Is there a way to knitr markdown straight out of your workspace using RStudio?
knitr, r, rstudio
Solution
RStudio opens a new R session to `knit()` your R Markdown file, so the objects in your current working space will not be available to that session (they are two separate sessions). Two solutions:
- file a feature request to RStudio, asking them to support knitting in the current R session instead of forcibly starting a new session;
- knit manually by yourself: `library(knitr); knit('your_file.Rmd')` (or `knit2html()` if you want HTML output in one step, or `rmarkdown::render()` if you are using R Markdown v2)
Problem
I wonder whether I can use `knitr` markdown to just create a report on the fly with objects stemming from my current workspace. Reproducibility is not the issue here. I also read this very fine thread here. But still I get an error message complaining that the particular object could not be found. 1) Suppose I open a fresh markdown document and save it. 2) write a chunk that refers to some `lm` object in my workspace. call `summary(mylmobject)` 3) knitr it. Unfortunately the report is generated but the regression output cannot be shown because the object could not be found. Note, it works in general if i just save the object to .Rdata and then load it directly from the markdown file. Is there a way to use objects in R markdown that are in the current workspace? This would be really nice to show non R people some output while still working.