similar to: Name spaces in R 1.7.0

Updating my 1.8.0 R installation (>update.packages() ) I obtain the following (SORRY FOR THE LENGTH OF THE LOG BUT IT HELPS!!!): ................ downloaded 135Kb KernSmooth : Version 2.22-11 in /usr/lib/R/library Version 2.22-12 on CRAN Update (y/N)? y mgcv : Version 0.9-3.1 in /usr/lib/R/library Version 0.9-6 on CRAN Update (y/N)? y trying URL

I'm trying to make a set of contour plots of bivariate kernel density estimates, showing three such plots overlaid, similar to this plot http://euclid.psych.yorku.ca/SCS/Private/Test/ridge-boot2.pdf except that I would like to have the contours *filled* (using transparent colors). To make this reproducible, I've saved the results of KernSmooth::bkde2D() in the following file:

It is known that function bkde2D (package "KernSmooth") returns a matrix of density estimates over the mesh induced by x1 and x2. In Details it is written that "... heights of the kernel, scaled by the bandwidths, at each datapoint are summed. This sum, after a normalization, is the corresponding fhat value in the output". There are several questions: 1) How to calculate

Hello, I'm using R 1.40 on MacOS X X.1.2 (installed via the fink package manager). To upgrade my installed packages, I tried to use update.packages() today. All went well for most packages, with the exception of KernSmooth and cluster. In both cases, libraries were not found although I think they are present. Here's what happened: ---------------------------------- >

Hi I hope this is going to the right place. I am trying to write a program which uses KernSmooth library to estimate mutual information between two time series at various different lags. At the moment it’s producing negative values, which is supposed to be impossible (something is fishy). I am summing across one row of the matrix to get p(value is in bin x) and summing across the columns to get

Dear all yesterday I got around to install R-1.5.1 on my machine at home which, admittedly, is running a very old version of RedHat Linux. I noticed two things: 1) My pdflatex version is too old to produce the pdf version of the manuals. `./configure' checks whether a recent version of makeinfo is installed and tells you whether you can produce the info version or not. (I was told I

I am trying to carry out density estimation for three dimensions (with anywhere between a few hundred and ~8000 data points). Which leads me to ask: a) is there any equivalent to kde2d (in MASS) or bkde2D (in KernSmooth) out there for three dimensions? b) if not, my skills only seem to extend as far as writing a function which measures density as the number of data points falling within a

Dear listers, After activating the name space for my bioconductor package (prada) I successfully ran R CMD check. However when loading the package in R and running the examples the imported function brewer.pal from package RColorBrewer is not found. I can directly call brewer.pal from the RColorBrewer name space typing RColorBrewer::brewer.pal, but it is not imported into my prada name space. When

Dear listers, After activating the name space for my bioconductor package (prada) I successfully ran R CMD check. However when loading the package in R and running the examples the imported function brewer.pal from package RColorBrewer is not found. I can directly call brewer.pal from the RColorBrewer name space typing RColorBrewer::brewer.pal, but it is not imported into my prada name space. When

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

If I have a contourplot (in the lattice package) and I want to add straight lines to it, how do I do this? I see that there are llines() and lsegement() functions for lattice plots, but they don't seem to do anything in this case: library(lattice) library(KernSmooth) x=rnorm(10000) y=x+rnorm(x,0,.5) a=bkde2D(cbind(x,y),.7) z=as.vector(a$fhat) grid=expand.grid(x=a$x1,y=a$x2) grid$z=z

Dear R-devel, my Bioconductor EDASeq package has a function MDPlot that uses the smoothScatter() function from the graphics package. When I test this package on travis-ci.org (R CMD check) I get the following error (which I don't get on my machine nor on the Bioconductor build system). * checking examples ... ERROR Running examples in ?EDASeq-Ex.R? failed The error most likely occurred in:

Hey everyone, Thanks for all the input. It's happening again. This time for the packages "DBI", "parallelly", "segmented", "survival", "V8". So, RStudio shows updates for those and updating them via RStudio leads to this output: ``` > install.packages(c("DBI", "parallelly", "segmented", "survival",

Hi all, people who don't follow Linux Today regularly may want to check out: http://linuxtoday.com/developer/2003082000626OSSVDV My apologies if this is considered spam. Cheers, Berwin ========================== Full address ============================ Berwin A Turlach Tel.: +61 (8) 9380 3338 (secr) School of Mathematics and Statistics +61

Hello, I am a newbie to R and the subject of density estimation in two dimensions or more. I would like to have some advice concerning a comparison between the R packages for density estimation in bivariate or higher order problems; I mean explicitly the packages: 1) ash 2) KernSmooth 3) locfit 4) sm. My specific problem now is having a set of numerical pairs (x_i, y_i), arising from a

Dear all, I noticed the following bug in points.formula > library(DAAG) > data(roller) > fm <- lm(depression ~ weight, data=roller) > plot( depression ~ weight, data=roller, type="n") > abline(fm) > attach(roller) > points( depression~weight, subset=1:7) > points( depression~weight, subset=8:10, col="blue") Error in if (length(x) == l) x[s] else x :

Dear all, When installing the usual packages that I use, after installing R 3.0.1, I noticed that the installation of some packages that query R about its configuration did not succeed. The problem is exemplified by: berwin at bossiaea:~$ R-3.0.1 CMD config CC /opt/R/R-3.0.1/lib/R/bin/config: 222: .: Can't open /opt/R/R-3.0.1/lib/R/etc/Renviron Prior to R 3.0.1 such commands worked fine:

Dear R developers, is there a preferred format or strategy for making a patch to contribute to a package that is maintained by R-core? Berwin Turlach and I have written a very minor extension to lmeControl to allow it to pass an argument to nlminb for the maximum number of evaluations of the objective function. I've edited the nlme/R/lme.R and nlme/man/lmeControl.Rd files. I can diff the

I always followed http://cran.r-project.org/bin/linux/ubuntu/ to install R on Ubuntu 8.1. I had no errors before! > install.packages("XML") Warning in install.packages("XML") : argument 'lib' is missing: using '/usr/local/lib/R/site-library' --- Please select a CRAN mirror for use in this session --- Loading Tcl/Tk interface ... done trying URL

G'day Duncan, On Tue, 12 Jan 2016 07:32:05 -0500 Duncan Murdoch <murdoch.duncan at gmail.com> wrote: > On 11/01/2016 11:59 PM, Berwin A Turlach wrote: > > G'day all, > > > > In Chapter 1.4 (Writing package vignettes) the Writing R Extensions > > manual states: > > > > By default @code{R CMD build} will run @code{Sweave} on all > >