How to specify figure names when `knit`ting with `fig.keep='all'`

Question

I'm using knitr to generate reports. However, I often first prepare "internal" documents which contain all plots, and then for a final report or paper want to include only some of the figures.

Say, I have a set of systematically produced figures, say I loop over my specimen:

<<sample, fig.keep = 'all'>>=
specimen <- c("436a", "783a", "10b")
for (s in specimen) # in reality it would e.g. be levels (specimen)
   plot (results [s])
@

This will produce a number of files figures/sample1.pdf, figures/sample2.pdf, etc. While the numbering with 1, 2, ... is good for the knitr-generated report, if I want to include one of the plots in a paper it is cumbersome and error prone to find out which .pdf belongs to which sample.

How can I tell knitr to use file names like "figures/sample-436a.pdf"?

I tried <<fig.path = sprintf ("figures/sample-%s", s)>>=, but that doesn't work: s is unknown, so I guess fig.path is evaluated right at the beginning of the chunk processing, not when saving the chunk.

PS: One obvious way to reduce the risk of errors are titles, but that is IMHO ugly in a paper.

Answer 1

Good question. Not sure if this could be a satisfactory answer:

\documentclass{article}

\begin{document}

<<prepare-src, include=FALSE>>=
s = names(iris)[-5]
# construct the source document
src = sprintf('<<sample-%s>>=
hist(iris[,"%s"], col="gray", border="white")
@', s, s)
@

% evaluate the source
\Sexpr{knit(text = src)}

\end{document}

In your case, you only need to decide which specimen to go into s.