similar to: Convert a List of Distances to a Distance Matrix

Hello, How can one write the output of a GLM/GEE model to a text file, such that the results appear in text file in the same (or similar) format they appear in the R console? For instance, I have the following model: Traitresult <- compar.gee(Y~X, data = data, family = "binomial", phy = tree, scale.fix = TRUE, scale.value = 1) How would I write "Traitresult" to a text

Hello, I am trying to test for non-linearity in a set of non-parametric data. Furthermore, I would like to do so in a multi-variate model. Frankly, I don't even know if this is possible, and if it is possible, I don't know if it is implemented in an R package. Any advice would greatly appreciated. Thank you! Charlie -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Charles G.

Hello, I am running the program COMPAR.GEE within the package APE. My dependent variable is binomial, while my independent variable is a multi-state categorical variable. The output reports an estimate for each state of the independent variable except the first one. For example, for the variable X with 3 states, the output is: intercept (estimate) X2 (estimate) X3 (estimate)

Hello, I am trying to preform a comparative analysis using the partial mantel method. However, i am having trouble creating compatible matrices. I can create matrices from my numerical data using the 'distance(x, method)' function from ecodist, but the row/column names are out put as numbers. While when i create a phyo-distance matrix using 'cophenetic(x)' from APE, the row/column

Hello, I am trying to run the APE program COMPAR.GEE with a model containing a categorical response variable and a mixture of continuous and categorical independent variables. The model runs when I have categorical (binary) response and two continuous independent variables (VAR1 and VAR2), but when I include a categorical (binary) independent variable (VAR3), I receive the following output with

Dear R-users: How does one calculate in R the odds ratios for a CATEGORICAL predictor variable that has 4 levels. I see r-help inquiries regarding odds ratios for what looked like a continuous predictor variable. I was wondering how to get the pairwise odds ratios for comparisons of levels of a categorical predictor variable. I can't seem to get the correct output using: >

Hi all, I am trying to bootstrap a small data set into 1000 "pseudodatasets" and then run an ANOVA on each one. Can anyone provide guidance on how I could do this? Thank you. -Dan Janes ************************************************ Dan Janes, Ph.D. Harvard University/OEB 26 Oxford St. Cambridge, MA 02138 Office: 617-496-2375 Fax: 617-495-5667 Email: djanes at oeb.harvard.edu

Dear list members, I am trying to use the maptools library to display geographical data. At the moment I have some trouble understanding how the " auxvar " variable is supposed to be used in the plot.Map function. I am using R Version 1.8.1 (2003-11-21) on Linux Looking at the plot.Map function itself, I see that it calls a color.ramp function (I am reporting only the relevant

Hello, I am having problems with plotting to a postscript device within a function call. When I do the same thing line by line in the command line interface, I have no problems, but the function creates an empty postscript file. If I remove the dev.off() call at the end of the function, I get one of the plots (the last), but not the others. Is there any way to get around this problem, or a

Hi All, Two weeks ago, I received instructions from the R list about creating pseudodatasets by bootstrapping an existing dataset 1000 times. I received code that bootstrapped my dataset and ran an ANOVA on each pseudodataset, producing a histogram of F-values. Here is the code I received that produces this F-histogram. X <- data.frame(b=rnorm(2162),c =factor(rep(1:47,each=46))) ##

Has anyone done any large scale intercom deployments with Asterisk? I've been asked about building a system to one-way page 500 phones simultaneously from a single server. My concerns are: - My limited math capabilities suggest 41 Mbps of RTP traffic, which seems like a lot, plus asterisk would be taking a single input stream and exploding it out to 500 endpoints. - There are 500

I'm trying to perform a mantel test that ignores specific pairs in my distance matrices. The reasoning is that some geographic distances below a certain threshold suffer from spatial autocorrelation, or perhaps ecological relationships become less relevant that stochastic processes above a certain threshold. The problem is that I can't find a way to do it. If I replace values in either or

Dear All, I've just installed Samba version 1.9.18p10 on one of our HP-UX boxes. The unix box is advertising itself with two WINS names. netbios name = ukswi0103 netbios aliases = ukswi0104 in smb.conf I've been playing with the idea of changing the behaviour of the server based on what the client calls it. What I'd like to do is have samba do security = user if the client

Hi, I'm very new to R. I want to know if there is any way to write only the lower half of a distance matrix created in R to a csv file for example. I get the 'cannot coerce class "dist" into a data.frame' message when I try. I have used as.matrix and can write to a file this way, but as a full matrix. The reason I only want the lower half is that I've been doing some

Greetings! I''m attempting to use the act_as_versioned plugin to provide versioning functionality for my rails app, but can''t think my way through this: How can you use act_as_versioned to perform versioning on a HABTM join table? It is easy to see how to do so for join models (:has_many :through) but not so for the join table. I want to use act_as_versioned to maintain

Dear UseRs, i want to apply mantel test by comparing a list of 124 distance matrices with a reference distance matrix "q". The list of distance matrices was created by the following command.. u<-lapply(el, function(x) dist(x)) where "el" is a data frame of 75 columns and 124 rows. Therefore, the list of distances matrices, made out of it should have 75 elements each

Hello I'm trying to do the following vector operation: given vector x = c(x1,x2,x3,x4...xn), produce vector y = c(x1,x1+x2,x1+x2+x3,...x1+...+xn). E.g., from x = c(1,3,2,2,5), produce y = c(1,4,6,8,13). The underlying problem is finding the cumulative distribution function given the empirical density distribution function. I have done some research on this but the only relevant

When I `sudo gem install mysql` I get the following: --snip-- $ sudo gem install mysql Attempting local installation of ''mysql'' Local gem file not found: mysql*.gem Attempting remote installation of ''mysql'' Updating Gem source index for: http://gems.rubyforge.org /usr/local/lib/ruby/1.8/yaml.rb:133: [BUG] Segmentation fault ruby 1.8.4 (2005-12-24)

Hi there, I would like to find a more efficient way of permuting the rows and columns of a symmetrical matrix that represents ecological or actual distances between objects in space. The permutation is of the type used in a Mantel test. Specifically, the permutation has to accomplish something like this: Original matrix addresses: a11 a12 a13 a21 a22 a23 a31 a32 a33 Example

Hi, i'm looking to test if two distance matrices are statistically different from each others. These two matrices have been computed on the same set of data (several population samples) 1. using a particular genetic distance 2. weighting that genetic distance with an extra factor (we can look at this as one set is computed before applying a treatment and the second one after applying