Sorry for the confusion. I am using a .Rnw file format. I have the .Rnw file weaved using Knitr. Also, I have tinytex clicked.
My references are showing up nicely in a reference section using the LaTeX command \bibliography{}. The problem is that the references are not showing up inline. I get this.
It is an interesting historical fact that the inverse probability theorem was actually
developed by the mathematician Pierre-Simon Laplace (?, ?).
The citation to Laplace shows up in the Reference section, but not here inline.
Also, equation numbers are not showing up inline. Specifically, the equation is
\begin{equation}\label{condprob}
p(C | S) = \frac{p(C \cap S)}{p(S)}.
\end{equation}
and in the sentence is
\par An interesting feature of Equation \ref{condprob} sets the axiomatic foundation for Bayes' theorem.
But when I typeset the document I get this
An interesting feature of Equation ?? sets the
So, the label is not being processed in the sentence.