\n", "

\n", "

\n", "\n", "---\n", "[](Beetle.ipynb)\n", "## [Beetle](Beetle.ipynb) \n", "Key Features:\n", "- Sending objects within MCMC data structure.\n", "- Managing objects within sum-of-squares evaluation.\n", "- Chain/Pairwise-correlation panels.\n", "- Credible interval generation and plotting.\n", "\n", "

\n", "

\n", "

\n", "

\n", "

\n", "\n", "---\n", "[](Banana.ipynb)\n", "## [Banana](Banana.ipynb) \n", "Key Features:\n", "- Sending class objects in MCMC data structure.\n", "- Defining parameter covariance matrix.\n", "- Pairwise correlation and generation of ellipse contours.\n", "\n", "

\n", "

\n", "

\n", "

\n", "

\n", "

\n", "\n", "---\n", "[](Algae.ipynb)\n", "## [Algae](Algae.ipynb)\n", "Key Features:\n", "- Using multiple data sets.\n", "- Solving system of ODE's as model response. \n", "- Chain/Density/Pairwise-correlation panels.\n", "- Generating prediction/credible intervals for multiple quantities of interest.\n", "\n", "---\n", "[](Viscoelasticity.ipynb)\n", "## [Viscoelasticity](Viscoelasticity.ipynb)\n", "Key Features:\n", "- Loading data from `*.mat` file.\n", "- Calling C++ model using `ctypes` packages.\n", "- Specifying model parameters to be included in the sampling chain.\n", "- Plotting prediction/credible intervals with respect to time or deformation.\n", "\n", "

\n", "

\n", "

\n", "

\n", "\n", "---\n", "[](Landau_Energy.ipynb)\n", "## [Landau Energy](Landau_Energy.ipynb)\n", "Key Features:\n", "- Evaluating multidimensional functions (3-D polarization space).\n", "- Loading data from `*.mat` file.\n", "- Specifying model parameters to be included in the sampling chain.\n", "- Specifying number of observations.\n", "- Enhanced visualization using [mcmcplot](https://github.com/prmiles/mcmcplot).\n", "- Plotting prediction/credible intervals.\n", "\n", "

\n", "

\n", "

\n", "\n", "---\n", "[](Radiation_Source_Localization.ipynb)\n", "## [Radiation Source Localization](Radiation_Source_Localization.ipynb)\n", "Key Features:\n", "- Embedding user defined objects in the data structure.\n", "- Enhanced visualization using [mcmcplot](https://github.com/prmiles/mcmcplot).\n", "- Specifying model parameters to be included in the sampling chain.\n", "\n", "

\n", "

\n", "

\n", "

\n", "

\n", "

\n", "

\n", "

\n", "

\n", "\n", "---\n", "[](Running_Parallel_Chains.ipynb)\n", "## [Running Parallel Chains](Running_Parallel_Chains.ipynb)\n", "Key Features:\n", "- Running multiple chains simultaneously.\n", "- Using Gelman-Rubin chain diagnostics.\n", "- Enhanced visualization using [mcmcplot](https://github.com/prmiles/mcmcplot)." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "---\n", "# Advanced Topics\n", "These tutorials address very specific features of using the package.\n", "\n", "## [Using Chain Log Files](Chain_Log_Files.ipynb)\n", "Key Features:\n", "- Saving chain logs in binary and text formats.\n", "- Loading log files for post processing.\n", "- Assessing log history to ascertain status of simulation.\n", "\n", "## [Restarting Simulations From Chain Log Files](Restarting_Simulations.ipynb)\n", "Key Features:\n", "- Saving chain logs in text format and meta data to .json.\n", "- Loading log files for simulation restart.\n", "\n", "## [Setting the RNG Seed](Setting_Random_Seed.ipynb)\n", "Key Features:\n", "- Set seed for random number generator within [pymcmcstat](https://github.com/prmiles/pymcmcstat/wiki).\n", "- Produce repeatable simulation results.\n", "\n", "## [Calling Models Written in C++](Running_Model_Using_Ctypes.ipynb)\n", "Key Features:\n", "- Call arbitrarily complex models written in other languages (e.g., C++) using the `ctypes` package.\n", "- Generating credible/prediction intervals using C++ based model.\n", "\n", "## [Specifying Sample Variables](Specifying_Sample_Variables.ipynb)\n", "Key Features:\n", "- Specify which model parameters should be included in sampling chain.\n", "\n", "## [Estimating Error Variance for Multiple Data Sets](Estimate_Error_Variance.ipynb)\n", "Key Features:\n", "- Setting up multiple data sets in the MCMC data structure.\n", "- Defining sum-of-squares function to accomodate multiple data sets.\n", "- Estimating a separate observation error variance for each data set.\n", "- Plotting prediction/credible intervals for each data set.\n", "\n", "## [Using Normal Prior Distributions](Using_Normal_Prior_Functions.ipynb)\n", "Key Features:\n", "- Enforcing normally distributed prior functions.\n", "- Defining non-linear parameter constraints via custom prior functions.\n", "\n", "## [Advanced Interval Plotting](Advanced_Interval_Plotting.ipynb)\n", "Key Features:\n", "- Change model, data, and interval display options when plotting credible and prediction intervals.\n", "- This highlights available features as of version 1.5.0." ] } ], "metadata": { "kernelspec": { "display_name": "Python 3", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.8.3" }, "latex_envs": { "LaTeX_envs_menu_present": true, "autoclose": false, "autocomplete": true, "bibliofile": "biblio.bib", "cite_by": "apalike", "current_citInitial": 1, "eqLabelWithNumbers": true, "eqNumInitial": 1, "hotkeys": { "equation": "Ctrl-E", "itemize": "Ctrl-I" }, "labels_anchors": false, "latex_user_defs": false, "report_style_numbering": true, "user_envs_cfg": false }, "toc": { "base_numbering": 1, "nav_menu": { "height": "317px", "width": "322px" }, "number_sections": true, "sideBar": true, "skip_h1_title": false, "title_cell": "Table of Contents", "title_sidebar": "Contents", "toc_cell": false, "toc_position": { "height": "calc(100% - 180px)", "left": "10px", "top": "150px", "width": "165px" }, "toc_section_display": true, "toc_window_display": true } }, "nbformat": 4, "nbformat_minor": 2 }