Merge pull request #42 from JuBiotech/review-joss-editor

Review from JOSS editor
JuBiotech · Nov 25, 2024 · 7e07f7f · 7e07f7f
2 parents bd7723c + 5e256e7
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diff --git a/docs/source/literature.bib b/docs/source/literature.bib
@@ -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,
@@ -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},
 }
 
 
@@ -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,
@@ -176,7 +179,7 @@ @article{RN146
   volume  = {11},
   pages   = {3571-3594},
   year    = {2010},
-  type    = {Journal Article}
+  type    = {Journal Article},
 }
 
 @article{RN147,
@@ -221,6 +224,7 @@ @article{vivo2012bayesian
   number={6},
   pages={2622--2630},
   year={2012},
+	doi={https://doi.org/10.1021/ac202124t},
   publisher={ACS Publications}
 }
 
@@ -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}
 }
 
@@ -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}
 }
 
@@ -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}
 }
 
@@ -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}
 }
 
@@ -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}
 }
diff --git a/paper/literature.bib b/paper/literature.bib
@@ -1,4 +1,4 @@
-@softmisc{nutpie,
+@misc{nutpie,
   author   = {Seyboldt, Adrian and {PyMC Developers}},
   keywords = {Software},
   license  = {MIT},
@@ -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,
@@ -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},
@@ -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,
@@ -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},
@@ -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},
@@ -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,
@@ -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},
@@ -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,
@@ -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}
 }
 
@@ -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}
 }