Accessing data generated by an R script with r markdown and knitr - r

Question

I am new to R markdown and knitr and haven't found the answer to this question:
I have R scripts where I've written functions and have assigned data to position 1 (.GlobalEnv). How do I access my data and run my functions within R markdown and generate the .html file with knitr?
Here's a trivial example. In a script file I generate:
some.x.data<-1:10
some.y.data<-1:10
toy.fn<-function(){
tot<-some.x.data + some.y.data
tot
}
toy.fn() works in the script file.
My R markdown file contains:
---
title: "trivial test"
author: "me"
date: "July 9, 2015"
output: html_document
---
```{r}
plot(some.x.data, some.y.data)
toy.fn()
```
When I click knit HTML, I get the following error:
Error in plot(some.x.data, some.y.data) : object 'some.x.data' not found
Calls: ... withCallingHandlers -> withVisible -> eval -> eval -> plot
Thanks

Answer 1

RStudio opens a new R session to knit() your Rmd file, so the objects in .GlobalEnv will not be available to that session (they are two separate sessions), so when you are knitring HTML there is not way to know what some.x.data, some.y.data and toy.fn is.
Either you need to recreate them in your Rmd file. If you don't want any output just do:
```{r, echo = FALSE, message = FALSE}
some.x.data<-1:10
some.y.data<-1:10
toy.fn<-function(){
tot<-some.x.data + some.y.data
tot
}
```
Full Rmd:
---
title: "trivial test"
author: "me"
date: "July 9, 2015"
output: html_document
---
```{r, echo = FALSE, message = FALSE}
some.x.data<-1:10
some.y.data<-1:10
toy.fn<-function(){
tot<-some.x.data + some.y.data
tot
}
```
```{r}
plot(some.x.data, some.y.data)
toy.fn()
```
Or
knit manually by yourself: library(knitr); knit('your_file.Rmd')