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I am having trouble with setting global options in my R Markdown documents. A simple example follows. In this case I've attempted to set global.par = TRUE. The expectation is that any par() specifications I make in one chuck are carried into subsequent chunks. However, this is not happening.
```{r package_options, include=FALSE}
knitr::opts_knit$set(global.par = TRUE)
```
```{r}
lambda <- 0.2; n <- 1000
exp <- rexp(n, lambda)
par(cex = 0.7)
hist(exp)
```
```{r}
lambda <- 0.02; n <- 1000
exp <- rexp(n, lambda)
hist(exp)
```
Specs: Max OS 10.11, R version 3.2.0 (2015-04-16), RStudio 0.98.1062, knitr 1.12.3
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knitr is an engine for dynamic report generation with R. It is a package in the programming language R that enables integration of R code into LaTeX, LyX, HTML, Markdown, AsciiDoc, and reStructuredText documents. The purpose of knitr is to allow reproducible research in R through the means of literate programming.
The first code chunk: ```{r setup, include=FALSE} knitr::opts_chunk$set(echo = TRUE) ``` is used to specify any global settings to be applied to the R Markdown script. The example sets all code chunks as “echo=TRUE”, meaning they will be included in the final rendered version.
The following sections dive into the three components of an R Markdown document in more details: the markdown text, the code chunks, and the YAML header.
Chunk Options include = FALSE prevents code and results from appearing in the finished file. R Markdown still runs the code in the chunk, and the results can be used by other chunks. echo = FALSE prevents code, but not the results from appearing in the finished file. This is a useful way to embed figures.
This issue has been fixed in knitr (>= v1.12.17), and you may test the current development version of knitr on Github. I just discovered that setting mfcol/mfrow will reset cex to 1, and that was the root cause of knitr not being able to restore cex correctly.
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