similar to: How to get the number of modes using kde2d

Dear R users, I used sm.density function in the sm package and kde2d() in the MASS package to estimate the bivariate density. Then I calculated the Kullback leibler divergence meassure between a distribution and the each of the estimated densities, but the asnwers are different. Is there any difference between the kde2d and sm.density estimates? if there is a difference, then which is the best

Hi, as Conrad suggested, I've made a complete list of all points in the specification, which I beleive are errors, or where the explanation is unclear, contains unneccessary steps and so on. I hope someone has time to look through the points and if and when accepting or rejecting them be so very kind and inform me about it. I will also once again try to work through the residue

Hi, I've found some more errors in the file format specification (or at least points, where the specification and actual libvorbis implementation mismatch): - Floor 1 / curve computation / step 1: amplitude value synthesis 21) vector [floor1_final_Y] element [i] = [predicted] - (([val] - 1) divided by 2 using integer division) hould be: 21) vector [floor1_final_Y] element [i] =

Hello! I am trying to do a smooth with the kde2d function, and I'm getting an error message about NAs. Does anyone have any suggestions? Does this function not do well with NAs in general? fit <- kde2d(X, Y, n=100,lims=c(range(X),range(Y))) Error in if (from == to || length.out < 2) by <- 1 : missing value where TRUE/FALSE needed Thanks in advance!! Jen [[alternative

Dear all, Please, look at the following code: attach(geyser) f1 <- kde2d(duration, waiting, n = 5) a <- 0 for (i in 1:5){ for (j in 1:5){ a <- a + f1$z[i,j] } } As far as I understood from Help kde2d returns matrix elements of which are values of joint probability mass function Pr(X=x,Y=y) therefore, sum of its elements should sum to 1. Which is not the case from my check. Where is

Hello, I am a little bit confused regarding the density values obtained from the function kde2d() from the package MASS because the are not in the intervall [0,1] as I would expect them to be. Here is an example: x <- c(0.0036,0.0088,0.0042,0.0022,-0.0013,0.0007,0.0028,-0.0028,0.0019,0.0026,-0.0029,-0.0081,-0.0024,0.0090,0.0088,0.0038,0.0022,0.0068,0.0089,-0.0015,-0.0062,0.0066) y <-

Good evening, I am Marta Colombo, student at Milan's Politecnico. Thank you very much for your kindness, this mailing list is really useful. I am using the function kde2d for two-dimensional kernel density estimation and I'd like to know something more about this kind of density estimator. In particular I'd like to know: what bandwidth is used ? Thank you in advance for your attention

I want to create a 3d plot with densities. I use the function density to first create a 2d dimensional plot for specific x values, the function then creates the density and puts them into a y variable. Now I have a second set of x values and put it again into the density function and I get a second set of y variables and so on.... I want to put those sets into a 3d plot, I hope you know what I

Hallo, I want to use kde2d to visualize data on a sphere given in spherical coordinates. Now the problem is, that "phi == 2*pi = 0", so in principal I have to connect (in a graphical view) the left and right border of my plot (and the bottom and top). Has anyone any idea how to do that ? Thanks, Manuel -- ------------------------------------- Manuel Metz Sternwarte der

Estimate region of highest probabilty density Dear R-community I have data consisting of x and y. To each pair (x,y) a z value (weight) is assigned. With kde2d I can estimate the densities on a regular grid and based on this make a contour plot (not considering the z-values). According to an earlier post in the list I adjusted the kde2d to kde2d.weighted (see code below) to estimate the

Hi, I guess I have a naive question. I use kde2d function in a standard way to estimate kernel densities of x and y (x and y are vectors) and plot them using image(). f1=kde2d(x,y) image(f1) But what if I want to see kernel estimates of three variables, x, y and z (a vector) plotted together ? Something in which x<->y is plotted and colored according to the corresponding value of z ?

Hi all, I'm fairly new to R, so I'm still trying to feel out what is available to me. I would like to be able to plot joint density in a two dimensional plot where density is indicated by color or darkness gradients, like a 2d color coded topographic map. Ideally, the output would be something I could then plot other points or lines on. Currently, I'm calculating joint density with

Dear wizaRds, I use the MASS::kde2d function to estimate density of the two first principal components. I do that to have a graphic visualisation of a "group structure" in my dataset. So far, no problem. But i would like to estimate that density using weights according to the COS?? values that tells me if my observation is well represented on the factorial plan 1-2. I would like to

R'istas: I am trying to plot a marginal distribution on the plane behind a persp() plot. My existing code is: library(MASS) X <- mvrnorm(1000,mu=c(0,0),Sigma=matrix(c(1,0,0,1),2)) X.kde <- kde2d(X[,1],X[,2],n=25) # X.kde is list: $x 1*n, $y 1*n, $z n*n persp(X.kde,phi=30,theta=60,xlab="x_b",ylab="x_a",zlab="f") ->res Any suggestions are very

Hi guys, After all the discussion yesterday about persp and color, I decided to have a more closer look at demo(persp), and decided to write a function to generate 'topo-like' colours to plot perspectives (Thanks a lot to Uwe Ligges for his enlightning comments regarding the code in the demo). Here it goes, I believe that this function will be pretty useful to a lot of people:

Hi, I'd like to partition a 2d probability density function into regions of equal probability. It is straightforward in the 1d case, like qnorm(seq(0,1,length=5)) but for 2d I'd need more constraints. Any suggestions for how to approach this? Is seems like a spatial sampling problem but I'm not sure where to look. Thanks for your time, Dave -- Dr. David Forrest drf at

Hi, Does anyone know how to count the number of modes in 2 dimensions using kde2d function? Thanks Pat

I have spatial data in 2 dimensions - say (x,y). The correlation between x and y is fairly substantial. My goal is to use a non-parametric approach to estimate the multivariate density describing the spatial locations. Ultimately, I would like to use this estimated density to determine the area associated with a 95% probability contour for the data. Given the strong correlation between x and

You'll find that it is a lot easier to do it in R: # lets first simulate a bivariate normal sample library(MASS) bivn <- mvrnorm(1000, mu = c(0, 0), Sigma = matrix(c(1, .5, .5, 1), 2)) # now we do a kernel density estimate bivn.kde <- kde2d(bivn[,1], bivn[,2], n = 50) # now plot your results contour(bivn.kde) image(bivn.kde) persp(bivn.kde, phi = 45, theta = 30) # fancy contour with

Hello, I'd be very grateful for help with some ggplot2's stat_density2d issues. First issue is with data limits. xlim() and ylim() doesn't seem to work; instead, estimates (and plotting) seems to be constrained to range(x), range(y) no matter what i do. The documentation says i can pass in kde2d's parameters to ... but pussing kde2d's "lims" parameter achieves