similar to: Fitted probabilities from glmmPQL?

Hi everyone, How might I go about configuring R to keep add-on packages loaded from session to session? Is this undesireable for some reason? At present, I keep a file called "pckgs.txt" in my working directory with, e.g., library(gnlm) library(Hmisc) ... and then type source("add-ons.txt") every time I start a new session. I suspect there's a more elegant way to hold

Hi All, Is it possible for system.time() to measure the time it takes for a machine to evaluate more than one R expression? For example, # This I can do: > system.time(x <- rnorm(100000)) [1] 0.07 0.00 0.13 0.00 0.00 # But this I can't: > system.time(x <- rnorm(100000); new <- sample(x, 100000, replace=T)) Error: syntax error # Nor this: > system.time(x <-

Within a function I'm assigning dynamic variable names and values to them using the "assign" function. I want to pass back the results but am uncertain how to do this. Basically, my function reads a number of data files and uses the filename of each file as the variable name for a list-to-become-dataframe. I want then to pass all these lists back, but again, the names of the

Dear all, I've come across a problem using strptime, can anyone explain what's going on? I'm using version 2.7.0 on Windows XP. Thank you Caroline First read in a data file using read.table alldata = read.table(file, header=F, skip=4, colClasses = c("character","numeric")) dim(alldata) [1] 223960 2 # inefficient, safe way of sorting out missing or dodgy

Hi ! I try to compare some models obtained from glmmPQL. model1 <- glmmPQL(y~red*yellow+I(red^2)+I(yellow^2)+densite8+I(densite8^2)+freq8_4 +I(freq8_4^2), random=~1|num, binomial); model2 <- glmmPQL(y~red*yellow+I(red^2)+I(yellow^2)+densite8+I(densite8^2)+freq8_4 , random=~1|num, binomial); anova(model1, model2) here is the answer : Erreur dans anova.lme(model1, model2) : Objects must

Hi R-users, I am using lme to fit a linear mixed model with the nlme package, does anyone know if it is possible to obtain standard error estimates of the variance components estimators and an adequate method to test the significance of the variance component? Thanks, Berta. [[alternative HTML version deleted]]

Hi, am a rails newbie. I had problems with 2 tasks i have created a guestbook app just to try out rails users sign guestbook by leaving name and message currently, the list action shows plain text like this: Joe Smith love your guestbook but i would like to add formating to the name field, say different colour, bold, and add time eg: Joe Smith (in red colour) wrote 5 days ago love your

[My very deepest apologies in advance if this is not plain text; I am recently at a new job in a windows-based environment and have not yet set up my favorite old (pine) system. I have tried my best to strip all formatting from the message..] I'm overlaying plots of tree locations mapped before and after logging activities and checking my matched individuals using several arguments to

Hey there all, Is there some way to tell rails or sql server to ignore the time in a datetime field when doing a comparison? For example, if I do something like select * from users where registration_date = ?, @date where @date might equal some user input like ''03/14/2006'' The result is nothing returned, because in my tables the datetime field looks like this: 3/14/2006

Is the labeling/naming of levels in the documentation for the predict.glmmPQL function "backwards"? The documentation states "Level values increase from outermost to innermost grouping, with level zero corresponding to the population predictions". Taking the sample in the documentation: fit <- glmmPQL(y ~ trt + I(week > 2), random = ~1 | ID, family =

Full_Name: Caroline Keef Version: 2.6.1 OS: Windows XP Submission from: (NULL) (195.171.203.131) I have tried to install the package rggobi which if I'm right requires the package RGtk2 If I install RGtk2 using the install.packages (I used the UK (Bristol) mirror, I haven't tried any other mirror) within R and then use library(RGtk2) I get the following message box "This

Dear All, I would like to analyse the residuals from a generalized linear mixed model (GLMM) that I estimated, with random effects, by means of the command glmmPQL, from the MASS package. It is not very clear to me what the actual residuals to analyse are (Y - Yhat): I obtain two columns of residuals, of which the first are population residuals, and the second refer to the grouping used in the

I am trying to use lme to fit a mixed effects model to get the same results as when using the following SAS code: proc mixed; class refseqid probeid probeno end; model expression=end logpgc / ddfm=satterth; random probeno probeid / subject=refseqid type=cs; lsmeans end / diff cl; run; There are 3 genes (refseqid) which is the large grouping factor, with 2 probeids nested within each refseqid,

hello all, i'm an R newbie struggling a bit with the glmmPQL function (from the nlme pack). i think i've managed to run the model successfully, but can't seem to plot the resulting function. plot(glmmPQL(...)) plots the residuals rather than the model... i know this should be basic, but i can't seem to figure it out. many thanks in advance. j -- View this message in context:

Dear Rusers, I have used R,S-PLUS and SAS to analyze the sample data "bacteria" in MASS package. Their results are listed below. I have three questions, anybody can give me possible answers? Q1:From the results, we see that R get 'NAs'for AIC,BIC and logLik, while S-PLUS8.0 gave the exact values for them. Why? I had thought that R should give the same results as SPLUS here.

Hello: In the example below (or for a censored data) using survfit.coxph, can anyone point me to a link or a pdf as to how the probabilities appearing in bold under "summary(pred$surv)" are calculated? Do these represent acumulative probability distribution in time (not including censored time)? Thanks very much, parmee *fit <- coxph(Surv(futime, fustat) ~ age, data = ovarian)*

Hi, I'm trying to perform a power simulation for a simple multilevel model, using the function glmmPQL in R version 2.8.1. I want to extract the p-value for the fixed-effects portion of the regression, but I'm having trouble doing that. I can extract the coefficients (summary(fit)$coeff), and the covariance matrix (summary(fit)$varFix), but I can't grab the p-value (or the

Hi! Can anyone let me know how can I get the stdDev of the random intercept from the output of glmmPQL? Thanks Salom?

Hi all, I'm using R 1.5.1 on Windows 2000. The following snippet of code doesn't seem to do anything - no error is reported, and there is no name change. names(myFrame[,c(1:3)]) <- c("name1", "name2", "name3") This code however works nicely: names(myFrame)[c(1:3)] <- c("name1", "name2", "name3") Can anyone suggest why

Dear listers, glmmPQL (package MASS) is given to work by repeated call to lme. In the classical outputs glmmPQL the Variance Structure is given as " fixed weights, Formula: ~invwt". The script shows that the function varFixed() is used, though the place where 'invwt' is defined remains unclear to me. I wonder if there is an easy way to specify another variance