diff --git a/Chapter2_MorePyMC/Ch2_MorePyMC_PyMC2.ipynb b/Chapter2_MorePyMC/Ch2_MorePyMC_PyMC2.ipynb index 3bc78f7f..9c2212bf 100644 --- a/Chapter2_MorePyMC/Ch2_MorePyMC_PyMC2.ipynb +++ b/Chapter2_MorePyMC/Ch2_MorePyMC_PyMC2.ipynb @@ -2172,7 +2172,7 @@ "\n", "We will be doing this graphically as well, which may seem like an even less objective method. The alternative is to use *Bayesian p-values*. These are still subjective, as the proper cutoff between good and bad is arbitrary. Gelman emphasises that the graphical tests are more illuminating [7] than p-value tests. We agree.\n", "\n", - "The following graphical test is a novel data-viz approach to logistic regression. The plots are called *separation plots*[8]. For a suite of models we wish to compare, each model is plotted on an individual separation plot. I leave most of the technical details about separation plots to the very accessible [original paper](http://mdwardlab.com/sites/default/files/GreenhillWardSacks.pdf), but I'll summarize their use here.\n", + "The following graphical test is a novel data-viz approach to logistic regression. The plots are called *separation plots*[8]. For a suite of models we wish to compare, each model is plotted on an individual separation plot. I leave most of the technical details about separation plots to the very accessible [original paper](https://onlinelibrary.wiley.com/doi/10.1111/j.1540-5907.2011.00525.x), but I'll summarize their use here.\n", "\n", "For each model, we calculate the proportion of times the posterior simulation proposed a value of 1 for a particular temperature, i.e. compute $P( \\;\\text{Defect} = 1 | t, \\alpha, \\beta )$ by averaging. This gives us the posterior probability of a defect at each data point in our dataset. For example, for the model we used above:" ] diff --git a/Chapter2_MorePyMC/Ch2_MorePyMC_PyMC3.ipynb b/Chapter2_MorePyMC/Ch2_MorePyMC_PyMC3.ipynb index 3eae5093..431b43de 100644 --- a/Chapter2_MorePyMC/Ch2_MorePyMC_PyMC3.ipynb +++ b/Chapter2_MorePyMC/Ch2_MorePyMC_PyMC3.ipynb @@ -2236,7 +2236,7 @@ "\n", "We will be doing this graphically as well, which may seem like an even less objective method. The alternative is to use *Bayesian p-values*. These are still subjective, as the proper cutoff between good and bad is arbitrary. Gelman emphasises that the graphical tests are more illuminating [7] than p-value tests. We agree.\n", "\n", - "The following graphical test is a novel data-viz approach to logistic regression. The plots are called *separation plots*[8]. For a suite of models we wish to compare, each model is plotted on an individual separation plot. I leave most of the technical details about separation plots to the very accessible [original paper](http://mdwardlab.com/sites/default/files/GreenhillWardSacks.pdf), but I'll summarize their use here.\n", + "The following graphical test is a novel data-viz approach to logistic regression. The plots are called *separation plots*[8]. For a suite of models we wish to compare, each model is plotted on an individual separation plot. I leave most of the technical details about separation plots to the very accessible [original paper](https://onlinelibrary.wiley.com/doi/10.1111/j.1540-5907.2011.00525.x), but I'll summarize their use here.\n", "\n", "For each model, we calculate the proportion of times the posterior simulation proposed a value of 1 for a particular temperature, i.e. compute $P( \\;\\text{Defect} = 1 | t, \\alpha, \\beta )$ by averaging. This gives us the posterior probability of a defect at each data point in our dataset. For example, for the model we used above:" ] diff --git a/Chapter2_MorePyMC/Ch2_MorePyMC_TFP.ipynb b/Chapter2_MorePyMC/Ch2_MorePyMC_TFP.ipynb index 6f04a856..1e8752ee 100644 --- a/Chapter2_MorePyMC/Ch2_MorePyMC_TFP.ipynb +++ b/Chapter2_MorePyMC/Ch2_MorePyMC_TFP.ipynb @@ -3884,7 +3884,7 @@ "\n", "We will be doing this graphically as well, which may seem like an even less objective method. The alternative is to use *Bayesian p-values*. These are still subjective, as the proper cutoff between good and bad is arbitrary. Gelman emphasises that the graphical tests are more illuminating [3] than p-value tests. We agree.\n", "\n", - "The following graphical test is a novel data-viz approach to logistic regression. The plots are called *separation plots*[4]. For a suite of models we wish to compare, each model is plotted on an individual separation plot. I leave most of the technical details about separation plots to the very accessible [original paper](http://mdwardlab.com/sites/default/files/GreenhillWardSacks.pdf), but I'll summarize their use here.\n", + "The following graphical test is a novel data-viz approach to logistic regression. The plots are called *separation plots*[4]. For a suite of models we wish to compare, each model is plotted on an individual separation plot. I leave most of the technical details about separation plots to the very accessible [original paper](https://onlinelibrary.wiley.com/doi/10.1111/j.1540-5907.2011.00525.x), but I'll summarize their use here.\n", "\n", "For each model, we calculate the proportion of times the posterior simulation proposed a value of 1 for a particular temperature, i.e. compute $P( \\;\\text{Defect} = 1 | t, \\alpha, \\beta )$ by averaging. This gives us the posterior probability of a defect at each data point in our dataset. For example, for the model we used above:" ] @@ -4028,7 +4028,7 @@ "def separation_plot( p, y, **kwargs ):\n", " \"\"\"\n", " This function creates a separation plot for logistic and probit classification. \n", - " See http://mdwardlab.com/sites/default/files/GreenhillWardSacks.pdf\n", + " See https://onlinelibrary.wiley.com/doi/10.1111/j.1540-5907.2011.00525.x\n", " \n", " p: The proportions/probabilities, can be a nxM matrix which represents M models.\n", " y: the 0-1 response variables.\n", diff --git a/Chapter2_MorePyMC/separation_plot.py b/Chapter2_MorePyMC/separation_plot.py index a5316bed..15433149 100644 --- a/Chapter2_MorePyMC/separation_plot.py +++ b/Chapter2_MorePyMC/separation_plot.py @@ -1,6 +1,6 @@ # separation plot # Author: Cameron Davidson-Pilon,2013 -# see http://mdwardlab.com/sites/default/files/GreenhillWardSacks.pdf +# see https://onlinelibrary.wiley.com/doi/10.1111/j.1540-5907.2011.00525.x import matplotlib.pyplot as plt @@ -11,7 +11,7 @@ def separation_plot( p, y, **kwargs ): """ This function creates a separation plot for logistic and probit classification. - See http://mdwardlab.com/sites/default/files/GreenhillWardSacks.pdf + See https://onlinelibrary.wiley.com/doi/10.1111/j.1540-5907.2011.00525.x p: The proportions/probabilities, can be a nxM matrix which represents M models. y: the 0-1 response variables.