In the following commuting diagram, I would like to draw a box containing the bottom triangle defined by nodes D, E and F. Do you know how I could do that?
\documentclass{article}
\usepackage{amsmath}
\usepackage{tikz-cd}
\begin{document}
\[
\begin{tikzcd}[row sep=2.5em]
& \text{A} \\
\arrow[rightarrow]{d}{R_4}\text{B} \arrow[leftarrow]{ur}{R_1}
\arrow[dashed,leftrightarrow]{rr}{R_3} && \text{C} \\
\arrow[leftrightarrow]{rd}{R_1}\text{D}\arrow[leftrightarrow]{rr}{R_3} & &
\text{E} \arrow[leftrightarrow]{ld}{R_2}\\
& \text{F} &
\end{tikzcd}
\]
\end{document}

Searching here and there, I put together the following:
\documentclass{article}
\usepackage{amsmath}
%\usepackage{tikz-cd}
\usepackage{tikz}
\usetikzlibrary{cd}
\usetikzlibrary{fit, patterns}
\begin{document}
\[
\tikz[%remember picture,
overlay]{
\filldraw[fill=yellow!50,draw=red!50!yellow] (-.5,-3.2) rectangle (3.8,-.4);
}
\begin{tikzcd}[row sep=2.5em]
& \text{A} \\
\arrow[rightarrow]{d}{R_4}\text{B} \arrow[leftarrow]{ur}{R_1}
\arrow[dashed,leftrightarrow]{rr}{R_3} && \text{C} \\[3em]
\arrow[leftrightarrow]{rd}{R_1}\text{D}\arrow[leftrightarrow]{rr}{R_3} & &
\text{E} \arrow[leftrightarrow]{ld}{R_2}\\
& \text{F} &
\end{tikzcd}
\]
\end{document}
It outputs:

I didn't edit any of your code within \[ and \], except for adding [3em] in line 18 for the sake of vertical spacing.
The style (colors, margins) may be changed up to your personal taste!
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