R Knitr PDF:是否有可能通过循环自动保存 PDF 报告(从 .Rmd 生成)? [英] R Knitr PDF: Is there a posssibility to automatically save PDF reports (generated from .Rmd) through a loop?

问题描述

我想创建一个循环，它允许我自动保存从 .Rmd 文件生成的 PDF 报告.例如，如果变量ID"有 10 行，我希望 R 自动将 10 个报告保存到特定目录中.这些报告应根据选择的 ID 而有所不同.

I would like to create a loop, which allows me to automatically save PDF reports, which were generated from a .Rmd file. For instance, if a variable "ID" has 10 rows, I would like R to automatically save me 10 reports, into a specific directory. These reports shall vary based on the ID selected.

以前的帖子(使用带有 knitr 的循环生成多个 pdf 报告...需要一点帮助才能让我克服困难) 已经处理了从 .Rnw 生成的多个 pdf 报告的创建文件.我尝试按如下方式应用该方法:

A previous post (Using loops with knitr to produce multiple pdf reports... need a little help to get me over the hump) has dealt with the creation of multiple pdf reports generated from .Rnw files. I tried to apply the approach as follows:

#Data

```{r, include=FALSE}
set.seed(500)
Score <- rnorm(40, 100, 15)
Criteria1<-rnorm(40, 10, 5)
Criteria2<-rnorm(40, 20, 5)
ID <- sample(1:1000,8,replace=T)
df <- data.frame(ID,Score,Criteria1,Criteria2)

#instead of manually choosing the ID:

subgroup<- subset(df, ID==1) 

# I would like to subset the Data through a loop. My approach was like like this:

for (id in unique(df$ID)){
subgroup<- df[df$ID == id,]}

```

```{r, echo=FALSE}
#Report Analysis

summary(subgroup)
```
#Here will be some text about the summary.



# At the end the goal is to produce automatic pdf reports with the ID name as a filename:

library("rmarkdown")
render("Automated_Report.rmd",output_file = paste('report.', id, '.pdf', sep=''))

推荐答案

调整你的例子:

您需要一个 .rmd 模板"文件.可能是这样的，另存为template.rmd.

You need one .rmd "template" file. It could be something like this, save it as template.rmd.

This is a subgroup report.

```{r, echo=FALSE}
#Report Analysis
summary(subgroup)
```

然后，你需要一个 R 脚本来加载你想要的数据，遍历数据子集，并为每个子集

Then, you need an R script that will load the data you want, loop through the data subsets, and for each subset

1. 定义模板内部使用的subgroup对象
2. 将模板渲染为所需的输出

所以，在这个单独的脚本中:

# load data 
set.seed(500)
Score <- rnorm(40, 100, 15)
Criteria1<-rnorm(40, 10, 5)
Criteria2<-rnorm(40, 20, 5)
ID <- sample(1:1000,8,replace=T)
df <- data.frame(ID,Score,Criteria1,Criteria2)

library("rmarkdown")

# in a single for loop
#  1. define subgroup
#  2. render output
for (id in unique(df$ID)){
    subgroup <- df[df$ID == id,]
    render("template.rmd",output_file = paste0('report.', id, '.html'))    
}

这在我的工作目录中生成了 8 个 html 文件，每个文件都有不同数据子集的摘要.

This produced 8 html files in my working directory, each with a summary of a different subset of the data.

请注意，如果您尝试单击 RStudio 中的knit"按钮，这将不起作用，因为它会在单独的 R 会话中运行 R 代码.但是，当您使用 render(或 knit2pdf)从控制台显式运行时，rmd 文件中的 R 代码仍然可以访问全局环境.

Note that this will not work if you try clicking the "knit" button inside RStudio, as that runs the R code in a separate R session. However, when you run from the console explicitly using render (or knit2pdf) the R code in the rmd file still has access to the global environment.

不是依赖全局变量，另一种选择是使用参数化报告，在 YAML 头中定义参数，并将参数值作为参数传递给 rmarkdown::render.

Rather than relying on global variables, another option would be to use parametrized reports, defining parameters in the YAML header, and passing the parameter values in as arguments to rmarkdown::render.

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