DOC tidy notebooks (#1535)

* Removed discrete_find_MAP.ipynb

Cleanup of several notebooks

Additional cleanup of notebooks

Cleanup of additional notebooks

Removed discrete_find_MAP.ipynb

Cleanup of several notebooks

Additional cleanup of notebooks

Cleanup of additional notebooks

WIP: Notebooks updated rugby analytics

* Removed discrete_find_MAP.ipynb

* Removed discrete_find_MAP.ipynb

Cleanup of several notebooks

Additional cleanup of notebooks

Cleanup of additional notebooks

Removed discrete_find_MAP.ipynb

Cleanup of several notebooks

Additional cleanup of notebooks

Cleanup of additional notebooks

WIP: Notebooks updated rugby analytics

* Cleanup of several notebooks

* Additional cleanup of notebooks

* Cleanup of additional notebooks

* More cleaned up notebooks (including divergent LKJ)

* Removed discrete_find_MAP.ipynb

Cleanup of several notebooks

Additional cleanup of notebooks

Cleanup of additional notebooks

Removed discrete_find_MAP.ipynb

Cleanup of several notebooks

Additional cleanup of notebooks

Cleanup of additional notebooks

WIP: Notebooks updated rugby analytics

* Cleanup of several notebooks

* More cleaned up notebooks (including divergent LKJ)

* DOC Rename pmf example.

* DOC Remove glm-logistic as it timeouts on reading data.

* DOC Revert LKJ model use Metropolis sampler as NUTS runs into non-singular errors.

* DOC Remove NUTS scaling NB as it stops running and is mostly obsolete now that we auto-init in this manner.

* DOC Change some samplers in model selection NB to make it faster.

* DOC Change getting started guide to use auto-init and auto-assigned samplers.

* DOC Remove link to paper as it's out-of-date.

Author: fonnesbeck

README.rst

@@ -35,9 +35,7 @@ Features
 Getting started
 ---------------
 
--  The `PyMC3
-   tutorial <http://pymc-devs.github.io/pymc3/notebooks/getting_started.html>`__ or
-   `journal publication <https://peerj.com/articles/cs-55/>`__
+-  The `PyMC3 tutorial <http://pymc-devs.github.io/pymc3/notebooks/getting_started.html>`__ 
 -  `PyMC3 examples <http://pymc-devs.github.io/pymc3/examples.html>`__
    and the `API reference <http://pymc-devs.github.io/pymc3/api.html>`__
 -  `Probabilistic Programming and Bayesian Methods for Hackers <https://github.com/CamDavidsonPilon/Probabilistic-Programming-and-Bayesian-Methods-for-Hackers>`__

docs/source/examples.rst

@@ -9,7 +9,6 @@ Howto
 
 .. toctree::
    notebooks/posterior_predictive.ipynb
-   notebooks/NUTS_scaling_using_ADVI.ipynb
    notebooks/howto_debugging.ipynb
    notebooks/LKJ.ipynb
 
@@ -19,7 +18,7 @@ Applied
 .. toctree::
    notebooks/BEST.ipynb
    notebooks/stochastic_volatility.ipynb
-   notebooks/pmf-pymc.ipynb
+   notebooks/probabilistic-matrix-factorization.ipynb
    notebooks/rugby_analytics.ipynb
    notebooks/survival_analysis.ipynb
    notebooks/GP-smoothing.ipynb
@@ -33,7 +32,6 @@ GLM
    notebooks/GLM-robust-with-outlier-detection.ipynb
    notebooks/GLM-model-selection.ipynb
    notebooks/GLM-rolling-regression.ipynb
-   notebooks/GLM-logistic.ipynb
    notebooks/GLM-hierarchical.ipynb
    notebooks/GLM-poisson-regression.ipynb