Plot animation in knitr rmarkdown - r

Question

Problem:
Hi, I try to make an animated plot in a rmarkdown document. Here is my code:
```{r lmSim, fig.show='animate'}
library(animation)
library(plyr)
oopt = ani.options(interval = 0.3, nmax = 101)
a <- sort(rnorm(100, 2))
b <- sort(rnorm(100, 7))
out <- vector("list", 101)
for (i in 1:ani.options("nmax")) {
ji <- seq(from = 0, to = 5, by = .05)
a <- jitter(a, factor = 1, amount = ji[i])
fab1 <- lm(a ~ b)
coe <- summary(fab1)$coefficients
r2 <- summary(fab1)$r.squared
if (coe[2, 4] < .0001) p <- " < .0001"
if (coe[2, 4] < .001 & coe[2, 4] > .0001) p <- " < .001"
if (coe[2, 4] > .01) p <- round(coe[2, 4], 3)
plot(a ~ b, main = "Linear model")
abline(fab1, col = "red", lw = 2)
text(x = min(b) + 2, y = max(a) - 1,
labels = paste("t = ", round(coe[2, 3], 3), ", p = ", p, ", R2 = ", round(r2, 3)))
out[[i]] <- c(coe[2, 3], coe[2, 4], r2)
ani.pause()
}
ani.options(oopt)
```
The loop work fine, and passed into a function, I'am able to save it in several formats with 'saveLatex', 'saveHTML' or 'saveVideo'. However, when 'knit' the .Rmd file in order to obtain a PDF, the animation does not appear, there is just this line written:
video of chunk lmSim
If I knit it in HTML, only the play button of the video is displayed. However, If I open the HTML in my browser (firefox) it is displayed correctly.
There is no error message displayed. I'm using R version 3.2.0, the latest R Studio version, 1.10.5 knitr version on a MacBook Pro Yosemite. I didn't find any relevant information or documentation to solve my problem.
Questions:
So, is it simply possible to have an embeded animation into a PDF generated with rmarkdown/knitr ?
Do I have to install another program to deal with videos in PDF (I have ffmpeg on my computer)?
Many thanks!
Thanks Yihui! It works very well with the following settings (reading the PDF with Adobe):
---
title: "Sim"
author: ""
header-includes:
- \usepackage{animate}
...
---
```{r lmSim, fig.show='animate', out.width = '6in'}

Answer 1

Have you tried with ggplot and gganimation? For example:
library(gapminder)
library(gganimate)
library(ggplot)
head(gapminder)
theme_set(theme_bw())
p <- ggplot(gapminder, aes(gdpPercap, lifeExp, size = 1, color = continent, frame = year)) +
geom_point() +
scale_x_log10()
animation<-gganimate(p, "your_animation.gif")#Or to your path
See that you need to save first your animation. You need to have establish your work directory.
After you can call it from the chat or html in markdown (not from the R chuck) like:
![your caption here](your_animation.gif)

Answer 2

May be it’s too late for this answer, but hopefully should help others. I recommend to save and run the R code as a separate file in the same directory and only import the animation as a gif to reduce lag in the presentation. This works for me in ioslides:
## Time series visualization
![time series](myanimation.gif){width=80%}