[R] Using rmarkdown with many plots created in a loop

[Thierry Onkelinx]

Dear Don,

Have a look at the knit_expand() function. Then you can create two Rmd
files. One main file and one template file for the subsets. knit_expand()
will find and replace anything between double curly brackets ("{{x}}" in
the example below) with the value of the variable.

The main file:

---
title: "main"
output: html_document
---

```{r setup, include=FALSE}
library(knitr)
```

```{r}
mydf <- data.frame(
  id = 1:4,
  x = rnorm(100),
  y = rnorm(100)
)
```

```{r}
rmd <- sapply(
  1:4,
  function(x) {
    knit_expand("child.Rmd", x = x)
  }
)
rmd <- paste(rmd, collapse = "\n")
cat(rmd)
```
```{r results = "asis"}
rendered <- knit(text = rmd, quiet = TRUE)
cat(rendered, sep = "\n")
```


The child.Rmd file

## ID {{x}}

```{r, fig.cap = "The caption: ID = {{x}}", echo = FALSE}
i <- {{x}}
detail <- subset(mydf, id == i)
plot(x ~ y, data = detail)
```

Best regards,


ir. Thierry Onkelinx
Statisticus / Statistician

Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkelinx using inbo.be
Havenlaan 88 bus 73, 1000 Brussel
www.inbo.be

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<https://www.inbo.be>

2018-08-17 1:44 GMT+02:00 MacQueen, Don via R-help <r-help using r-project.org>:

> I would appreciate some suggestions of a good way to prepare a report
> using rmarkdown,
> in which I loop through subsets of a data set, creating a plot of each
> subset, and interspersing
> among the figures some text relevant to each figure.
>
> One way is to have an R script write the rmd file, then render it.
> It works, but it's cumbersome and difficult to get the rmd syntax correct.
> I would very much appreciate suggestions for a better way.
>
> Reproducible example below.
>
> Thanks
> -Don
>
>
> Example data (other data structures could be used), and an example using
> this approach.
>
> myd <- lapply( 1:3,
>               function(i) list(df=data.frame(x=1:5, y=rnorm(5)),
>                                comment=paste('Data', LETTERS[i]))
>               )
>
> Example interactive review (details would change depending on data
> structure)
> (I would typically insert pauses when working interactively)
>
> for (i in 1:3) {
>   cat(paste('Figure',i,'shows',myd[[i]]$comment),'\n')
>   with(myd[[i]]$df , plot(x,y))
>   mtext(myd[[i]]$comment)
>   mtext( paste(nrow(myd[[i]]$df),'points'), adj=1)
> }
>
> Note that along with the data I've saved some comments relevant to each
> subset.
> I've calculated them in the example data, but in general they could be
> completely
> arbitrary and come from anywhere.
>
> Now I'd like to get the same plots and comments into a report prepared
> using rmarkdown.
> Here's one way, having the loop create an rmd file, then rendering it.
>
> ### example script begins
> library(rmarkdown)
>
> myf <- 'myd.rmd'
> sink(myf)
> cat('---
> title: Example
> ---
>
> Here are some figures with a comment appearing before each.\n\n'
> )
> sink()
>
> for (i in 1:3) {
>   cat(paste('Figure',i,'comment:',myd[[i]]$comment),'\n', file=myf,
> append=TRUE)
>
>   cat("
> ```{r  echo=FALSE, fig.cap='",paste('fig',i),"caption.'}
>   with(myd[[",i,"]]$df , plot(x,y))
>   mtext(myd[[",i,"]]$comment)
>   mtext( paste(nrow(myd[[",i,"]]$df),'points'), adj=1)
> ```
> ", file=myf, append=TRUE)
>
> }
>
> cat('Done with report\n', file=myf, append=TRUE)
>
> render(myf)
>
> --
> Don MacQueen
> Lawrence Livermore National Laboratory
> 7000 East Ave., L-627
> Livermore, CA 94550
> 925-423-1062
> Lab cell 925-724-7509
>
>
>
> ______________________________________________
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> PLEASE do read the posting guide http://www.R-project.org/
> posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

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