similar to: power in generalized linear models with categorical independent variables

Dear R list., I am running a script to get a compact letter display. library(lme4) library(multcomp) library(gplots) ####### Mixed Effects Model ######### data <- read.table("AJmix.txt",header=TRUE, sep="\t") attach(data) y<-cbind(positive,negative) treatment<-factor(treatment) mouse<-factor(mouse) data$obs<-1:nrow(data) names(data) detach(data) attach(data)

Dear R-list, In the R-book, p.464, Michael Crawley recommends that error bars for bar plots of normally distributed continuous response variables with categorical explanatory variables be given by 1/2 of the least significant difference, where the least significant difference is defines as qt(0.975,degrees_of_freedom)*standard_error_of_the_difference. The idea is that the above quantity

Dear R-help-list, I have a problem in which the explanatory variables are categorical, the response variable is a proportion, and experiment contains technical replicates (pseudoreplicates) as well as biological replicated. I am new to both generalized linear models and mixed- effects models and would greatly appreciate the advice of experienced analysts in this matter. I analyzed the

Dear Wizards - Thank you so much for your help. That was exactly what I was looking for. Now, I have been working on conditional selection of columns in a data frame. My goal is to calculate the total revenue per sales representative per status in a table. I have come to a complete stop: Let's say, we have a data.frame called df with several columns and a number of rows: df <-

Hello, I have a question about running R in a cluster environment. The shell script I am running looks like this: #!/bin/bash cd /nfs/apollo/2/c2b2/users/mb0001/Data /nfs/apollo/1/shares/software/core_facility/local/x86_64_rocks/R/current/bin/ R --save < calculate.R >& script.out I have used the "-save" command to save the R workspace (If, I understand it

Hi R users,   I am doing multiscale bootstrapping for clustering through pvclust package. I have large data set (observations 182 and variables 5546). When i tried to make bootstrapping, then i got message as "Bootstrap (r = 0.5)............Error: cannot allocate vector of size 117.3 Mb". I am new R user and could not understand what is the problem and also don't know the easiet

Dear WizaRds! A trivial question indeed on selecting subsets in data frames. I am sorry. Unfortunately, I did not find any helpful information on the introduction, searched the help archive and read in introductory books. Please help: I want to select column "KB" which is read via read.csv2 as a data.frame into d. I checked that it is indeed a data.frame object and included the

Hi all, I have a matrix with 10000 rows and 10 columns. The last columns contains another identifiers but the values are not uniques so that I want to generate another matrix with rows with unique values in the last column. If I did tmp<-unique(my_mat$col10) this will give me 8560 unique entries so the ideal matrix will be 8560X10 columns now then. I tried sub_mat<-my_mat[tmp,] but

Hello, I'm wondering how I can merge two featuresets into one. My dataset is two sets of microarray data and it looks like followings: > rawData $v1 TilingFeatureSet (storageMode: lockedEnvironment) assayData: 2197815 features, 59 samples element names: channel1, channel2 protocolData rowNames: LT290677RU_D1_2011-02-16 LT286300LU_D1_2010-07-24 ... LT003990RU_D1_2010-11-04 (59

Dear R users, It is my pleasure to announce the availability of package stepR (1.0-2) on CRAN. The main purpose of the package is to fit piecewise constant functions (a.k.a. step-functions or block signals) to serial data in a fully data-driven manner under certain (Gaussian or non-Gaussian) distributional assumptions. It mainly implements the algorithms described in the references below -

Dear R users, It is my pleasure to announce the availability of package stepR (1.0-2) on CRAN. The main purpose of the package is to fit piecewise constant functions (a.k.a. step-functions or block signals) to serial data in a fully data-driven manner under certain (Gaussian or non-Gaussian) distributional assumptions. It mainly implements the algorithms described in the references below -

*Postdoc Position Computational Systems Biology 'Systems Bioinformatics: Computational Modelling Methods' f/m * * VU University Amsterdam, the Netherlands * *Research project * The goal of the project is to develop and implement computer methods for computational modelling of biological systems. This encompasses methods for computational model assembly, execution, analysis and

Hi all, here's a proposal for a SoC project on wildlife movement patterns analysis. A MSc student is available to anwser the call, of course. The idea has already been briefly discussed with the mantainer of the adehabitat package and the AniMov project community. Short description Develop some add-on functions to use the adehabitat package to perform basic movement ecology analysis, in

Hi everyone, Can anyone give me more details about the 'lp', 'risk', 'terms', and 'expected' options from the predict.coxph function? I actually found that risk is obtained from exp(lp). I can't find information on 'expected' type however. Is anybody can expand the information on this function? Thank you in advance, I will appreciate it.

This may be an FAQ, but a (perfunctory) search failed to turn it up. Suppose I have a function foo(...){<something>} and I want to obtain, inside foo, the names of items comprising the ``...''. E.g. if I call foo(melvin,clyde,irving) I want to be able to loop through the ``...'' and successively obtain the text strings "melvin", "clyde", and

Hello, I have a matrix with 6 columns and 12 rows. I want to extract out those IDs (rownames) from my matrix which have a negative values. For each ID(row) if the negative value is even under 1 column it needs to be extracted out. I will be grateful for any correct suggestion. Thanks Manisha Here is the matrix that I am working on: ID A B C D E F 1 -4.18972 -3.8946

After verifying my smb.conf file, the only thing that changed was this "panic action" command was added. My smb.conf is attached. All our workstations stopped working. If I change the computer name, switch to workgroup, then try to re-join the domain under a different computer name, it works. Do you know what .tdb file machine information is stored in. Also I exported all

Okay, I've traced it to a bug in configparser, which on my python 2.7.4 system is a backport of configparser from python 3. Here is a clean patch that works around the problem. Geoffrey On Wed, Nov 6, 2013 at 10:24 AM, Geoffrey Irving <irving at naml.us> wrote: > LLVM builds with me on the release_33 branch, but fails on trunk. I > bisected the problem to this commit: > >

If one specifies new options in a package, using the options() function, where does/should one document these new options? E.g. suppose that I put the line options(melvin=42) in a file zzz.R in the R directory of the package source, where the package contains functions foo(), bar(), clyde(), and irving() which all query options("melvin") and take some action based on the value of

Hello everybody, I frequently have to produce barplots from variables the natural variation of which is far away from zero. A typical range would be, say from -16 to -28. So, the following example should give an "honest" presentation: x<-c(-20,-22,-21,-28) barplot(x,beside=T,ylim=c(-18,-30)) But using anything else but "0" for the first element of ylim leads to strange