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repository. **No contribution to the code base or documentation is too small.**
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Contributors and maintainers to this project are are expected to abide the [Contributor Code of Conduct](https://github.com/TerrainBento/umami/blob/master/CODE_OF_CONDUCT.md).
Copy file name to clipboardExpand all lines: joss/paper.bib
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@Article{hobley2017creative,
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AUTHOR = {Hobley, D. E. J. and Adams, J. M. and Nudurupati, S. S. and Hutton, E. W. H. and Gasparini, N. M. and Istanbulluoglu, E. and Tucker, G. E.},
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TITLE = {Creative computing with Landlab: an open-source toolkit for building, coupling, and exploring two-dimensional numerical models of Earth-surface dynamics},
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TITLE = {{Creative computing with Landlab: an open-source toolkit for building, coupling, and exploring two-dimensional numerical models of Earth-surface dynamics}},
author = {Adams, Brian M and Eldred, Michael S and Geraci, Gianluca and Hooper, Russell W and Jakeman, John D and Maupin, Kathryn A and Monschk, Jason A and Rushdi, Ahmad A and Stephens, J Adam and Swiler, Laura P and Wildey, Timothy M and Bohnhoff, William J and Dalbey, Keith R and Ebeida, Mohamed S and Eddy, John P and Hough, Patricia D and Khalil, Mohammad and Hu, Kenneth T and Ridgway, Elliott M and Vigil, Dena M and Winokur, Justin G},
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author = {Adams, B. M. and Eldred, S. and Geraci, G. and Hooper, R. W. and Jakeman, J. D. and Maupin, K. A. and Monschk, J. A. and Rushdi, A. A. and Stephens, J. A. and Swiler, L. P. and Wildey, T. M. and Bohnhoff, W. J. and Dalbey, K. R. and Ebeida, M. S. and Eddy, J. P. and Hough, P. D. and Khalil, M. and Hu, K. T. and Ridgway, E. M. and Vigil, D. M. and Winokur, J. G.},
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title = {{Dakota, A Multilevel Parallel Object-Oriented Framework for Design Optimization, Parameter Estimation, Uncertainty Quantification, and Sensitivity Analysis: Version 6.10 User{\textquoteright}s Manual}},
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journal = {Sandia National Laboratories, Tech. Rep. SAND2014-4633},
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journal = {{Sandia National Laboratories, Tech. Rep. SAND2014-4633}},
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year = {2019}
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}
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@Article{forte2019tak,
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AUTHOR = {Forte, A. M. and Whipple, K. X.},
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TITLE = {Short communication: The Topographic Analysis Kit (TAK) for TopoToolbox},
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TITLE = {{Short communication: The Topographic Analysis Kit (TAK) for TopoToolbox}},
Copy file name to clipboardExpand all lines: notebooks/DiscretizedMisfit.ipynb
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Part 4: Application using the Discretized Misfit calculation\n",
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"# Part 5: Application using the Discretized Misfit calculation\n",
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"\n",
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"\n",
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"By now, you should have looked through [Part 1](IntroductionToMetric.ipynb) and [Part 2](IntroductionToResidual.ipynb) of the introductory notebook series. These introduced the umami `Metric` and `Residual` classes. You should have also worked through [Part 3](ExampleApplication.ipynb), which provides an example application of umami. \n",
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"By now, you should have looked through [Part 1](IntroductionToMetric.ipynb), [Part 2](IntroductionToResidual.ipynb) of the introductory notebook series, and [Part 3](OtherIO_options.ipynb) of the introductory notebook series. These introduced the umami `Metric` and `Residual` classes. You should have also worked through [Part 4](ExampleApplication.ipynb), which provides an example application of umami. \n",
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"\n",
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"## Scope\n",
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"\n",
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"Similar to [Part 3](ExampleApplication.ipynb), this application will use umami alongside the [terrainbento](https://terrainbento.readthedocs.io/en/latest/) package. As in the prior example, we will define a \"synthetic truth\" model evaluation with a specific set of input parameters, and then do a grid search letting some of those parameters vary. In this way we will explore which statistics for model-data comparison do best at identifying the \"true\" parameters. \n",
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"Similar to [Part 4](ExampleApplication.ipynb), this application will use umami alongside the [terrainbento](https://terrainbento.readthedocs.io/en/latest/) package. As in the prior example, we will define a \"synthetic truth\" model evaluation with a specific set of input parameters, and then do a grid search letting some of those parameters vary. In this way we will explore which statistics for model-data comparison do best at identifying the \"true\" parameters. \n",
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"\n",
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"This application focuses on the least intuitive of the umami calculations: the [`discretized_misfit`](https://umami.readthedocs.io/en/latest/umami.calculations.residual.discretized_misfit.html). \n",
Copy file name to clipboardExpand all lines: notebooks/ExampleApplication.ipynb
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Part 3: Example application\n",
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"# Part 4: Example application\n",
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"\n",
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"By now, you should have looked through [Part 1](IntroductionToMetric.ipynb) and [Part 2](IntroductionToResidual.ipynb) of the introductory notebook series. These introduced the umami `Metric` and `Residual` classes. \n",
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"By now, you should have looked through [Part 1](IntroductionToMetric.ipynb), [Part 2](IntroductionToResidual.ipynb) of the introductory notebook series, and [Part 3](OtherIO_options.ipynb). These introduced the umami `Metric` and `Residual` classes. \n",
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"\n",
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"## Scope\n",
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"\n",
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"source": [
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"# Next steps\n",
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"\n",
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"The next step is the final notebook in the four part introductory series: [Part 4: Application using the Discretized Misfit calculation](DiscretizedMisfit.ipynb)."
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"The next step is the final notebook in the four part introductory series: [Part 5: Application using the Discretized Misfit calculation](DiscretizedMisfit.ipynb)."
Copy file name to clipboardExpand all lines: notebooks/IntroductionToMetric.ipynb
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"source": [
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"# Part 1: Introduction to Umami and the `Metric` Class\n",
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"\n",
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"Umami is a package for calculating metrics for use with for Earth surface dynamics models. This notebook is the first half of a two-part introduction to using umami.\n",
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"Umami is a package for calculating metrics for use with for Earth surface dynamics models. This notebook is the first part of a three-part introduction to using umami.\n",
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"\n",
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"Umami was designed to work well with the [terrainbento](https://terrainbento.readthedocs.io/en/latest/) model package, as well as other models built using the [Landlab Toolkit](https://github.com/landlab/landlab). \n",
Copy file name to clipboardExpand all lines: notebooks/IntroductionToResidual.ipynb
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"source": [
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"# Part 2: Introduction to Umami and the `Residual` Class\n",
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"\n",
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"Umami is a package for calculating metrics for use with for Earth surface dynamics models. This notebook is the second half of a two-part introduction to using umami.\n",
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"Umami is a package for calculating metrics for use with for Earth surface dynamics models. This notebook is the second notebook in a three-part introduction to using umami.\n",
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"\n",
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"## Scope of this tutorial\n",
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"\n",
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"# Next steps\n",
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"\n",
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"Now that you have a sense for how the `Metric` and `Residual` classes are used, try the next notebook: [Part 3: Example application](ExampleApplication.ipynb)."
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"Now that you have a sense for how the `Metric` and `Residual` classes are used, try the next notebook: [Part 3: Other IO options (using umami without Landlab or terrainbento)](OtherIO_options.ipynb)."
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