Default custom options - r

Question

I would like to create a default chunk option for my documents, so that I can choose which chunks are included in the appendix. Here is my MWE:
```{r setup, include=FALSE, appendix=FALSE}
knitr::opts_chunk$set(echo=FALSE)
knitr::opts_chunk$set(appendix=TRUE)
```
```{r}
# some code included in the appendix
```
```{r appendix=FALSE}
# some code not included in the appendix
```
# Appendix
```{r, ref.label=knitr::all_labels(appendix), echo = T, eval = F}
```
I would like to include all the chunks that do not explicitly say appendix=TRUE. If I add that, it works as expected, but the default knitr::opts_chunk$set(appendix=TRUE) does not seem to work.
I am probably missing something in my setup. Any help is greatly appreciated.

Answer 1

You need to explicitly set:
Appendix <- TRUE in setOptions
you then set -
knitr::opts_chunk$set(appendix = TRUE)
now any chunk without Appendix = FALSE is included in the Appendix.
Note: It is important to include Appendix = FALSE in the Appendix chunk.
I hope the above helps, it is how I do this.
---
title: "47085866-2"
author: "Technophobe1"
date: "11/5/2017"
output:
html_document:
keep_md: yes
---
```{r setOptions, echo = FALSE, Appendix = FALSE}
Appendix <- TRUE
knitr::opts_chunk$set(echo = FALSE, message = FALSE, error = FALSE, warning = FALSE, results = 'hide')
knitr::opts_chunk$set(appendix = TRUE)
```
## Appendix = TRUE
```{r code}
# some code included in the appendix
setClass(
"CStruct",
slots = list(
powerLevel = "numeric",
size = "numeric"
)
)
CStructure <- new("CStruct", powerLevel = 5, size = 10)
CStructure
str(CStructure)
CStructure#powerLevel
CStructure#size
```
## Appendix = FALSE
```{r ref.label='code', Appendix = FALSE}
# some code not included in the appendix
setClass(
"CStruct2",
slots = list(
n = "numeric",
s = "character",
b = "logical"
)
)
CStructure2 <- new("CStruct2", n = c(2, 3, 5),
s = c("aa", "bb"),
b = c(TRUE, FALSE, TRUE) )
str(CStructure2)
CStructure2#n
CStructure2#s
CStructure2#b
```
# Code Appendix
```{r, ref.label=knitr::all_labels(Appendix), Appendix = FALSE, echo=TRUE, eval=FALSE}
## Code Appendix
```
Output: