stitch: Automatically create a report based on an R script and a...

Description Usage Arguments Details Value See Also Examples

View source: R/template.R

Description

This is a convenience function for small-scale automatic reporting based on an R script and a template. The default template is an Rnw file (LaTeX); stitch_rhtml() and stitch_rmd() are wrappers on top of stitch() using the R HTML and R Markdown templates respectively.

Usage

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stitch(script, template = system.file("misc", "knitr-template.Rnw", package = "knitr"), 
    output = NULL, text = NULL, envir = parent.frame())

stitch_rhtml(..., envir = parent.frame())

stitch_rmd(..., envir = parent.frame())

Arguments

script

path to the R script

template

path of the template to use (by default the Rnw template in this package; there is also an HTML template in knitr)

output

the output filename (passed to knit); by default it uses the base filename of the script

text

a character vector as an alternative way to provide the input file

envir

the environment in which the code chunks are to be evaluated (for example, parent.frame(), new.env(), or globalenv())

...

arguments passed to stitch()

Details

The first two lines of the R script can contain the title and author of the report in comments of the form ## title: and ## author:. The template must have a token %sCHUNK_LABEL_HERE, which will be used to input all the R code from the script. See the examples below.

The R script may contain chunk headers of the form ## ---- label, opt1=val1, opt2=val2, which will be copied to the template; if no chunk headers are found, the whole R script will be inserted into the template as one code chunk.

Value

path of the output document

See Also

spin (turn a specially formatted R script to a report)

Examples

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s = system.file("misc", "stitch-test.R", package = "knitr")
if (interactive()) stitch(s)  # compile to PDF

# HTML report
stitch(s, system.file("misc", "knitr-template.Rhtml", package = "knitr"))

# or convert markdown to HTML
stitch(s, system.file("misc", "knitr-template.Rmd", package = "knitr"))

Example output

processing file: stitch-test.Rhtml

  |                                                                       
  |                                                                 |   0%
  |                                                                       
  |.........                                                        |  14%
label: setup (with options) 
List of 2
 $ include: logi FALSE
 $ cache  : logi FALSE


  |                                                                       
  |...................                                              |  29%
   inline R code fragments


  |                                                                       
  |............................                                     |  43%
label: auto-report

  |                                                                       
  |.....................................                            |  57%
  ordinary text without R code


  |                                                                       
  |..............................................                   |  71%
label: session-info (with options) 
List of 1
 $ cache: logi FALSE

sh: 1: cannot create /dev/null: Permission denied

  |                                                                       
  |........................................................         |  86%
label: clean-up (with options) 
List of 1
 $ include: logi FALSE


  |                                                                       
  |.................................................................| 100%
  ordinary text without R code


output file: stitch-test.html

[1] "stitch-test.html"


processing file: stitch-test.Rmd

  |                                                                       
  |                                                                 |   0%
  |                                                                       
  |.............                                                    |  20%
   inline R code fragments


  |                                                                       
  |..........................                                       |  40%
label: auto-report

  |                                                                       
  |.......................................                          |  60%
  ordinary text without R code


  |                                                                       
  |....................................................             |  80%
label: session-info (with options) 
List of 1
 $ cache: logi FALSE

sh: 1: cannot create /dev/null: Permission denied

  |                                                                       
  |.................................................................| 100%
label: clean-up (with options) 
List of 1
 $ include: logi FALSE


output file: stitch-test.md

HTML output at: stitch-test.html
[1] "stitch-test.md"

knitr documentation built on Aug. 10, 2017, 9:02 a.m.