[R-sig-eco] 3d density plot

[ONKELINX, Thierry]

Here is a solution using ggplot2 

Positions <- expand.grid(Run = seq_len(100), ID = seq_len(101))
Positions$X <- runif(nrow(Positions), -.5, .5)
Positions$Y <- runif(nrow(Positions), -.5, .5)
Positions[Positions$ID == 1, c("X", "Y")] <- Positions[Positions$ID == 1, c("X", "Y")] + matrix(c(50, 40), ncol = 2, nrow = 100, byrow = TRUE)
library(plyr)
Positions <- ddply(Positions, "Run", function(x){
	x <- x[order(x$ID), ]
	x$X <- cumsum(x$X)
	x$Y <- cumsum(x$Y)
	x
})
library(ggplot2)
ggplot(Positions, aes(x = X, y = Y)) + geom_density2d()

HTH,

Thierry


----------------------------------------------------------------------------
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest
Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium
tel. + 32 54/436 185
Thierry.Onkelinx at inbo.be
www.inbo.be

To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of.
~ Sir Ronald Aylmer Fisher

The plural of anecdote is not data.
~ Roger Brinner

The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey

-----Oorspronkelijk bericht-----
Van: r-sig-ecology-bounces at r-project.org [mailto:r-sig-ecology-bounces at r-project.org] Namens Kingsford Jones
Verzonden: zaterdag 20 juni 2009 0:05
Aan: Nabeil Salama
CC: r-sig-ecology at r-project.org
Onderwerp: Re: [R-sig-eco] 3d density plot

Hi Nabeil,

I'm not sure I understand what you'd like to accomplish, but perhaps the following will be helpful:

example(kde2d, package='MASS')


hth,

Kingsford Jones


On Fri, Jun 19, 2009 at 10:32 AM, Nabeil Salama<N.Salama at marlab.ac.uk> wrote:
> Dear all.
>
>
>
> I am new to R so I am probably asking something that will be sneered at.
>
>
>
>
> I am moving 100 "particles" in both x,y dimensions and would like to 
> plot the density of particles at each Cartesian coordinate.
>
>
>
> I can simply use:
>
>
>
> plot(density(positionX)
>
> plot(density(positionY)
>
>
>
> to produce the relevant density of particles at either an X or a Y 
> point, however how would it be possible to overlay the densities so 
> that I obtain a density at a particular coordinate.
>
>
>
> An mock example of what I am currently doing is
>
>
>
> posX    <- matrix (nrow=101,ncol=100,data=0)
>
> posY     <- matrix (nrow=101,ncol=100,data=0)
>
>
>
> posX[1,]<-50
>
> posY[1,]<-40
>
>
>
> for (j in 1:100) {
>
> posX[j+1,]<- posX[j,]+(runif(100)-0.5)
>
> posY[j+1,]<- posY[j,]+(runif(100)-0.5)
>
>
>
> }
>
>
>
> matplot(posX,posY,type="l")
>
> plot(density((posY[,j])))
>
> plot(density((posX[,j])))
>
>
>
> Simply I would like to know the density of particles at coordinates of 
> the matplot.
>
> >From the example given the density of particles at 50,40 will be 
> >higher
> than at the edges. But to quantifiably see this would be an advantage.
>
>
>
>
>
> Any help?
>
>
>
> I hope that is understandable.
>
>
>
> Many thanks
>
>
>        [[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-ecology mailing list
> R-sig-ecology at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>

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