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Hi, Using Vegan package I was wondering if there's a way to use a distance matrix as an input for adonis (or any of the other similar hypothesis testing functions) instead of the usual species by sample table. Working in the field of microbial ecology, what I'm trying to do is to overcome the problem of having to use discrete units such as species or OTUs, which are problematic in microbial ecology (if not outright theoretically false). What I have instead is a phylometric distance matrix between all my samples based on a phylo...

...the clusters formed by resampling the data set. A similar type of analysis is used in molecular taxonomy and the confidence values of each cluster are placed in the nodes of the dendogram. Any ideas on how to do this in R will be appreciated. Thanks H?ctor L. Ayala-del-R?o, Ph.D. Center for Microbial Ecology & Center for Genomic and Evolutionary Studies on Microbial Life at Low Temperatures Michigan State University 545 Plant & Soil Sciences Building East Lansing, MI 48824-1325 Phone: 517-353-9021 Fax: 517-353-2917

...update.packages" function should be on it but did not work. Also I tried read.table and did not work either. Does anybody know if the base package from Macinthosh port is different to the regular base package from the Unix port?? Thanks Hector H?ctor L. Ayala-del-R?o, Ph.D. Center for Microbial Ecology & Center for Genomic and Evolutionary Studies on Microbial Life at Low Temperatures Michigan State University 545 Plant & Soil Sciences Building East Lansing, MI 48824-1325 Phone: 517-353-9021 Fax: 517-353-2917

...doesn't work in the Aqua GUI. Can someone tell me how to change the Vcells? Although to the best of my understanding (which is limited) I shouldn't have to do that. Any suggestions would be greatly appreciated. thanks, betty -- Betty Gilbert lgilbert at berkeley.edu Taylor Lab Plant and Microbial Biology 321 Koshland Hall U.C. Berkeley Berkeley, Ca 94720

...X109 26Y 0.011736659 0.000000000 0.009536035 0.019622226 0.000000000 0.000000000 C-50 0.004679457 0.000000000 0.005053814 0.005240992 0.000000000 0.000000000 C-90 0.000000000 0.000000000 0.007591623 0.000000000 0.000000000 0.007940663 H??ctor L. Ayala-del-R??o, Ph.D. Center for Microbial Ecology & Center for Genomic and Evolutionary Studies on Microbial Life at Low Temperatures Michigan State University 545 Plant & Soil Sciences Building East Lansing, MI 48824-1325 Phone: 517-353-9021 Fax: 517-353-2917

...e cuticles and the surrounding environment over a 3 year period. I am attempting to analyze the effect of several factors on these counts (termite nest volume, temperature, humidity, light, incubation temperature, habitat, year, sample location, etc.) to determine which account for the variance in microbial communities. These data are observations, so there are many missing values....which may be part of the problem. I've tried many different combinations of variables, and also have tried reducing my data set to remove as many NA's and confounding variables as possible, but I still can'...

Hello guys I am new to this list and for R too. I am wondering if there is a patch for the SPSS reading code on the foreign package, in order to be able to read long variable names. Right now read.spss() just trunc the names to 8 characters. Or if someone could help me on other way: I have to process everyday a lot of SPSS Syntax Files and Dat files that come from one system that can only export

...ns. Keith Jewell ================================== sessionInfo() is given below. I think the toy example above is enough to demonstrate my problem, but in case it is relevant (I don't think it is) here is some more info about the models I'm fitting: I'm fitting sigmoidal models to microbial growth over time. The specific model giving me problems at the moment is only one of a whole class of such models which I need to work with. I specify it here to illustrate that it is not always obvious what the bounds on the parameters are. SSbaranyiBR94<-selfStart( model=function(Time, y...

Hi, As part of my dissertation, I'm going to be doing an Anova, comparing the "dead zone" diameters on plates of microbial growth with little paper disks "loaded" with antimicrobial, a clear zone appears where death occurs, the size depending on the strength and succeptibility. So it's basically 4 different treatments, and I'm comparing the diameters (in mm) of circles. I'm concerned however...

Our lab just picked up a G4 Powerbook (1 GHz, 1GB RAM, OS X 10.2.6). None of us have any experience with Macs but for various reasons we need to have one around for development. In any case, we've installed fink, all the Apple Developer Tools and the Dec2002updater to gcc 3.3. We're now trying to compile R 1.7.1 without too much success. First we had to get g77, which turned out to

...entation includes many examples taken from the literature, as well as calculations of the metastability relationships in systems of proteins. The protein examples were developed to explore the chemical features of thermophilic adaptation, subcellular localization, proteomic stress response, and microbial diversity. Calculation of the standard Gibbs energies of proteins is based on a published group additivity algorithm and is further supported in this package by the inclusion of data files for the amino acid compositions of selected proteins and of proteins in yeast and E. coli. A paper desc...

...hould add to make it run under this operation system? I had problems upgrading to 2.3 (problem downloading packages) so I'm not sure an upgrade will work out with me. I just want a publication quality histogram... thank you, betty -- Betty Gilbert lgilbert@berkeley.edu Taylor Lab Plant and Microbial Biology 321 Koshland Hall U.C. Berkeley Berkeley, Ca 94720 [[alternative HTML version deleted]]

...but the entire column and their associated rows. I've looked at order , sort, and match and can't figure out a way to do it based on the alphanumeric name of the columns. Does anyone have any suggestions? Sincerely, Betty -- Betty Gilbert lgilbert@berkeley.edu Taylor Lab Plant and Microbial Biology 321 Koshland Hall U.C. Berkeley Berkeley, Ca 94720 [[alternative HTML version deleted]]

...entation includes many examples taken from the literature, as well as calculations of the metastability relationships in systems of proteins. The protein examples were developed to explore the chemical features of thermophilic adaptation, subcellular localization, proteomic stress response, and microbial diversity. Calculation of the standard Gibbs energies of proteins is based on a published group additivity algorithm and is further supported in this package by the inclusion of data files for the amino acid compositions of selected proteins and of proteins in yeast and E. coli. A paper desc...

hello I need basic explanation of variogram and how to use in R. I will appreciate if you supply them. regards Ahmet Temiz ______________________________________ XamimeLT - installed on mailserver for domain @deprem.gov.tr Queries to: postmaster at deprem.gov.tr ______________________________________ The views and opinions expressed in this e-mail message are ...{{dropped}}

The Biostatistics Analytics Team at the FDA Center for Food Safety and Applied Nutrition seeks an MS/PhD in computer science (or related field) with experience in bioinformatics. The Analytics Team is responsible for computational support for projects involving large chemical and microbial hazard data sets, including bioinformatic and statistical analysis of bacterial genomic data for foodborne pathogens. The individual works with a team of statisticians and bioinformaticians to develop and improve methods for detecting and identifying bacterial pathogens from food and environment...

...0,78.4), seq(78.5,81.9), seq(82.0,86.4), seq(86.5, 94.5), seq(94.5,100.0)) Is it possible to pass this sequential ordering to key.xtickfun? May i ask for an example code? Thank you very much! -- Tim Richter-Heitmann (M.Sc.) PhD Candidate International Max-Planck Research School for Marine Microbiology University of Bremen Microbial Ecophysiology Group (AG Friedrich) FB02 - Biologie/Chemie Leobener Stra?e (NW2 A2130) D-28359 Bremen Tel.: 0049(0)421 218-63062 Fax: 0049(0)421 218-63069

...this for thousands of trees ( which i have to process according to my PhD committee :) ) Does anyone know how to get the individual trees into usable variables? I apologize for my lack of familiarity with the package. thanks, betty -- Betty Gilbert lgilbert@berkeley.edu Taylor Lab Plant and Microbial Biology 321 Koshland Hall U.C. Berkeley Berkeley, Ca 94720 [[alternative HTML version deleted]]

...doesn't work in the Aqua GUI. Can someone tell me how to change the Vcells? Although to the best of my understanding (which is limited) I shouldn't have to do that. Any suggestions would be greatly appreciated. thanks, betty -- Betty Gilbert lgilbert at berkeley.edu Taylor Lab Plant and Microbial Biology 321 Koshland Hall U.C. Berkeley Berkeley, Ca 94720 ______________________________________________ R-help at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html

...try and get as many opinions on it as possible. -Ben W. > On Fri, Feb 25, 2011 at 9:08 AM, Ben Ward<benjamin.ward at bathspa.org> wrote: >> Hi, As part of my dissertation, I'm going to be doing an Anova, comparing >> the "dead zone" diameters on plates of microbial growth with little paper >> disks "loaded" with antimicrobial, a clear zone appears where death occurs, >> the size depending on the strength and succeptibility. So it's basically 4 >> different treatments, and I'm comparing the diameters (in mm) of circl...