R: Read chunks from an external script

read_chunk {knitr} | R Documentation

## Read chunks from an external script

### Description

Chunks can be put in an external script, and this function reads chunks into the current knitr session; `read_demo()` is a convenience function to read a demo script from a package.

### Usage

    read_chunk(path, lines = readLines(path, warn = FALSE), labels = NULL, from = NULL,
        to = NULL, from.offset = 0L, to.offset = 0L, roxygen_comments = TRUE)

    read_demo(topic, package = NULL, ...)

### Arguments

`path` | Path to the R script.
`lines` | Character vector of lines of code. By default, this is read from `path`.
`labels` | Character vector of chunk labels (default `NULL`).
`from, to` | Numeric vector specifying the starting/ending line numbers of code chunks, or a character vector; see Details.
`from.offset, to.offset` | Offsets to be added to `from`/`to`.
`roxygen_comments` | Logical dictating whether to keep trailing roxygen-style comments from code chunks in addition to whitespace
`topic, package` | Name of the demo and the package. See `demo`.
`...` | Arguments passed to `read_chunk`.

### Details

There are two approaches to read external code into the current session: (1) Use a special separator of the from `## ---- chunk-label` (at least four dashes before the chunk label) in the script; (2) Manually specify the labels, starting and ending positions of code chunks in the script.

The second approach will be used only when `labels` is not `NULL`. For this approach, if `from` is `NULL`, the starting position is 1; if `to` is `NULL`, each of its element takes the next element of `from` minus 1, and the last element of `to` will be the length of `lines` (e.g. when `from = c(1, 3, 8)` and the script has 10 lines in total, `to` will be `c(2, 7, 10)`). Alternatively, `from` and `to` can be character vectors as regular expressions to specify the positions; when their length is 1, the single regular expression will be matched against the `lines` vector, otherwise each element of `from`/`to` is matched against `lines` and the match is supposed to be unique so that the numeric positions returned from `grep()` will be of the same length of `from`/`to`. Note `labels` always has to match the length of `from` and `to`.

### Value

As a side effect, code chunks are read into the current session so that future chunks can (re)use the code by chunk label references. If an external chunk has the same label as a chunk in the current session, chunk label references by future chunks will refer to the external chunk.

### Note

This function can only be used in a chunk which is not cached (chunk option `cache = FALSE`), and the code is read and stored in the current session without being executed (to actually run the code, you have to use a chunk with a corresponding label).

### Author(s)

Yihui Xie; the idea of the second approach came from Peter Ruckdeschel (author of the SweaveListingUtils package)

### References

https://yihui.name/knitr/demo/externalization/

### Examples

    ## put this in foo.R and read_chunk('foo.R')

    ## ---- my-label ----
    1 + 1
    lm(y ~ x, data = data.frame(x = 1:10, y = rnorm(10)))

    ## later you can use <<my-label>>= to reference this chunk

    ## the 2nd approach
    code = c("#@a", "1+1", "#@b", "#@a", "rnorm(10)", "#@b")
    read_chunk(lines = code, labels = "foo")  # put all code into one chunk named foo
    read_chunk(lines = code, labels = "foo", from = 2, to = 2)  # line 2 into chunk foo
    read_chunk(lines = code, labels = c("foo", "bar"), from = c(1, 4), to = c(3, 6))
    # automatically figure out 'to'
    read_chunk(lines = code, labels = c("foo", "bar"), from = c(1, 4))
    read_chunk(lines = code, labels = c("foo", "bar"), from = "^#@a", to = "^#@b")
    read_chunk(lines = code, labels = c("foo", "bar"), from = "^#@a", to = "^#@b",
        from.offset = 1, to.offset = -1)

    ## later you can use, e.g., <<foo>>=
    knitr:::knit_code$get()  # use this to check chunks in the current session
    knitr:::knit_code$restore()  # clean up the session

[Package knitr version 1.20 Index]