使用带有knitr的循环来生成多个pdf报告...需要一点帮助来帮助我克服麻烦 [英] Using loops with knitr to produce multiple pdf reports... need a little help to get me over the hump

问题描述

首先，我必须承认我对knitr和可重现分析的概念非常陌生，但是我可以看到它在改进当前工作流程(包括大量复制粘贴到word文档中)方面的潜力.

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).

我经常必须按组(在此示例中为医院)生成多个报告，并且在每家医院内，可能有许多我要报告结果的病房.以前，我使用循环在R中运行所有绘图和分析，然后开始复制/粘贴工作.但是，在阅读了这篇文章之后( Sweave可以自动产生许多pdf吗?)，这给了我希望，我实际上可以跳过很多步骤，直接从R直接通过Rnw/knitr进行报告.

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 (Can Sweave produce many pdfs automatically?), 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.

但是，尝试一下之后，我发现有些东西还没有完全解决(因为Rnw中的R环境似乎无法识别我试图传递给它的循环变量?) .

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??).

   ##  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)


##  Here is my current work flow-- produce all plots, but export as png and cut/paste
for(hosp in unique(df$Hospital)){
  subgroup <- df[ df$Hospital == hosp,]
  for(ward in unique(subgroup$Ward)){
    subgroup2 <- subgroup[subgroup$Ward == ward,]
    savename <- 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}
<<loaddata, echo=FALSE, message=FALSE>>=
  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)
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}


##  To be then turned into pdf with this
tools::texi2pdf("C:file.path\\report_A.tex", clean = TRUE, quiet = TRUE)

尝试运行knit()代码块后，出现此错误:

After trying to run my knit() code chunk I get this error:

Error in file(con, "w") : invalid 'description' argument

当我查看要创建* .tex文件的目录时，我可以看到生成了医院A的2个pdf图(B都没有)，并且没有医院特定的* .tex文件可以编织成pdf.预先感谢您提供的任何帮助！

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!

推荐答案

您不需要重新定义.Rnw文件中的数据，我认为警告来自您放置输出的事实名称与Hospital(医院的完整向量)一起使用，而不是与hosp(循环索引)一起使用.

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).

按照您的示例，testingloops.Rnw应该是

\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}

驱动程序R文件就是

##  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'))
}

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