forgot to stash pop

Author: tbrown122387

README.md

@@ -2,10 +2,14 @@
 
 [![DOI](https://zenodo.org/badge/130237492.svg)](https://zenodo.org/badge/latestdoi/130237492)
 
-This is a template library for fast particle filtering. Templated abstract base classes for different particle filters are provided (e.g. the Bootstrap Filter, the Auxiliary Particle Filter, Rao-Blackwellized particle filter, etc.), as well as non-abstract (but indeed templated) base classes for closed form filtering algorithms (e.g. Kalman Filter, Hidden Markov Model filter, etc.). Once you have a certain model in mind, all you have to do is make it into a class that inherits from the filter you want to use!
+This is a template library for fast particle filtering. Templated abstract base classes for different particle filters are provided (e.g. the Bootstrap Filter, the Auxiliary Particle Filter, Rao-Blackwellized particle filter, etc.), as well as non-abstract (but indeed templated) base classes for closed form filtering algorithms (e.g. Kalman Filter, Hidden Markov Model filter, etc.). 
+
+Once you have a certain model in mind, all you have to do is make it into a class that inherits from the filter you want to use!
 
 ## Installation
-This is a header-only library, so there is no building necessary. When you use it in another project, make sure to compile with C++11 enabled (`-std=c++11`), and to include the `include` directory of this project. Note, also, that this code all makes use of the [Eigen library](http://eigen.tuxfamily.org/).
+This is a header-only library, so there is no building necessary. When you use it in another project, make sure to compile with C++11 enabled (`-std=c++11`), and to include the `include` directory of this project. 
+
+Note, also, that this code all makes use of [Eigen](http://eigen.tuxfamily.org/) and [Boost](https://www.boost.org/).
 
 ## Examples
 Don't know how to use this? Check out the [`examples`](https://github.com/tbrown122387/pf/tree/master/examples) directory! Check `pf/examples/Makefile` to make sure it jives with your directories, and then run `make`. After that, run `./examples ./data/svol_y_data.csv` and you'll see the filtering output from `examples/svol_comparison.cpp`.

docs/html/annotated.html

@@ -90,23 +90,32 @@
 <tr id="row_0_1_" class="even"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classrvsamp_1_1k__gen.html" target="_self">k_gen</a></td><td class="desc">A class that performs sampling with replacement (useful for the index sampler in an <a class="el" href="classAPF.html" title="A base-class for Auxiliary Particle Filtering. Filtering only, no smoothing. ">APF</a>) </td></tr>
 <tr id="row_0_2_"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classrvsamp_1_1MVNSampler.html" target="_self">MVNSampler</a></td><td class="desc">A class that performs sampling from a multivariate normal distribution </td></tr>
 <tr id="row_0_3_" class="even"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classrvsamp_1_1rvsamp__base.html" target="_self">rvsamp_base</a></td><td class="desc">Base class for all random variable sampler types. Primary benefit is that it sets the seed for you </td></tr>
-<tr id="row_0_4_"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classrvsamp_1_1UniformSampler.html" target="_self">UniformSampler</a></td><td class="desc">A class that performs sampling from a continuous uniform distribution </td></tr>
-<tr id="row_0_5_" class="even"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classrvsamp_1_1UnivNormSampler.html" target="_self">UnivNormSampler</a></td><td class="desc">A class that performs sampling from a univariate Normal distribution </td></tr>
+<tr id="row_0_4_"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classrvsamp_1_1TruncUnivNormSampler.html" target="_self">TruncUnivNormSampler</a></td><td class="desc">Default-constructor .. </td></tr>
+<tr id="row_0_5_" class="even"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classrvsamp_1_1UniformSampler.html" target="_self">UniformSampler</a></td><td class="desc">A class that performs sampling from a continuous uniform distribution </td></tr>
+<tr id="row_0_6_"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classrvsamp_1_1UnivLogNormSampler.html" target="_self">UnivLogNormSampler</a></td><td class="desc">A class that performs sampling from a univariate Log-Normal distribution </td></tr>
+<tr id="row_0_7_" class="even"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classrvsamp_1_1UnivNormSampler.html" target="_self">UnivNormSampler</a></td><td class="desc">A class that performs sampling from a univariate Normal distribution </td></tr>
 <tr id="row_1_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classAPF.html" target="_self">APF</a></td><td class="desc">A base-class for Auxiliary Particle Filtering. Filtering only, no smoothing </td></tr>
-<tr id="row_2_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classBSFilter.html" target="_self">BSFilter</a></td><td class="desc">A base class for the boostrap particle filter </td></tr>
-<tr id="row_3_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classBSFilterWC.html" target="_self">BSFilterWC</a></td><td class="desc">A base class for the boostrap particle filter with covariates </td></tr>
-<tr id="row_4_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classcf__filter.html" target="_self">cf_filter</a></td><td class="desc">Abstract Base Class for Kalman filter and HMM filter </td></tr>
-<tr id="row_5_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classhmm.html" target="_self">hmm</a></td><td class="desc">A class template for HMM filtering </td></tr>
-<tr id="row_6_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classkalman.html" target="_self">kalman</a></td><td class="desc">A class template for Kalman filtering </td></tr>
-<tr id="row_7_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classmn__resampler.html" target="_self">mn_resampler</a></td><td class="desc">Performs multinomial resampling </td></tr>
-<tr id="row_8_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classmn__resampler__rbpf.html" target="_self">mn_resampler_rbpf</a></td><td class="desc">Performs multinomial resampling for a Rao-Blackwellized pf </td></tr>
-<tr id="row_9_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classpf__base.html" target="_self">pf_base</a></td><td class="desc"></td></tr>
-<tr id="row_10_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classrbase.html" target="_self">rbase</a></td><td class="desc">Base class for all resampler types </td></tr>
-<tr id="row_11_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classrbpf__hmm.html" target="_self">rbpf_hmm</a></td><td class="desc">Rao-Blackwellized/Marginal Particle Filter with inner HMMs </td></tr>
-<tr id="row_12_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classrbpf__hmm__bs.html" target="_self">rbpf_hmm_bs</a></td><td class="desc">Rao-Blackwellized/Marginal Bootstrap Filter with inner HMMs </td></tr>
-<tr id="row_13_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classrbpf__kalman.html" target="_self">rbpf_kalman</a></td><td class="desc">Rao-Blackwellized/Marginal Particle Filter with inner Kalman Filter objectss </td></tr>
-<tr id="row_14_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classrbpf__kalman__bs.html" target="_self">rbpf_kalman_bs</a></td><td class="desc">Rao-Blackwellized/Marginal Bootstrap Filter with inner Kalman Filter objectss </td></tr>
-<tr id="row_15_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classSISRFilter.html" target="_self">SISRFilter</a></td><td class="desc">A base class for the Sequential Important Sampling with Resampling (SISR) </td></tr>
+<tr id="row_2_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classBSFilter.html" target="_self">BSFilter</a></td><td class="desc">A base class for the bootstrap particle filter </td></tr>
+<tr id="row_3_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classBSFilterWC.html" target="_self">BSFilterWC</a></td><td class="desc">A base class for the bootstrap particle filter with covariates </td></tr>
+<tr id="row_4_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classcf__filter.html" target="_self">cf_filter</a></td><td class="desc">Abstract Base Class for all closed-form filters </td></tr>
+<tr id="row_5_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classForwardMod.html" target="_self">ForwardMod</a></td><td class="desc"></td></tr>
+<tr id="row_6_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classgamFilter.html" target="_self">gamFilter</a></td><td class="desc">A class template for Gamma filtering </td></tr>
+<tr id="row_7_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classhmm.html" target="_self">hmm</a></td><td class="desc">A class template for HMM filtering </td></tr>
+<tr id="row_8_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classkalman.html" target="_self">kalman</a></td><td class="desc">A class template for Kalman filtering </td></tr>
+<tr id="row_9_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classmn__resampler.html" target="_self">mn_resampler</a></td><td class="desc"></td></tr>
+<tr id="row_10_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classmn__resampler__rbpf.html" target="_self">mn_resampler_rbpf</a></td><td class="desc"></td></tr>
+<tr id="row_11_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classmultivGamFilter.html" target="_self">multivGamFilter</a></td><td class="desc">Another class template for Gamma filtering, but this time </td></tr>
+<tr id="row_12_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classpf__base.html" target="_self">pf_base</a></td><td class="desc"></td></tr>
+<tr id="row_13_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classrbase.html" target="_self">rbase</a></td><td class="desc">Base class for all resampler types </td></tr>
+<tr id="row_14_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classrbpf__base.html" target="_self">rbpf_base</a></td><td class="desc"></td></tr>
+<tr id="row_15_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classrbpf__hmm.html" target="_self">rbpf_hmm</a></td><td class="desc">Rao-Blackwellized/Marginal Particle Filter with inner HMMs </td></tr>
+<tr id="row_16_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classrbpf__hmm__bs.html" target="_self">rbpf_hmm_bs</a></td><td class="desc">Rao-Blackwellized/Marginal Bootstrap Filter with inner HMMs </td></tr>
+<tr id="row_17_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classrbpf__kalman.html" target="_self">rbpf_kalman</a></td><td class="desc">Rao-Blackwellized/Marginal Particle Filter with inner Kalman Filter objectss </td></tr>
+<tr id="row_18_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classrbpf__kalman__bs.html" target="_self">rbpf_kalman_bs</a></td><td class="desc">Rao-Blackwellized/Marginal Bootstrap Filter with inner Kalman Filter objectss </td></tr>
+<tr id="row_19_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classresid__resampler.html" target="_self">resid_resampler</a></td><td class="desc"></td></tr>
+<tr id="row_20_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classSISRFilter.html" target="_self">SISRFilter</a></td><td class="desc">A base class for the Sequential Important Sampling with Resampling (SISR) </td></tr>
+<tr id="row_21_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classstratif__resampler.html" target="_self">stratif_resampler</a></td><td class="desc"></td></tr>
+<tr id="row_22_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classsystematic__resampler.html" target="_self">systematic_resampler</a></td><td class="desc"></td></tr>
 </table>
 </div><!-- directory -->
 </div><!-- contents -->

docs/html/annotated_dup.js

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