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Review from JOSS editor #42

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Review from JOSS editor #42

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98731ef
fix typos, update bibliography
Y0dler Nov 25, 2024
9315947
unite conclusion and summary, then remove conclusion
Y0dler Nov 25, 2024
6732e12
test protecting cases
Y0dler Nov 25, 2024
cfbde16
fix all cases
Y0dler Nov 25, 2024
5e256e7
actually fix all cases
Y0dler Nov 25, 2024
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24 changes: 17 additions & 7 deletions docs/source/literature.bib
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -82,11 +82,12 @@ @article{RN150
@book{RN162,
author = {Kruschke, John K.},
title = {Doing Bayesian Data Analysis},
edition = {1st Edition},
edition = {Second Edition},
publisher={Academic Press},
isbn = {9780123814852},
year = {2010},
type = {Book}
year = {2015},
type = {Book},
doi = {http://dx.doi.org/10.1016/B978-0-12-405888-0.00001-5}
}

@article{RN144,
Expand All @@ -96,7 +97,8 @@ @article{RN144
volume = {12},
pages = {171-178},
year = {1985},
type = {Journal Article}
type = {Journal Article},
url = {http://www.jstor.org/stable/4615982},
}


Expand All @@ -107,7 +109,8 @@ @article{RN152
volume = {7},
number = {4},
year = {1992},
type = {Journal Article}
type = {Journal Article},
doi = {10.1214/ss/1177011136}
}

@article{RN153,
Expand Down Expand Up @@ -176,7 +179,7 @@ @article{RN146
volume = {11},
pages = {3571-3594},
year = {2010},
type = {Journal Article}
type = {Journal Article},
}

@article{RN147,
Expand Down Expand Up @@ -221,6 +224,7 @@ @article{vivo2012bayesian
number={6},
pages={2622--2630},
year={2012},
doi={https://doi.org/10.1021/ac202124t},
publisher={ACS Publications}
}

Expand All @@ -232,6 +236,7 @@ @article{woldegebriel2015probabilistic
number={14},
pages={7345--7355},
year={2015},
doi={https://doi.org/10.1021/acs.analchem.5b01521},
publisher={ACS Publications}
}

Expand All @@ -242,6 +247,7 @@ @article{briskot2019prediction
volume={1587},
pages={101--110},
year={2019},
doi={https://doi.org/10.1016/j.chroma.2018.11.076},
publisher={Elsevier}
}

Expand All @@ -252,6 +258,7 @@ @article{yamamoto2021uncertainty
volume={175},
pages={223--237},
year={2021},
doi={https://doi.org/10.1016/j.cherd.2021.09.003},
publisher={Elsevier}
}

Expand All @@ -263,6 +270,7 @@ @article{wiczling2016much
number={1},
pages={997--1002},
year={2016},
doi={https://doi.org/10.1021/acs.analchem.5b03859},
publisher={ACS Publications}
}

Expand All @@ -274,16 +282,18 @@ @article{kelly1971estimation
number={10},
pages={1170--1183},
year={1971},
doi={https://doi.org/10.1021/ac60304a011},
publisher={ACS Publications}
}

@article{kelly1971application,
title={Application of method of maximum posterior probability to estimation of gas-chromatographic peak parmeters},
title={Application of method of maximum posterior probability to estimation of gas-chromatographic peak parameters},
author={Kelly, PC and Harris, WE},
journal={Analytical Chemistry},
volume={43},
number={10},
pages={1184--1195},
year={1971},
doi={https://doi.org/10.1021/ac60304a005},
publisher={ACS Publications}
}
63 changes: 32 additions & 31 deletions paper/literature.bib
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
@softmisc{nutpie,
@misc{nutpie,
author = {Seyboldt, Adrian and {PyMC Developers}},
keywords = {Software},
license = {MIT},
Expand Down Expand Up @@ -44,9 +44,9 @@ @article{matplotlib
year = 2007
}

@softmisc{matplotlibzenodo,
@misc{matplotlibzenodo,
author = {{The Matplotlib Development Team}},
title = {Matplotlib: Visualization with Python},
title = {{Matplotlib: Visualization with Python}},
keywords = {software},
month = may,
year = 2024,
Expand All @@ -58,16 +58,15 @@ @softmisc{matplotlibzenodo

@article{RN173,
author = {Hoffmann, Matthew D. and Gelman, Andrew},
title = {The No-U-Turn Sampler: Adaptively Setting Path Lengths in Hamiltonian Monte Carlo},
title = {{The No-U-Turn Sampler: Adaptively Setting Path Lengths in Hamiltonian Monte Carlo}},
journal = {Journal of Machine Learning Research},
volume = {15},
year = {2014},
type = {Journal Article}
}

@article{RN150,
author = {Abril-Pla, O. and Andreani, V. and Carroll, C. and Dong, L. and Fonnesbeck, C. J. and Kochurov, M. and Kumar, R. and Lao, J. and Luhmann, C. C. and Martin, O. A. and Osthege, M. and Vieira, R. and Wiecki, T. and Zinkov, R.},
title = {{PyMC}: a modern, and comprehensive probabilistic programming framework in Python},
title = {{PyMC}: a modern, and comprehensive probabilistic programming framework in {P}ython},
journal = {PeerJ Comput Sci},
volume = {9},
pages = {e1516},
Expand All @@ -76,16 +75,17 @@ @article{RN150
doi = {10.7717/peerj-cs.1516},
url = {https://www.ncbi.nlm.nih.gov/pubmed/37705656},
year = {2023},
type = {Journal Article}
}

@book{RN162,
author = {Kruschke, John K.},
title = {Doing Bayesian Data Analysis},
edition = {1st Edition},
title = {{Doing Bayesian Data Analysis}},
edition = {Second Edition},
publisher={Academic Press},
isbn = {9780123814852},
year = {2010},
type = {Book}
year = {2015},
type = {Book},
doi = {http://dx.doi.org/10.1016/B978-0-12-405888-0.00001-5}
}

@article{RN144,
Expand All @@ -95,23 +95,23 @@ @article{RN144
volume = {12},
pages = {171-178},
year = {1985},
type = {Journal Article}
url = {http://www.jstor.org/stable/4615982},
}


@article{RN152,
author = {Gelman, Andrew and Rubin, Donald B.},
title = {Inference from Iterative Simulation Using Multiple Sequences},
title = {{Inference from Iterative Simulation Using Multiple Sequences}},
journal = {Statistical Science},
volume = {7},
number = {4},
year = {1992},
type = {Journal Article}
doi = {10.1214/ss/1177011136}
}

@article{RN153,
author = {Grushka, E.},
title = {Characterization of exponentially modified Gaussian peaks in chromatography},
title = {{Characterization of exponentially modified Gaussian peaks in chromatography}},
journal = {Anal Chem},
volume = {44},
number = {11},
Expand All @@ -121,12 +121,11 @@ @article{RN153
doi = {10.1021/ac60319a011},
url = {https://www.ncbi.nlm.nih.gov/pubmed/22324584},
year = {1972},
type = {Journal Article}
}

@article{RN149,
author = {Hemmerich, J. and Noack, S. and Wiechert, W. and Oldiges, M.},
title = {Microbioreactor Systems for Accelerated Bioprocess Development},
title = {{Microbioreactor Systems for Accelerated Bioprocess Development}},
journal = {Biotechnol J},
volume = {13},
number = {4},
Expand All @@ -136,7 +135,6 @@ @article{RN149
doi = {10.1002/biot.201700141},
url = {https://www.ncbi.nlm.nih.gov/pubmed/29283217},
year = {2018},
type = {Journal Article}
}

@article{RN148,
Expand All @@ -151,12 +149,11 @@ @article{RN148
doi = {10.1002/1097-0290(20010205)72:3<346::aid-bit12>3.0.co;2-x},
url = {https://www.ncbi.nlm.nih.gov/pubmed/11135205},
year = {2001},
type = {Journal Article}
}

@article{RN145,
author = {Vehtari, Aki and Gelman, Andrew and Gabry, Jonah},
title = {Practical Bayesian model evaluation using leave-one-out cross-validation and WAIC},
title = {{Practical Bayesian model evaluation using leave-one-out cross-validation and WAIC}},
journal = {Statistics and Computing},
volume = {27},
number = {5},
Expand All @@ -165,29 +162,26 @@ @article{RN145
1573-1375},
doi = {10.1007/s11222-016-9696-4},
year = {2016},
type = {Journal Article}
}

@article{RN146,
author = {Watanabe, Sumio},
title = {Asymptotic Equivalence of Bayes Cross Validation and Widely Applicable Information Criterion in Singular Learning Theory},
title = {{Asymptotic Equivalence of Bayes Cross Validation and Widely Applicable Information Criterion in Singular Learning Theory}},
journal = {Journal of machine learning research},
volume = {11},
pages = {3571-3594},
year = {2010},
type = {Journal Article}
}

@article{RN147,
author = {Kumar, Ravin and Carroll, Colin and Hartikainen, Ari and Martin, Osvaldo},
title = {ArviZ a unified library for exploratory analysis of Bayesian models in Python},
title = {{ArviZ a unified library for exploratory analysis of Bayesian models in Python}},
journal = {Journal of Open Source Software},
volume = {4},
number = {33},
issn = {2475-9066},
doi = {10.21105/joss.01143},
year = {2019},
type = {Journal Article}
}

@article{harris2020array,
Expand All @@ -213,55 +207,60 @@ @article{harris2020array
}

@article{vivo2012bayesian,
title={Bayesian approach for peak detection in two-dimensional chromatography},
title={{Bayesian approach for peak detection in two-dimensional chromatography}},
author={Viv{\'o}-Truyols, Gabriel},
journal={Analytical chemistry},
volume={84},
number={6},
pages={2622--2630},
year={2012},
doi={https://doi.org/10.1021/ac202124t},
publisher={ACS Publications}
}

@article{woldegebriel2015probabilistic,
title={Probabilistic model for untargeted peak detection in LC--MS using Bayesian statistics},
title={{Probabilistic model for untargeted peak detection in LC--MS using Bayesian statistics}},
author={Woldegebriel, Michael and Viv{\'o}-Truyols, Gabriel},
journal={Analytical chemistry},
volume={87},
number={14},
pages={7345--7355},
year={2015},
doi={https://doi.org/10.1021/acs.analchem.5b01521},
publisher={ACS Publications}
}

@article{briskot2019prediction,
title={Prediction uncertainty assessment of chromatography models using Bayesian inference},
title={{Prediction uncertainty assessment of chromatography models using Bayesian inference}},
author={Briskot, Till and St\"{u}ckler, Ferdinand and Wittkopp, Felix and Williams, Christopher and Yang, Jessica and Konrad, Susanne and Doninger, Katharina and Griesbach, Jan and Bennecke, Moritz and Hepbildikler, Stefan and others},
journal={Journal of Chromatography A},
volume={1587},
pages={101--110},
year={2019},
doi={https://doi.org/10.1016/j.chroma.2018.11.076},
publisher={Elsevier}
}

@article{yamamoto2021uncertainty,
title={Uncertainty quantification for chromatography model parameters by Bayesian inference using sequential Monte Carlo method},
title={{Uncertainty quantification for chromatography model parameters by Bayesian inference using sequential Monte Carlo method}},
author={Yamamoto, Yota and Yajima, Tomoyuki and Kawajiri, Yoshiaki},
journal={Chemical Engineering Research and Design},
volume={175},
pages={223--237},
year={2021},
doi={https://doi.org/10.1016/j.cherd.2021.09.003},
publisher={Elsevier}
}

@article{wiczling2016much,
title={How much can we learn from a single chromatographic experiment? A Bayesian perspective},
title={{How much can we learn from a single chromatographic experiment? A Bayesian perspective}},
author={Wiczling, Pawe{\l} and Kaliszan, Roman},
journal={Analytical chemistry},
volume={88},
number={1},
pages={997--1002},
year={2016},
doi={https://doi.org/10.1021/acs.analchem.5b03859},
publisher={ACS Publications}
}

Expand All @@ -273,16 +272,18 @@ @article{kelly1971estimation
number={10},
pages={1170--1183},
year={1971},
doi={https://doi.org/10.1021/ac60304a011},
publisher={ACS Publications}
}

@article{kelly1971application,
title={Application of method of maximum posterior probability to estimation of gas-chromatographic peak parmeters},
title={Application of method of maximum posterior probability to estimation of gas-chromatographic peak parameters},
author={Kelly, PC and Harris, WE},
journal={Analytical Chemistry},
volume={43},
number={10},
pages={1184--1195},
year={1971},
doi={https://doi.org/10.1021/ac60304a005},
publisher={ACS Publications}
}
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