similar to: plot.hclust with lots of objects

Hi! I am newbee to R and I am facing the problem in plotting the dedrogram with lot of objects. The lines and labels are overlapped very badly, and writing the graphic to postscript and zooming there is not helping either. I tried cut.dendrogram method, but getting the error that it doesn't exist even though I get the man pages for it. I would not find any solution in web as well, and I

I have a data set with 6 variables and 251 cases. The people who supplied me with this data set believe that it falls naturally into three groups, and have given me a rule for determining group number from these 6 variables. If I do scaled.stuff <- scale(stuff, TRUE, c(...the design ranges...)) stuff.dist <- dist(scaled.stuff) stuff.hc <- hclust(stuff.dist)

Hello, I wonder why the control parameter REPORT is not supported by method SANN. Looking into optim.c I found an internal constant: #define STEPS 100 ... and decreasing this to 10 helped me fine-tuning the annealing parameters in an actual problem. Is there any reason why not passing nREPORT to samin and setting something like: STEPS = nREPORT / tmax Thomas P. -- Thomas Petzoldt

Dear R developers, I recently observed a NOTE on several MaxOS X package checks: sh: line 1: gs: command not found !!! Error: Closing Ghostscript (exit status: 127)! /usr/bin/texi2dvi: thumbpdf exited with bad status, quitting. See for details: http://www.r-project.org/nosvn/R.check/r-release-macosx-ix86/simecol-00check.html or

Dear R developers, I tried to use nlminb instead of optim for a current problem (fitting parameters of a differential equation model). The PORT algorithm converged much better than any of optim's methods and the identified parameters are plausible. However, it took me a while before spotting the reason of a technical problem that nlminb, in contrast to optim, does not pass names of the

Dear R developers, some of our packages come with additional programming examples in a directory called "/examples" which is created from "/inst/examples". This directory is linked from the docs (e.g. in inst/doc/index.html): <dl> <dt><a href="../examples/">examples</a>: <dd>Source code of examples </dl> Given, that we have a

Special Volume on Spectroscopy and Chemometrics in R Guest Edited by Katharine M. Mullen and Ivo H.M. van Stokkum 11 contributions, with software packages and examples Similar volumes on R in Psychometrics (guest edited by Jan de Leeuw) and R in Political Methodology (guest edited by Micah Altman and Simon Jackman) are close to being finished. Additional volumes are being worked on. Proposals

Dear list The deSolve package allows you to specify the model code in C or Fortran. Thanks to the excellent vignette this works fine. However I have not yet managed to use forcing functions in C code. In pure R code this works very well with approxfun() specified outside the model: ############################################### #Model lvml <- function(t, x, parms) {

Dear list - Does anyone have any ideas / comments about why I am receiving the following warning when I run lsoda: 1: lsoda-- at t (=r1), too much accuracy requested in: lsoda(start, times, model, parms) 2: for precision of machine.. see tolsf (=r2) in: lsoda(start, times, model, parms) I have tried changing both rtol and atol but without success. I saw the thread in the

Hello, first of all, thanks to LT for \pkg{codeutils}. I agree that it is indeed very useful to identify errors and also to encourage re-thinking past solutions. My problem: I want to compare different sets of related sub-functions which should be used alternatively by the same top-level function. Sets of related functions should be bound together (as lists) and the workspace should be as clean

Hello R Developers, This is my first foray into using c-code with R, so please forgive my foolishness. I had a look at the archives and did not find anything on this, so hopefully I am not doubling up. I have tried to use R cmd to create an object file from the odesolve dynload example. I am using windows and have just installed rtools, and have the latest version of stable R (2..7.2). This is

Hello One of my packages, untb_1.3-2, passes R CMD check under MacOSX (and apparently the systems used in the package check summary page on CRAN) but fails with the following message on R-2.6.0.tgz compiled last night on my (home) linux box. I hasten to add that I have never seen this error before on home-compiled pre-releases of R-2.6.0. Can anyone help me understand what is going on?

We've added a column at http://cran.r-project.org/web/checks/check_summary.html of test results using the Sun Studio compiler: it is intended that these will be updated weekly. The Sun Studio compiler is that used on Solaris: these runs were on the Linux version. All the other platforms are using gcc 4, so this provides an opportunity for checking for use of gcc-specific features and

All- I am interested in estimating a parameter that is the starting value for an ODE model. That is, in the typical combined fitting procedure using nls and lsoda (alternatively rk4), I first defined the ODE model: minmod <- function(t, y, parms) { G <- y[1] X <- y[2] with(as.list(parms),{ I_t <- approx(time, I.input, t)$y dG <- -1*(p1 + X)*G +p1*G_b dX <-

I've been trying to get plot.hclust to work with a hclust object I created and have not had much success. It seems that there is some "hidden" characteristic of a hclust object that I can't see. This is most easily seen in the following example, where plot.hclust works on one object, but when this object is "dumped" and then re-read, plot.hclust no longer works. Is

Hello, how can I get the similarity value (i.e., the inner cluster similarity) that was used to cut a hierarchical tree at a specific height? I would appreciate your help! Best regards, Madeleine

Hi all, Prefix: I am a frustrated Java coder in R. I am coding a medium sized ecosystem modelling program in R. I have changed to using S4 objects and it has cost me an order of magnitude in execution speed over the functional model. I cannot afford this penalty and have found that it is the result of all the passing-by-value of objects. I see that you can now safely inherit from

library(mva) data(USArrests) hc <- hclust(dist(USArrests), "ave") plot(hc) # OK dump(c("hc"), "tst") rm(hc) source("tst") plot(hc) # Error in plot.hclust(hc) : invalid dendrogram input The same problem occurs with dput/dget --please do not edit the information below-- Version: platform =

Buenas tardes a todos, Estoy interesado en cambiar los límites del eje y en un dendograma construído utilizando la función hclust(). A continuación un ejemplo: hc <- hclust(dist(USArrests), "ave") plot(hc) Hasta aquí todo bien. Si quisiera cambiar los límites del eje "y" de c(0, 200)? Al usar plot(hc, ylim = c(0, 200)) no observo efecto alguno. Qué puedo hacer?

Dear R-users, I tried to receive the merge details of a clustering by using the summary function of hclust. For illustration I use the Longley data as done by Prof Ripley (Wed 11 Apr 2001) d <- dist(longley.y) d <- d/max(d) hc <- hclust(d, "ave") But instead of getting a matrix for $merge I get: >summary(hc) Length Class Mode merge 30 -none- numeric