similar to: standardization of values before call to pam() or clara()

Greetings, I have had good success using the clara() function to perform a simple cluster analysis on a large dataset (1 million+ records with 9 variables). Since the clara function is a wrapper to pam(), which will accept known medoid data - I am wondering if this too is possible with clara() ... The documentation does not suggest that this is possible. Essentially I am trying to

Hi, I have developed a logistic regression model in the form of (factor_1~ numeric + factor_2) and would like to perform a cross-validation or some similar form of sensitivity analysis on this model. using cv.glm() from the boot package: # dataframe from which model was built in 'z' # model is called 'm_geo.lrm' # as suggested in the man page for a binomial model: cost <-

Greetings: As I am not a windows user, I cannot try this: is it possible to install rgdal on windows without having to compile it from source ? Compilation on MacOS is within my abilities, however each time i try and install the rgdal package it dies complaining that it cannot find gdal-config --- which was recently installed with GRASS. I have updated my PATH environment variable, logged

Hello: I would like to superimpose vector polygons (state outlines) from a Shape file on top of a satellite image, imported into a SpatialGridDataFrame from GEOTIFF via gdal_translate and readGDAL. When I plot polygon and point shape files in R, into SpatialPointDataFrame and SpatialPolygonDataFrame, the two feature sets line up geographically, so it seems logical that a SpatialGridDataFrame

Is there a function that calculates the inter-rater agreement index (kappa) in R? Thanks ../Murli [[alternative HTML version deleted]]

Hi everyone, Suppose I have a count the occurrences of positive results, and the total number of occurrences: pos <- 14 total <- 15 testing that the proportion of positive occurrences is greater than 0.5 gives a p-value and confidence interval: prop.test( pos, total, p=0.5, alternative='greater') 1-sample proportions test with continuity correction data: 14 out of

I need informations about the clara routine. The on-line doc say that the argument stand is a logical, indicating if the measurements in x are standardized before calculating the dissimilarities. Measurements are standardized for each variable (column), by subtracting the variable's mean value and dividing by the variable's mean absolute deviation. If we note STAND = TRUE, I suppose that

Greetings, A couple general questions regarding the use of splines to interpolate depth profile data. Here is an example of a set of depths, with associated attributes for a given soil profile, along with a function for calculating midpoints from a set of soil horizon boundaries: #calculate midpoints: mid <- function(x) { for( i in 1:length(x)) { if( i > 1) { a[i] = (x[i] -

Greetings, I am trying to add an extra labled axis in position 3 (top x-axis), with numbers that do not match up with the existing axes. Surely this must be possible, and I am just doing it incorectly. So far I have tried the following: #make a plot plot(TIK, type="l", cex=.25, xlim=c(2,32), ylim=c(0,1600)) #try and add a new axis with different numbers in position 3

Getting a very strange error with a new install of R from source on x86; make[3]: Leaving directory `/tmp/R.INSTALL.r20887/cluster/src' ** R ** data ** moving datasets to lazyload DB Error in factor(c(1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1), : invalid labels; length 2 should be 1 or 1 Execution halted ERROR: lazydata failed for package 'cluster' ** Removing

Hello R-help, I am a recent convert to R from SAS and I am having some difficulty with output of a for loop into a matrix. I have searched the help manuals and the archives, but I can't get my code to work. It is probably a syntax error that I am not spotting. I am trying to make a distance matrix by extracting the distances from each point to all others in a vector (the for loop). I can

hi to all, frustated for this error, to day i buy a 1 GB memory slot for my laptop now it have 1,28GB instead the old 512, but i've the same error :-( damn!damn!....how can i do? repeat for a little area (about 20X20 km and res=20m) it work fine! have you any suggestion? is ther a method for look if this error depend from my ram or other....? thanks foe any suggestion! i need your help.

I've been asked in private, (and am replying BCC to the asker), >> I saw your post on the R-help archives page about the possibility of >> porting a function from S-Plus called peaks() to R. I am looking for >> some way to locate peaks in a simple x,y data set, and thought that R >> might be the way to go. "of course" it is the way to go, don't get

Greetings, After pouring over the documentation for the 'colorspace' package, I have not been able to figure out how the plot() method converts colorspace coordinates to RGB values for display on the screen. I am convert between colorspaces with the various as() methods... but cannot seem to find a way to extract RGB (i.e. for displaying on a computer screen) triplets from color space

Greetings: are there any simple ways to convert an sp class object to a splancs ppp class object, outside of reading the coordinates and computing a bounding box? cheers, -- Dylan Beaudette Soils and Biogeochemistry Graduate Group University of California at Davis 530.754.7341

Greetings, I am using both the lrm() {Design} and glm( , family=binomial()) to perform a a logisitic regression in R. Apart from the typical summary() methods, what other methods of diagnosing logistic regression models does R provide? i.e. plotting an 'lm' object, etc. Secondly, is there any facility to calculate the R^{2)_{L} as suggested by Menard in "Applied Logistic

This may sound like a very naive question, but... give two lists of coordinate pairs (x,y - Cartesian space) is there any simple way to compute the affine transformation matrix in R. I have a set of data which is offset from where i know it should be. I have coordinates of the current data, and matching coordinates of where the data should be. I need to compute the composition of the affine

Dear all: I have a shapefile in UTM coordinate system and I would like to transform it to Lat/Log coordinates (WSG84). The package PBSmapping contains function convUL to transform between the two coordinate systems when data is in the form of a data frame with attributes specifying the coordinate system. However, when shapefiles are imported using function read.shape (package maptools), a list

Hi, I have been trying to use the new .parallel argument with the most recent version of plyr [1] to speed up some tasks. I can run the example in the NEWS file [1], and it seems to be working correctly. However, R will only use a single core when I try to apply this same approach with ddply(). 1. http://cran.r-project.org/web/packages/plyr/NEWS Watching my CPUs I see that in both cases

Hi, Is anyone on the list familiar with an R implementation of Piper Diagrams? Example: http://faculty.uml.edu/nelson_eby/89.315/IMAGES/Figure%209-78.jpg I am thinking that two calls to triax.plot (plotrix) along with some kind of affine-transformed standard plot would do the trick. Not so sure about the final layout, or a nice generalized version for something like lattice. Cheers, Dylan