I am trying to include knitr in my document and print INLA graphics :
Using a trivial example
\documentclass{article}
\begin{document}
<<c1>>=
library("INLA")
n = 100
z = runif(n)
eta = 1 + 0.1*z
N = 20
p = exp(eta)/(1+exp(eta))
y = rbinom(n, size = N, prob = p)
r = inla(y ~ 1 + z,
data = data.frame(y, z),
family = "binomial",
Ntrials = rep(N, n),
control.family = list(link = "logit"),
control.predictor = list(compute=TRUE)
)
@
<<c2>>=
plot(r, single=TRUE)
@
\end{document}
When I run this code interactively inside RStudio, everything works fine and I get a series of graphs. However, after knitting a document - not one of them is turned on.
How can i fix this?
UPDATE 1 I sent a question asking for clarification to the developer of the Google group package package .
UPDATE 2 INLA's Havard Rue posted a Sweave solution on Google Groups. Trick:
<<results=tex, echo=FALSE>>=
figs = plot(r, single=TRUE, postscript=TRUE, prefix="Sweave/ex1/figure-")
cat("\\begin{figure}[tbp]\n")
cat("\n")
cat("\\centering\n")
for(i in 1:length(figs)) {
cat("\\includegraphics[width=7cm,height=7cm,angle=-90]{",
gsub("[.]eps$","",figs[i]), "}\n", sep="")
}
cat("\\caption{XXX}\n")
cat("\\label{fig:11}\n")
cat("\\end{figure}\n")
@
. , pdf. , knitr, , .