I have a .Rmd file called f1.Rmd (containing a mix of text and R chunks) and an R script called f2.R.
I would like to insert a set of R instructions in f2.R that would execute all the R chunks contained in f1.Rmd, in such a way that all variables created in f1.Rmd would be created in my current R session if I source f2.R
(similarly to what happens when clicking on "Run" -> "Run all chunks below from the Rstudio menu").
If you render the f1.Rmd file from your current environment, this should happen.
You can use rmarkdown::render() from the console or a .R script. This will create all the variables in your current environment. It will also have the side effect of making the document.
When you use the knit button in RStudio, this launches the render in a new r session as a background process.
See also the envir option for render.
See also this answer for other options. knitr: run all chunks in an Rmarkdown document
It also depends what your .Rmd is doing.
Related
I have a large Markdown file (*.Rmd) and want to execute only the R commands in that file (not the text) in RStudio. How can this be done?
If I mark the whole document and try to execute it, R tries to execute also the text in the Markdown file, which, of course, results in errors.
Click on the arrows at the top right of the chunks:
I have an RMarkdown document with some R code in it. The code works fine when I'm running it interactively in the console. However, when I try to knit the document (using the "knit" button in RStudio), R throws error messages that some objects cannot be found.
When you compile a document (using the "knit" button in RStudio), knitting takes place in a separate R session. Therefore, your document must be self-contained:
Objects from the Global Environment of your interactive sessions are not available when knitting. You must create/load all objects from within your document.
You must load all packages used from within your document.
Also note that while knitting, your working directory is changed to the directory containing your document (by default). Therefore, relative paths (for example, paths to data sets you want to read) might not point to the expected files.
I wish to use libraries across multiple .Rmd files in an r notebook without having to reload the library each time.
An example: I have loaded the library kableExtra in the index.Rmd file but when I call it in another .Rmd file such as ExSum.Rmd I would get this error:
Error in Kable....: could not find funciton "kable" Calls:...
If I load the kableExtra library again this problem goes away. Is there a workaround?
R Markdown files are intended to be standalone, so you shouldn't do this. There are two workarounds that come close:
If you process your .Rmd files within the R console by running code like rmarkdown::render("file.Rmd") then any packages attached in the session will be available to the code in the .Rmd file.
You can put all the setup code (e.g. library(kableExtra)) into a file (called setup.R, for example), and source it into each document in the first code chunk using source('setup.R'). Every file will run the same setup, but you only need to type it once.
The second is the better approach.
I've been moving some of the code for a report I'm writing to child .rmd files. I want to run these chunks by clicking on the green arrow (top right):
But this doesn't work in RStudio, is this a feature or a bug?
This has not been implemented in RStudio yet, and probably won't be for some time.
However, you can write your R code in a separate file, reference it in R Markdown chunks, and execute those chunks interactively in RStudio. The way to do this is with knitr's code externalization feature. You can read about how to use it in R Markdown notebooks here:
https://rmarkdown.rstudio.com/r_notebooks.html#executing_code (scroll down a bit to Executing External Chunks)
More on code externalization with knitr here:
https://yihui.name/knitr/demo/externalization/
I'm trying to write a Bash script in Ubuntu 10.04 that opens a Python file which exports a CSV, and then runs the following Rscript with the goal of exporting a HTML with plots from Dashboard.Rmd:
require(knitr)
setwd('/home/sensors/Desktop/')
knit2html('Dashboard.Rmd')
browseURL('Dashboard.html')
Dashboard.Rmd is an R markdown that calls read.csv on the csv from the first step, makes a data frame and creates plots, but that part's working fine. According to this, I figure that Rscript should replicate the action of pressing "Knit HTML" in R Studio. However, the html it creates is identical to the last time Knit HTML was pressed; i.e. even if the CSV is different, the html doesn't reflect the change.
I also tried using a separate line for knit and markdownToHTML with the same effect. It seems like it doesn't source the code from the Rmd when performing knit. It does update the html properly when I enter the commands from that Rscript into the console of R Studio with Dashboard.Rmd open. However I'm not sure how to translate that into a Bash script. I also tried knit2html with envir=new.env(), envir=R_GlobalEnv, and envir=parent.frame() with no luck. Any help would be appreciated!
So it turns out that this was an artifact of cache=TRUE -- the HTML file was not changed because everything was cached.