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I have just installed the preview release of RStudio, Version 0.98.864 (May 24th, 2014). Also, I have installed the development versions of knitr and shiny, via
devtools::install_github(c("yihui/knitr", "rstudio/shiny"))
I am trying to create a Shiny Document (using Rstudio dialog with Shiny Document template) to:
1) Set the value of a variable, e.g. x. The following code is the contents of my Rmd file: (I have to place this as an image as the formatting is playing up)
2) Source an R script (testExternalisation.R) in the same directory that uses the variable, x, set in the .Rmd file; code as follows:
y <- x + 3
However, on running the .Rmd document I get the following message: "Error: object 'x' not found. Now, if I remove the first 3 lines of my .Rmd file, i.e. the front matter for a Shiny html_document, I am perfectly able to knit the resulting .Rmd document. Is there a solution for sourcing external scripts in Shiny Documents that rely on variables in the calling Shiny Doc?
Edit: When knitting the document, environment() returns <environment: R_GlobalEnv> for both the .Rmd and .R files. However, when running the Shiny document, the .Rmd environment is <environment: 0x05828968> and source environment is <environment: R_GlobalEnv>, so I need to ensure the two are using the same environment ...
Thanks.
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To share R code like function definitions, you can put this code in an R script and import it in each file with the function source() To share common R Markdown text and code chunks, you can use child documents.
You can execute R script as you would normally do by using the Windows command line. If your R version is different, then change the path to Rscript.exe. Use double quotes if the file path contains space.
R Markdown provides an unified authoring framework for data science, combining your code, its results, and your prose commentary. R Markdown documents are fully reproducible and support dozens of output formats, like PDFs, Word files, slideshows, and more.
R Markdown is a file format for making dynamic documents with R. An R Markdown document is written in markdown (an easy-to-write plain text format) and contains chunks of embedded R code, like the document below.
The following seems to solve the problem: change the source() function to
source("testExternalisation.R", local=environment())
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