similar to: model.matrix() may be misleading for "lme" models

Dear list members, After further testing, I found that the following simplified version of model.matrix.lme(), which omits passing xlev to the default method, is more robust. The previous version generated spurious warnings in some circumstances. model.matrix.lme <- function(object, ...){ data <- object$data if (is.null(data)){ NextMethod(formula(object),

Dear Ivan, Thank you for addressing my questions with your usual thoroughness. Please see below: On 2024-09-21 2:51 p.m., Ivan Krylov wrote: > [You don't often get email from ikrylov at disroot.org. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ] > > Caution: External email. > > > Dear Prof. John Fox, > > ? Sat, 21 Sep 2024 12:47:49

Dear Prof. John Fox, ? Sat, 21 Sep 2024 12:47:49 -0400 John Fox <jfox at mcmaster.ca> ?????: > NextMethod(formula(object), data=eval(object$call$data), > contrasts.arg=object$contrasts) The use of NextMethod worries me a bit. It will work as intended as long as everyone gives fully-named arguments to the generic, without relying on positional or partial

? Sun, 22 Sep 2024 10:23:50 -0400 John Fox <jfox at mcmaster.ca> ?????: > > Evaluating object$call$data in the environment of the suggested > > nlme:::model.matrix.lme function may also not work right. Without an > > explicit copy of the data, the best environment to evaluate it in > > would be parent.frame(). > > I'm afraid that I don't understand

Dear R-users: I can't run the following code from "Mixed Effects Models in S and S-plus". library( nlme ) options( width = 65, digits = 5 ) options( contrasts = c(unordered = "contr.helmert", ordered = "contr.poly") ) # Chapter 5 Extending the Basic Linear Mixed-Effects Models # 5.1 General Formulation of the Extended Model data( Orthodont ) vf1Fixed

Full_Name: Glenn Stone Version: 1.5.1 and 1.6.0 OS: win2000 Submission from: (NULL) (168.140.227.9) The following code produces incorrect fitted values in version 1.5.1 and an error in 1.6.0 Error in "contrasts<-"(*tmp*, value = "contr.treatment") : contrasts apply only to factors In addition: Warning message: variable ihalf is not a factor in:

> I can't tell whether evaluating object$call$data in environment(object$formula) is a better or worse idea than parent.frame(). I have struggled with this a lot over the years. There is a bunch of wonky code in lme4, e.g. here <https://github.com/lme4/lme4/blob/master/R/lmer.R#L814-L838>, that tries to look for data in different possible locations, but I don't think anything

Dear experts: Is it possible to create a new function based on stats:::model.matrix.default so that an alternative factor coding is used when the function is called instead of the default factor coding? Basically, I'd like to reproduce the results in 'mat' below, without having to explicitly specify my desired factor coding (identity matrices) in the 'contrasts.arg'. dd

There is a bug in `predict' whereby the order of variables sometimes gets re-arranged compared to the original fit, and then disaster results. Specifically, the 'variables' and 'predvars' attributes of a 'terms' object get out of synch. This only happens when the terms in the original formula get re-ordered during fitting: test> scrunge.data_ data.frame(

Hi, I have run into another problem using offsets, this time with the predict function, where there seems to be a contradiction again between the behavior and the help page. On the man page for predict.lm, it says Offsets specified by offset in the fit by lm will not be included in predictions, whereas those specified by an offset term in the formula will be. While it indicates nothings about

I think there are two bugs in aov() that shows up when the right hand side of `formula' contains both `-1' and an Error() term, e.g., aov(y ~ a + b - 1 + Error(c), ...). Without `-1' or `Error()' there is no problem. I've included and example, and the source of aov() with suggested fixes below. The first bug (labeled BUG 1 below) creates an extra, empty stratum inside

I believe you are right, but can you please explain why anyone would want to fit this model? It differs only in the coding from aov(y ~ a + b + Error(c), data=test.df) and merely lumps together the top two strata. There is a much simpler fix: in the line if(intercept) nmstrata <- c("(Intercept)", nmstrata) remove the condition (and drop the empty stratum later if you

Dear R-helpers, I try to perform glm's with negative binomial distributed data. So I use the MASS library and the commands: model_1 = glm.nb(response ~ y1 + y2 + ...+ yi, data = data.frame) and predict(model_1, newdata = data.frame) So far, I think everything should be ok. But when I want to perform a glm with a subset of the data, I run into an error message as soon as I want to predict

Dear R-project! How do i create 1 dummy from 2 already existing dummys. To be more precise, I want to create a dummy from a dummy called "sex" and another called "sex1" when both thoose dummys are 1 I want my created dummy "samesex" to take 1. Thanks for the help! Paulie [[alternative HTML version deleted]]

Hello everyone, I am trying to fit the following model All X. variables are continuous, while the conditions are categoricals. model <- lm(X2

I would like to ask for advice from R experts about the benefits or dangers of using attr to return information with an object that is returned from a function. I have a feeling as though I have cheated by using attributes, and wonder if I've done something fishy. Maybe I mean to ask, where is the dividing line between attributes and instance variables? The separation is not clear in my mind

Over a decade ago there was a problem with model.frame when the variable names were long: https://stat.ethz.ch/pipermail/r-help/2002-August/024492.html I have similar symptoms with R 2.15.3 on Windows 7: Browse[2]> x <- model.matrix(formula(myform), p$data) Error in model.frame.default(object, data, xlev = xlev) (from mice.R#601) : object is not a matrix My attempt at a work-around

Hi everybody! I'm sure that I overlook something and feel quite stupid to ask, but I have not found an easy solution to the following problem: Take e.g. the Orthodont data from the nlme package: > head(Orthodont) Grouped Data: distance ~ age | Subject distance age Subject Sex 1 26.0 8 M01 Male 2 25.0 10 M01 Male 3 29.0 12 M01 Male 4 31.0 14 M01 Male

Consider the following plot that shows separate regression lines ~ age for each subject in the Pothoff-Roy Orthodont data, with separate panels by Sex: library(nlme) #plot(Orthodont) xyplot(distance ~ age|Sex, data=Orthodont, type='r', groups=Subject, col=gray(.50), main="Individual linear regressions ~ age") I'd like to also show in each panel the pooled OLS

Dear R-devel list members, I've discovered an inconsistency in how lm() and similar functions handle logical predictors as opposed to factor or character predictors. An "lm" object for a model that includes factor or character predictors includes the levels of a factor or unique values of a character predictor in the $xlevels component of the object, but not the FALSE/TRUE values