Calling functions in a second file when compiling .Rmd files with knitr - r

Question

I want to use knitr to format an R markdown file, lets call it Main.rmd. Some code in Main.rmd relies on helper functions in a second file, lets call it Functions.rmd.
When I first run Functions.rmd and then Main.rmd, the code in Main.rmd runs fine. When I first run Functions.rmd and then try to knit Main.rmd, I receive an evaluation:
Error "Object 'myfunction' not found
How can I fix this without combining Main.rmd and Functions.rmd into a single document, which I would like to avoid doing?
Edit: I've added a toy example below. There are very useful suggestions so far for how to call the functions in Functions.rmd from Main.rmd, but they all require converting Functions.rmd to a .R file. However, for my current purpose, it is important that Functions.rmd can also be read as a standalone markdown document.
First, Main.rmd:
---
title: "Main_test"
author: "Matt Nolan"
date: "25/06/2018"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## Background.
This is the main body of text and code used to display results of analyses, some of which are created by calling functions in Functions.Rmd.
```{r cars}
myexamplefunction(1,2)
```
And, here is Functions.rmd:
---
title: "Functions_test"
author: "Matt Nolan"
date: "25/06/2018"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## Background
This is a document containing functions used in the document "Main_test".
Because it contains functions and formatted text to explain the functions for an interested reader, it should be usable as a standalone markdown document.
For example, this is a function that adds two numbers.
```{r cars}
myexamplefunction <- function(a, b) {a + b}
```

Answer 1

30Jun2018 Update: R Markdown does not support combining Rmd files
Matt's 25Jun2018 update clarifies the question, asking how to embed one Rmd document in another Rmd document. Per the R Markdown website, R Markdown requires a single Rmd file. It does not currently support the embedding of one Rmd file within another Rmd document.
That said, with the bookdown package, you could structure the Rmd files as chapters in a book, where each Rmd file is a chapter in the book. For details, see Bookdown: Authoring Books with R Markdown 1.4 - Two Rendering Approaches, the Getting Started page, and the Bookdown Demo github repository for an example book built in bookdown.
25Jun2018 Update: Printing the code in an Appendix
Per the comments from the OP, the reason for including the functions in an Rmd file instead of an R file was to obtain a formatted printout of the code in an Appendix. This is possible with the technique I originally posted plus a few changes.
Use named chunks to put the code in an appendix, and use the arguments echo=TRUE and eval=FALSE to avoid executing it multiple times.
Execute code from the Appendix in main flow of the document by way of the ref.label= argument, and keep the code from printing in the main document with the echo=FALSE argument.
In addition to using the source() function, one must print each function in another chunk in the appendix in order to obtain formatted print of each function.
An updated version of my example Rmd file is listed below.
---
title: "TestIncludedFiles"
author: "Len Greski"
date: "June 24, 2018"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## Background
A question was posted on [Stackoverflow](https://stackoverflow.com/questions/51013924/calling-functions-in-a-second-file-when-compiling-rmd-files-with-knitr) about how to include functions from one Rmd file while knitting another.
If the second file contains R functions to be accessed in the second Rmd file, they're best included as R files rather than Rmd. In this example we'll include three files of functions from the Johns Hopkins University *R Programming* course: `pollutantmean()`, `corr()`, and `complete()`. We'll execute them in a subsequent code block.
After an update to the original post where the original poster noted that he included the functions in an Rmd file in order to provide a formatted printout of the code in the report as an appendix, I've modified this example to account for this additional requirement.
```{r ref.label="sourceCode",echo=FALSE}
# execute sourceCode chunk from appendix
```
## Executing the sourced files
Now that the required R functions have been sourced, we'll execute them.
```{r runCode, echo=TRUE}
pollutantmean("specdata","nitrate",70:72)
complete("specdata",1:10)
corr("specdata",threshold=500)
```
# Appendix
```{r sourceCode,echo=FALSE,eval=FALSE}
# use source() function to source the functions we want to execute
source("./rprogramming/oneLine_pollutantmean.r")
source("./rprogramming/oneLine_complete.r")
source("./rprogramming/oneLine_corr.r")
```
The following is an inventory of the functions used in this Rmd file.
```{r }
pollutantmean
complete
corr
```
...and the output for the Appendix section of the document (with redactions to avoid publishing answers to a class programming assignment).
Original Answer
If the second Rmd file only contains functions, you're better off saving them as an R file and using source() to include them in Main.Rmd. For example:
date: "June 24, 2018"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## Background
A question was posted on [Stackoverflow](https://stackoverflow.com/questions/51013924/calling-functions-in-a-second-file-when-compiling-rmd-files-with-knitr) about how to include functions from one Rmd file while knitting another.
If the second file contains R functions to be accessed in the second Rmd file, they're best included as R files rather than Rmd. In this example we'll include three files of functions from the Johns Hopkins University *R Programming* course: `pollutantmean()`, `corr()`, and `complete()`. We'll execute them in a subsequent code block.
```{r sourceCode,echo=TRUE}
# use source() function to source the functions we want to execute
source("./rprogramming/pollutantmean.r")
source("./rprogramming/complete.r")
source("./rprogramming/corr.r")
```
## Executing the sourced files
Now that the required R functions have been sourced, we'll execute them.
```{r runCode, echo=TRUE}
pollutantmean("specdata","nitrate",70:72)
complete("specdata",1:10)
corr("specdata",threshold=500)
```
...produces the following output:
DISCLOSURE: This answer includes techniques that I previously posted as a blog article in 2016, ToothGrowth Assignment: Accessing R Code from an Appendix in Knitr.