R Knitr PDF: Is there a posssibility to automatically save PDF reports (generated from .Rmd) through a loop?

Solution 1:

Adapting your example:

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)
```

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

1. Define the subgroup object used inside the template
2. render the template to the desired output

So, in this separate script:

# 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'))    
}

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

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.

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.