使用与knitr循环产生多个PDF报告…需要一点帮助，让我在驼峰

首先，我必须承认，我对knitr和可重复分析的概念很陌生，但是我可以看到它在改进我目前的工作stream程（其中包括大量复制到word文档中）上的潜力。

我经常不得不按小组（医院在这个例子中）生成多个报告，在每个医院内，可能会有许多不同的病房，我正在报告一个结果。 以前我用R语言把所有的图表和分析都用R语言进行，然后复制/粘贴工作就开始了。 然而，读完这篇文章后（ Sweave会自动生成许多PDF文件？ ），这让我希望我可以跳过许多步骤，从R直接通过Rnw / knitr进行报告。

然而，在尝试一下之后，我发现有些东西没有完全解决（因为Rn中的R环境似乎没有认识到我正试图传递给它的循环variables？）。

## 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) 

试图运行我的knit（）代码块后，我得到这个错误：

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

当我查看要创build* .tex文件的目录时，我可以看到医院A的2个pdf图（没有B），也没有医院特定的* .tex文件编织成pdf。 预先感谢您提供的任何帮助！

Answer 1

您不需要重新定义.Rnw文件中的数据，我认为警告来自于您将输出名称与Hospital （ Hospital的完整vector）而不是hosp （循环索引）。

按照你的例子， testingloops.Rnw会

 \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} 

和驱动程序R文件将是公正的

 ## 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')) } 

Answer 2

好问题！ 这适用于您在问题中提供的其他位。 请注意，我用x代替了你的hosp 。 我打电话给你的Rnw文件test.rnw

 # input 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) # 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)) 

我用lapply和anonymous函数取代了你的循环，这些函数通常被认为是更加R 。

在这里你可以看到我在rnw文件中用xreplace了rnw ：

 \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$Hospital == x,] @ \begin{document} <<setup, echo=FALSE >>= opts_chunk$set(fig.path = paste("test", x , sep="")) @ Some informative text about hospital \Sexpr{x} <<plots, echo=FALSE >>= for(ward in unique(subgroup$Ward)){ subgroup2 <- subgroup[subgroup$Ward == ward,] # subgroup2 <- subgroup2[ order(subgroup2$Month),] savename <- paste(x, ward) plot(subgroup2$Month, subgroup2$Outcomes, type="o", main=paste("Trend plot for", savename)) } @ \end{document} 

结果是两个tex文件（report_A.tex，report_B.tex），四个PDF（A1，A2，B1，B2）和两个PDF（报告_A.pdf，report_B.pdf），每个都带有数字在他们中。 那是你以后的事吗？