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POUsing loops with knitr to produce multiple pdf reports... need a little help to get me over the hump
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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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    copied!<p>First of all, I must admit that I'm very new to knitr and the concept of reproducible analysis, but I can see its potential in improving my current workflow (which includes much copy-pasting into word docs).</p> <p>I often have to produce multiple reports by group (Hospital in this example) and within each hospital, there may be many different Wards that I'm reporting an outcome on. Previously I ran all of my plots and analysis in R using loops, then the copy/pasting work commenced; however, after reading this post (<a href="https://stackoverflow.com/questions/8519128/can-sweave-produce-many-pdfs-automatically">Can Sweave produce many pdfs automatically?</a>), and it gave me hope that I may actually be able to skip many steps and go straight from R to report through Rnw/knitr.</p> <p>However, after giving it a try I see that there is something that isn't quite working out (as the R environment within the Rnw does not appear to recognize the looping variables I'm trying to pass to it??). </p> <pre><code> ## make my 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) ## Here is my current work flow-- produce all plots, but export as png and cut/paste for(hosp in unique(df$Hospital)){ subgroup &lt;- df[ df$Hospital == hosp,] for(ward in unique(subgroup$Ward)){ subgroup2 &lt;- subgroup[subgroup$Ward == ward,] savename &lt;- paste(hosp, ward) plot(subgroup2$Month, subgroup2$Outcomes, type="o", main=paste("Trend plot for", savename)) } } # followed by much copy/pasting ## Here is what I'm trying to go for using knitr library(knitr) for (hosp in unique(df$Hospital)){ knit("C:file.path\\testing_loops.Rnw", output=paste('report_', Hospital, '.tex', sep="")) } ## With the following *Rnw file ## start *.Rnw Code \documentclass[10pt]{article} \usepackage[margin=1.15 in]{geometry} &lt;&lt;loaddata, echo=FALSE, message=FALSE&gt;&gt;= Hospital &lt;- c(rep("A", 20), rep("B", 20)) Ward &lt;- rep(c(rep("ICU", 10), rep("Medicine", 10)), 2) Month &lt;- rep(seq(1:10), 4) Outcomes &lt;- rnorm(40, 20, 5) df &lt;- data.frame(Hospital, Ward, Month, Outcomes) subgroup &lt;- df[ df$Hospital == hosp,] @ \begin{document} &lt;&lt;setup, echo=FALSE &gt;&gt;= opts_chunk$set(fig.path = paste("test", hosp , sep="")) @ Some infomative text about hospital \Sexpr{hosp} &lt;&lt;plots, echo=FALSE &gt;&gt;= for(ward in unique(subgroup$Ward)){ subgroup2 &lt;- subgroup[subgroup$Ward == ward,] # subgroup2 &lt;- subgroup2[ order(subgroup2$Month),] savename &lt;- paste(hosp, ward) plot(subgroup2$Month, subgroup2$Outcomes, type="o", main=paste("Trend plot for", savename)) } @ \end{document} ## To be then turned into pdf with this tools::texi2pdf("C:file.path\\report_A.tex", clean = TRUE, quiet = TRUE) </code></pre> <p>After trying to run my knit() code chunk I get this error:</p> <pre><code>Error in file(con, "w") : invalid 'description' argument </code></pre> <p>And when I look into the directory where the *.tex file was to be created, I can see the 2 pdf plots from hospital A were produced (none for B) and no hospital specific *.tex file to knit into a pdf. Thanks in advance for any help you can offer!</p>
 

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