Create Parametric R Markdown Documentation

Create parametric R markdown documentation?

I would use a combination of brew and knitr to achieve this. I would create a brew template called doc.brew which looks like this

<% for (res in names(results)) { -%>

### Results for: <%= res %>

```{r}
plot(results[["<%= res %>"]]$x, results[["<%= res %>"]]$y)
```

<% } %>

You can now run the following code to get your desired output

results = list(
  result1 = data.frame(x=rnorm(3), y=rnorm(3)), 
  result2=data.frame(x=rnorm(3), y=rnorm(3))
)
brew::brew('doc.brew', 'doc.Rmd')
knit2html('doc.Rmd')

How do I knit child documents with parameters into a main RMarkdown document?

What worked for me (derived from the documentation once I properly understood it.):

Instead of using the params field in the YAML header, set the values of the parameters inside the main document and call cat on the output of knitr::knit_child. The below files achieved the desired result.

parameterized.Rmd

---
title: "Parameterized report"
output: html_document
---

```{r}
head(df[, 1:2])
```

main.Rmd

---
title: "Main report"
output: html_document
---

# mtcars
```{r mtcars, echo=FALSE, results='asis'}
df <- mtcars 
cat(
  knitr::knit_child('parameterized.Rmd', envir = environment(), quiet = TRUE)
  )
```

# iris
```{r iris, echo=FALSE, results='asis'}
df <- iris 
cat(
  knitr::knit_child('parameterized.Rmd', envir = environment(), quiet = TRUE)
  )
```

Knitting main.Rmd applied the parameterized report to each dataframe.

Setting document title in Rmarkdown from parameters

Try to use a second YAML metadata block, and put the parameterized metadata in there.

I got the following code to work as expected (i.e., producing a document title from the list of params):

---
output: html_document
params: 
    set_title: "My Title!"
---

---
title: `r params$set_title`
---

The RMarkdown documentation notes that YAML metadata blocks are combined by Pandoc. Use the first block to define the parameter set, and the second one to use the parameters as metadata. Knitr will execute the R code to interpret the parameters in the second block.Then Pandoc will merge the metadata blocks together.

Update (2017):

This can be accomplished in a single block, like so:

---
output: html_document
params: 
    set_title: "My Title!"
title: "`r params$set_title`"
---

This works because the title comes after the params definition. I put quotes around the in-line R code to prevent "Scanner errors".

Is it possible to create a self-rendering Rmarkdown document?

You can treat an Rmd file as an Rscript. For instance, assume that your Rmd file looks like this

---
title: "Untitled"
author: "ekoam"
date: "`r Sys.Date()`"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

## R Markdown

This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.

When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:

```{r cars}
summary(cars)
```

## Including Plots

You can also embed plots, for example:

```{r pressure, echo=FALSE}
plot(pressure)
```

Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.

You can then prepend the following code to that Rmd file

#!/usr/bin/env Rscript

args <- commandArgs()
fname <- normalizePath(sub("--file=", "", args[grepl("--file=", args)]))
thisfile <- readLines(fname)
newfname <- paste0(tempdir(), "/", basename(fname))
writeLines(thisfile[-1:-which(thisfile == "q(\"no\")")], newfname)
rmarkdown::render(newfname, output_dir = dirname(fname))
q("no")

The trick here is q("no"). This line terminates the R session, and, thus, whatever written after it will be ignored. Such an effect also means high flexibility for coding because you can write almost any valid R code before that q("no"). The code above simply creates another temporary Rmd file with the same content as what is after q("no"). Then, we rmarkdown::render that temporary file and dump the output to the current directory.

The complete Rmd file looks like this

#!/usr/bin/env Rscript

args <- commandArgs()
fname <- normalizePath(sub("--file=", "", args[grepl("--file=", args)]))
thisfile <- readLines(fname)
newfname <- paste0(tempdir(), "/", basename(fname))
writeLines(thisfile[-1:-which(thisfile == "q(\"no\")")], newfname)
rmarkdown::render(newfname, output_dir = dirname(fname))
q("no")

---
title: "Untitled"
author: "ekoam"
date: "`r Sys.Date()`"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

## R Markdown

This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.

When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:

```{r cars}
summary(cars)
```

## Including Plots

You can also embed plots, for example:

```{r pressure, echo=FALSE}
plot(pressure)
```

Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.

Passing Parameters to R Markdown

In my case it worked, just had to change the indentation in the header and some names which are available in my folder...

Here my jnk.Rmd

---
title: "Liquidity Report"
output: pdf_document
params: 
  client: "NAMESPACE"
---
```{r plot, echo=FALSE, warning=FALSE}
cftest <- read.csv(params$client)
```

And this is what I called in the console : render('jnk.Rmd',params= list( client= "NAMESPACE"))

Passing parameters through an RMarkdown document?

I think the step you were missing was specifying the output filename so that each "vendor" would have its own file; otherwise, the same filename is overwritten each time leaving you with a single HTML document.

An example:

---
title: mtcars cyl
author: r2evans
params:
  cyl: null
---

We have chosen to plot a histogram of `mtcars` where `$cyl` is equal to `r params$cyl`:

```{r}
dat <- subset(mtcars, cyl == params$cyl)
if (nrow(dat) > 0) {
  hist(dat$disp)
}
```

Calling this with:

for (cy in c(4,6,8)) {
  rmarkdown::render("~/StackOverflow/10466439/67525642.Rmd", 
                    output_file = sprintf("cyl_%s.html", cy),
                    params = list(cyl = cy))
}

will render three HTML files, cyl_4.html, cyl_6.html, and cyl_8.html, each with differing content:

---

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