[REVIEW]: UltraNest - a robust, general purpose Bayesian inference engine

whedon commented 3 years ago

Submitting author: @JohannesBuchner (Johannes Buchner) Repository: https://github.com/JohannesBuchner/UltraNest/ Version: v3.2.0 Editor: @fboehm Reviewer: @mattpitkin, @ziatdinovmax Archive: 10.5281/zenodo.4653423

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Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/85b49ded8945434bdc1343d14cad7b6e/status.svg)](https://joss.theoj.org/papers/85b49ded8945434bdc1343d14cad7b6e)

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

@mattpitkin & @ziatdinovmax, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

Make sure you're logged in to your GitHub account
Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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

Review checklist for @mattpitkin

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 (@JohannesBuchner) 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 @ziatdinovmax

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 (@JohannesBuchner) 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

Attempting dry run of processing paper acceptance...

whedon commented 3 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2162

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2162, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true from branch joss-paper

whedon commented 3 years ago

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

OK DOIs

- 10.1063/1.1835238 is OK
- 10.1214/aoms/1177730491 is OK
- 10.1137/1116083 is OK
- 10.1126/science.220.4598.671 is OK
- 10.1103/PhysRevLett.57.2607 is OK
- 10.1080/01621459.1995.10476572 is OK
- 10.1214/aos/1056562461 is OK
- 10.1111/j.1468-4004.2006.47430.x is OK
- 10.1086/501068 is OK
- 10.1103/PhysRevD.73.123523 is OK
- 10.1063/1.2821265 is OK
- 10.1111/j.1365-2966.2007.11871.x is OK
- 10.1111/j.1365-2966.2007.12353.x is OK
- 10.1007/978-0-387-71887-3 is OK
- 10.1088/0264-9381/25/18/184010 is OK
- 10.1088/0264-9381/26/11/114011 is OK
- 10.1088/0264-9381/26/11/114008 is OK
- 10.1088/0264-9381/26/21/215003 is OK
- 10.1111/j.1365-2966.2009.14548.x is OK
- 10.1088/0264-9381/26/22/225004 is OK
- 10.1103/PhysRevD.80.095013 is OK
- 10.1111/j.1365-2966.2008.14005.x is OK
- 10.1007/JHEP04(2010)057 is OK
- 10.1093/biomet/asq021 is OK
- 10.2140/camcos.2010.5.65 is OK
- 10.1103/PhysRevD.81.062003 is OK
- 10.1088/1475-7516/2011/04/012 is OK
- 10.1088/1475-7516/2011/07/002 is OK
- 10.1063/1.3573613 is OK
- 10.1007/JHEP06(2011)042 is OK
- 10.1186/1752-0509-5-97 is OK
- 10.1111/j.1365-2966.2011.18474.x is OK
- 10.1145/1921598.1921600 is OK
- 10.1063/1.3573612 is OK
- 10.1111/j.1365-2966.2011.20288.x is OK
- 10.1111/j.1365-2966.2012.20540.x is OK
- 10.1103/PhysRevD.85.104045 is OK
- 10.1088/0004-637X/778/2/153 is OK
- 10.1371/journal.pone.0082317 is OK
- 10.1063/1.4819989 is OK
- 10.1051/0004-6361/201220063 is OK
- 10.1088/0004-637X/778/1/32 is OK
- 10.1093/mnras/stt2190 is OK
- 10.1007/s11222-014-9512-y is OK
- 10.1051/0004-6361/201322971 is OK
- 10.1051/0004-6361/201424181 is OK
- 10.1088/0264-9381/31/20/205006 is OK
- 10.1063/1.4903724 is OK
- 10.1103/PhysRevX.4.031034 is OK
- 10.1371/journal.pone.0088419 is OK
- 10.1093/mnras/stu109 is OK
- 10.1093/mnras/stv199 is OK
- 10.1098/rsos.150030 is OK
- 10.1063/1.4905971 is OK
- 10.1093/mnrasl/slv047 is OK
- 10.1093/mnras/stv1911 is OK
- 10.1088/0004-637X/802/2/107 is OK
- 10.1063/1.4933309 is OK
- 10.1103/PhysRevB.93.174108 is OK
- 10.1093/mnras/stv2370 is OK
- 10.1051/0004-6361/201527522 is OK
- 10.1093/mnras/stv2217 is OK
- 10.3847/0004-6256/152/6/203 is OK
- 10.1002/2016RS005965 is OK
- 10.1063/1.4985355 is OK
- 10.1007/s11222-018-9844-0 is OK
- 10.1088/1538-3873/aae7fc is OK
- 10.1021/acs.jctc.9b00567 is OK
- 10.1093/mnras/sty3090 is OK
- 10.1093/mnras/sty3307 is OK
- 10.21105/joss.01809 is OK
- 10.1093/mnras/staa1469 is OK
- 10.3847/1538-3881/ab5190 is OK
- 10.1093/mnras/staa278 is OK
- 10.3390/e22020185 is OK
- 10.21105/joss.00024 is OK
- 10.1086/670067 is OK

MISSING DOIs

- 10.1214/aoms/1177732360 may be a valid DOI for title: The large-sample distribution of the likelihood ratio for testing composite hypotheses
- 10.1287/opre.32.6.1296 may be a valid DOI for title: Efficient Monte Carlo procedures for generating points uniformly distributed over bounded regions
- 10.1016/s0951-8320(02)00056-x may be a valid DOI for title: An approximate epistemic uncertainty analysis approach in the presence of epistemic and aleatory uncertainties
- 10.1093/nar/gki282 may be a valid DOI for title: NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequence
- 10.1063/1.2149795 may be a valid DOI for title: Using Nested Sampling in the Analysis of Multi-Rate Sound Energy Decay in Acoustically Coupled Rooms
- 10.1214/06-ba127 may be a valid DOI for title: Nested sampling for general Bayesian computation
- 10.1021/ci7000633.s004 may be a valid DOI for title: Gaussian processes: a method for automatic QSAR modeling of ADME properties
- 10.1186/1471-2105-9-19 may be a valid DOI for title: NestedMICA as an ab initio protein motif discovery tool
- 10.1016/j.marpetgeo.2009.01.003 may be a valid DOI for title: Markov chain Monte Carlo (MCMC) sampling methods to determine optimal models, model resolution and model choice for Earth Science problems
- 10.1063/1.3275622 may be a valid DOI for title: Computational methods for Bayesian model choice
- 10.1063/1.3275625 may be a valid DOI for title: Nested sampling’s convergence
- 10.1142/s0217751x11052323 may be a valid DOI for title: Bayesian model selection for electromagnetic kaon production on the nucleon
- 10.1021/jp1012973 may be a valid DOI for title: Efficient sampling of atomic configurational spaces
- 10.1007/s11222-010-9198-8 may be a valid DOI for title: Diffusive nested sampling
- 10.1111/j.1365-2966.2011.18962.x may be a valid DOI for title: Detecting extrasolar planets from stellar radial velocities using Bayesian evidence
- 10.1201/b10905-6 may be a valid DOI for title: MCMC using Hamiltonian dynamics
- 10.1109/tim.2011.2105030 may be a valid DOI for title: A model-based probabilistic inversion framework for characterizing wire fault detection using TDR
- 10.1016/j.bpj.2011.12.053 may be a valid DOI for title: Exploring the energy landscapes of protein folding simulations with Bayesian computation
- 10.1121/1.4754550 may be a valid DOI for title: Nested sampling applied in Bayesian room-acoustics decay analysis a
- 10.1111/j.1365-2966.2012.22124.x may be a valid DOI for title: An analytic model for rotational modulations in the photometry of spotted stars
- 10.1186/1752-0509-7-72 may be a valid DOI for title: Nested sampling for parameter inference in systems biology: application to an exemplar circadian model
- 10.1201/b18502-11 may be a valid DOI for title: Hamiltonian Monte Carlo for Hierarchical Models
- 10.1002/2012wr013406 may be a valid DOI for title: Nested sampling algorithm for subsurface flow model selection, uncertainty quantification, and nonlinear calibration
- 10.21105/astro.1306.2144 may be a valid DOI for title: Importance Nested Sampling and the MultiNest Algorithm
- 10.1093/mnras/stt2122 may be a valid DOI for title: TEMPONEST: a Bayesian approach to pulsar timing analysis
- 10.1063/1.4821761 may be a valid DOI for title: Nested sampling in the canonical ensemble: Direct calculation of the partition function from NVT trajectories
- 10.1016/j.cma.2013.11.001 may be a valid DOI for title: Efficient Bayesian inference of subsurface flow models using nested sampling and sparse polynomial chaos surrogates
- 10.1002/qj.2245 may be a valid DOI for title: A nested sampling particle filter for nonlinear data assimilation
- 10.1016/j.jcp.2013.10.001 may be a valid DOI for title: Hybrid nested sampling algorithm for Bayesian model selection applied to inverse subsurface flow problems
- 10.1063/1.4903717 may be a valid DOI for title: Parallelized nested sampling
- 10.1093/bioinformatics/btu675 may be a valid DOI for title: SYSBIONS: nested sampling for systems biology
- 10.1103/physreve.89.022302 may be a valid DOI for title: Nested sampling for materials: The case of hard spheres
- 10.1002/2014wr016062 may be a valid DOI for title: Model selection on solid ground: Rigorous comparison of nine ways to evaluate Bayesian model evidence
- 10.1007/s11222-015-9617-y may be a valid DOI for title: Point Process-based Monte Carlo estimation
- 10.1016/j.strusafe.2015.02.002 may be a valid DOI for title: Moving Particles: a parallel optimal Multilevel Splitting method with application in quantiles estimation and meta-model based algorithms
- 10.1016/j.advwatres.2014.10.006 may be a valid DOI for title: Calibration of channelized subsurface flow models using nested sampling and soft probabilities
- 10.1088/1742-6596/626/1/012070 may be a valid DOI for title: Ellipsoidal nested sampling, expression of the model uncertainty and measurement
- 10.1088/0264-9381/32/21/215012 may be a valid DOI for title: Classification methods for noise transients in advanced gravitational-wave detectors
- 10.1051/ps/2015017 may be a valid DOI for title: Rare Event Simulation and Splitting for Discontinuous Random Variables
- 10.1002/2014wr016718 may be a valid DOI for title: Evaluating marginal likelihood with thermodynamic integration method and comparison with several other numerical methods
- 10.1063/1.4959055 may be a valid DOI for title: Equidistribution testing with Bayes factors and the ECT
- 10.1103/physreve.96.043311 may be a valid DOI for title: Constant-pressure nested sampling with atomistic dynamics
- 10.3390/e19080422 may be a valid DOI for title: Computing Entropies With Nested Sampling
- 10.3847/1538-3881/aa7ed8 may be a valid DOI for title: HELIOS–RETRIEVAL: An Open-source, Nested Sampling Atmospheric Retrieval Code; Application to the HR 8799 Exoplanets and Inferred Constraints for Planet Formation
- 10.1093/sysbio/syy050 may be a valid DOI for title: Model selection and parameter inference in phylogenetics using Nested Sampling
- 10.1063/1.4985378 may be a valid DOI for title: New prior sampling methods for nested sampling-Development and testing
- 10.1093/mnras/staa2345 may be a valid DOI for title: Nested sampling cross-checks using order statistics

INVALID DOIs

- https://doi.org/10.1016/j.bpj.2011.12.053 is INVALID because of 'https://doi.org/' prefix
- http://dx.doi.org/10.1063/1.3703630 is INVALID because of 'https://doi.org/' prefix
- http://dx.doi.org/10.1016/j.cpc.2015.12.005 is INVALID because of 'https://doi.org/' prefix
- http://dx.doi.org/10.1016/j.dsp.2017.07.021 is INVALID because of 'https://doi.org/' prefix

JohannesBuchner commented 3 years ago

I saw in the proof that there is a parenthesis issue near where MLFriends is mentioned, which swallowed a reference. I pushed this commit: https://github.com/JohannesBuchner/UltraNest/commit/50a5b5d60cf7cd881f87a457890dafc59217836f Otherwise, I think it is all good.

fboehm commented 3 years ago

@whedon accept from branch joss-paper

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

whedon commented 3 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2163

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2163, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true from branch joss-paper

whedon commented 3 years ago

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

OK DOIs

- 10.1063/1.1835238 is OK
- 10.1214/aoms/1177730491 is OK
- 10.1137/1116083 is OK
- 10.1126/science.220.4598.671 is OK
- 10.1103/PhysRevLett.57.2607 is OK
- 10.1080/01621459.1995.10476572 is OK
- 10.1214/aos/1056562461 is OK
- 10.1111/j.1468-4004.2006.47430.x is OK
- 10.1086/501068 is OK
- 10.1103/PhysRevD.73.123523 is OK
- 10.1063/1.2821265 is OK
- 10.1111/j.1365-2966.2007.11871.x is OK
- 10.1111/j.1365-2966.2007.12353.x is OK
- 10.1007/978-0-387-71887-3 is OK
- 10.1088/0264-9381/25/18/184010 is OK
- 10.1088/0264-9381/26/11/114011 is OK
- 10.1088/0264-9381/26/11/114008 is OK
- 10.1088/0264-9381/26/21/215003 is OK
- 10.1111/j.1365-2966.2009.14548.x is OK
- 10.1088/0264-9381/26/22/225004 is OK
- 10.1103/PhysRevD.80.095013 is OK
- 10.1111/j.1365-2966.2008.14005.x is OK
- 10.1007/JHEP04(2010)057 is OK
- 10.1093/biomet/asq021 is OK
- 10.2140/camcos.2010.5.65 is OK
- 10.1103/PhysRevD.81.062003 is OK
- 10.1088/1475-7516/2011/04/012 is OK
- 10.1088/1475-7516/2011/07/002 is OK
- 10.1063/1.3573613 is OK
- 10.1007/JHEP06(2011)042 is OK
- 10.1186/1752-0509-5-97 is OK
- 10.1111/j.1365-2966.2011.18474.x is OK
- 10.1145/1921598.1921600 is OK
- 10.1063/1.3573612 is OK
- 10.1111/j.1365-2966.2011.20288.x is OK
- 10.1111/j.1365-2966.2012.20540.x is OK
- 10.1103/PhysRevD.85.104045 is OK
- 10.1088/0004-637X/778/2/153 is OK
- 10.1371/journal.pone.0082317 is OK
- 10.1063/1.4819989 is OK
- 10.1051/0004-6361/201220063 is OK
- 10.1088/0004-637X/778/1/32 is OK
- 10.1093/mnras/stt2190 is OK
- 10.1007/s11222-014-9512-y is OK
- 10.1051/0004-6361/201322971 is OK
- 10.1051/0004-6361/201424181 is OK
- 10.1088/0264-9381/31/20/205006 is OK
- 10.1063/1.4903724 is OK
- 10.1103/PhysRevX.4.031034 is OK
- 10.1371/journal.pone.0088419 is OK
- 10.1093/mnras/stu109 is OK
- 10.1093/mnras/stv199 is OK
- 10.1098/rsos.150030 is OK
- 10.1063/1.4905971 is OK
- 10.1093/mnrasl/slv047 is OK
- 10.1093/mnras/stv1911 is OK
- 10.1088/0004-637X/802/2/107 is OK
- 10.1063/1.4933309 is OK
- 10.1103/PhysRevB.93.174108 is OK
- 10.1093/mnras/stv2370 is OK
- 10.1051/0004-6361/201527522 is OK
- 10.1093/mnras/stv2217 is OK
- 10.3847/0004-6256/152/6/203 is OK
- 10.1002/2016RS005965 is OK
- 10.1063/1.4985355 is OK
- 10.1007/s11222-018-9844-0 is OK
- 10.1088/1538-3873/aae7fc is OK
- 10.1021/acs.jctc.9b00567 is OK
- 10.1093/mnras/sty3090 is OK
- 10.1093/mnras/sty3307 is OK
- 10.21105/joss.01809 is OK
- 10.1093/mnras/staa1469 is OK
- 10.3847/1538-3881/ab5190 is OK
- 10.1093/mnras/staa278 is OK
- 10.3390/e22020185 is OK
- 10.21105/joss.00024 is OK
- 10.1086/670067 is OK

MISSING DOIs

- 10.1214/aoms/1177732360 may be a valid DOI for title: The large-sample distribution of the likelihood ratio for testing composite hypotheses
- 10.1287/opre.32.6.1296 may be a valid DOI for title: Efficient Monte Carlo procedures for generating points uniformly distributed over bounded regions
- 10.1016/s0951-8320(02)00056-x may be a valid DOI for title: An approximate epistemic uncertainty analysis approach in the presence of epistemic and aleatory uncertainties
- 10.1093/nar/gki282 may be a valid DOI for title: NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequence
- 10.1063/1.2149795 may be a valid DOI for title: Using Nested Sampling in the Analysis of Multi-Rate Sound Energy Decay in Acoustically Coupled Rooms
- 10.1214/06-ba127 may be a valid DOI for title: Nested sampling for general Bayesian computation
- 10.1021/ci7000633.s004 may be a valid DOI for title: Gaussian processes: a method for automatic QSAR modeling of ADME properties
- 10.1186/1471-2105-9-19 may be a valid DOI for title: NestedMICA as an ab initio protein motif discovery tool
- 10.1016/j.marpetgeo.2009.01.003 may be a valid DOI for title: Markov chain Monte Carlo (MCMC) sampling methods to determine optimal models, model resolution and model choice for Earth Science problems
- 10.1063/1.3275622 may be a valid DOI for title: Computational methods for Bayesian model choice
- 10.1063/1.3275625 may be a valid DOI for title: Nested sampling’s convergence
- 10.1142/s0217751x11052323 may be a valid DOI for title: Bayesian model selection for electromagnetic kaon production on the nucleon
- 10.1021/jp1012973 may be a valid DOI for title: Efficient sampling of atomic configurational spaces
- 10.1007/s11222-010-9198-8 may be a valid DOI for title: Diffusive nested sampling
- 10.1111/j.1365-2966.2011.18962.x may be a valid DOI for title: Detecting extrasolar planets from stellar radial velocities using Bayesian evidence
- 10.1201/b10905-6 may be a valid DOI for title: MCMC using Hamiltonian dynamics
- 10.1109/tim.2011.2105030 may be a valid DOI for title: A model-based probabilistic inversion framework for characterizing wire fault detection using TDR
- 10.1016/j.bpj.2011.12.053 may be a valid DOI for title: Exploring the energy landscapes of protein folding simulations with Bayesian computation
- 10.1121/1.4754550 may be a valid DOI for title: Nested sampling applied in Bayesian room-acoustics decay analysis a
- 10.1111/j.1365-2966.2012.22124.x may be a valid DOI for title: An analytic model for rotational modulations in the photometry of spotted stars
- 10.1186/1752-0509-7-72 may be a valid DOI for title: Nested sampling for parameter inference in systems biology: application to an exemplar circadian model
- 10.1201/b18502-11 may be a valid DOI for title: Hamiltonian Monte Carlo for Hierarchical Models
- 10.1002/2012wr013406 may be a valid DOI for title: Nested sampling algorithm for subsurface flow model selection, uncertainty quantification, and nonlinear calibration
- 10.21105/astro.1306.2144 may be a valid DOI for title: Importance Nested Sampling and the MultiNest Algorithm
- 10.1093/mnras/stt2122 may be a valid DOI for title: TEMPONEST: a Bayesian approach to pulsar timing analysis
- 10.1063/1.4821761 may be a valid DOI for title: Nested sampling in the canonical ensemble: Direct calculation of the partition function from NVT trajectories
- 10.1016/j.cma.2013.11.001 may be a valid DOI for title: Efficient Bayesian inference of subsurface flow models using nested sampling and sparse polynomial chaos surrogates
- 10.1002/qj.2245 may be a valid DOI for title: A nested sampling particle filter for nonlinear data assimilation
- 10.1016/j.jcp.2013.10.001 may be a valid DOI for title: Hybrid nested sampling algorithm for Bayesian model selection applied to inverse subsurface flow problems
- 10.1063/1.4903717 may be a valid DOI for title: Parallelized nested sampling
- 10.1093/bioinformatics/btu675 may be a valid DOI for title: SYSBIONS: nested sampling for systems biology
- 10.1103/physreve.89.022302 may be a valid DOI for title: Nested sampling for materials: The case of hard spheres
- 10.1002/2014wr016062 may be a valid DOI for title: Model selection on solid ground: Rigorous comparison of nine ways to evaluate Bayesian model evidence
- 10.1007/s11222-015-9617-y may be a valid DOI for title: Point Process-based Monte Carlo estimation
- 10.1016/j.strusafe.2015.02.002 may be a valid DOI for title: Moving Particles: a parallel optimal Multilevel Splitting method with application in quantiles estimation and meta-model based algorithms
- 10.1016/j.advwatres.2014.10.006 may be a valid DOI for title: Calibration of channelized subsurface flow models using nested sampling and soft probabilities
- 10.1088/1742-6596/626/1/012070 may be a valid DOI for title: Ellipsoidal nested sampling, expression of the model uncertainty and measurement
- 10.1088/0264-9381/32/21/215012 may be a valid DOI for title: Classification methods for noise transients in advanced gravitational-wave detectors
- 10.1051/ps/2015017 may be a valid DOI for title: Rare Event Simulation and Splitting for Discontinuous Random Variables
- 10.1002/2014wr016718 may be a valid DOI for title: Evaluating marginal likelihood with thermodynamic integration method and comparison with several other numerical methods
- 10.1063/1.4959055 may be a valid DOI for title: Equidistribution testing with Bayes factors and the ECT
- 10.1103/physreve.96.043311 may be a valid DOI for title: Constant-pressure nested sampling with atomistic dynamics
- 10.3390/e19080422 may be a valid DOI for title: Computing Entropies With Nested Sampling
- 10.3847/1538-3881/aa7ed8 may be a valid DOI for title: HELIOS–RETRIEVAL: An Open-source, Nested Sampling Atmospheric Retrieval Code; Application to the HR 8799 Exoplanets and Inferred Constraints for Planet Formation
- 10.1093/sysbio/syy050 may be a valid DOI for title: Model selection and parameter inference in phylogenetics using Nested Sampling
- 10.1063/1.4985378 may be a valid DOI for title: New prior sampling methods for nested sampling-Development and testing
- 10.1093/mnras/staa2345 may be a valid DOI for title: Nested sampling cross-checks using order statistics

INVALID DOIs

- https://doi.org/10.1016/j.bpj.2011.12.053 is INVALID because of 'https://doi.org/' prefix
- http://dx.doi.org/10.1063/1.3703630 is INVALID because of 'https://doi.org/' prefix
- http://dx.doi.org/10.1016/j.cpc.2015.12.005 is INVALID because of 'https://doi.org/' prefix
- http://dx.doi.org/10.1016/j.dsp.2017.07.021 is INVALID because of 'https://doi.org/' prefix

JohannesBuchner commented 3 years ago

@whedon accept deposit=true from branch joss-paper

whedon commented 3 years ago

I'm sorry @JohannesBuchner, I'm afraid I can't do that. That's something only editor-in-chiefs are allowed to do.

JohannesBuchner commented 3 years ago

Ah ok, wasn't sure if that was for me. All ready from my side.

kthyng commented 3 years ago

So why is there a giant pile of missing or invalid dois?

kthyng commented 3 years ago

@JohannesBuchner I'm looking at your Zenodo archives and they look out of order. The most recent one is associated with an older version of the code. Can I verify this is the correct DOI even though Zenodo tells me there is a more recent one when I click on it: 10.5281/zenodo.4636924.

kthyng commented 3 years ago

@JohannesBuchner Just a couple of notes for your paper:

there is a typo in the 2nd paragraph: chose > choose.
why are there extra periods in the [2] affiliation line?

fboehm commented 3 years ago

So why is there a giant pile of missing or invalid dois?

@kthyng - I verified that the dois in the generated pdf work. Should I also be concerned with the output of whedon's check on references? I had thought that it was imperfect. I don't know the algorithm that whedon uses for reference check. Does it look a the bib file? Do we need the bib file to contain only those references that are used in paper.md? Or is it ok if the bib file has unused references?

JohannesBuchner commented 3 years ago

@JohannesBuchner I'm looking at your Zenodo archives and they look out of order. The most recent one is associated with an older version of the code. Can I verify this is the correct DOI even though Zenodo tells me there is a more recent one when I click on it: 10.5281/zenodo.4636924.

Thanks, I think zenodo got confused there because I did a bunch at the same time.

The latest version is now 3.2.0. doi: 10.5281/zenodo.4653423

JohannesBuchner commented 3 years ago

@whedon set v3.2.0 as version

whedon commented 3 years ago

I'm sorry @JohannesBuchner, I'm afraid I can't do that. That's something only editors are allowed to do.

JohannesBuchner commented 3 years ago

@JohannesBuchner Just a couple of notes for your paper:
* there is a typo in the 2nd paragraph: chose > choose.

* why are there extra periods in the [2] affiliation line?

Thank you, these are fixed in the updated branch.

JohannesBuchner commented 3 years ago

@whedon generate pdf from branch joss-paper

whedon commented 3 years ago

Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...

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:

fboehm commented 3 years ago

@whedon set v3.2.0 as version

whedon commented 3 years ago

OK. v3.2.0 is the version.

fboehm commented 3 years ago

@whedon set 10.5281/zenodo.4653423 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.4653423 is the archive.

kthyng commented 3 years ago

@fboehm @JohannesBuchner As long as the DOIs in the paper are ok, it is fine. I would be remiss not to check in though with the unusual listing of doi's coming through our whedon check.

kthyng commented 3 years ago

Looks like everything is in order now!

kthyng commented 3 years ago

@whedon accept deposit=true from branch joss-paper

whedon commented 3 years ago

Doing it live! Attempting automated processing of paper acceptance...

whedon commented 3 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 3 years ago

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/2176
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.03001
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kthyng commented 3 years ago

Congrats on your new publication @JohannesBuchner! Thanks to editor @fboehm and reviewers @mattpitkin and @ziatdinovmax for your hard work, time, and expertise!!

whedon commented 3 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.03001/status.svg)](https://doi.org/10.21105/joss.03001)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03001">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03001/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03001/status.svg
   :target: https://doi.org/10.21105/joss.03001

This is how it will look in your documentation:

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Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://joss.theoj.org/reviewer-signup.html
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JohannesBuchner commented 3 years ago

Many thanks @mattpitkin and @ziatdinovmax for your useful comments, and @fboehm for the guidance through the process. It helped me a lot, as this was my first submission!

openjournals / joss-reviews