similar to: Bivariate Partial Dependence Plots in Random Forests

Hi, I have been trying to plot density plots using the example on: http://addictedtor.free.fr/graphiques/graphcode.php?graph=139 I used to use this function, but I cannot get any old code or even the example to work. library("geneplotter") require("RColorBrewer") x1 <- matrix(rnorm(1e4), ncol=2) x2 <- matrix(rnorm(1e4, mean=3, sd=1.5), ncol=2) x <-

Hi there I'm trying to construct a model of mortality risk in 2D space that requires numerical integration of a hazard function, for which I'm using the integrate function. I'm occasionally encountering parameter combinations that cause integrate to terminate with error "Error in integrate... the integral is probably divergent", which I'm not sure how to interpret. The

Can you please tell me the minimum system spec for R on a windows machine? Thanks _______________________________________ Matthew Longley IT Administrator Zoological Society of London Regent's Park London NW1 4RY Charity No: 208728 Tel: 020 74496412 Fax: 020 74496294 email: Matthew.Longley at zsl.org WWW: www.zsl.org _______________________________________

Hello, new Linux user here and I cannot mount a new (empty) WD MyBook Essentials 3TB USB external hard drive (Model WDBACW0030HBK-NESN). I'm only about 3 weeks into this linux thing and so please forgive me if any of my syntax is off My linux OS is CentOS 5.4 x86-64 running on a dedicated HP z400. The WD MyBook is to back up the large data files we are creating on the HP400 (it's

Dear all, I have encounter an odd situation. I have various R scripts interconnected via the source () function. After examining the results I noticed that not all the functions or procedures within a script were adequately conducted. Especially with the longest script ( about 180 lines) Then, I ran every scripts individually (not using source () ) selecting all (Ctrl + a) and running the

Dear R users, When I try to resize a graphics device in R, I often get this warning message (mostly when I already have several other graphics devices open) : "Not enough memory to modify the size. Alpha blending is desactivated" (translation from the french message: "Mémoire insuffisante pour modifier la taille. L'"alpha blending" est désactivé"). Following

Hi there! I have found a trange problem with getting pairs()-plots to show properly in latex \subfloat environments. If i generate images of these plots with pdf() and include them in subfloats, they will either show up in grayscale, or sometimes the datapoints of the pairplots are missing. Mind you, the PDFs themselves are properly colored and look perfectly fine, both as pdf-image in acrobat

Douglas Bates wrote: >From 0.62 onward you should not have to create a symbolic link in >/usr/local/bin. It should be that you can run > cd $RSOURCE > ./configure --prefix=/usr/local > make install >and you will end up with the R script installed in /usr/local/bin and >all the files needed to run R in /usr/local/lib/R. > >Can you tell what the prefix is set to after

Hi, I wonder if anyone has written any code to implement the suggestions of Smart et al (2004) in the Bulletin of the Ecological Society of America for a new way of graphically presenting the results of logistic regression (see www.esapubs.org/bulletin/backissues/085-3/bulletinjuly2004_2column.htm#t ools1 for the full text)? I couldn't find anything relating to this sort of graphical

I am trying to set up R-0.62.1 on an alphastation running digital unix 3.2D. I had R-0.61.1 working fine, but have had a number of problems getting 0.62.1 going.... The next problem is that plotting to any device causes R to hang. Looking at processor usage it would appear that it gets stuck in an infinite loop rather than pausing for input. I have managed to track the problem down to plot.new().

I was wondering if someone could help me with a problem getting locfit running. I am running Digital Unix 3.2D on an alphastation, with R 0.61.1 I downloaded the CRAN distribution of locfit. I had no problems installing it with R INSTALL (I installed it into my library rather than the default base library; the output is attached at the end of this email message). I then tried to test it with the

Dear R-helpers, a S-code for piecewise regressions was provided by Toms & Lesperance (2003) Ecology, 84, 2034-2041 (paper can be found on the web).The code is quite complete with different types of transitions around breakpoints and model selection fonctions. It doesn't work directly under R due to some "translation" problems I guess. However I reckon that it would be a

Hello, To thank you for telling me if this message is not posted on the good list. After installing Xen 4 on a workstation HP Z400, the hypervisor is extremely slow, both on a Fedora machine on a Debian Squeeze, whether in 32-bit or 64-bit version. Unable to install a DomU. The problem seems to come from the hardware configuration of the HP Z400 - Xeon - W3550-4 processors - 16 GB of

I am trying to make the R-0.62.1 distribution on a DEC alpha running Digital Unix 3.2d. I have run into a few problems..... (1) the Makefile in src/graphics need to have INCLUDES= -I../include not -I ../include (2) I have the standard DEC fortran 90 compiler which needs to link R.binary with a -nofor_main flag. The appropriate slot in config.site appears to be ignored, which means Makeconf

I am analysing some binary data with a mixed effects model using glmmPQL. I am aware that I cannot use the AIC values to help me find the minimum adequate model so how do I perform likelihood ratio tests? I need to fix on the minimum adequate model but I'm not sure of the proper way to do this. Thank you very much, Elizabeth Boakes Elizabeth Boakes PhD Student Institute of Zoology

I am analysing binomial data using a generalised mixed effects model. I understand that if I use glmmPQL it is not appropriate to compare AIC values to obtain a minimum adequate model. I am assuming that this means it is also inappropriate to use AIC values from lmer since, when analysing binomial data, lmer also uses PQL methods. However, I wasn't sure so please could somebody clarify

Hello, I'm using R code that includes a residual permutation that was written as a supplement to the paper: Turner et al. 2010. A general hypothesis-testing framework for stable isotopes ratios in ecological studies. Ecology 91:2227-2233. The supplemental code is available at: http://www.esapubs.org/archive/ecol/E091/157/suppl-1.htm When I execute the function, no warnings are given

Dear R users! Does someone know about any algorithms / packages in R, that perform classification / regression / decision trees using multivariate splits? I have done some research, but I found nothing. Packages "tree" and "rpart" seem only to be able to do CART with univariate splits. Thank you for your help! B?lint -- Cz?cz B?lint PhD hallgat? BCE KTK Talajtan ?s

We would like to announce version 2.0.8 of Brodgar. Software Package for Multivariate Analysis and Multivariate Time Series Analysis NEW: INTERFACE TO R SOFTWARE Examples: http://www.brodgar.com/brodgarandr.htm and http://www.brodgar.com/ordination.htm http://www.brodgar.com/timeseries.htm Key phrases: Interface to R, dynamic factor analysis, MAFA, (partial) canonical correspondence

Dear R users, I used nndist() to gain the distance of 2 nearest neighbours of the points in my dataset. Is there a way of getting the ID numbers of these nearest neighbours (along with their distances). The command I used: nn2 <- nndist(X2, k=1:2). This is the output of the nearest neighbour distances I got (the IDs of the given points are there but their IDs aren't). Any help or