I am using Rmarkdown and Knitr using Rstudio.
The following both print script and output to html.
```{r}
summary(cars)
```
However the following will only print the output, that is embedded plot.
```{r, echo=FALSE}
plot(cars)
```
I have situation different than above, I want to present the script but should not run in html as this will take very long time (hours if not days) to run. So I just did was put comment sign.
```{r}
#summary(cars)
```
But I need a better way to do this - Is there any better way presenting script without running it.
eval = FALSE
Checkout The R Markdown Cheat Sheet http://blog.rstudio.org/2014/08/01/the-r-markdown-cheat-sheet/
It summarizes the options for code chunks
Related
I use ProjectTemplate and Knitr to produce reports. Most of the analysis is stored in the src directory, whilst the report contains the presentation R markdown.
I would like the main text to include only the results of the analysis, and the document appendix to contain some code chunks from the analysis. The only way I have found to achieve this is as follows:
First, run the actual analysis in the main body of the document:
```{r runanalysis, warning=FALSE, message=FALSE}
# run the analysis code to generate the objects
source('../src/rf-model-caret.R')
```
Secondly, in the appendix, two knitr chunks are needed. The first reads in the actual code (and executes it). The second displays the code.
```{r analysis, eval=TRUE, echo=FALSE}
knitr::read_chunk('../src/rf-model-caret.R')
```
```{r analysis2, ref.label="analysis", eval=FALSE, echo=TRUE}
```
This works but seems very inefficient because:
The analysis has to be run twice - firstly in the source in the main document, and again in the appendix just to produce the code.
reading a knitr chunk and then referencing it again immediately to display the code
Is there a better way to achieve the goal of executing external source in the main document and printing the code in the appendix?
You may try this:
In the main body:
```{r runanalysis, code=readLines('../src/rf-model-caret.R'), echo=FALSE, eval=TRUE}
```
In the appendix:
```{r runanalysis, code=readLines('../src/rf-model-caret.R'), echo=TRUE, eval=FALSE}
```
I created a custom function which sets mfrow to nxn and creates n^2 scatter plots, with multiple data sets on each plot, based on an input list of data frames. The signature of my plotting function looks like this:
plot.return.list<-function(df.list,num.plot,title)
Where df.list is my list of data frames, num.plot is the total number of plots to generate (used to set mfrow) and title is the overall plot title (the function generates titles for each individual sub-graph).
This creats plots fine when I run the function from the console. However, I'm trying to get this figure into a markdown document using RStudio, like so:
```{r, fig.height=6,fig.width=6}
plot.return.list(f.1.list,4,bquote(atop("Numerical Approximations vs Exact Soltuions for "
,dot(x)==-1*x*(t))))
```
Since I haven't set the echo option in my {r} statement, this prints both the plotting code as well as the plot itself. However, if my first line instead reads:
{r, fig.height=6,fig.width=6,echo=FALSE}
Then both the code AND the plot disappear from the final document.
How do I make the plot appear WITHOUT the code? According to the example RStudio gives, setting echo=FALSE should make the plot appear without the code, but that isn't the behavior I'm observing.
EDIT: I seem to have tracked my problem down to kable. Whether or not I'm making a custom plot-helper function, any call to kable kills my plot. This can be reproduced in a markdown:
---
title: "repro"
author: "Frank Moore-Clingenpeel"
date: "October 9, 2016"
output: pdf_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(knitr)
options(default=TRUE)
repro.df<-data.frame((0.1*1:10)%*%t(1:10))
```
```{r, echo=FALSE}
kable(repro.df)
```
```{r, fig.height=6,fig.width=6,echo=FALSE}
plot(repro.df[,1],repro.df[,2])
```
In this code, the plot won't plot because I have echo set to false; removing the flag makes the plot visible
Also note that in my repro code, kable produces a table with a bunch of garbage in the last line--I don't know why, but this isn't true for my full original code, and I don't think it's related to my problem.
Thanks for the reproducible example. From this I can see that the problem is you don't have a newline between your table chunk and your plot chunk.
If you were to knit this and examine the MD file produced by knit (or set html_document as your output format and have keep_md: true to look at it), you would see that the table code and plot code are not separated by any newline. Pandoc needs this to delimit the end of the table. Without it, it thinks your  is part of the table and hence puts it as a "junk line" in the table rather than an image on its own.
Just add a newline between the two chunks and you will be fine. (Tables need to be surrounded with blank lines).
(I know you are compiling to LaTeX so it may confuse you why I am talking about markdown. In case it does, when you do Rmd -> PDF, Rmarkdown uses knit to go from RMD to MD, and then pandoc to go from MD to tex. This is why you still need to make sure your markdown looks OK).
I use ProjectTemplate and Knitr to produce reports. Most of the analysis is stored in the src directory, whilst the report contains the presentation R markdown.
I would like the main text to include only the results of the analysis, and the document appendix to contain some code chunks from the analysis. The only way I have found to achieve this is as follows:
First, run the actual analysis in the main body of the document:
```{r runanalysis, warning=FALSE, message=FALSE}
# run the analysis code to generate the objects
source('../src/rf-model-caret.R')
```
Secondly, in the appendix, two knitr chunks are needed. The first reads in the actual code (and executes it). The second displays the code.
```{r analysis, eval=TRUE, echo=FALSE}
knitr::read_chunk('../src/rf-model-caret.R')
```
```{r analysis2, ref.label="analysis", eval=FALSE, echo=TRUE}
```
This works but seems very inefficient because:
The analysis has to be run twice - firstly in the source in the main document, and again in the appendix just to produce the code.
reading a knitr chunk and then referencing it again immediately to display the code
Is there a better way to achieve the goal of executing external source in the main document and printing the code in the appendix?
You may try this:
In the main body:
```{r runanalysis, code=readLines('../src/rf-model-caret.R'), echo=FALSE, eval=TRUE}
```
In the appendix:
```{r runanalysis, code=readLines('../src/rf-model-caret.R'), echo=TRUE, eval=FALSE}
```
I opened a new R Markdown file in R studio and got the default small working example.
---
title: "test"
author: "Katharina Zweig"
date: "30. Januar 2016"
output: html_document
---
This is an R Markdown document. Markdown is a simple formatting syntax
for authoring HTML, PDF, and MS Word documents. For more details on using
R Markdown see <http://rmarkdown.rstudio.com>.
When you click the **Knit** button a document will be generated that
includes both content as well as the output of any embedded R code chunks
within the document. You can embed an R code chunk like this:
```{r}
summary(cars)
```
You can also embed plots, for example:
```{r, echo=FALSE}
plot(cars)
```
Note that the `echo = FALSE` parameter was added to the code chunk to
prevent printing of the R code that generated the plot.
It says, you only need to press the knit button to create an HTML
containg the text, the code and the results of the code. I got some long
error logs that were hardly helpful. Neither did changing the output to
PDF and Word - same result: text was there, code was there, no results of
running the code. By producing the output, the original file vanished.
What is wrong?
When the knit button is used on a file not yet saved, it asks you under which name to save it. The file needs to be saved as an Rmd file - just give no extension and R-Studio will do it right. Then, the file does not vanish and the resulting document contains the results of the r commands. I thought it asked where to save the output and gave it the extension of the output file, i.e., either myfile.html / myfile.pdf / myfile.doc.
In the chunk option try this:
{r, results='asis'}
summary(cars)
You can also embed plots, for example:
{r, echo=FALSE, results='asis'}
plot(cars)
The results = 'asis' command should output the tables and graphs if not please let me know.
I'm using the rmarkdown library to convert an Rmd file with code and plots to a PDF file, which I do with these commands:
library(rmarkdown)
render("test.Rmd", "pdf_document")
Here is my test.Rmb file:
Title
========================================================
This is an R Markdown document. Markdown is a simple formatting syntax for authoring web pages (click the **Help** toolbar button for more details on using R Markdown).
When you click the **Knit HTML** button a web page will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
# cars
```{r}
summary(cars)
```
You can also embed plots, for example:
```{r}
plot(cars)
```
# mtcars
```{r}
summary(mtcars)
```
You can also embed plots, for example:
```{r}
plot(mtcars)
```
This is the HTML result from that Rmd file. When I make the PDF, rmarkdown adds page breaks by pushing plots that can't fit on the current page to the next one. This is the resultant PDF.
As you can see, the first plot can't fit on the first page, so it gets bumped to the second. That's fine, but then code that comes after the first plot is bumped back to the first page, which makes no sense to me. The only way I've figured out how to avoid this problem is to add manual $\pagebreak$ LaTeX commands all over the place to prevent this behavior.
Is there a better way to stop rmarkdown from moving code that comes after plots before those plots?