[R] step.gam with a list of data frames

Dear R-helpers, I used the step.gam function (package gam, Trevor Hastie) on a data frame without problems. Then I created a list of several bootstrap samples from this data frame. Now I want to use the step.gam function on this list using a for-loop. The code is working well until the step.gam

[R] error in step.gam

Dear r-helpers, I use function step.gam (package gam, T. Hastie) with several explanatory variables to build a model. Unfortunately, I obviously have too many variables. This message occurs on my 4 core 64bit machine with 8GB RAM in R2.11.1 for Windows (64bit build): Error in array(FALSE, term.

[R] vegan: grafical problem in ordiplot/ordisurf

Dear vegan-helpers, I calculated an NMDS with metaMDS and then displayed the results with ordiplot. The NMDS consist of 4 axes. I want to plot two diagrams: 1st vs. 2nd and 3rd vs. 4th axis. I used the ordiplot-command choices = c(1,2) and c(3,4), respectively. 1st vs. 2nd does not make any prob

[R] vegan (ordisurf): R² for smoothed surf aces

Dear r-helpers, I just read in an article by Virtanen et al. (2006) where vegetation-environment relationships are studied by fitting smoothed surfaces on an NMDS ordination using GAMs (Wood 2000). The authors describe, that they used R² as goodness-of-fit statistic, which they compare to the R

[R] distance matrix, podani, package: proxy

Dear r-helpers, I just wanted to calculate a distance matrix using the function dist, with method = 'Podani' (package: proxy). The calculation is starting without error. Now the hourglass is running and won't stop. Since more than 20 hours! I do not think that the problem is with my input matrix.

[R] cross validation/GAM/package Daim

Dear r-helpers, I estimated a generalized additive model (GAM) using Hastie's package GAM. Example: gam1 <- gam(vegetation ~ s(slope), family = binomial, data=aufnahmen_0708, trace=TRUE) pred <- predict(gam1, type = "response") vegetation is a categorial, slope a numerical variable. Now I want

[R] mann-whitney test with more groups

Dear r-helpers, I want to test groups of samples for significant differences. Question: Does Group1 differ significantly from group2. This is a question to be answered by mann-whitney-u-test. I know that I can use wilcox.test with 2 samples. My problem: How can r perform the test automatically if

[R] metaMDS NMDS: use of alternative distances?

Dear r-helpers! How can I integrate other distances (in the form of a dist object) into function metaMDS? The problem: metaMDS needs the original data.frame for the calculation and only the default distances of function vegdist are allowed. Any suggestions are greatly appreciated! Thank you, Kim

[R] previous.best in metaMDS

Dear R-community, dear Jari Oksanen! I use metaMDS (package vegan) to calculate NMDS. In a lot of papers I read that it is recommended to use previous best solutions as a new starting configuration to get better results and to avoid local minima. On the help page I found that a previous.best-comma

[R] k-modes (Huang) in package klaR?

Dear R-Users and Developers, I want to calculate something like k-means clustering, but with ordinal data (Braun-Blanquet) to combine this classification technique with a NMDS-Ordination. I found an algorithm especially developed for categorical data: k-modes (Huang 1998). Is there a function im

[R] "predict"-fuction for metaMDS (vegan)

now a similar function to the predict function which works with NMDS or does anybody know how to modify the predict function so that it will work also for NMDS? Thank you very much! Kim Original-Nachricht > Datum: Fri, 04 Sep 2009 18:11:09 +0100 > Von: Gavin Simpson > An

[R] NA in cca (vegan)

Dear all, I would like to calculate a cca (package vegan) with species and environmental data. One of these environmental variables is cos(EXPOSURE). The problem: for flat releves there is no exposure. The value is missing and I can't call it 0 as 0 stands for east and west. The cca does not run

Re: [R] rcorr.cens Goodman-Kruskal gamma

eleves. Further suggestions would be greatly appreciated, Thank you very much, Kim Original-Nachricht > Datum: Mon, 09 Mar 2009 13:27:29 -0500 > Von: Frank E Harrell Jr > An: David Winsemius > CC: Kim Vanselow , r-help@r-project.org > Betreff: Re: [R] rcorr.ce

[R] rcorr.cens Goodman-Kruskal gamma

Dear r-helpers! I want to classify my vegetation data with hierachical cluster analysis. My Dataset consist of Abundance-Values (Braun-Blanquet ordinal scale; ranked) for each plant species and relevé. I found a lot of r-packages dealing with cluster analysis, but none of them is able to calculat

[R] Problem installing MASS-Package

Dear R-Help-Team, I tried to use isoMDS-Function of the MASS-Package: Message: Fehler: konnte Funktion "isoMDS" nicht finden (error: could not find function "isoMDS") so I tried to install the package MASS: > utils:::menuInstallPkgs() versuche URL 'http://cran.rakanu.com/bin/windows/contrib/2.8