similar to: different DF in package nlme and lme4

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

All, I'm trying to create an augPred plot in the nlme library, similar to the plot on p.43 of Pinheiro & Bates (Mixed Effects Models in S and S-Plus) for their Pixel data. My data structure is the same as the example but I still get the error msg below. > comp.adj.UKV <- groupedData(adj.UKV ~ Time | Patient_no/Lisinopril, data = comp.adj.UKV.frm, order.groups = F) >

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 am running the following model: > glm89.nb <- glm.nb(AvGUD ~ Year*Trt*Micro) where Year has 3 levels, Trt has 2 levels and Micro has 3 levels. However when I run it has a zero inflated negative binomial (as I have lots of zeros) I get the below error message: > Zinb <- zeroinfl(AvGUD ~ Year*Trt*Micro |1, data = AvGUD89, dist = "negbin") Error in optim(fn =

Hi, 1/ I wonder why a anova.lme on a single lme object does not print the sum of squares (as expected from the help: "a data frame with the sums of squares, numerator degrees of freedom, denominator degrees of freedom, F-values, and P-values"). Example: > fm2 <- lme(distance ~ age + Sex, data = Orthodont, random = ~ 1) > anova(fm2) numDF denDF F-value p-value

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 R core team Using the following code produces an empty plot (similar to col = NA): > plot(1:9, col = factor(rep(1:3,3), labels = c("red", "blue", "black"))) My question: Shouldn't one get at least a warning (or an error) if one tries to use a factor as col argument? Thanks for an answer. Regards, Christoph Buser

Dear R gurus I've a question concerning the transformation of a new S4 class (that I defined) and the existing class "POSIXlt". I did the following: ## Definition of the new class: setClass("dtime", representation(data = "POSIXlt"), prototype(data = as.POSIXlt("2004/06/01"))) ## Transformation between the new class "dtime"

Dear R core team Please apologize for posting the same question twice on R-help and R-devel. Since I was not sure which list is appropriate I tried R-help (Tue Mar 22), but got no answer. Now I do not know if the formulation of my question was unclear or the question is not so easy to answer or to easy (what I do not hope). My problem: I create a new S4 class, containing one slot, data (of

Hy all, I apologize i've used rownames instead of colnames in my first exemple. (that's why i changed the mail object) I was on mars when i wrote my question... Every answer where correct ... but, because i've made a wrong question, people wern't able to understand... So finally i'm speaking about colnames : Let's be more precise: I've got a query that gives me for

Dear R-core There is a different output for the apply function due to the change of unlist as mentioned in the R news. Newly, applying as.factor() (or factor()) in str(dat <- data.frame(x = 1:10, f1 = gl(2,5,labels = c("A", "B")))) (d1 <- apply(dat,2,as.factor)) newly returns a character matrix while in R-2.3.1 the same command resulted in an integer matrix that was

Dear R core team I've a proprosal to improve the function interaction.plot. It should be allowed to use type = "b". This can be done by changing the function's header from function( , type = c("l", "p"), ) to function( , type = c("l", "p", "b"), ) Then it works. This type = "b" is useful, if

Dear R Core Team I've a proposal to improve drop1(). The function should change the contrast from the default ("treatment") to "sum". If you fit a model with an interaction (which ist not signifikant) and you display the main effect with drop1( , scope = .~., test = "F") If you remove the interaction, then everything's okay. There is no way to fit a

Dear R-list I have a question concerning the argument "adjustSigma" in the function "lme" of the package "nlme". The help page says: "the residual standard error is multiplied by sqrt(nobs/(nobs - npar)), converting it to a REML-like estimate." Having a look into the code I found: stdFixed <- sqrt(diag(as.matrix(object$varFix))) if (object$method

Dear R-users I have a problem choosing initial points for the function arms() in the package HI I intend to implement a Gibbs sampler and one of my conditional distributions is nonstandard and not logconcave. Therefore I'd like to use arms. But there seem to be a strong influence of the initial point y.start. To show the effect I constructed a demonstration example. It is reproducible

Hello! I've tried to use extprograms pipe feature but stuck with "Broken pipe" errors in mail log: May 17 15:18:57 backend1 dovecot: lmtp(20338, user at domain.tld): Debug: 3VMVFWFKllFyTwAArRg8UA: sieve: action pipe: running program: learn May 17 15:18:57 backend1 dovecot: script: Error: write(response) failed: Broken pipe May 17 15:18:57 backend1 dovecot: lmtp(20338, user at

Dear Prof. Ripley and Christoph, thank you very much for your comments. You have helped me a lot. Thanks, Tomas Goicoa >Dear Prof. Ripley > >Thank you for your email. Yes, this is of course the correct >syntax to save us the extra calculation. And I forgot the >"lower.tail = FALSE" for pf() in my example to obtain the >p-value. > >Thank you for the

Hello! I've tried to use extprograms pipe feature but stuck with "Broken pipe" errors in mail log: May 17 15:18:57 backend1 dovecot: lmtp(20338, user at domain.tld): Debug: 3VMVFWFKllFyTwAArRg8UA: sieve: action pipe: running program: learn May 17 15:18:57 backend1 dovecot: script: Error: write(response) failed: Broken pipe May 17 15:18:57 backend1 dovecot: lmtp(20338, user at

I create multiple server instances for the samba with systemd, everything ok, but after reboot server, the service nmb does not work randomly. selinux disable samba version 4.2.10 config smb [global] workgroup = WORKGROUP3 netbios name = net3 security = user interfaces = enp7s0f3 bind interfaces only =

Hello, I've been using rsync to keep two boxes in sync until one replaces the other. To make things a bit more to my liking and to make apache's userdir config a bit simpler, I have added a number of symlinks in the new machine's /home. Both boxes have hashed userdirs, ie: /home/a/auser, /home/b/buser, etc. So I have some symlinks like /home/a/aweirdo -> /home/CORP/aweirdo.