CODEWITHSUNDEEP
rknitrrstudio
Farrel
Farrel

Reputation: 10444

Making knitr run a r script: do I use read_chunk or source?

I am running R version 2.15.3 with RStudio version 0.97.312. I have one script that reads my data from various sources and creates several data.tables. I then have another r script which uses the data.tables created in the first script. I wanted to turn the second script into a R markdown script so that the results of analysis can be outputted as a report.

I do not know the purpose of read_chunk, as opposed to source. My read_chunk is not working, but source is working. With either instance I do not get to see the objects in my workspace panel of RStudio.

Please explain the difference between read_chunk and source? Why would I use one or the other? Why will my .Rmd script not work

Here is ridiculously simplified sample

It does not work. I get the following message

Error: object 'z' not found

Two simple files...

test of source to rmd.R

x <- 1:10
y <- 3:4
z <- x*y

testing source.Rmd

Can I run another script from Rmd
========================================================

Testing if I can run "test of source to rmd.R"

```{r first part}
require(knitr)
read_chunk("test of source to rmd.R")
a <- z-1000
a
```

The above worked only if I replaced "read_chunk" with "source". I 
can use the vectors outside of the code chunk as in inline usage. 
So here I will tell you that the first number is `r a[1]`. The most 
interesting thing is that I cannot see the variables in RStudio 
workspace but it must be there somewhere.

Upvotes: 23

Views: 14621

Answers (3)

Omar Wasow
Omar Wasow

Reputation: 2040

In case it helps anyone else, I've found using read_chunk() to read a script without evaluating can be useful in two ways. First, you might have a script with many chunks and want control over which ones run where (e.g., a plot or a table in a specific place). I use source when I want to run everything in a script (for example, at the start of a document to load a standard set of packages or custom functions). I've started using read_chunk early in the document to load scripts and then selectively run the chunks I want where I need them.

Second, if you are working with an R script directly or interactively, you might want a long preamble of code that loads packages, data, etc. Such a preamble, however, could be unnecessary and slow if, for example, prior code chunks in the main document already loaded data.

Upvotes: 1

russellpierce
russellpierce

Reputation: 4711

There isn't an option to run a chunk interactively from within knitr AFAIK. However, this can be done easily enough with something like:

#' Run a previously loaded chunk interactively
#'
#' Takes labeled code loaded with load_chunk and runs it in the /global/ envir (unless otherwise specified)
#'
#' @param chunkName The name of the chunk as a character string
#' @param envir The environment in which the chunk is to be evaluated 
run_chunk <- function(chunkName,envir=.GlobalEnv) {
    chunkName <- unlist(lapply(as.list(substitute(.(chunkName)))[-1], as.character))    
    eval(parse(text=knitr:::knit_code$get(chunkName)),envir=envir) 
} 
NULL

Upvotes: 1

Yihui Xie
Yihui Xie

Reputation: 30194

read_chunk() only reads the source code (for future references); it does not evaluate code like source(). The purpose of read_chunk() was explained in this page as well as the manual.

Upvotes: 14

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