Merge e447419 into d6a0325

arviz/plots/forestplot.py

@@ -150,7 +150,7 @@ def forestplot(trace, models=None, varnames=None, alpha=0.05, quartiles=True, rh
     all_quants = []
     bands = [(0.05, 0)[i % 2] for i in range(len(varnames))]
     var_old = 0.5
-    for v_idx, varname in enumerate(varnames):
+    for v_idx, varname in enumerate(sorted(varnames)):
         for h_idx, tr in enumerate(traces):
             if plot_rhat[h_idx]:
                 gr_stat = gelman_rubin(tr)

doc/index.rst

@@ -39,28 +39,32 @@ Contributions and issue reports are very welcome at `the github repository
     </div>
     <div class="col-md-6">
         <div class="container-fluid hidden-xs hidden-sm">
-            <a href="examples/energyplot.html">
-            <div class="col-md-3 thumbnail">
-                <img src="_static/energyplot_thumb.png">
+            <a href="examples/parallelplot.html">
+            <div class="col-md-4 thumbnail">
+                <img src="_static/parallelplot_thumb.png">
             </div>
             </a>
             <a href="examples/traceplot.html">
-            <div class="col-md-3 thumbnail">
+            <div class="col-md-4 thumbnail">
                 <img src="_static/traceplot_thumb.png">
             </div>
             </a>
-            <a href="examples/densityplot.html">
-            <div class="col-md-3 thumbnail">
-                <img src="_static/densityplot_thumb.png">
+            <a href="examples/energyplot.html">
+            <div class="col-md-4 thumbnail">
+                <img src="_static/energyplot_thumb.png">
+            </div>
+            <a href="examples/jointplot.html">
+            <div class="col-md-4 thumbnail">
+                <img src="_static/jointplot_thumb.png">
             </div>
             </a>
-            <a href="examples/compareplot.html">
-            <div class="col-md-3 thumbnail">
-                <img src="_static/compareplot_thumb.png">
+            <a href="examples/ppcplot.html">
+            <div class="col-md-4 thumbnail">
+                <img src="_static/ppcplot_thumb.png">
             </div>
             </a>
             <a href="examples/autocorrplot.html">
-            <div class="col-md-3 thumbnail">
+            <div class="col-md-4 thumbnail">
                 <img src="_static/autocorrplot_thumb.png">
             </div>
             </a>

examples/forestplot.py

@@ -0,0 +1,12 @@
+"""
+Forest Plot
+===========
+
+_thumb: .5, .8
+"""
+import arviz as az
+
+az.style.use('arviz-darkgrid')
+
+trace = az.load_trace('data/centered_eight_trace.gzip')
+az.forestplot(trace, varnames=('theta__0', 'theta__1', 'theta__2'))

examples/jointplot.py

@@ -0,0 +1,12 @@
+"""
+Joint Plot
+==========
+
+_thumb: .5, .8
+"""
+import arviz as az
+
+az.style.use('arviz-darkgrid')
+
+trace = az.load_trace('data/non_centered_eight_trace.gzip')
+az.jointplot(trace, kind='hexbin', varnames=('tau', 'mu'))

examples/kdeplot.py

@@ -0,0 +1,15 @@
+"""
+KDE Plot
+========
+
+_thumb: .2, .8
+"""
+import arviz as az
+import matplotlib.pyplot as plt
+
+az.style.use('arviz-darkgrid')
+
+trace = az.load_trace('data/non_centered_eight_trace.gzip')
+
+fig, ax = plt.subplots(figsize=(12, 8))
+az.kdeplot(trace.tau, fill_alpha=0.1, ax=ax)

examples/pairplot.py

@@ -0,0 +1,28 @@
+"""
+Pair Plot
+=========
+
+_thumb: .2, .5
+"""
+import arviz as az
+import numpy as np
+import pymc3 as pm
+
+az.style.use('arviz-darkgrid')
+
+# Data of the Eight Schools Model
+J = 8
+y = np.array([28.,  8., -3.,  7., -1.,  1., 18., 12.])
+sigma = np.array([15., 10., 16., 11.,  9., 11., 10., 18.])
+
+
+with pm.Model() as centered_eight:
+    mu = pm.Normal('mu', mu=0, sd=5)
+    tau = pm.HalfCauchy('tau', beta=5)
+    theta = pm.Normal('theta', mu=mu, sd=tau, shape=J)
+    obs = pm.Normal('obs', mu=theta, sd=sigma, observed=y)
+    centered_eight_trace = pm.sample()
+
+az.pairplot(centered_eight_trace,
+            varnames=['theta__0', 'theta__1', 'tau', 'mu'],
+            divergences=True)

examples/parallelplot.py

@@ -0,0 +1,26 @@
+"""
+Parallel Plot
+=============
+
+_thumb: .2, .5
+"""
+import arviz as az
+import numpy as np
+import pymc3 as pm
+
+az.style.use('arviz-darkgrid')
+
+# Data of the Eight Schools Model
+J = 8
+y = np.array([28.,  8., -3.,  7., -1.,  1., 18., 12.])
+sigma = np.array([15., 10., 16., 11.,  9., 11., 10., 18.])
+
+
+with pm.Model() as centered_eight:
+    mu = pm.Normal('mu', mu=0, sd=5)
+    tau = pm.HalfCauchy('tau', beta=5)
+    theta = pm.Normal('theta', mu=mu, sd=tau, shape=J)
+    obs = pm.Normal('obs', mu=theta, sd=sigma, observed=y)
+    centered_eight_trace = pm.sample()
+
+az.parallelplot(centered_eight_trace, varnames=['theta', 'tau', 'mu'])

examples/posteriorplot.py

@@ -0,0 +1,12 @@
+"""
+Posterior Plot
+==============
+
+_thumb: .5, .8
+"""
+import arviz as az
+
+az.style.use('arviz-darkgrid')
+
+trace = az.load_trace('data/non_centered_eight_trace.gzip')
+az.posteriorplot(trace, varnames=['theta__0', 'theta__1', 'tau', 'mu'])

examples/ppcplot.py

@@ -0,0 +1,29 @@
+"""
+Posterior Predictive Check Plot
+===============================
+
+_thumb: .6, .5
+"""
+import arviz as az
+import numpy as np
+import pymc3 as pm
+
+az.style.use('arviz-darkgrid')
+
+# Data of the Eight Schools Model
+J = 8
+y = np.array([28.,  8., -3.,  7., -1.,  1., 18., 12.])
+sigma = np.array([15., 10., 16., 11.,  9., 11., 10., 18.])
+
+
+with pm.Model() as centered_eight:
+    mu = pm.Normal('mu', mu=0, sd=5)
+    tau = pm.HalfCauchy('tau', beta=5)
+    theta = pm.Normal('theta', mu=mu, sd=tau, shape=J)
+    obs = pm.Normal('obs', mu=theta, sd=sigma, observed=y)
+    centered_eight_trace = pm.sample()
+
+with centered_eight:
+    ppc_samples = pm.sample_ppc(centered_eight_trace)
+
+az.ppcplot(y, ppc_samples)