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Paper: Parameter Estimation Using the Python Package pymcmcstat #466

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eeef073
added initial rst and bib files
prmiles May 13, 2019
7e3bbfe
added doi numbers for code and articles
prmiles May 13, 2019
a497739
made changes - successfully compiled
prmiles May 13, 2019
7aaed40
added additional references
prmiles May 16, 2019
e8a0f44
added methodology section
prmiles May 16, 2019
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prmiles May 16, 2019
9af8bd3
first complete rough draft
prmiles May 20, 2019
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added images
prmiles May 20, 2019
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final edits for first draft submission
prmiles May 21, 2019
6af8feb
updated reference to pymcmcstat 1.7.1
prmiles May 21, 2019
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updated intro
prmiles Jun 21, 2019
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reordered methodology
prmiles Jun 21, 2019
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updated abstract
prmiles Jun 21, 2019
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prmiles Jun 21, 2019
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prmiles Jun 21, 2019
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updated joss ref
prmiles Jun 21, 2019
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prmiles Jun 21, 2019
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updated key components list
prmiles Jun 22, 2019
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explain MCMC relation to Bayes
prmiles Jun 22, 2019
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added ref for Metropolis
prmiles Jun 22, 2019
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updated initial example
prmiles Jun 22, 2019
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added basic visualization example
prmiles Jun 22, 2019
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prmiles Jun 23, 2019
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prmiles Jun 23, 2019
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prmiles Jun 23, 2019
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prmiles Jun 23, 2019
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add Metropolis section
prmiles Jun 23, 2019
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removed monodomain section
prmiles Jun 23, 2019
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minor update to conclusion
prmiles Jun 23, 2019
ff41d67
minor upd to several sections
prmiles Jun 23, 2019
9e8eda2
fixed bug and upd case studies
prmiles Jun 23, 2019
82844d7
upd visco section
prmiles Jun 24, 2019
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upd rsl section
prmiles Jun 24, 2019
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updated conclusions
prmiles Jun 24, 2019
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add ref for mcmcplot
prmiles Jun 24, 2019
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added URLs via footnotes
prmiles Jun 26, 2019
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moved caption to above table
prmiles Jun 26, 2019
0307283
fixed typo in visc. section
prmiles Jun 26, 2019
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prmiles Jun 26, 2019
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@article{brooks1998assessing,
title={Assessing Convergence of Markov chain Monte Carlo Algorithms},
author={Brooks, Stephen P and Roberts, Gareth O},
journal={Statistics and Computing},
volume={8},
number={4},
pages={319--335},
year={1998},
}

@article{cattafesta2011actuators,
title={Actuators for active flow control},
author={Cattafesta III, Louis N and Sheplak, Mark},
journal={Annual Review of Fluid Mechanics},
volume={43},
pages={247--272},
year={2011},
publisher={Annual Reviews},
doi={10.1146/annurev-fluid-122109-160634}
}

@article{davidson2013nonaffine,
title={A nonaffine network model for elastomers undergoing finite deformations},
author={Davidson, Jacob D and Goulbourne, NC},
journal={Journal of the Mechanics and Physics of Solids},
volume={61},
number={8},
pages={1784--1797},
year={2013},
publisher={Elsevier},
doi={10.1016/j.jmps.2013.03.009},
}

@article{gelman1992inference,
title={Inference from iterative simulation using multiple sequences},
author={Gelman, Andrew and Rubin, Donald B and others},
journal={Statistical science},
volume={7},
number={4},
pages={457--472},
year={1992},
publisher={Institute of Mathematical Statistics},
doi={10.1214/ss/1177011136}
}

@article{haario2001adaptive,
title={An Adaptive Metropolis Algorithm},
author={Haario, Heikki and Saksman, Eero and Tamminen, Johanna and others},
journal={Bernoulli},
volume={7},
number={2},
pages={223--242},
year={2001},
publisher={Bernoulli Society for Mathematical Statistics and Probability},
}

@article{haario2006dram,
title={\mbox{DRAM}: Efficient Adaptive MCMC},
author={Haario, Heikki and Laine, Marko and Mira, Antonietta and Saksman, Eero},
journal={Statistics and computing},
volume={16},
number={4},
pages={339--354},
year={2006},
publisher={Springer},
doi={10.1007/s11222-006-9438-0},
}

@article{hite2019bayesian,
title={Bayesian Metropolis methods for source localization in an urban environment},
author={Hite, Jason and Mattingly, John},
journal={Radiation Physics and Chemistry},
volume={155},
pages={271--274},
year={2019},
publisher={Elsevier},
doi={10.1016/j.radphyschem.2018.06.024},
}

@article{hite2019localization,
title={Localization of a radioactive source in an urban environment using Bayesian Metropolis methods},
author={Hite, Jason and Mattingly, John and Archer, Dan and Willis, Michael and Rowe, Andrew and Bray, Kayleigh and Carter, Jake and Ghawaly, James},
journal={Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment},
volume={915},
pages={82--93},
year={2019},
publisher={Elsevier},
doi={10.1016/j.nima.2018.09.032},
}

@article{leon2018analysis,
title={Analysis of a multi-axial quantum-informed ferroelectric continuum model: Part 2—sensitivity analysis},
author={Leon, Lider S. and Smith, Ralph C. and Oates, William S. and Miles, Paul R.},
journal={Journal of Intelligent Material Systems and Structures},
volume={29},
number={13},
pages={2840--2860},
year={2018},
publisher={SAGE Publications Sage UK: London, England},
doi={10.1177/1045389X18781024},
}

@book{lines2001principles,
title={Principles and applications of ferroelectrics and related materials},
author={Lines, Malcolm E and Glass, Alastair M},
year={2001},
publisher={Oxford university press}
}

@article{mashayekhi2018fractional,
title={Fractional viscoelasticity in fractal and non-fractal media: Theory, experimental validation, and uncertainty analysis},
author={Mashayekhi, Somayeh and Miles, Paul R. and Hussaini, M. Yousuff and Oates, William S.},
journal={Journal of the Mechanics and Physics of Solids},
volume={111},
pages={134--156},
year={2018},
publisher={Elsevier},
doi={10.1016/j.jmps.2017.10.013}
}

@article{miles2015bayesian,
title={Bayesian uncertainty analysis of finite deformation viscoelasticity},
author={Miles, Paul R. and Hays, Michael and Smith, Ralph C. and Oates, William S.},
journal={Mechanics of Materials},
volume={91},
pages={35--49},
year={2015},
publisher={Elsevier},
doi={10.1016/j.mechmat.2015.07.002},
}

@article{miles2018analysis,
title={Analysis of a multi-axial quantum informed ferroelectric continuum model: Part 1—uncertainty quantification},
author={Miles, Paul R. and Leon, Lider S. and Smith, Ralph C. and Oates, William S.},
journal={Journal of Intelligent Material Systems and Structures},
volume={29},
number={13},
pages={2823--2839},
year={2018},
publisher={SAGE Publications Sage UK: London, England},
doi={10.1177/1045389X18781023},
}

@misc{pymcmcstat2019v1.7.1,
author = {Paul Miles},
title = {prmiles/pymcmcstat: v1.7.1},
month = may,
year = 2019,
doi = {10.5281/zenodo.2660145},
}

@book{rubinstein2003polymer,
title={Polymer physics},
author={Rubinstein, Michael and Colby, Ralph H. and others},
volume={23},
year={2003},
publisher={Oxford university press New York}
}

@book{smith2005smart,
title={Smart material systems: model development},
author={Smith, Ralph C.},
year={2005},
publisher={SIAM}
}

@book{smith2014uncertainty,
title={Uncertainty Quantification: Theory, Implementation, and Applications},
author={Smith, Ralph C.},
volume={12},
year={2014},
publisher={SIAM}
}
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