Lars Relund NielsenLars Relund Nielsen
Department of Economics and Business Economics
Fuglesangs Allé 4
DK-8210 Aarhus V
Office 2621-114
Phone: +45 871 65145/+45 61 300 299 (mobile)
E-mail: lars@relund.dk
ORCID: 0000-0002-4802-3071

Cand.scient.oecon. (M.Sc.), Ph.D. 2004 in Mathematics and Economics at the University of Aarhus. Professor at Department of Economics and Business Economics, Business and Social Sciences, Aarhus University.

Accessing an array created in R from C++

R 28. August 2009

Assume that you have created a 3-dim array in R containing vectors of various size:

> a<-array(list(),c(2,2,2))   # array where each element contain a numeric vector
> a[[1,1,1]]<-rnorm(1)
> a[[1,1,2]]<-rnorm(3)
> a[[2,1,1]]<-rnorm(2)
> a[[2,1,2]]<-rnorm(3)
> a[[1,2,1]]<-rnorm(4)
> a[[1,2,2]]<-rnorm(3)
> a[[2,2,1]]<-rnorm(5)
> a[[2,2,2]]<-rnorm(1)
> d = dim(a)
> d
[1] 2 2 2
> i<-1; j<-1; k<-2
> q<-i + j*d[1] + k*(d[1]*d[2]) - (d[1] + d[1]*d[2])
> a[[i,j,k]]      # access an element
[1] -0.2370040 -0.6009635  3.0550405
> a[[q]]          # access the same element using a single index
[1] -0.2370040 -0.6009635  3.0550405

Note you can access the array in two ways. Next you want to copy the array to a vector on the C++ side. For instance in a package you may need to do some operations in C++ to speed up time.

On the C++ side you can create a function: Læs mere »

Testing external pointers with finalization in R using C++

R 27. February 2009

I the past days I have been experimenting with how to use R as an interface to an C++ library. I have made a small test package in R that show how it can be done. The idea is to be able to create a C++ object from R and call methods of the C++ class from R before freeing the object from memory in R.

The package/function description goes as follows: Læs mere »

Highlighting R code in LaTeX using SweaveListingUtils

LaTeX, R 4. February 2009

It is well known that you can use Sweave to integrate R code into a LaTeX document. However, how do we highlight R code in LaTeX? LaTeX got its own powerful package listings that can highlight source code from various languages. Moreover, the package SweaveListingUtils provides utilities for defining R as a listings “language”. To highlight your R code in your Sweave document you have to include the following code chunk: Læs mere »

Using an array for storing an object in R

R 1. February 2009

Often you need fast access/lookup in R. For instance assume that you have the following data frame/matrix dat

>head(dat)
     x y z
[1,] 1 1 1  0.46 -0.89  0.88 -0.21 0.46  0.93 1.06
[2,] 1 1 2  0.72 -0.40  1.71 -0.52 0.95    NA   NA
[3,] 1 1 3 -0.49 -0.42 -0.26 -0.06 1.07  1.48 1.08
[4,] 1 1 4 -1.55 -0.90  0.15 -0.60 1.86 -1.15   NA
[5,] 1 1 5 -0.46 -1.54 -0.40    NA   NA    NA   NA
[6,] 1 1 6  0.14  1.13 -2.42  0.86 0.13 -1.60 0.62

x, y and z represent an unique index and the rest of the columns represent a vector. The vectors may be of various length. To find the vector corresponding to index (x,y,z) you can do a normal search: Læs mere »

Five days at KU Life

R, Research 11. November 2007

nyt_logo.gif.ashxThe last days 5-9 November I have been visiting Professor Anders Ringgaard Kristensen at KU Life. We have been working on a package in R “MDP” which will provide tools for solving Markov decision processes and their extension multi-level hirarchic Markov decision processes. The package will be based on a solver made by Anders in Java.

Creating an animation (gif/mpeg) in R using intermediate files

R 20. June 2007

I recent had a discussion with Søren about how one could create an animation of some plots in R. After searching the mail-list it seems that the best way to do it is using ImageMagick which is a free set of tools to create, edit, and compose bitmap images. To use the following guide you must install ImageMagick.

Creating an animated gif

We create an animated gif file in two steps. First, we save all the plots used in the animation as png files (vector file format) and second, we merge them into a gif animation.

Lets try a simple example:

> x<-1:10
> y<-runif(10,1.5,2.5)
> xlim<-c(0,10)
> ylim<-c(0,4)
> png(file="plot%02d.png", bg="transparent")
> plot(x, y, type="n", xlim=xlim, ylim=ylim)
> title("Create 10 uniform distributed samples")
> for (i in 1:10) plot(x[i], y[i], axes=F, xlab="", ylab="", xlim=xlim, ylim=ylim)
> dev.off()

We have now created intermediate files plot01.png to plot11.png. Note

  1. Plot plot01.png only contains the axes and titles of the plot
  2. The rest of the plots only contain the single point we want to add to the animation. That is we want to put the point on top of the frames (keeping the old ones).

Finally we merge the files

 > system('convert -delay 10 -dispose None plot*.png -loop 0 plot.gif', invisible = F, wait=T)

Simple animation

The -despose option ensures that the images are put on top of each other (therefore the background must be transparent). Option -despose background can be used if you don’t use transparent images. Many other options can be added see the ImageMagick documentation of convert for more details. It might be usefull to reduce the file size of the gif (takes longer than creating plot.gif)

> system('convert -coalesce -layers OptimizeFrame plot.gif plot1.gif', invisible = F, wait=T)

Creating an mpeg

Unfortunately, gifs cannot be embedded into a pdf file so if you have a pdf presentation you must create an mpeg movie instead. The easiest way is just converting your gif into a mpeg; however, since the convert program in ImageMagick is not so fund of transparent backgrounds in gifs when converting to an mpeg you must fix this first

> png(file="background.png", bg="white")
> plot(x,y,type="n",xlim=xlim,ylim=ylim)
> dev.off()
> system('convert  background.png  null: ( plot.gif -coalesce ) -gravity Center -layers Composite -layers Optimize plot2.gif',invisible = F,wait=T)
> system('convert plot2.gif plot.mpeg',invisible = F,wait=T)

First we create a no transparent background and merge it to all the frames and afterwards we convert the gif to an mpeg which fills much more 🙁 You may use option -quality 1 to reduce file size.

© Lars Relund Nielsen
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