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ericmjlericmjl
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Merge branch 'master' into travis-ghpages
2 parents 62df3d5 + e4ca1db commit 5016eab

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lines changed

‎notebooks/02-Instructor-Parameter_estimation_hypothesis_testing.ipynb‎

Lines changed: 6 additions & 5 deletions
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@@ -20,6 +20,7 @@
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"import matplotlib.pyplot as plt\n",
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"import pymc3 as pm\n",
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"from ipywidgets import interact\n",
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"import arviz as az\n",
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"%matplotlib inline\n",
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"sns.set()"
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]
@@ -374,7 +375,7 @@
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"with Model:\n",
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" samples = pm.sample(2000, njobs=1)\n",
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"\n",
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"pm.plot_posterior(samples);"
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"az.plot_posterior(samples, kind='hist');"
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]
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},
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{
@@ -458,7 +459,7 @@
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"with model:\n",
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" samples = pm.sample(2000, njobs=1)\n",
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" \n",
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"pm.plot_posterior(samples);"
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"az.plot_posterior(samples);"
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]
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},
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{
@@ -540,7 +541,7 @@
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"source": [
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"with Model:\n",
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" samples = pm.sample(2000, njobs=1)\n",
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"pm.plot_posterior(samples);"
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"az.plot_posterior(samples, kind='hist');"
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]
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},
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{
@@ -598,7 +599,7 @@
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"# bust it out & sample\n",
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"with model:\n",
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" samples = pm.sample(2000, njobs=1)\n",
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"pm.plot_posterior(samples, varnames=['μ_1', 'μ_2', 'diff_means', 'effect_size']);"
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"az.plot_posterior(samples, var_names=['μ_1', 'μ_2', 'diff_means', 'effect_size'], kind='hist');"
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]
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}
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],
@@ -618,7 +619,7 @@
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.6.6"
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"version": "3.6.8"
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}
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},
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"nbformat": 4,

‎notebooks/02-Student-Parameter_estimation_hypothesis_testing.ipynb‎

Lines changed: 6 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -20,6 +20,7 @@
2020
"import matplotlib.pyplot as plt\n",
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"import pymc3 as pm\n",
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"from ipywidgets import interact\n",
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"import arviz as az\n",
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"%matplotlib inline\n",
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"sns.set()"
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]
@@ -366,7 +367,7 @@
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" samples = ___\n",
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"\n",
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"# Plot posterior\n",
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"pm.plot_posterior(samples);"
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"az.plot_posterior(samples);"
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]
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},
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{
@@ -451,7 +452,7 @@
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" samples = ___\n",
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"\n",
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"# Plot posterior\n",
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"pm.plot_posterior(samples);"
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"az.plot_posterior(samples);"
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]
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},
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{
@@ -533,7 +534,7 @@
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"source": [
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"with Model:\n",
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" samples = pm.sample(2000, njobs=1)\n",
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"pm.plot_posterior(samples);"
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"az.plot_posterior(samples);"
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]
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},
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{
@@ -588,7 +589,7 @@
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"# bust it out & sample\n",
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"with model:\n",
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" samples = pm.sample(2000, njobs=1)\n",
591-
"pm.plot_posterior(samples, varnames=['μ_1', 'μ_2', 'diff_means', 'effect_size']);"
592+
"az.plot_posterior(samples, var_names=['μ_1', 'μ_2', 'diff_means', 'effect_size']);"
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]
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}
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],
@@ -608,7 +609,7 @@
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.6.6"
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"version": "3.6.8"
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}
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},
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"nbformat": 4,

‎notebooks/03-instructor-two-group-iq.ipynb‎

Lines changed: 8 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -11,6 +11,7 @@
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"import matplotlib.pyplot as plt\n",
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"import pymc3 as pm\n",
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"import seaborn as sns\n",
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"import arviz as az\n",
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"from utils import ECDF\n",
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"from data import load_kruschke\n",
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"\n",
@@ -290,7 +291,7 @@
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"outputs": [],
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"source": [
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"# Use `pm.plot_posterior()`\n",
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"pm.plot_posterior(trace, varnames=['mu_drug', 'mu_placebo'])"
294+
"az.plot_posterior(trace, var_names=['mu_drug', 'mu_placebo'])"
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]
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},
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{
@@ -377,7 +378,7 @@
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"metadata": {},
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"outputs": [],
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"source": [
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"pm.plot_posterior(trace=trace, varnames=['diff_means', 'effect_size'])"
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"az.plot_posterior(trace=trace, var_names=['diff_means', 'effect_size'])"
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]
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},
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{
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"metadata": {},
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"outputs": [],
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"source": [
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"traces = pm.traceplot(trace_alt)"
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"traces = az.traceplot(trace_alt)"
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]
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},
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{
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"metadata": {},
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"outputs": [],
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"source": [
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"pm.plot_posterior(trace_alt, varnames=['mu', 'effect_size'])"
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"az.plot_posterior(trace_alt, var_names=['mu', 'effect_size'])"
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]
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},
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{
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],
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"metadata": {
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"kernelspec": {
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"display_name": "bayesian-modelling-tutorial",
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"display_name": "Python 3",
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"language": "python",
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"name": "bayesian-modelling-tutorial"
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.6.6"
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"version": "3.6.8"
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},
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"toc": {
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"base_numbering": 1,

‎notebooks/03-student-two-group-iq.ipynb‎

Lines changed: 8 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -11,6 +11,7 @@
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"import matplotlib.pyplot as plt\n",
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"import pymc3 as pm\n",
1313
"import seaborn as sns\n",
14+
"import arviz as az\n",
1415
"from utils import ECDF\n",
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"from data import load_kruschke\n",
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"\n",
@@ -287,7 +288,7 @@
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"metadata": {},
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"outputs": [],
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"source": [
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"# Use `pm.plot_posterior()`\n",
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"# Use `az.plot_posterior()`\n",
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"pm.__________________"
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]
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},
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"metadata": {},
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"outputs": [],
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"source": [
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"# Use `pm.plot_posterior`, but pass in different varnames\n",
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"# Use `az.plot_posterior`, but pass in different varnames\n",
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"_______________________"
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]
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},
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"metadata": {},
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"outputs": [],
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"source": [
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"traces = pm.traceplot(trace_alt)"
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"traces = az.plot_trace(trace_alt)"
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]
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},
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{
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"metadata": {},
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"outputs": [],
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"source": [
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"pm.plot_posterior(trace_alt, varnames=['mu', 'effect_size'])"
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"az.plot_posterior(trace_alt, var_names=['mu', 'effect_size'])"
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]
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},
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{
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],
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"metadata": {
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"kernelspec": {
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"display_name": "bayesian-modelling-tutorial",
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"display_name": "Python 3",
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"language": "python",
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"name": "bayesian-modelling-tutorial"
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.6.6"
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"version": "3.6.8"
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},
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"toc": {
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"base_numbering": 1,

‎notebooks/04-instructor-multi-group-comparsion-sterilization.ipynb‎

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Original file line numberDiff line numberDiff line change
@@ -14,6 +14,7 @@
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"from sklearn.preprocessing import LabelEncoder\n",
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"import theano.tensor as tt\n",
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"from utils import ECDF\n",
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"import arviz as az\n",
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"\n",
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"%load_ext autoreload\n",
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"%autoreload 2\n",
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"outputs": [],
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"source": [
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"# Plot the trace plots.\n",
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"pm.traceplot(trace)"
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"az.plot_trace(trace)"
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]
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},
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{
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"metadata": {},
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"outputs": [],
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"source": [
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"# Use the `forestplot` or `plot_posterior` functions.\n",
244-
"pm.forestplot(trace, varnames=['perc_reduction'], ylabels=sorted(mapping))"
244+
"# Use the `plot_forest` or `plot_posterior` functions.\n",
245+
"az.plot_forest(trace, var_names=['perc_reduction'], ylabels=sorted(mapping))"
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]
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},
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{
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],
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"metadata": {
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"kernelspec": {
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"display_name": "bayesian-modelling-tutorial",
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"display_name": "Python 3",
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"language": "python",
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"name": "bayesian-modelling-tutorial"
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.6.6"
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"version": "3.6.8"
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}
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},
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"nbformat": 4,

‎notebooks/04-student-multi-group-comparsion-sterilization.ipynb‎

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"from sklearn.preprocessing import LabelEncoder\n",
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"import theano.tensor as tt\n",
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"from utils import ECDF\n",
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"import arviz as az\n",
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"\n",
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"%load_ext autoreload\n",
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"%autoreload 2\n",
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"outputs": [],
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"source": [
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"# Use the `forestplot` or `plot_posterior` functions.\n",
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"pm._______(_______, varnames=______)"
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"az._______(_______, var_names=______)"
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]
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},
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{
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],
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"metadata": {
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"kernelspec": {
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"display_name": "bayesian-modelling-tutorial",
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"display_name": "Python 3",
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"language": "python",
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"name": "bayesian-modelling-tutorial"
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.6.8"
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}
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},
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"nbformat": 4,

‎notebooks/05-instructor-two-group-comparison-finches.ipynb‎

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"import seaborn as sns\n",
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"import numpy as np\n",
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"from utils import ECDF\n",
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"import arviz as az\n",
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"\n",
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"%load_ext autoreload\n",
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"%autoreload 2\n",
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"metadata": {},
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"outputs": [],
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"source": [
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"traces = pm.traceplot(trace)"
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"traces = az.plot_trace(trace)"
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]
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},
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{
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"metadata": {},
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"outputs": [],
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"source": [
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"pm.forestplot(trace, varnames=['mean'])"
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"az.plot_forest(trace, var_names=['mean'])"
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{
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3",
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"language": "python",
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"name": "bayesian-modelling-tutorial"
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"name": "python3"
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"language_info": {
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"codemirror_mode": {
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.6.8"
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}
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},
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"nbformat": 4,

‎notebooks/05-student-two-group-comparison-finches.ipynb‎

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"import seaborn as sns\n",
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"import numpy as np\n",
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"from utils import ECDF\n",
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"import arviz as az\n",
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"\n",
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"%load_ext autoreload\n",
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"%autoreload 2\n",
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3",
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"language": "python",
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"name": "bayesian-modelling-tutorial"
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.6.6"
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"version": "3.6.8"
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}
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},
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"nbformat": 4,

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