similar to: nlme - sum of squares - permutation test

Hi, I'm having some problems regarding the packages lme4 and nlme, more specifically in the denominator degrees of freedom. I used data Orthodont for the two packages. The commands used are below. require(nlme) data(Orthodont) fm1<-lme(distance~age+ Sex, data=Orthodont,random=~1|Subject, method="REML") anova(fm1) numDF DenDF F-value p-value (Intercept) 1

Dear All, I've come across a problem in predict.lme. Assigning a model formula to a variable and then using this variable in lme (instead of typing the formula into the formula part of lme) works as expect. However, when performing a predict on the fitted model I gan an error messag - predict.lme (but not predictlm) seems to expect a 'properly' typed in formula and a cannot extract

Dear list members, how can multiple imputation realized for anova tables in R? Concretely, how to combine F-values and R^2, R^2_adjusted from multiple imputations in R? Of course, the point estimates can be averaged, but how to get standarderrors for F-values/R^2 etc. in R? For linear models, lm.mids() works well, but according to Rubins rules, standard errors have to be used together with

Hi all I tried to reproduce an example with lme and used the Orthodont dataset. library(nlme) fm2a.1 <- lme(distance ~ age + Sex, data = Orthodont, random = ~ 1 | Subject) anova(fm2a.1) > numDF denDF F-value p-value > (Intercept) 1 80 4123.156 <.0001 > age 1 80 114.838 <.0001 > Sex 1 25 9.292 0.0054 or alternatively

Dear All -- I am trying to use within a little table producing code an anova comparison of two gls fitted objects, contained in a list of such object, obtained using nlme function gls. The anova procedure fails to locate the second of the objects. The following code, borrowed from the help page of anova.gls, exemplifies: --------------- start example code --------------- library(nlme) ##

Full_Name: Madeleine Yeh Version: 1.9.1 OS: AIX 5.2 Submission from: (NULL) (151.121.225.1) After compiling R-1.9.1 on AIX 5.2 using the IBM cc compiler, I ran the checks. One of them failed. Here is the output from running the check solo. root@svweb:/fsapps/test/build/R/1.9.1/R-1.9.1/tests/Examples: ># ../../bin/R --vanilla < stats-Ex.R R : Copyright 2004, The R

Hello, It seems that, unlike Splus, the anova.lm function of R does not take the argument ssType=3 into account. How can one get an anova table with the adjusted sum of squares in R? Thanks in advance, Patrick Giraudoux University of Franche-Comté Department of Environmental Biology EA3184 af. INRA F-25030 Besançon Cedex tel.: +33 381 665 745 fax.: +33 381 665 797 http://lbe.univ-fcomte.fr

Dear all, Does someone know an R function implementing the method of Sison and Glaz (1995) (see full ref below) for computing Simultaneous confidence intervals for multinomial proportions? As alternative method, I think to boostrap the mean of each proportion and get in that way confidence interval of the mean. I observed 21 times a response that could be one out of 8 categories

Hi, We had some exchanges off the list with Deepayan Sarkar about a bug (?) we cannot fix (it seems it does not occur under Unix). It likely needs the help of somebody on Windows. The initial problem was that when running the following script (Windows XP, R 1.8.1 as well as R 1.9.0): > lset(col.whitebg()) > xyplot(rdens ~ annee | habitat, > groups = sp, type = 'b', >

Hello, I'd like to sum the weights of each independent variable across linear models that have been evaluated using AIC. For example: > library(MuMIn) > data(Cement) > lm1 <- lm(y ~ ., data = Cement) > dd <- dredge(lm1, beta = TRUE, eval = TRUE, rank = "AICc") > get.models(dd, subset = delta <4) There are 5 models with a Delta AIC Score of

Hi All, I have tried every fix on my try or tryCatch that I have found on the internet, but so far have not been able to get my R code to continue with the "for loop" after the lmer model results in an error. Here is two attemps of my code, the input is a 3D array file, but really any function would do.... metatrialstry<-function(mydata){ a<-matrix(data=NA, nrow=dim(mydata)[3],

Hi all, I am having issues comparing models with lmer. As an example, when I run the code below the model summaries (AIC, BIC, loglik) differ between the summary() and anova() commands. Can anyone clear up what's wrong? Thank you! Darren Ward library(lme4) data(sleepstudy) fm1<-lmer(Reaction ~ Days + (1|Subject), sleepstudy) summary(fm1) fm2<-lmer(Reaction ~ Days +

Hello, I've written a simple (although probably overly roundabout) function to test whether two regression slope coefficients from two linear models on independent data sets are significantly different. I'm a bit concerned, because when I test it on simulated data with different sample sizes and variances, the function seems to be extremely sensitive both of these. I am wondering if

Dear R-help list, I would like to perform multiple comparisons for lme. Can you report to me if my way to is correct or not? Please, note that I am not nor a statistician nor a mathematician, so, some understandings are sometimes quite hard for me. According to the previous helps on the topic in R-help list May 2003 (please, see Torsten Hothorn advices) and books such as Venables &

My question concerns the logic behind hypothesis tests for fixed-effect terms in models fitted with lme. Suppose the levels of Subj indicate a grouping structure (k subjects) and Trt is a two-level factor (two treatments) for which there are several (n) responses y from each treatment and subject combination. If one suspects a subject by treatment interaction, either of the following models seem

This continues the message "data.frame within a function (PR#9294)" that was posted on 2006/10/12. Duncan Murdoch kindly replied. I'm using the current version R 2.4.0, but the same issue exists. Just copy and paste the following code under R, and compare the output of f1() and f2() and the output of f3() and f4(). Does anybody have any idea? Thanks.

Hi, I have a string that I want to use in a variable call. How can I remove the quotes and/or the string properties of the string to use it in a variable call? Here's an example: library(lme) fm2 <- lme(distance ~ age, data = Orthodont, random = ~ 1) summary(fm2) I want to update the above regression to include new predictors according to what is in a string: predictors <-

Could someone please tell me how to stop the package/function name from being included before the command prompt? This started happening today after I made some changes to my Rprofile.site file and I don't know why. For example: if I enter example(AIC), instead of just getting the regular '>' before each output line, I get 'AIC>' instead. I only want the '>'

I am not sure a previous e-mail reached the list (no mail aknowledgement from R-boundle etc.). The question was how to write polygon or segment coordinates into a shapefile set or any other ArcGIS supported format. The library shapefiles seems to do something but the documentation is a bit beyond of my mind.... and I cannot get the meaning of the functions write**** and its application to the case

Hello, I wanted to fit a linear mixed model to a data that is similar in terms of design to the 'Machines' data in 'nlme' package except that each worker (with triplicates) only operates one machine. I created a subset of observations from 'Machines' data such that it looks the same as the data I wanted to fit the model with (see code below). I fitted a model in