I have a print statement in R as a macro in Markdown
```{r chunk_name, echo=FALSE}
if ( any(so.results$Duration <0.0))
{print("there are non-positive durations")
} else
{print("all durations are fine!")}
```
and I want to generate a PDF, not an XML! How can I print "all durations are fine!" in colour for example green or red?
Using HERE and HERE and the hints given by User I wrote the following:
```{r, results='asis', echo=FALSE}
if ( any(so.results$Duration <0.0))
{cat("\n") print("\textcolor{blue}
{print("there are non-positive durations}")
} else
{cat("\n") print("\textcolor{red}{print("all durations are fine!}")}
```
which solves the problem.
Related
Say I have the following code in knitr. How can I run it multiple times with different values of i?
```{r, echo=FALSE}
i<-0.1
```
### X,Y plot of Y=X+e where e is a standard normal distro: mean=0, sd=`r i`
```{r, echo=FALSE}
r<-rnorm(100,mean=0,sd=i)
x<-seq(0,1,length.out=100)
y<-x+r
plot(x,y)
```
EDIT:
As has been suggested ... I tried to do something like this: start a loop in an R code block, have a template in between and then close the loop -- R throws and error.
```{r, echo=FALSE}
for (i in 1:4) {
```
# bla
```{r, echo=FALSE}
}
```
What makes this question tricky is that not only the chunk content (the plot) must be repeated, but the heading as well. That's why we can neither simply reuse the chunk nor just loop over the plot command like
for (i in 1:3) { plot(rnorm(100, sd = i)) }
But it's almost that simple: We loop over the code that produces the plot and output the heading from inside the loop. This requires the chunk option results="asis" and cat to get verbatim markdown output:
```{r, echo=FALSE, results = "asis"}
sdVec <- c(0.1, 0.2, 0.3)
for (sd in sdVec) {
cat(sprintf("\n### X,Y plot of Y=X+e where e ~ N(0, %s)", sd))
r<-rnorm(100,mean=0,sd=sd)
x<-seq(0,1,length.out=100)
y<-x+r
plot(x,y)
}
```
See this answer for related issues.
I label my figures like this.
---
title: "xxx"
output:
pdf_document:
fig_caption: true
---
And then in each chunk
```{r, fig.cap="some caption"}
qplot(1:5)
```
This works quite nicely. However in chunks where I plot multiple figures within a loop I can't specify a caption. This produces no caption at all:
```{r, fig.cap="another caption"}
qplot(1:5)
qplot(6:10)
```
How can I specify a figure that counts from the same number as the first chunk for each plot?
You can use a fig.cap argument of length 2 (or the size of your loop):
```{r, fig.cap=c("another caption", "and yet an other")}
qplot(1:5)
qplot(6:10)
```
Found an easy way to dynamically produce plots and add them to the pdf with individual captions, using knitr::fig_chunk as described here. This is also a workaround for OPs comment that message=false (or echo=False or results='asis' for that matter) supresses the fig.cap argument.
```{r my-plots, dev='png', fig.show='hide', echo=FALSE}
# generate plots first
qplot(1:5)
qplot(6:10)
```
```{r, echo=FALSE, results='asis'}
# then put them in the document with the captions
cat(paste0("![some caption](", fig_chunk(label = "my-plots", ext = "png", number = 1), ")\n\n"))
cat(paste0("![another caption](", fig_chunk(label = "my-plots", ext = "png", number = 2), ")\n\n"))
```
Hopefully this helps someone who stumbles upon this question in the future.
Supposing if I have this function to print a plot in a PDF file:
generatePlot<-function(values) {
pdf(file = "foo.pdf")
barplot(values, main = "A simple example")
dev.off()
}
And then I am doing this in a "test.Rmd", parameterizing r warning=FALSE, message=FALSE, echo=FALSE, that will output a PDF document:
tmp.values <- sample(10, 6)
generatePlot(tmp.values)
The problem is: plot just is appearing on "foo.pdf" and not on "test.pdf".
In the second one, I observe only the following:
## pdf
## 2
What do I have to do for the plot to be printed in both files?
Try the following:
---
title: "My HTML page"
output: pdf_document
---
```{r, warning=FALSE, message=FALSE, echo=FALSE}
generatePlot<-function(values) {
barplot(values, main = "A simple example")
dev.copy(pdf, "foo.pdf")
invisible(dev.off())
}
```
```{r warning=FALSE, message=FALSE, echo=F}
generatePlot(mtcars$mpg)
```
As you can see I am using dev.copy instead to make sure that the plot is printed on the default device first and then copied to the pdf device which saves the plot at the location of the Rmd document. In order to suppress the output of dev.off() use invisible().
When typesetting an R Markdown document to PDF, if a function draws multiple plots, those plots often appear side-by-side, with only the first plot fully within the margins of the page.
Minimal R Markdown example:
---
title: "Example re plotting problem"
author: "Daniel E. Weeks"
date: "May 3, 2016"
output: pdf_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## Multiple plots within a loop
```{r}
plots <- function() {
plot(rnorm(100))
hist(rnorm(100))
}
for (i in 1:3) {
plots()
}
```
Here is a screenshot of page 2 of the generated PDF
which shows the problem. I have searched online, but haven't yet found a solution to this problem.
Thank you.
The plot hook solution proposed by user2554330 is simple and works well. So this code draws all the plots within the margins of the resulting PDF:
---
title: "Example re plotting problem"
author: "Daniel E. Weeks"
date: "May 3, 2016"
output: pdf_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## Multiple plots within a loop
```{r}
plots <- function() {
plot(rnorm(100))
hist(rnorm(100))
}
```
## Call plotting function
```{r}
my_plot_hook <- function(x, options)
paste("\n", knitr::hook_plot_tex(x, options), "\n")
knitr::knit_hooks$set(plot = my_plot_hook)
for (i in 1:3) {
plots()
}
```
The problem is that the generated .tex file has no spaces between the \includegraphics{} calls. LaTeX gives warnings about overfull hboxes, because the graphics aren't big enough to sit alone on a line, and are too big when it puts two on each line.
You can tell LaTeX (TeX really) to output the bad lines without putting two figures on each line by adding
\pretolerance=10000
in the text before the code chunk. You'll probably want to set it back to its default value
\pretolerance=100
after the code chunk, or LaTeX won't try hyphenation afterwards, and text can look really ugly.
Another way to fix this would be to force each figure to be in its own paragraph. You can do this by adding this code
my_plot_hook <- function(x, options)
paste("\n", knitr::hook_plot_tex(x, options), "\n")
knitr::knit_hooks$set(plot = my_plot_hook)
into a code chunk before you do your plotting. This puts a blank line
before and after each figure.
I have a dataframe dataof nobservations of several numeric and factor variables. I would like to produce a html report in which class and describe are reported and a histogram (qplotor ggplot) is plotted for every variable.
How can I do that?
Is it possible in R Markdown to produce an automatic header preceding every variable analysis?
Thank you for your help.
Corrado
You can put a loop in your R chunks in Markdown files. Something like that for example :
```{r, echo=FALSE}
library(ggplot2)
```
This is an introductory sentence with absolutely no interest.
```{r, results="asis", eval=TRUE, echo=FALSE}
data(cars)
for (varname in names(cars)) {
var <- cars[,varname]
cat(paste0("<h2>",varname,"</h2>"))
cat(paste0("Class : <pre>",class(var),"</pre>"))
cat("Summary : <pre>")
print(summary(var))
cat("</pre>")
if (is.numeric(var)) print(qplot(var, binwidth=diff(range(var))/30))
}
```
This is an astonishing conclusion.
Which gives the following result : http://rpubs.com/juba/mdloop