You shall reap what you sew… on reproducible research and taking the plunge with S-weave and knitr

kittensewingAfter reading a lot about reproducible research with R and kntir (and Sweave/LaTeX and R Markdown), I have finally made the commitment to buckle my chin strap and get after it. Knitting my first “minimal” *.Rnw file was easy (thanks to the help of Riccardo Klinger’s most excellent example). In addition, to get quickly up to speed on the coding conventions of LaTeX, Tobi Oetikers document found here will give you just enough to be dangerous–in a good way).

After producing my first report, I quickly ran up against an issue that proved to be a major stumbling block for me. In my work, I find that I often have to produce reports for multiple clients (from the same db) and in those reports, I’m looping over many variables to produce the same plot (e.g., for example displaying trend of units sold by month over all the products in a clients inventory). I did what I normally do in those cases, produce a toy example of my problem and take it to stack overflow, and without fail, my solution (actually 2) were contributed kindly by Ben and Brian Diggs. The recipients of my virtual beer (or other beverage of their choice award) of the week!

As I had the most success with Brian’s code, I offer it up below! Cheers to you both, Brian and Ben!

##  Example *.Rnw File
\usepackage[margin=1.15 in]{geometry}
<<loaddata, echo=FALSE, message=FALSE>>=
subgroup <- df[ df$Hospital == hosp,]

<<setup, echo=FALSE >>=
  opts_chunk$set(fig.path = paste("test", hosp , sep=""))

Some infomative text about hospital \Sexpr{hosp}

<<plots, echo=FALSE >>=
  for(ward in unique(subgroup$Ward)){
    subgroup2 <- subgroup[subgroup$Ward == ward,]
    #     subgroup2 <- subgroup2[ order(subgroup2$Month),]
    savename <- paste(hosp, ward)
    plot(subgroup2$Month, subgroup2$Outcomes, type="o", main=paste("Trend plot for", savename))

## example R file that processes the *.Rnw
##  make my data
Hospital <- c(rep("A", 20), rep("B", 20))
Ward <- rep(c(rep("ICU", 10), rep("Medicine", 10)), 2)
Month <- rep(seq(1:10), 4)
Outcomes <- rnorm(40, 20, 5)
df <- data.frame(Hospital, Ward, Month, Outcomes)

## knitr loop
for (hosp in unique(df$Hospital)){
  knit2pdf("testingloops.Rnw", output=paste0('report_', hosp, '.tex'))


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