similar to: Marginal Predicitions from nlme and lme4

I'm using groupedData from nlme. I set up a groupedData data.frame with outer=~group1. When I try to plot with outer=TRUE, I get "subscript out of bounds." This happens most of the time. When it works, I get spaghetti-type plots for comparing groups. But I don't understand why it doesn't usually work. > longa.mod.1.gd <- groupedData(mod1.logit~time|

Hello! I want to calculate the intra- and interrater reliability of my study. The design is very simple, 5 raters rated a diagnostic score 3 times for 19 patients. Are there methods/funtions in R? I only found packages to calculate interrater variability and intraclass correlation coefficients for matrices of n*m (n subjects, m raters) - I have n subjects, m raters and r repetitions. Can

Using the weight argument with a variance function in lme (nlme), you can allow for heteroscedasticity of the within-group error. Is there a way to do this for the other variance components? For example, suppose you had subjects, days nested within subjects, and visits nested within days within subjects (a fully nested two-way design) and you had, say men and women subjects. Could you allow for

Dear R-users, I was wondering if anybody knows if it's possible to obtain a p value for the full model of a GLMM with the lme4 package. I was told that I should check whether the full model including all the predictor variables is significant before doing stepwise regression or further analysis, but I can't figure out how to do this. I also wanted to know if there's a way of

Dear community, can anyone provide a snippet of code to force the lm() to fit a model with terms in the formula in an arbitrary order? I am interested in something like: lm(y ~ A * B + C, data=data) where the interaction of A and B should be in the formula before C. My goal is to simplify my presentation of models using the anova() statement. I have found that this should be possible using

Hello! So, my problem is following. I have bird offspring growth data and I'd like to model individual growth curves (aim is to study asymptotes and inflection points) with nlme according to Pinheiro & Bates 2000: first using nlsList to generate individual curves and then nlme to study the parameters and fixed effects. The data is structured to two levels. I have broods and

Dear All, How can I sort a data frame (using one of the column)? Thanks for your support. Regards. Abd. Rahman Kassim (PhD) Head Forest Ecology Branch Forest Management & Ecology Program Forestry and Conservation Division Forest Research Institute Malaysia Kepong 52109 Selangor, Malaysia ***************************************** Checked by TrendMicro Interscan Messaging Security. For any

Hi all, I need to put two different axis to one plot. On the top of the plot, I need to put one axis, with increments from left side to the right side; then at the bottom of the same plot, I need to put another axis, with increments from right side to the left side and showing a different unit. How do I do that? By the way, is there a "hold" command for plotting? If I first plot a

Hi, How can I execute some scripts from within R. I have a large data file which I process (for instance with gawk, but not only) before performing some statistics. I would like to do this in R, so that I do not have to save many data files and then making analysis on them (which proved to be unefficient) Thank you Marco Grazzi

Hi everyone, I was wondering if anyone has any code they could share for creating thumbnail plots in Sweave. For example, I'd like a plot like the following: y <- c(40, 46, 39, 44, 23, 36, 70, 39, 30, 73, 53, 74) x <- c(6, 4, 3, 6, 1, 5, 6, 2, 1, 8, 4, 6) opar <- par(mar=c(3,3,0,0)) plot(x, y, xlab="", ylab="") abline(h=mean(y), col="red") par(opar)

Hi, I have great problems with my work in R. I look for to model the growth of fish. I have "Longitudinal data", a serie of repeated measures for each individual. Using the corresponding packages "nlme" in R. I treat to fit to the data different growth functions, wich were entered by me. Unfortunately for no it was arrived at the convergence, several error messages appeared. I

Dear R community, I'm trying to figure out if there is any way to split the printed output of some commands, for example summary.lme, so that I can intersperse comments in Sweave. I don't mind running the command numerous times and masking various portions of the output, or saving the output as an object and printing it, but I can't figure out how to do either. Does anyone have any

Hi, Does anyone know if: with R can you take a set of numbers and aggregate them like you can in SPSS? For example, could you calculate the percentage of people who smoke based on a dataset like the following: smoke = 1 non-smoke = 2 variable 1 1 1 2 2 1 1 1 2 2 2 2 2 2 When aggregated, SPSS can tell you what percentage of persons are smokers based on the frequency of 1's and 2's. Can

Hi, Can anyone explain how the standard error in arima() is calculated? Also, how can I extract it from the Arima object? I don't see it in there. > x <- rnorm(1000) > a <- arima(x, order = c(4, 0, 0)) > a Call: arima(x = x, order = c(4, 0, 0)) Coefficients: ar1 ar2 ar3 ar4 intercept -0.0451 0.0448 0.0139 -0.0688 0.0010 s.e.

Dear helpers, I'm estimating multilevel regression models, using the lme-function from the nlme-package. Let's say that I estimated a model and stored it inside the object named 'model'. The summary of that model is shown below: Using summary(model)$tTable , I receive the following output: > summary(model)$tTable Value Std.Error DF t-value

Dear All, I'm trying to model heteroscedasticity using a multilevel model. To do so, I make use of the nlme package and the weigths-parameter. Let's say that I hypothesize that the exam score of students (normexam) is influenced by their score on a standardized LR test (standLRT). Students are of course nested in "schools". These variables are contained in the

Dear community, I'm trying to track down a quote, but can't recall the source or the exact structure - not very helpful, I know - something along the lines that: 80% of [applied] statistics is linear regression ... ? Does this ring a bell for anyone? Thanks, Andrew -- Andrew Robinson Department of Mathematics and Statistics Tel: +61-3-8344-9763 University of

Hi everyone, I'm involved in a discussion with a colleague. He suggested a sample design for a finite-sized process that (to all intents and purposes) involves tossing a coin and examining the unit if the coin shows Heads. I should emphasize that we're both approaching the problem from a design-based sampling theory point of view. So I have no argument about the appropriateness of the

Hello R-users Is it possible to fit a three level linear mixed effect model in R? If anyone has an idea or sample code, i will appreciate it very much if i can receive it. I am reading the book by Pinheiro and Bates but have not come across that yet! Kind regards Pryseley --------------------------------- [[alternative HTML version deleted]]

Dear R-users, Does anyone knows how I can order my serie of boxplots from lowest to highest median (which is much better for visualization purposes). thanks in advance, willem [[alternative HTML version deleted]]