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    <p>Great question! This works for me with the other bits you've supplied in your question. Note that I've replaced your <code>hosp</code> with just <code>x</code>. I've called your <code>Rnw</code> file <code>test.rnw</code></p> <pre><code># input data Hospital &lt;- c(rep("A", 20), rep("B", 20)) Ward &lt;- rep(c(rep("ICU", 10), rep("Medicine", 10)), 2) Month &lt;- rep(seq(1:10), 4) Outcomes &lt;- rnorm(40, 20, 5) df &lt;- data.frame(Hospital, Ward, Month, Outcomes) # generate the tex files, one for each hospital in df library(knitr) lapply(unique(df$Hospital), function(x) knit("C:\\emacs\\test.rnw", output=paste('report_', x, '.tex', sep=""))) # generate PDFs from the tex files, one for each hospital in df lapply(unique(df$Hospital), function(x) tools::texi2pdf(paste0("C:\\emacs\\", paste0('report_', x, '.tex')), clean = TRUE, quiet = TRUE)) </code></pre> <p>I've replaced your loops with<code>lapply</code> and anonymous functions, which often seem to be considered more <code>R</code>-ish.</p> <p>Here you can see where I replaced the <code>hosp</code> with <code>x</code> in the <code>rnw</code> file:</p> <pre><code>\documentclass[10pt]{article} \usepackage[margin=1.15 in]{geometry} &lt;&lt;loaddata, echo=FALSE, message=FALSE&gt;&gt;= Hospital &lt;- c(rep("A", 20), rep("B", 20)) Ward &lt;- rep(c(rep("ICU", 10), rep("Medicine", 10)), 2) Month &lt;- rep(seq(1:10), 4) Outcomes &lt;- rnorm(40, 20, 5) df &lt;- data.frame(Hospital, Ward, Month, Outcomes) subgroup &lt;- df[ df$Hospital == x,] @ \begin{document} &lt;&lt;setup, echo=FALSE &gt;&gt;= opts_chunk$set(fig.path = paste("test", x , sep="")) @ Some informative text about hospital \Sexpr{x} &lt;&lt;plots, echo=FALSE &gt;&gt;= for(ward in unique(subgroup$Ward)){ subgroup2 &lt;- subgroup[subgroup$Ward == ward,] # subgroup2 &lt;- subgroup2[ order(subgroup2$Month),] savename &lt;- paste(x, ward) plot(subgroup2$Month, subgroup2$Outcomes, type="o", main=paste("Trend plot for", savename)) } @ \end{document} </code></pre> <p>The result is two tex files (report_A.tex, report_B.tex), four PDFs for the figures (A1, A2, B1, B2) and two PDFs for the reports (report_A.pdf, report_B.pdf), each with their figures in them. Is that what you were after?</p>
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    1. POUsing loops with knitr to produce multiple pdf reports... need a little help to get me over the hump
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    1. COAbsolutely! I'm having trouble (right now) getting the second lapply chunk to behave as it loops through tools:texi2pdf, but I can figure that out myself. Just having the first lapply knit my *.tex files is fantastic! Many, many THANKS!!
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    2. COGlad that helped, have you tried `knit2pdf` as in Brian Diggs' answer? You could replace the second `lapply` with: `library(knitr); lapply(unique(df$Hospital), function(x) knit2pdf("C:\\emacs\\test.rnw", output=paste0('report_', x, '.tex')))`
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    3. COBy 'replace' I mean 'do away with' the second `lapply`, pardon me.
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