Using loops with knitr to produce multiple pdf reports… need a little help to get me over the hump

by

You don’t need to re-define the data in the .Rnw file and I think the warning is coming from the fact that you are putting the output name together with Hospital (the full vector of hospitals) rather than hosp (the loop index).

Following your example, testingloops.Rnw would be

\documentclass[10pt]{article}
\usepackage[margin=1.15 in]{geometry}
<<loaddata, echo=FALSE, message=FALSE>>=
subgroup <- df[ df$Hospital == hosp,]
@

\begin{document}
<<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))
  }
@
\end{document}

and the driver R file would be just

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

More Related Contents:

  1. How to combine two RMarkdown (.Rmd) files into a single output?
  2. How to use objects from global environment in Rstudio Markdown
  3. Rstudio rmarkdown: both portrait and landscape layout in a single PDF
  4. knitr/rmarkdown/Latex: How to cross-reference figures and tables?
  5. Generate Dynamic R Markdown Blocks
  6. Subfigures or Subcaptions with knitr?
  7. Using stargazer with Rstudio and Knitr
  8. R knitr: Possible to programmatically modify chunk labels?
  9. Conditionally display a block of text in R Markdown
  10. Align multiple tables side by side
  11. two-column layouts in RStudio presentations/slidify/pandoc
  12. R Markdown – variable output name
  13. Code chunk font size in Rmarkdown with knitr and latex
  14. knitr gets tricked by data.table `:=` assignment
  15. Can Sweave produce many pdfs automatically?
  16. knitr: How to prevent text wrapping in output?
  17. r knitr chunk options for figure height / width are not working
  18. Create a loop that includes both a code chunk and text
  19. Insert a logo in upper right corner of R markdown pdf document
  20. Use loop to generate section of text in rmarkdown
  21. R – Markdown avoiding package loading messages
  22. Unicode with knitr and Rmarkdown
  23. Add an image to a table-like output in R
  24. R: why kable doesn’t print inside a for loop?
  25. Programmatically insert header and plot in same code chunk with R markdown using results=’asis’
  26. New R-Studio version 0.98.932 deletes .md file – how to prevent?
  27. Reduce file size of R Markdown HTML output
  28. Wrap text around plots in Markdown
  29. Create parametric R markdown documentation?
  30. Automatically adjust LaTeX table width to fit pdf using knitr and Rstudio

Leave a Comment