similar to: Bar plots with stacked columns marked with askterisks

Hi, I'm trying to save heatmaps as PDFs. However, the PDF version of the heatmaps (Heatmap_CAFvsTNF_run2.pdf) is blurred when compared to its counterpart, which was saved manually by using the software "Grab" (Heatmap_CAFvsTNF_run2.tiff). -----R code-------- sample_output <- "stroma_run2" filename <-

Hi, I tried to use rmnlIndepMetrop (bayesm package) for my MNL model with 4 choice alternatives, 5 independent variables, 69 observations, dim(X) [1] 276 5, nu=6. So I run such code: if(nchar(Sys.getenv("LONG_TEST")) != 0) {R=2000} else {R=10} set.seed(66) df=read.table("X_metrop.dat",header=TRUE) inp=as.matrix(df) y=as.numeric(inp[,1]) n=length(y) p=4

Hi, I have recently been playing with the grid package in an attempt to create some pages containing multiple lattice plots on the same page. However, when I specify a grid layout with different widths, such as: pushViewport(viewport(layout = grid.layout(1, 2, unit(c(2, 1), "null")))) the individual graphs do not end up as the same height - which is a feature I would prefer to have.

Hello, I am a new user of R, and I am not able to read/scan external files. I am working in a Linux environment. I have read through the R FAQ and documents and have not been successful using the recommendations. Below are several scripts I've used and the error messages. . I've cc'd Brandon Whitcher because it was recommended in another FAQ. I read that this is a bug that

rly there would be a heavy penalty to launching a shell so you would want t= o carefully evaluate the frequency this is executed on your system.<br /> <div class=3D"container"> <div class=3D"line number1 index0 alt2"><code class=3D"sql plain"><br /> DELIMITER @@</code></div> <div class=3D"line number2 index1

Hi! Wondering if anyone can tell me what''s wrong with my code? I''m trying to use the onChange event of a select list to update multiple divs... Agile Web Development with Rails (p. 403) suggests using ":complete => eval(request.responseText) instead of :update" I''ve attempted the following test code: # in the view <select name="plist",

Hi, I am sure this has come up before, but my searches of the archive didn't give any results (maybe I didn't use the right keywords, but if I use too many, the search times out). I have a vector of dimensions n, length is not fixed, eg n <- c(4,5,7) or n <- c(19,4,5,7) and a function f that takes a vector of indices, same length of n, and gives a scalar. I would like to fill

Does lme prediction work correctly with poly() terms? In the following simulated example, the predictions are wildly off. Or am I doing something daft? Milk yield for five cows is measured weekly for 45 weeks. Yield is simulated as cubic function of weekno + random cow effect (on intercept) + residual error. I want to recover an estimate of the fixed curve. ############### library(nlme)

Hi, I read the example in http://wiki.rubyonrails.com/rails/pages/HowtoUseMultipleDatabases, it show us how to connect to other database, each time we start a new action, however, this doesn''t work while you try to connect to two different database within the same action. SO I wonder is it possible to bind to two or more database within the same action???? Thanks you very much Saiho

Hey guys, I'm having trouble getting the correct colors, when they are read from a csv file. Here's an example: 1 1 black 1 2 green 1 3 green 1 4 black 1 5 peachpuff Call it blah.csv. Then I ran: data <- read.csv("blah.csv",header=FALSE,sep="") and then to plot the data, I ran: plot(data[,1],data[,2],col=data[,3]) But the output reports a vertical line with

Hi, I would like to know how (if) I can extract some of the information from the summary of my nlme. at present, I get a summary looking something like this: > summary(fit.nlme) Nonlinear mixed-effects model fit by maximum likelihood Model: MLKYLD ~ W4(DIM, logA, B, C) Data: ADHIS.x0 AIC BIC logLik 265314 265401.6 -132647 Random effects: Formula: list(logA ~ 1 , B ~

Hello. I recently tried installing NetBSD-5 on xen-4.0.1-rc5, which resulted in no network (xennet0 can''t get IPs per dhclient and has no connectivity if set by hand). Tried it with netBSD-5.1-RC3-1 i386 PAE & amd64, netBSD-5.0 and even 4, all with the same result. On a older xen version (3.3.1) networking works fine, so I assume it''s a xen bug, and not a netBSD-kernel

I am attempting to run a glm with a binomial model to analyze proportion data. I have been following Crawley's book closely and am wondering if there is an accepted standard for how much is too much overdispersion? (e.g. change in AIC has an accepted standard of 2). In the example, he fits several models, binomial and quasibinomial and then accepts the quasibinomial. The output for residual

Dear All, I'm not sure of the interpretation of interactions with contrasts. Can anyone help? I do an ANCOVA, dryweight is covariate, block and treatment are factors, c4 the response variable. model<-aov(log(c4+1)~dryweight+treatment+block+treatment:block) summary(model); Df Sum Sq Mean Sq F value Pr(>F) dryweight 1 3.947 3.947 6.6268 0.01076 *

I am using R for the first time in one of my classes. My students have alerted me to a problem for which we have not found an answer. We find that some means returned by the model.tables function are not correct when missing data is present in analysis of variance problems. We have duplicated the problem using R 1.2.0, 1.2.1, and 1.2.2 under Windows 98 and several distributions of Linux (Redhat

Dear R-list, I am wondering how to perform a bootstrap in R for the weighted time dependent Cox model? (Andersen?Gill format, with multiple observations from each patients) to obtain the bootstrap standard error of the treatment effect. Below is an example dataset. Would 'censboot' be appropriate to use in this context? Any suggestions/references/direction to R-package will be highly

Ok, now we have the mapping of color names to color codes (see below) and conversion to rgb (something like Ben Bolker's function), but how to convert rgb to hsv? Thanks to Brian Ripley, Peter Dalgaard and Ben Bolker Details below Regards Jens etc/colors.big maps 455 names to rgb in S syntax etc/rgb.txt maps 657 names to rgb in C syntax, but unlike colors() it has mixed upper and

I have: RedHat 9.0 TDM40B asterisk-0.9.0 compiled from sources zaptel-0.9.1 likewise /etc/zaptel.conf contains fxoks=1-4 loadzone = us defaultzone=us loaded modules zaptel and wcfxs /etc/askterisk/zapata.conf contains [channels] language = en signalling = fxo_ks context = phones channel => 1-4 /etc/askterisk/extensions.conf contains [general]

Sadly you failed to set your email program to send plain text and the data is corrupted at my end. I also think you need to reduce the size of the data set... the intent here is to increase your understanding, not debug your particular analysis. I will say that I am having a very challenging time understanding what you are trying to accomplish though. What are the equations that you think need

Hi I have a linear model and I want to tests whether the model terms are significant I used anova but F and P value depend on the order of the terms in the model. I have repeated the same analysis in another stat software and F and P value did not differ with order of terms in the model. Can anyone can explain what happen or what am I doing wrong ? In R > anova (lm(Y~X.1+X.2)) Analysis of