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added meta-analysis example to slides 7 and minted improvements
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@avehtari
avehtari committed Oct 10, 2024
1 parent 6674dee commit 82b30ae
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Binary file modified slides/BDA_lecture_6.pdf
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13 changes: 11 additions & 2 deletions slides/BDA_lecture_6.tex
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Expand Up @@ -23,11 +23,13 @@
\usepackage{rotating}
\usepackage{listings}
\usepackage{lstbayes}
\usepackage{minted}
\setminted{highlightcolor=lightyellow}
\usepackage{natbib}
\bibliographystyle{apalike}

%minted
\usepackage{minted}
\setminted{highlightcolor=yellow!25}
\newmintinline{r}{}
\makeatletter
\newcommand{\minted@style@bw}{%
\renewcommand\fcolorbox[3][]{##3}%
Expand All @@ -42,6 +44,13 @@
{\minted@style@bw}{}%
}}
\makeatother
\newcommand{\reducedstrut}{\vrule width 0pt height .9\ht\strutbox depth .9\dp\strutbox\relax}
\newcommand{\highlight}[1]{%
\begingroup
\setlength{\fboxsep}{0pt}%
\colorbox{yellow!30}{\reducedstrut\detokenize{#1}\/}%
\endgroup
}

\mode<presentation>
{
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Binary file modified slides/BDA_lecture_7.pdf
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155 changes: 139 additions & 16 deletions slides/BDA_lecture_7.tex
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Expand Up @@ -21,27 +21,34 @@
\usepackage{rotating}
\usepackage{listings}
\usepackage{lstbayes}
\usepackage{minted}
\setminted{highlightcolor=lightyellow}
\newmintinline{r}{}
\usepackage[all,poly,ps,color]{xy}
\usepackage{natbib}
\bibliographystyle{apalike}

% minted
\usepackage{minted}
\setminted{highlightcolor=yellow!25}
\newmintinline{r}{}
\makeatletter
\newcommand{\minted@style@bw}{%
\renewcommand\fcolorbox[3][]{##3}%
\renewcommand\textcolor[3][]{##3}%
\color{gray}
}

% define new minted option "gray"
\minted@def@opt@switch{gray}
\fvset{formatcom*={%
\ifthenelse{\equal{\minted@get@opt{gray}{true}}{true}}
{\minted@style@bw}{}%
}}
\makeatother
\newcommand{\reducedstrut}{\vrule width 0pt height .9\ht\strutbox depth .9\dp\strutbox\relax}
\newcommand{\highlight}[1]{%
\begingroup
\setlength{\fboxsep}{0pt}%
\colorbox{yellow!30}{\reducedstrut\detokenize{#1}\/}%
\endgroup
}

\mode<presentation>
{
Expand All @@ -61,7 +68,10 @@
/Keywords (Bayesian data analysis)
}

\definecolor{lightyellow}{rgb}{1,1,0.878}
%\definecolor{lightyellow}{rgb}{1,1,0.5}
%\definecolor{lightgoldenrodyellow}{rgb}{0.98, 0.98, 0.82}
\definecolor{lightyellow}{rgb}{1, 1, 0.6}

\definecolor{hutblue}{rgb}{0,0.2549,0.6784}
\definecolor{forestgreen}{rgb}{0.1333,0.5451,0.1333}
\definecolor{navyblue}{rgb}{0,0,0.5}
Expand Down Expand Up @@ -570,15 +580,15 @@
sigma ~ normal(0, 1);

// Observation model
%\fboxsep0pt\colorbox{lightyellow}{weight}% ~ normal(mu_diet[diet_idx], sigma);
%\highlight{weight}% ~ normal(mu_diet[diet_idx], sigma);
}
\end{minted}

brms formula
\vspace{-0.5\baselineskip}
%\begin{minted}[escapeinside=\%\%,beameroverlays]{r}
\begin{minted}[escapeinside=\%\%]{r}
brm(%\fboxsep0pt\colorbox{lightyellow}{weight}% ~ 1 + (1 | Diet),
brm(%\highlight{weight}% ~ 1 + (1 | Diet),
\end{minted}
}

Expand All @@ -595,7 +605,7 @@
\begin{minted}[escapeinside=\%\%]{stan}
model {
// Priors
mu_diet ~ normal(%\fboxsep0pt\colorbox{lightyellow}{mu\_0}%, sd);
mu_diet ~ normal(%\highlight{mu_0}%, sd);
mu_0 ~ normal(0, 1);
sd ~ normal(0, 1)
sigma ~ normal(0, 1);
Expand All @@ -609,7 +619,7 @@
\vspace{-0.5\baselineskip}
%\begin{minted}[escapeinside=\%\%,beameroverlays]{r}
\begin{minted}[escapeinside=\%\%]{r}
brm(weight ~%\fboxsep0pt\colorbox{lightyellow}{ 1 }%+ (1 | Diet),
brm(weight ~%\highlight{ 1 }%+ (1 | Diet),
\end{minted}
}

Expand All @@ -626,7 +636,7 @@
\begin{minted}[escapeinside=\%\%]{stan}
model {
// Priors
%\fboxsep0pt\colorbox{lightyellow}{mu\_diet ~ normal(mu\_0, sd)}%;
%\highlight{mu_diet ~ normal(mu_0, sd)}%;
mu_0 ~ normal(0, 1);
sd ~ normal(0, 1)
sigma ~ normal(0, 1);
Expand All @@ -640,7 +650,7 @@
\vspace{-0.5\baselineskip}
%\begin{minted}[escapeinside=\%\%,beameroverlays]{r}
\begin{minted}[escapeinside=\%\%]{r}
brm(weight ~%\fboxsep0pt\colorbox{lightyellow}{ 1 + (1 | Diet)}%,
brm(weight ~%\highlight{ 1 + (1 | Diet)}%,
\end{minted}
}

Expand Down Expand Up @@ -670,7 +680,7 @@
brms formula
\vspace{-0.5\baselineskip}
\begin{minted}[escapeinside=\%\%]{r}
brm(weight ~ 1 + (1 | Diet), %\fboxsep0pt\colorbox{lightyellow}{data=Chick12}%,
brm(weight ~ 1 + (1 | Diet), %\highlight{data=Chick12}%,
\end{minted}
}

Expand Down Expand Up @@ -1199,7 +1209,7 @@

\vspace{-0.5\baselineskip}
\begin{minted}[escapeinside=\%\%,fontsize=\footnotesize]{r}
nstudents | trials(nstudents1) ~ assignment + %\fboxsep0pt\colorbox{lightyellow}{(assignment || year)}%, ...
nstudents | trials(nstudents1) ~ assignment + %\highlight{(assignment || year)}%, ...
\end{minted}

\begin{minted}[highlightlines={8-12,14-17},fontsize=\scriptsize,xleftmargin=-5mm]{r}
Expand Down Expand Up @@ -1228,7 +1238,7 @@

\vspace{-0.5\baselineskip}
\begin{minted}[escapeinside=\%\%,fontsize=\footnotesize]{r}
nstudents | trials(nstudents1) ~ assignment + %\fboxsep0pt\colorbox{lightyellow}{(assignment | year)}%, ...
nstudents | trials(nstudents1) ~ assignment + %\highlight{(assignment | year)}%, ...
\end{minted}

\begin{minted}[highlightlines={8-13},fontsize=\scriptsize,xleftmargin=-5mm]{r}
Expand Down Expand Up @@ -1555,7 +1565,7 @@
\rinline/bf()/

\begin{minted}[fontsize=\footnotesize,escapeinside=\%\%]{r}
fit_lin <- brm(%\colorbox{lightyellow}{bf(temp ~ year, center=FALSE)}%, data = data_lin)
fit_lin <- brm(%\highlight{bf(temp ~ year, center=FALSE)}%, data = data_lin)
\end{minted}

\end{frame}
Expand Down Expand Up @@ -1599,6 +1609,120 @@
\end{tabular}


\end{frame}

\begin{frame}[fragile]{Meta-analysis}
\framesubtitle{Pharmacologic treatments for chronic obstructive pulmonary disease}

\begin{minted}[fontsize=\footnotesize]{r}
> head(dat.baker2009)
study year id treatment exac total
1 Llewellyn-Jones 1996 1996 1 Fluticasone 0 8
2 Llewellyn-Jones 1996 1996 1 Placebo 3 8
3 Boyd 1997 1997 2 Salmeterol 47 229
4 Boyd 1997 1997 2 Placebo 59 227
5 Paggiaro 1998 1998 3 Fluticasone 45 142
6 Paggiaro 1998 1998 3 Placebo 51 139
\end{minted}

\end{frame}

\begin{frame}[fragile]{Meta-analysis}
\framesubtitle{Pharmacologic treatments for chronic obstructive pulmonary disease}

\only<1>{A big variation in the number of patients per study}
\only<2>{2--4 drugs tested per study, and some not including placebo}

\begin{minipage}[t][][t]{1.2\linewidth}
\hspace{-10mm}
\only<1>{\includegraphics[width=12.5cm]{baker2009_n_patients_per_study.pdf}}
\only<2>{\includegraphics[width=12.5cm]{baker2009_treatments_and_studies.pdf}}
\end{minipage}
\end{frame}

\begin{frame}[fragile]{Meta-analysis}
\framesubtitle{Pharmacologic treatments for chronic obstructive pulmonary disease}

\vspace{-0.75\baselineskip}
Pooled over studies, separate for treatments

\vspace{-0.25\baselineskip}
\begin{minted}[fontsize=\footnotesize,escapeinside=\%\%]{r}
fit_pooled <- brm(%\highlight{exac | trials(total) ~ 0 + treatment}%,
prior = prior(student_t(7, 0, 1.5), class='b'),
family=binomial(), data=dat.baker2009)
\end{minted}
\vspace{-0.25\baselineskip}
\phantom{\includegraphics[width=9cm]{baker2009_pooled_studies_odds_ratio.pdf}}

\end{frame}

\begin{frame}[fragile]{Meta-analysis}
\framesubtitle{Pharmacologic treatments for chronic obstructive pulmonary disease}

\vspace{-0.75\baselineskip}
Pooled over studies, separate for treatments

\vspace{-0.25\baselineskip}
\begin{minted}[fontsize=\footnotesize,escapeinside=\%\%]{r}
fit_pooled <- brm(exac | trials(total) ~ 0 + %\highlight{treatment}%,
prior = prior(student_t(7, 0, 1.5), class='b'),
family=binomial(), data=dat.baker2009)
\end{minted}
\vspace{-0.25\baselineskip}
{\includegraphics[width=9cm]{baker2009_pooled_studies_odds_ratio.pdf}}

\end{frame}

\begin{frame}[fragile]{Meta-analysis}
\framesubtitle{Pharmacologic treatments for chronic obstructive pulmonary disease}

\vspace{-0.75\baselineskip}
Hirerachical for studies, hierarchical for treatments

\vspace{-0.25\baselineskip}
\begin{minted}[fontsize=\footnotesize,escapeinside=\%\%]{r}
fit_hier <- brm(%\highlight{exac | trials(total) ~ (1 | treatment) + (1 | study)}%,
family=binomial(), data=dat.baker2009)
\end{minted}
%\vspace{-0.25\baselineskip}
\phantom{\includegraphics[width=9cm]{baker2009_hier1_odds_ratio.pdf}}

\end{frame}

\begin{frame}[fragile]{Meta-analysis}
\framesubtitle{Pharmacologic treatments for chronic obstructive pulmonary disease}

\vspace{-0.75\baselineskip}
Hirerachical for studies, hierarchical for treatments

\vspace{-0.25\baselineskip}
\begin{minted}[fontsize=\footnotesize,escapeinside=\%\%]{r}
fit_hier <- brm(exac | trials(total) ~ %\highlight{(1 | treatment)}% + (1 | study),
family=binomial(), data=dat.baker2009)
\end{minted}
%\vspace{-0.25\baselineskip}
{\includegraphics[width=9cm]{baker2009_hier1_odds_ratio.pdf}}

\end{frame}

\begin{frame}[fragile]{Meta-analysis}
\framesubtitle{Pharmacologic treatments for chronic obstructive pulmonary disease}

\vspace{-0.75\baselineskip}
Hirerachical for studies, hierarchical for treatments

\vspace{-0.25\baselineskip}
\begin{minted}[fontsize=\footnotesize,escapeinside=\%\%]{r}
fit_hier <- brm(exac | trials(total) ~ (1 | treatment) + %\highlight{(1 | study)}%,
family=binomial(), data=dat.baker2009)
\end{minted}

\begin{minipage}[t][][t]{1.2\linewidth}
\hspace{-10mm}
{\includegraphics[width=12.5cm]{baker2009_hier1_study_effects.pdf}}
\end{minipage}

\end{frame}

\begin{frame}[fragile]{BDA course demo for brms}
Expand All @@ -1610,7 +1734,6 @@

\end{frame}


\begin{frame}{Exchangeability}

\begin{itemize}
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14 changes: 11 additions & 3 deletions slides/BDA_lecture_8a.tex
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Expand Up @@ -22,14 +22,15 @@
\usepackage{subcaption}
\usepackage{listings}
\usepackage{lstbayes}
\usepackage{minted}
\setminted{highlightcolor=lightyellow}
\newmintinline{r}{}
\usepackage[all,poly,ps,color]{xy}
\usepackage{eurosym}
\usepackage{natbib}
\bibliographystyle{apalike}

% minted
\usepackage{minted}
\setminted{highlightcolor=yellow!25}
\newmintinline{r}{}
\makeatletter
\newcommand{\minted@style@bw}{%
\renewcommand\fcolorbox[3][]{##3}%
Expand All @@ -44,6 +45,13 @@
{\minted@style@bw}{}%
}}
\makeatother
\newcommand{\reducedstrut}{\vrule width 0pt height .9\ht\strutbox depth .9\dp\strutbox\relax}
\newcommand{\highlight}[1]{%
\begingroup
\setlength{\fboxsep}{0pt}%
\colorbox{yellow!30}{\reducedstrut\detokenize{#1}\/}%
\endgroup
}

\mode<presentation>
{
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