[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,

[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

[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] 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

[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 to

[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

[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

[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

[R] predict-fuction for metaMDS (vegan)

An: Kim Vanselow vanse...@gmx.de CC: r-help@r-project.org Betreff: Re: [R] NA in cca (vegan) On Fri, 2009-09-04 at 17:15 +0200, Kim Vanselow wrote: Dear all, I would like to calculate a cca (package vegan) with species and environmental data. One of these environmental variables is cos

[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

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 f.harr...@vanderbilt.edu An: David Winsemius dwinsem...@comcast.net CC: Kim Vanselow vanse...@gmx.de, r-help@r-project.org Betreff

[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

[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