OK
- 10.1029/WR010i001p00106 is OK
- 10.1371/journal.pntd.0005429 is OK
- 10.1080/00221686909500264 is OK
- 10.1002/2013WR014227 is OK
- 10.1002/2014WR016139 is OK
- 10.1002/2017WR021859 is OK
- 10.1175/2008jcli2592.1 is OK
- 10.1139/e96-050 is OK
- 10.1007/s10533-018-0450-1 is OK
- 10.1016/j.advwatres.2015.01.004 is OK
- 10.5194/tc-13-557-2019 is OK
- 10.1029/2006jf000722 is OK
- 10.1038/nature19809 is OK
- 10.1002/wrcr.20250 is OK
- 10.1016/0022-1694(94)90095-7 is OK
- 10.1007/978-94-017-8863-2_12 is OK
- 10.1016/j.ejrs.2017.01.009 is OK
- 10.1134/s0097807814050029 is OK
- 10.1038/ncomms14592 is OK
- 10.1186/s12879-018-3124-7 is OK
- 10.1029/2012GL053387 is OK
- 10.1175/1525-7541(2000)001<0289:GCOSFS>2.0.CO;2 is OK
- 10.1073/pnas.1215218109 is OK
- 10.1073/pnas.1408439111 is OK
- 10.1016/S0278-4343(97)00003-4 is OK
- 10.1016/j.geomorph.2016.10.017 is OK
- 10.1016/j.cosust.2014.11.002 is OK
- 10.1002/rra.2682 is OK
- 10.1186/s13071-014-0544-0 is OK
- 10.1029/135GM09 is OK
- 10.1029/93TC01060 is OK
- 10.3390/rs11070750 is OK
- 10.1029/2020WR027199 is OK
- 10.1016/j.geomorph.2015.01.025 is OK
- 10.1016/j.earscirev.2019.04.009 is OK
- 10.1016/j.advwatres.2016.05.002 is OK
- 10.3390/w9100748 is OK
- 10.1017/S1049023X00008141 is OK
- 10.1007/s13280-011-0224-7 is OK
- 10.1007/s003820050269 is OK
- 10.1002/esp.3290120207 is OK
- 10.1016/j.envres.2016.07.026 is OK
- 10.1029/2010JF001955 is OK
- 10.1029/2010JG001300 is OK
- 10.1016/j.biocon.2010.08.013 is OK
- 10.1002/esp.3337 is OK
- 10.2475/ajs.266.6.417 is OK
- 10.1016/j.jtbi.2016.04.008 is OK
- 10.5194/gmd-9-1937-2016 is OK
- 10.5194/gmd-9-1937-2016 is OK
- 10.1002/esp.1016 is OK
- 10.1504/ijram.2012.047550 is OK
- 10.1007/s10588-013-9171-0 is OK
- 10.1029/2005RG000183 is OK
- 10.3334/ORNLDAAC/994 is OK
- 10.1016/j.jhydrol.2006.04.029 is OK
- 10.1002/hyp.7394 is OK
- 10.1038/nclimate2051 is OK
- 10.5589/m03-006 is OK
- 10.1111/j.1365-2311.2007.00927.x is OK
- 10.1002/hyp.11117 is OK
- 10.1016/j.ocemod.2010.09.002 is OK
- 10.1029/2019GL082027 is OK
- 10.1016/0169-555X(95)00047-9 is OK
- 10.1007/s10040-016-1386-y is OK
- 10.1130/G22633.1 is OK
- 10.1130/GES00065.1 is OK
- 10.1002/2013WR014283 is OK
- 10.1029/2018JC014510 is OK
- 10.1201/9781439833896 is OK
- 10.1016/j.csr.2011.12.001 is OK
- 10.1016/j.csr.2011.12.001 is OK
- 10.5194/essd-10-185-2018 is OK
- ARTN e100389210.1371/journal.pcbi.1003892 is OK
- 10.1111/j.1365-2486.2005.00966.x is OK
- Doi 10.2307/2986138 is OK
- 10.1002/(SICI)1096-9837(200004)25:4<421::AID-ESP65>3.0.CO;2-Q is OK
- 10.1016/j.jenvman.2013.03.026 is OK
- 10.1080/16742834.2018.1452520 is OK
- 10.1061/(ASCE)0733-9399(2007)133:4(400) is OK
- 10.1029/2018MS001603 is OK
- 10.1029/2018MS001603 is OK
- 10.1016/j.jhydrol.2009.02.007 is OK
- 10.1002/hyp.7795 is OK
- 10.1038/nature06958 is OK
- 10.1002/eap.1404 is OK
- 10.1002/ece3.3590 is OK
- 10.1016/j.geomorph.2005.09.008 is OK
- 10.1016/j.rse.2017.06.031 is OK
- 10.1016/S0169-555X(99)00032-X is OK
- 10.1029/WR017i004p01087 is OK
- 10.1002/esp.3290080204 is OK
- 10.1111/j.1461-0248.2006.01007.x is OK
- 10.3354/meps048057 is OK
- 10.1016/j.pocean.2006.10.001 is OK
- 10.1111/j.1467-9574.2011.00483.x is OK
- 10.1007/s00442-003-1382-5 is OK
- 10.5194/tc-6-221-2012 is OK
- 10.5194/tc-9-151-2015 is OK
- 10.1029/WR010i003p00499 is OK
- 10.1016/j.pce.2007.04.003 is OK
- 10.1002/2012WR013358 is OK
- 10.1016/0006-3207(81)90035-5 is OK
- 10.5194/gmd-9-4185-2016 is OK
- 10.1175/BAMS-D-12-00014.1 is OK
- 10.1175/JCLI-D-15-0415.1 is OK
- 10.1186/s40562-018-0109-8 is OK
- 10.1007/s10533-018-0431-4 is OK
- 10.1086/684223 is OK
- 10.1038/s41561-017-0056-6 is OK
- 10.1029/2003EO480001 is OK
- 10.5194/tcd-9-3351-2015 is OK
- 10.5194/tcd-9-3351-2015 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1175/jcli3532.1 is OK
- 10.1038/Nclimate3271 is OK
- 10.1177/0022343317691330 is OK
- 10.1002/2017WR021289 is OK
- 10.1029/2019JF005206 is OK
- 10.1130/0016-7606(1975)86<487:TCOCMO>2.0.CO;2 is OK
- ARTN e100423910.1371/journal.pcbi.1004239 is OK
- 10.1061/(ASCE)WR.1943-5452.0000258 is OK
- 10.1007/s10584-005-5352-2 is OK
- 10.1038/nclimate1911 is OK
- 10.1007/s10980-013-9902-0 is OK
- 10.1029/2006JC003642 is OK
- 10.1007/s12237-011-9386-6 is OK
- 10.1002/9781118470596.ch1 is OK
- 10.1002/9781118470596.ch1 is OK
- 10.1139/T09-058 is OK
- 10.1007/s13280-011-0219-4 is OK
- 10.1029/WR020i011p01659 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1175/BAMS-D-12-00121.1 is OK
- 10.1007/s10584-011-0153-2 is OK
- 10.1016/j.ocemod.2016.02.004 is OK
- 10.1016/S0341-8162(73)80016-5 is OK
- 10.1038/sdata.2018.224 is OK
- 10.1016/j.rse.2017.03.044 is OK
- 10.1002/2014JC010353 is OK
- 10.1002/2016GL070067 is OK
- 10.1002/2016GL070067 is OK
- 10.1007/s12665-017-6593-x is OK
- 10.1038/ngeo2636 is OK
- 10.1371/journal.pone.0039067 is OK
- 10.1186/s12889-017-4294-8 is OK
- 10.1002/2017JC013365 is OK
- 10.12952/journal.elementa.000124 is OK
- 10.1214/17-AOAS1090 is OK
- 10.1029/2008gl036205 is OK
- Artn 04402110.1088/1748-9326/8/4/044021 is OK
- Artn 08400310.1088/1748-9326/11/8/084003 is OK
- 10.1088/1748-9326/aae471 is OK
- 10.3390/rs11040374 is OK
- 10.5281/zenodo.3946761 is OK
- 10.1007/s00367-004-0188-8 is OK
- 10.1016/j.geomorph.2005.11.003 is OK
- 10.2307/2845334 is OK
- 10.1016/j.coldregions.2012.08.002 is OK
- 10.1007/s13253-014-0182-1 is OK
- 10.1007/s00227-012-2135-y is OK
- 10.1016/j.scitotenv.2017.10.044 is OK
- 10.1130/GSAB-P2-91-1119 is OK
- Doi 10.1111/1467-9868.00294 is OK
- 10.1130/0091-7613(1974)2<461:LEAODO>2.0.CO;2 is OK
- 10.1080/02723646.1981.10642205 is OK
- 10.14710/geoplanning.4.2.121-130 is OK
- 10.1007/s10584-013-0705-8 is OK
- 10.1016/0034-4257(82)90004-9 is OK
- 10.1111/j.1600-0870.2010.00475.x is OK
- 10.1002/esp.4073 is OK
- 10.1016/j.geomorph.2008.10.005 is OK
- 10.4230/LIPICS.SOCG.2017.48 is OK
- 10.2112/JCOASTRES-D-11-00060.1 is OK
- 10.1029/2019WR026867 is OK
- 10.2151/jmsj.2015-001 is OK
- 10.1111/j.1365-3091.1963.tb01216.x is OK
- 10.1002/2013EF000184 is OK
- 10.1623/hysj.54.1.43 is OK
- 10.1623/hysj.54.1.43 is OK
- 10.1175/2008JTECHO587.1 is OK
- 10.5194/essd-2016-36 is OK
- 10.1080/02626667.2012.745082 is OK
- 10.1029/2006JC003978 is OK
- 10.1016/j.advwatres.2004.02.020 is OK
- 10.3390/ijgi3020638 is OK
- 10.1016/j.jhydrol.2018.10.038 is OK
- 10.4269/ajtmh.2009.09-0115 is OK
- 10.1007/s12237-010-9362-6 is OK
- 10.1029/WR022i005p00731 is OK
- 10.1111/j.1752-1688.2006.tb04515.x is OK
- 10.1038/nature22333 is OK
- 10.1029/2006wr005528 is OK
- 10.1016/0022-1694(93)90157-5 is OK
- 10.1029/2008GL033985 is OK
- 10.1038/ncomms15611 is OK
- 10.1016/j.jhydrol.2004.03.028 is OK
- 10.1029/2008EO100001 is OK
- 10.1890/100125 is OK
- 10.1002/hyp.9740 is OK
- 10.1002/2016JC012006 is OK
- 10.1179/136485906X105516 is OK
- 10.1073/pnas.0705414105 is OK
- 10.1002/esp.3739 is OK
- 10.1175/JHM-D-12-015.1 is OK
- 10.1175/Jhm-D-12-015.1 is OK
- 10.1002/2015MS000471 is OK
- 10.1175/Jhm-D-14-0079.1 is OK
- 10.1016/j.geomorph.2016.10.018 is OK
- 10.1016/j.csda.2017.05.005 is OK
- 10.1175/JPO-D-17-0085.1 is OK
- 10.1002/wat2.1424 is OK
- 10.1016/j.tranpol.2015.09.002 is OK
- 10.1002/2015JG003120 is OK
- 10.1080/1088937X.2012.733893 is OK
- 10.1016/B978-0-12-814003-1.00039-3 is OK
- 10.1029/2018JG004659 is OK
- 10.1111/j.1365-3156.2008.02162.x is OK
- 10.1111/j.1365-3156.2011.02797.x is OK
- 10.1029/2018RG000607 is OK
- 10.1016/j.coldregions.2014.03.003 is OK
- 10.1002/esp.4613 is OK
- 10.1186/1297-9716-42-55 is OK
- 10.1016/j.jtbi.2014.04.033 is OK
- ARTN e0005255 10.1371/journal.pntd.0005255 is OK
- 10.2987/5578.1 is OK
- 10.2987/13-6350.1 is OK
- 10.1111/mve.12046 is OK
- 10.1029/2019JD031381 is OK
- 10.1029/2019JD031381 is OK
- 10.1016/j.rse.2016.12.029 is OK
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- 10.1007/s12237-010-9357-3 is OK
- 10.1038/nclimate2873 is OK
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- 10.1051/mmnp/20149211 is OK
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- Artn 2017090110.1098/Rspb.2017.0901 is OK
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MISSING DOIs

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- 10.1016/j.geoderma.2011.10.006 may be a valid DOI for title: Soil Carbon Distribution in Alaska in Relation to Soil-Forming Factors
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- 10.1029/2010wr009607 may be a valid DOI for title: River-to-Lake Connectivities, Water Renewal, and Aquatic Habitat Diversity in the Mackenzie River Delta
- 10.1016/j.geomorph.2005.01.011 may be a valid DOI for title: Morphology and Geotechnique of Active-Layer Detachment Failures in Discontinuous and Continuous Permafrost, Northern Canada
- 10.1002/ppp.522 may be a valid DOI for title: Frequency and Magnitude of Active-Layer Detachment Failures in Discontinuous and Continuous Permafrost, Northern Canada
- 10.1016/j.gloplacha.2004.12.007 may be a valid DOI for title: Long-Term Open-Water Season Stream Temperature Variations and Changes over Lena River Basin in Siberia
- 10.1186/1476-072x-13-50 may be a valid DOI for title: Modeling Tools for Dengue Risk Mapping-a Systematic Review
- 10.1002/esp.1947 may be a valid DOI for title: Modelling Mid-channel Bars in Meandering Channels
- 10.1590/s0074-02762007005000056 may be a valid DOI for title: Variation in Aedes Aegypti (Diptera: Culicidae) Container Productivity in a Slum and a Suburban District of Rio de Janeiro during Dry and Wet Seasons
- 10.1590/s0074-02762008000600016 may be a valid DOI for title: Mosquito Traps Designed to Capture Aedes Aegypti (Diptera: Culicidae) Females: Preliminary Comparison of Adultrap, MosquiTRAP and Backpack Aspirator Efficiency in a Dengue-Endemic Area of Brazil
- 10.1371/currents.outbreaks.f0b3978230599a56830ce30cb9ce0500 may be a valid DOI for title: Towards an Early Warning System for Forecasting Human West Nile Virus Incidence
- 10.1080/17513758.2015.1005698 may be a valid DOI for title: A Network-Patch Methodology for Adapting Agent-Based Models for Directly Transmitted Disease to Mosquito-Borne Disease
- 10.1111/tbed.12082 may be a valid DOI for title: Inter-Epidemic and Between-Season Persistence of Rift Valley Fever: Vertical Transmission or Cryptic Cycling?
- 10.1002/esp.3482 may be a valid DOI for title: Network Concepts to Describe Channel Importance and Change in Multichannel Systems: Test Results for the Jamuna River, Bangladesh
- 10.1029/97wr01033 may be a valid DOI for title: Hydrograph Separations in an Arctic Watershed Using Mixing Model and Graphical Techniques
- 10.1130/dnag-gna-o1.255 may be a valid DOI for title: Movement and Storage of Sediment in Rivers of the United States and Canada
- 10.1130/0016-7606(1996)108<1089:cfgats>2.3.co;2 may be a valid DOI for title: Channel-Floodplain Geomorphology along the Solimoes-Amazon River, Brazil
- 10.1002/rra.1360 may be a valid DOI for title: River Channel Cutoff Dynamics, Sacramento River, California, USA
- 10.1038/415514a may be a valid DOI for title: Increasing Risk of Great Floods in a Changing Climate
- 10.5194/tc-9-781-2015 may be a valid DOI for title: Sensitivity of Airborne Geophysical Data to Sublacustrine and Near-Surface Permafrost Thaw
- 10.1016/s0025-3227(98)00101-7 may be a valid DOI for title: River-Plume Sedimentation Modeling for Sequence Stratigraphy: Application to the Eel Margin, Northern California
- 10.1603/0022-2585-41.3.502 may be a valid DOI for title: Evaluation of a Sampling Methodology for Rapid Assessment of Aedes Aegypti Infestation Levels in Iquitos, Peru
- 10.1179/136485906x105534 may be a valid DOI for title: Aedes Aegypti (Diptera: Culicidae) Production from Non-Residential Sites in the Amazonian City of Iquitos, Peru
- 10.1016/s0169-555x(03)00046-1 may be a valid DOI for title: Estimation of Error in Bankfull Width Comparisons from Temporally Sequenced Raw and Corrected Aerial Photographs
- 10.1186/1471-2334-14-167 may be a valid DOI for title: Climate Change and Dengue: A Critical and Systematic Review of Quantitative Modelling Approaches
- 10.1130/0016-7606(1986)97<497:asaobe>2.0.co;2 may be a valid DOI for title: A Statistical Analysis of Bank Erosion and Channel Migration in Western Canada
- 10.1179/136485906x105462 may be a valid DOI for title: Pupal/Demographic Surveys to Inform Dengue-Vector Control
- 10.1111/j.1467-8306.1966.tb00541.x may be a valid DOI for title: Man and Geomorphic Process in the Chemung River Valley, New York and Pennsylvania
- 10.1007/s10021-009-9253-5 may be a valid DOI for title: Retention of Riverine Sediment and Nutrient Loads by Coastal Plain Floodplains
- 10.1016/j.geomorph.2013.03.014 may be a valid DOI for title: Multi-Scale Factors Controlling the Pattern of Floodplain Width at a Network Scale: The Case of the Rhône Basin, France
- 10.1111/j.1365-3091.1993.tb01347.x may be a valid DOI for title: Variability of Deltaic Processes in Terms of Sediment Supply, with Particular Emphasis on Grain-Size
- 10.1002/ppp.538 may be a valid DOI for title: Warming of Permafrost in the Arctic National Wildlife Refuge, Alaska
- 10.1016/j.geomorph.2008.02.007 may be a valid DOI for title: The Effects of Variability in Bank Material Properties on Riverbank Stability: Goodwin Creek, Mississippi
- 10.1029/2004jf000158 may be a valid DOI for title: Formation of Oriented Thaw Lakes by Thaw Slumping
- 10.1163/9789004408425_004 may be a valid DOI for title: China’s Arctic Policy
- 10.1126/science.1122593 may be a valid DOI for title: Trajectory Shifts in the Arctic and Subarctic Freshwater Cycle
- 10.1002/1099-1085(200011/12)14:16/17<3011::aid-hyp132>3.0.co;2-b may be a valid DOI for title: Channel Instability as a Control on Silting Dynamics and Vegetation Patterns within Perifluvial Aquatic Zones
- 10.1002/9781119940791.ch11 may be a valid DOI for title: Biophysical Characterisation of Fluvial Corridors at Reach to Network Scales
- 10.1590/s0036-46652002000500002 may be a valid DOI for title: Frequency, Diversity, and Productivity Study on the Aedes Aegypti Most Preferred Containers in the City of Manaus, Amazonas, Brazil
- 10.1002/9781444304473.ch32 may be a valid DOI for title: Turbidite Depositional Patterns and Flow Characteristics, Navy Submarine Fan, California Borderland
- 10.1641/0006-3568(2000)050[0807:reohao]2.0.co;2 may be a valid DOI for title: Regional Effects of Hydrologic Alterations on Riverine Macrobiota in the New World: Tropical-Temperate Comparisons
- 10.1002/hyp.369 may be a valid DOI for title: Climatic Control of River-Ice Hydrology: A Review
- 10.1139/l02-040 may be a valid DOI for title: Ice Breakup: A Neglected Factor in River Ecology
- 10.14358/pers.70.12.1383 may be a valid DOI for title: A Review of Techniques for Extracting Linear Features from Imagery
- 10.1111/gcb.12500 may be a valid DOI for title: Cumulative Geoecological Effects of 62 Years of Infrastructure and Climate Change in Ice-rich Permafrost Landscapes, Prudhoe Bay Oilfield, Alaska
- 10.1214/07-aoas108 may be a valid DOI for title: A Multivariate Semiparametric Bayesian Spatial Modeling Framework for Hurricane Surface Wind Fields
- 10.1016/j.geomorph.2004.07.013 may be a valid DOI for title: Statistical Analysis of Lateral Migration of the Rio Grande, New Mexico
- 10.1063/1.1745010 may be a valid DOI for title: Capillary Conduction of Liquids through Porous Mediums
- 10.3133/sir20135168 may be a valid DOI for title: Recent (circa 1998 to 2011) Channel-Migration Rates of Selected Streams in Indiana
- 10.1111/j.1752-1688.1995.tb03389.x may be a valid DOI for title: Comparison of the Magnitude of Erosion along Two Large Regulated Rivers
- 10.1603/0022-2585-41.4.634 may be a valid DOI for title: Adult Size and Distribution of Aedes Aegypti (Diptera: Culicidae) Associated with Larval Habitats in Iquitos, Peru
- 10.5194/esurf-8-87-2020 may be a valid DOI for title: Determining Flow Directions in River Channel Networks Using Planform Morphology and Topology
- 10.26719/2015.18.12.1217 may be a valid DOI for title: Dengue Vector Control and Surveillance during a Major Outbreak in a Coastal Red Sea Area in Sudan
- 10.1016/0022-5193(77)90265-x may be a valid DOI for title: Reaction Kinetics of Poikilotherm Development
- 10.1002/ppp.582 may be a valid DOI for title: Patterns of Permafrost Formation and Degradation in Relation to Climate and Ecosystems
- 10.3133/ofr91502 may be a valid DOI for title: Geomorphic and Vegetative Recovery Processes along Modified Stream Channels of West Tennessee
- 10.1146/annurev.earth.32.101802.120201 may be a valid DOI for title: River Avulsions and Their Deposits
- 10.2172/88648 may be a valid DOI for title: TRANSIMS: Transportation Analysis and Simulation System
- 10.1029/2007wr006133 may be a valid DOI for title: Estimation of River Discharge, Propagation Speed, and Hydraulic Geometry from Space: Lena River, Siberia
- 10.1590/s0037-86822012000200007 may be a valid DOI for title: Variation in Aedes Aegypti (Linnaeus) (Diptera, Culicidae) Infestation in Artificial Containers in Caxias, State of Maranhao, Brazil
- 10.1139/s04-032 may be a valid DOI for title: Large-Scale Flow Structures and Stability in Shallow Flows
- 10.4269/ajtmh.2003.68.209 may be a valid DOI for title: Dengue and Its Vectors in Thailand: Calculated Transmission Risk from Total Pupal Counts of Aedes Aegypti and Association of Wing-Length Measurements with Aspects of the Larval Habitat
- 10.1002/esp.2119 may be a valid DOI for title: Historical Channel Narrowing along the Rio Grande near Albuquerque, New Mexico in Response to Peak Discharge Reductions and Engineering: Magnitude and Uncertainty of Change from Air Photo Measurements
- 10.1016/0198-0254(85)92806-7 may be a valid DOI for title: The Prodelta Environment of a Fjord - Suspended Particle Dynamics
- 10.1016/0022-1694(94)02540-r may be a valid DOI for title: A Review of Baseflow Recession Analysis
- 10.1038/sdata.2017.4 may be a valid DOI for title: WorldPop, Open Data for Spatial Demography
- 10.1175/bams-d-11-00094.1 may be a valid DOI for title: An Overview of CMIP5 and the Experiment Design
- 10.4324/9781003026709-6 may be a valid DOI for title: Bank Processes, Bed Material Movement and Planform Development in a Meandering River
- 10.3376/1081-1710(2008)33[76:spoaad]2.0.co;2 may be a valid DOI for title: Seasonal Profiles of Aedes Aegypti (Diptera: Culicidae) Larval Habitats in an Urban Area of Costa Rica with a History of Mosquito Control
- 10.1016/j.ocemod.2016.08.002 may be a valid DOI for title: Impacts of the Representation of Riverine Freshwater Input in the Community Earth System Model
- 10.4269/ajtmh.1995.53.595 may be a valid DOI for title: Understanding Productivity, a Key to Aedes Aegypti Surveillance
- 10.4269/ajtmh.1996.54.543 may be a valid DOI for title: Critical Examination of Aedes Aegypti Indices: Correlations with Abundance
- 10.1111/j.1365-2486.2007.01381.x may be a valid DOI for title: The Disappearance of Relict Permafrost in Boreal North America: Effects on Peatland Carbon Storage and Fluxes
- 10.1002/ppp.3430020207 may be a valid DOI for title: Differential Frost Heave, Load Casting and Convection: Converging Mechanisms; a Discussion of the Origin of Cryoturbations
- 10.1002/ppp.3430020207 may be a valid DOI for title: Differential Frost Heave, Load Casting and Convection: Converging Mechanisms; a Discussion of the Origin of Cryoturbations
- 10.1515/ijnsns.2009.10.3.273 may be a valid DOI for title: Accelerating Markov Chain Monte Carlo Simulation by Differential Evolution with Self-Adaptive Randomized Subspace Sampling
- 10.1080/04353676.1987.11880197 may be a valid DOI for title: Riverbank Erosion in the Colville Delta, Alaska
- 10.1016/s0169-555x(03)00157-0 may be a valid DOI for title: Hydrologic and Geomorphic Processes in the Colville River Delta, Alaska
- 10.1038/nature05040 may be a valid DOI for title: Methane Bubbling from Siberian Thaw Lakes as a Positive Feedback to Climate Warming
- 10.1002/2017jd026899 may be a valid DOI for title: Hydrological Drought in the Anthropocene: Impacts of Local Water Extraction and Reservoir Regulation in the US
- 10.1002/(sici)1099-1530(199801/03)9:1<23::aid-ppp274>3.0.co;2-y may be a valid DOI for title: Permafrost Changes in Rock Walls and the Retreat of Alpine Glaciers: A Thermal Modelling Approach
- 10.1029/2006jf000696 may be a valid DOI for title: Time-Dependent Morphology of Thaw Lakes and Taliks in Deep and Shallow Ground Ice
- 10.1111/j.1752-1688.2007.00160.x may be a valid DOI for title: Use of Synthetic Aperture Radar for Selecting Alaskan Lakes for Winter Water Use1
- 10.1093/jmedent/45.6.1173 may be a valid DOI for title: Rapid Estimation of Aedes Aegypti Population Size Using Simulation Modeling, with a Novel Approach to Calibration and Field Validation
- 10.1029/2007gl030156 may be a valid DOI for title: Modeling Large-scale Inundation of Amazonian Seasonally Flooded Wetlands
- 10.2475/ajs.257.3.204 may be a valid DOI for title: Factors Influencing Erosion of a Cohesive River Bank
- 10.1016/b978-0-12-812365-2.00003-2 may be a valid DOI for title: Mosquito-Borne Diseases
- 10.1016/b978-0-12-812365-2.00003-2 may be a valid DOI for title: Mosquito-Borne Diseases
- 10.1306/819a4274-16c5-11d7-8645000102c1865d may be a valid DOI for title: Variations in Morphology of Major River Deltas as Functions of Ocean Wave and River Dischare Regimes
- 10.1086/628028 may be a valid DOI for title: Mississippi River Mouth Processes: Effluent Dynamics and Morphologic Development
- 10.1080/01431160600589179 may be a valid DOI for title: Modification of Normalised Difference Water Index (NDWI) to Enhance Open Water Features in Remotely Sensed Imagery
- 10.1016/j.ecolmodel.2008.10.005 may be a valid DOI for title: Uncertainty Analysis of Transient Population Dynamics
- 10.1016/j.csda.2010.06.028 may be a valid DOI for title: Understanding and Comparisons of Different Sampling Approaches for the Fourier Amplitudes Sensitivity Test (FAST)
- 10.1029/2010wr009726 may be a valid DOI for title: A Physically Based Description of Floodplain Inundation Dynamics in a Global River Routing Model
- 10.1002/ppp.451 may be a valid DOI for title: Shrinking Thermokarst Ponds and Groundwater Dynamics in Discontinuous Permafrost near Council, Alaska
- 10.1029/2009gb003481 may be a valid DOI for title: Rapid Carbon Accretion and Organic Matter Pool Stabilization in Riverine Floodplain Soils
- 10.1002/(sici)1099-1530(199701)8:1<45::aid-ppp240>3.0.co;2-k may be a valid DOI for title: Effects of Climate on the Active Layer and Permafrost on the North Slope of Alaska, U.S.A
- 10.1080/10889370802175895 may be a valid DOI for title: Statistics and Characteristics of Permafrost and Ground-Ice Distribution in the Northern Hemisphere
- 10.1016/j.gloplacha.2007.05.003 may be a valid DOI for title: Transient Projections of Permafrost Distribution in Canada during the 21st Century under Scenarios of Climate Change

INVALID DOIs

- 10.1590/S0120-41572015000200014 is INVALID
- 10.2987/8756-971X(2006)22[565:APIKTT]2.0.CO;2 is INVALID
- ARTN e2515: 10.1371/journal.pntd.0002515 is INVALID
- 10.1641/0006-3568(2004)054[0413:TNDHHC]2.0.CO;2 is INVALID
- Artn 20160005: 10.1098/Rsif.2016.0005 is INVALID
- Artn W12445: 10.1029/2008wr006917 is INVALID
- ARTN e0124037: 10.1371/journal.pone.0124037 is INVALID
- ARTN e2503: 10.1371/journal.pntd.0002503 is INVALID
- ARTN e0149282: 10.1371/journal.pone.0149282 is INVALID
- Artn Rg2004: 10.1029/2005rg000183 is INVALID
- 10.1002/rra is INVALID
- Artn 218: 10.1186/S13071-018-2779-7 is INVALID
- 10.1130/0016-7606(1972)83[475:ACDFSG]2.0.CO;2 is INVALID
- Artn 1046: 10.3390/Ijerph14091046 is INVALID
- 105194/bg-10-1-2013 is INVALID
- ARTN e08347: 10.7554/eLife.08347 is INVALID
- ARTN e22701: 10.1371/journal.pone.0022701 is INVALID
- ARTN e52235: 10.1371/journal.pone.0052235 is INVALID
- 10.1029/2010WR009712@10.1002/(ISSN)1944-7973.SBRS1 is INVALID
- ARTN e0005828: 10.1371/journal.pntd.0005828 is INVALID
- Artn 20: 10.1186/1756-3305-6-20 is INVALID
- ARTN e508: 10.1371/journal.pntd.0000508 is INVALID
- ARTN e0005347: 10.1371/journal.pntd.0005347 is INVALID
- ARTN e15272: 10.7554/eLife.15272 is INVALID
- Artn 167: 10.1186/1471-2334-14-167 is INVALID
- Artn 20162078: 10.1098/Rspb.2016.2078 is INVALID
- 10.1130/0016-7606(1994)106<1494 is INVALID
- 10.1579/0044-7447(2006)35[339:hciafe]2.0.co;2 is INVALID
- Artn 20120921: 10.1098/Rsif.2012.0921 is INVALID
- http://dx.doi.org/10.15585/mmwr.mm6717e1 is INVALID because of 'https://doi.org/' prefix
- Artn 180073: 10.1038/Sdata.2018.73 is INVALID
- ARTN e71247: 10.1371/journal.pone.0071247 is INVALID
- ARTN e1795: 10.1371/journal.pntd.0001795 is INVALID
- 10.1130/0016-7606(1966)77[859:MRBFFJ]2.0.CO;2 is INVALID
- ARTN e2207: 10.1371/journal.pntd.0002207 is INVALID
- ARTN e830: 10.1371/journal.pntd.0000830 is INVALID
- http://dx.doi.org/10.1016/j.apm.2013.05.036 is INVALID because of 'https://doi.org/' prefix

jonschwenk commented 3 years ago

@kbarnhart After a Zotero update, it started exporting my full library by default instead of just a particular collection. whedon's DOI check is thus of my entire library, not just the references in the paper. I have fixed the .bib file in the RivGraph repo to only contain the relevant refs, but I'm not sure how to ask whedon to re-run the DOI check.

kbarnhart commented 3 years ago

@whedon check references

whedon commented 3 years ago

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

OK DOIs

- 10.1029/2020WR027199 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1029/2019JF005206 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.5281/zenodo.3946761 is OK
- 10.1029/2019WR026867 is OK
- 10.1002/esp.3482 is OK
- 10.3390/ijgi9110658 is OK
- 10.1002/2016EA000196 is OK
- 10.13140/RG.2.2.31051.44323 is OK
- 10.5194/esurf-8-87-2020 is OK
- 10.5281/zenodo.3783866 is OK
- 10.1002/2014WR016604 is OK
- 10.1002/2014WR016577 is OK
- 10.1073/pnas.1708404114 is OK
- 10.1002/essoar.10502024.1 is OK
- 10.7717/peerj.453 is OK
- 10.1029/2019GL086710 is OK

MISSING DOIs

- None

INVALID DOIs

- None

kbarnhart commented 3 years ago

@jonschwenk done. for reference here is the list of things whedon can do

leotrs commented 3 years ago

In trying to install the package, I ran into some problems reported here. I will continue my review pending the fix.

Update: the mentioned issue is fixed and now I can continue my review.

whedon commented 3 years ago

:wave: @eriknes, please update us on how your review is going.

whedon commented 3 years ago

:wave: @leotrs, please update us on how your review is going.

kbarnhart commented 3 years ago

@eriknes and @leotrs, we have an automatic reminder two weeks into the review. Feel free to provide an update if you have one.

@leotrs making an issue in the main repo and linking it here is perfect. Thank you! If you paste openjournals/joss-reviews/issues/2952 into the issue then GitHub links the issues nicely.

leotrs commented 3 years ago

I have finished the review checklist and it is my opinion that the software and manuscript meet JOSS standards.

Issues in target repository associated to my review:

jonschwenk commented 3 years ago

@kbarnhart Just curious how things are going here. Haven't seen any movement from @eriknes...

eriknes commented 3 years ago

Hi,

Sorry for the late reply

I have a revision due this weekend and will complete this review over the weekend if that's ok?

Best,

Erik

On Thu, Feb 18, 2021 at 1:52 AM Jon Schwenk notifications@github.com wrote:

@kbarnhart https://github.com/kbarnhart Just curious how things are going here. Haven't seen any movement from @eriknes https://github.com/eriknes...

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/2952#issuecomment-780953979, or unsubscribe https://github.com/notifications/unsubscribe-auth/AF7R2DE6C345X6I3BBTUGP3S7RQFTANCNFSM4WBGVY7Q .

kbarnhart commented 3 years ago

@jonschwenk thanks for checking in. The review started Jan 13th, and JOSS is requesting reviewers complete their reviews within 6 weeks. @eriknes if you could complete the review by the middle of next week that would be great.

eriknes commented 3 years ago

Dear Katy,

It seems like the invitation may have expired - can you resend it to me? I will complete the review tomorrow morning CET time.

I am sorry it has taken some time.

Best regards,

Erik

On Thu, Feb 18, 2021 at 2:16 PM Katy Barnhart notifications@github.com wrote:

@jonschwenk https://github.com/jonschwenk thanks for checking in. The review started Jan 13th, and JOSS is requesting reviewers complete their reviews within 6 weeks. @eriknes https://github.com/eriknes if you could complete the review by the middle of next week that would be great.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/2952#issuecomment-781336163, or unsubscribe https://github.com/notifications/unsubscribe-auth/AF7R2DCIVC3Z6KDDYQ6AQ2DS7UHLFANCNFSM4WBGVY7Q .

kbarnhart commented 3 years ago

@whedon re-invite @eriknes as reviewer

whedon commented 3 years ago

OK, the reviewer has been re-invited.

@eriknes please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

kbarnhart commented 3 years ago

@eriknes this link should work. Let me know if it doesnt.

eriknes commented 3 years ago

I am sorry this took a while. I have installed and tested the software and it works as expected. I have a certain idea about the effort required to make network mapping of river deltas work, so I am actually very impressed!

I have a couple of comments regarding the documentation of the algorithms used and their performance. But it seems like that is not part of the review process? It is the first time I am reviewing for JOSS, and I understand it is a developer oriented journal, but I would have liked to see at least brief descriptions of the algorithms in the software paper, even if references are provided. Skeletonization and pruning methods, as far as I know, usually result in networks with noise.

jonschwenk commented 3 years ago

Hi @eriknes , glad you were successful in demo-ing RivGraph. It has been challenging and fun to develop, so I'm also glad that you see its value!

As for the algorithm documentation--I believe you are correct in that the purpose of the JOSS paper is not really to explain the algorithm logic, but more to demonstrate their utility. Please note that we do provide full API documentation for (nearly) every function of RG. We've also tried to leave comments throughout to help the curious understand what's going on. For example, take a look at the prune_delta() source code. The steps to prune the vectorized skeleton are laid out fairly explicitly there. If you dig into each of the steps, you'll find similar commenting. We've also tried to name functions as intuitively as possible, often at the expense of brevity. It's not perfect, but we hope it's enough for possible contributors and the curious to unravel the inner workings.

kbarnhart commented 3 years ago

Sorry for the delay on weighing in.

In a case such as this submission, it would be reasonable to add a bit more to the paper that describe the approach to skeletonization and pruning. Perhaps one more paragraph in "basic functionality" section. That would give the potential user a bit more context about why these methods can be tricky and the approaches that RivGraph takes to address them.

I would also expect that somewhere in the documentation (an overview section, examples, or in the API all seem reasonable places to me) there is sufficient description so that a reader can understand the algorithms conceptually. For example, this part of the delta example: https://jonschwenk.github.io/RivGraph/examples/delta_example/delta_example.html#pruning-the-network

If there are specific algorithmic details that @eriknes thinks should be highlighted in the docs, I'd recommend making an in-repo issue to state what they are and discuss. The balance to keep here is that the algorithm description should serve to help a user understand what the software is doing, and thus use the software correctly.

@jonschwenk Agreed! The comments you've left in the source code are really nice.

Hopefully my comment clarifies these questions, if not, please let me know.

eriknes commented 3 years ago

Thank you @kbarnhart for weighing in on this

A lot of design choices must have been made to make the output consistent. Although it may be outside the scope of the paper for this journal to give the full algorithmic details, I think it would be nice to briefly describe some of these choices and how well the software can be expected to perform. For instance, I expect that skeletonization of a river delta network with a lot of noise along the edges of the channels would get some false positive branching points / nodes. Maybe the authors could report how well the code performs compared to a few deltas where the nodes and edges have been manually delineated, e.g. the ones shown by Tejedor et al.?

Overall a nice piece of work in my opinion

Erik

On Mon, Mar 1, 2021 at 4:43 PM Katy Barnhart notifications@github.com wrote:

Sorry for the delay on weighing in.

In a case such as this submission, it would be reasonable to add a bit more to the paper that describe the approach to skeletonization and pruning. Perhaps one more paragraph in "basic functionality" section. That would give the potential user a bit more context about why these methods can be tricky and the approaches that RivGraph takes to address them.

I would also expect that somewhere in the documentation (an overview section, examples, or in the API all seem reasonable places to me) there is sufficient description so that a reader can understand the algorithms conceptually. For example, this part of the delta example: https://jonschwenk.github.io/RivGraph/examples/delta_example/delta_example.html#pruning-the-network

If there are specific algorithmic details that @eriknes https://github.com/eriknes thinks should be highlighted in the docs, I'd recommend making an in-repo issue to state what they are and discuss. The balance to keep here is that the algorithm description should serve to help a user understand what the software is doing, and thus use the software correctly.

@jonschwenk https://github.com/jonschwenk Agreed! The comments you've left in the source code are really nice.

Hopefully my comment clarifies these questions, if not, please let me know.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/2952#issuecomment-788046429, or unsubscribe https://github.com/notifications/unsubscribe-auth/AF7R2DBE3JTERUVUUISQDX3TBOYY3ANCNFSM4WBGVY7Q .

jonschwenk commented 3 years ago

We can add some to the text about what the functions are doing. I believe most of this is already in either the examples or the documentation, but I have no problem adding more to the manuscript.

In your example case, @eriknes, the bottom line is that the skeletonization will ~100% respect the mask that you provide. If the mask has many spurious loops (e.g. island "speckling"), those will be retained as RivGraph retains (almost) all connectivity of the mask. If it's just noise on the edges of a channel, these will get pruned if they're not part of a loop. It is up to the user to fill in spurious islands in their mask before applying RivGraph functions. Will clarify this and a few other points in the manuscript and post an update when ready.

Thanks for the feedback!

jonschwenk commented 3 years ago

@eriknes and @kbarnhart We have updated the paper to include a bit more about the masks and the algorithm reasoning. The edits are not extremely detailed, but hopefully they provide enough to assuage the questions posed by Erik (and similar ones). Most of the changes are in the Functionality section--one new paragraph was added, and more description is given in the method descriptions.

jonschwenk commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

kbarnhart commented 3 years ago

@eriknes please let me know if @jonschwenk 's updates have addressed your concerns.

@jonschwenk thanks for making these updates.

eriknes commented 3 years ago

Yes, I think this is probably sufficient as per the JOSS guidelines of software papers

Thank you

On Thu, Mar 4, 2021 at 4:44 PM Katy Barnhart notifications@github.com wrote:

@eriknes https://github.com/eriknes please let me know if @jonschwenk https://github.com/jonschwenk 's updates have addressed your concerns.

@jonschwenk https://github.com/jonschwenk thanks for making these updates.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/2952#issuecomment-790711796, or unsubscribe https://github.com/notifications/unsubscribe-auth/AF7R2DFEWLCQVYAPZXE62TTTB6TFXANCNFSM4WBGVY7Q .

kbarnhart commented 3 years ago

@leotrs and @eriknes based on the comments here, the in-repo issues, and the checklists it looks as if your reviews are complete an no remaining issues exits. If this is the case and you think this manuscript is ready to be accepted, please indicate so here.

@jonschwenk once the reviewers have indicated the submission is ready to move forward I will complete a couple of steps (e.g., copyediting), and then we can move forward with the final steps in the JOSS publication process.

eriknes commented 3 years ago

Yes, confirmed

On Fri, Mar 5, 2021 at 4:49 PM Katy Barnhart notifications@github.com wrote:

@leotrs https://github.com/leotrs and @eriknes https://github.com/eriknes based on the comments here, the in-repo issues, and the checklists it looks as if your reviews are complete an no remaining issues exits. If this is the case and you think this manuscript is ready to be accepted, please indicate so here.

@jonschwenk https://github.com/jonschwenk once the reviewers have indicated the submission is ready to move forward I will complete a couple of steps (e.g., copyediting), and then we can move forward with the final steps in the JOSS publication process.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/2952#issuecomment-791504258, or unsubscribe https://github.com/notifications/unsubscribe-auth/AF7R2DDBSVOR5VFMNPPN6OTTCD4QLANCNFSM4WBGVY7Q .

leotrs commented 3 years ago

Yes.

On Fri, Mar 5, 2021, 10:52 AM Erik Nesvold notifications@github.com wrote:

Yes, confirmed

On Fri, Mar 5, 2021 at 4:49 PM Katy Barnhart notifications@github.com wrote:

@leotrs https://github.com/leotrs and @eriknes https://github.com/eriknes based on the comments here, the in-repo issues, and the checklists it looks as if your reviews are complete an no remaining issues exits. If this is the case and you think this manuscript is ready to be accepted, please indicate so here.

@jonschwenk https://github.com/jonschwenk once the reviewers have indicated the submission is ready to move forward I will complete a couple of steps (e.g., copyediting), and then we can move forward with the final steps in the JOSS publication process.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub < https://github.com/openjournals/joss-reviews/issues/2952#issuecomment-791504258 , or unsubscribe < https://github.com/notifications/unsubscribe-auth/AF7R2DDBSVOR5VFMNPPN6OTTCD4QLANCNFSM4WBGVY7Q

.

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kbarnhart commented 3 years ago

@whedon check references

whedon commented 3 years ago

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

OK DOIs

- 10.1029/2020WR027199 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1029/2019JF005206 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.5281/zenodo.3946761 is OK
- 10.1029/2019WR026867 is OK
- 10.1002/esp.3482 is OK
- 10.3390/ijgi9110658 is OK
- 10.1002/2016EA000196 is OK
- 10.13140/RG.2.2.31051.44323 is OK
- 10.5194/esurf-8-87-2020 is OK
- 10.5281/zenodo.3783866 is OK
- 10.1002/2014WR016604 is OK
- 10.1002/2014WR016577 is OK
- 10.1073/pnas.1708404114 is OK
- 10.1002/essoar.10502024.1 is OK
- 10.7717/peerj.453 is OK
- 10.1029/2019GL086710 is OK

MISSING DOIs

- None

INVALID DOIs

- None

kbarnhart commented 3 years ago

@whedon compile pdf

whedon commented 3 years ago

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

@whedon commands

kbarnhart commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

kbarnhart commented 3 years ago

@jonschwenk I've proposed some very minor copyedits at jonschwenk/RivGraph/pull/48

Please consider, and if you don't disagree, merge. Once you've done that please double check that the paper compiles and complete the following next steps:

[ ] Make a tagged release of your software, and list the version tag of the archived version here.
[ ] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
[ ] Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
[ ] Please list the DOI of the archived version here.

I can then move forward with accepting the submission.

jonschwenk commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

jonschwenk commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

jonschwenk commented 3 years ago

@kbarnhart Checklist complete.

[x] Recompiled paper
[x] New tagged release has been created: v0.4
[x] v0.4 has been stored at Zenodo.
[x] Metadata matches title and authors, includes ORCIDs.
[x] Zenodo DOI: 10.5281/zenodo.4591559

kbarnhart commented 3 years ago

@whedon set 10.5281/zenodo.4591559 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.4591559 is the archive.

kbarnhart commented 3 years ago

@whedon set v0.4 as version

whedon commented 3 years ago

OK. v0.4 is the version.

kbarnhart commented 3 years ago

@whedon accept

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

openjournals / joss-reviews