Proper R Markdown Code Organization

Question

I have been reading about R Markdown (here, here, and here) and using it to create solid reports. I would like to try to use what little code I am running to do some ad hoc

Answer 1

Often times, I have many reports that need to run the same code with slightly different parameters. Calling all my "stats" functions separately, generating the results and then just referencing is what I typically do. The way to do this is as follows:

---
title: "Untitled"
author: "Author"
date: "August 4, 2015"
output: html_document
---

```{r, echo=FALSE, message=FALSE}
directoryPath <- "rawPath" ##Something like /Users/userid/RDataFile
fullPath <- file.path(directoryPath,"myROutputFile.RData") 
load(fullPath)
```

Some Text, headers whatever

```{r}
summary(myStructure$value1) #Where myStructure was saved to the .RData file
```  

You can save an RData file by using the save.image() command.

Hope that helps!

Answer 2

There is a solution for this sort of problem, explained here.

Basically, if you have an .R file containing your code, there is no need to repeat the code in the .Rmd file, but you can include the code from .R file. For this to work, the chunks of code should be named in the .R file, and then can be included by name in the .Rmd file.

test.R:

## ---- chunk-1 ----
table(cars.by.name$make)

test.Rmd

Just once on top of the .Rmd file:

```{r echo=FALSE, cache= F}
knitr::read_chunk('test.R')
```

For every chunk you're including (replace chunk-1 with the label of that specific chunk in your .R file):

```{r chunk-1}
```

Note that it should be left empty (as is) and in run-time your code from .R will be brought over here and run.