similar to: incorrect MCMC CIs in pvals.fnc (languageR) ?

Hi everybody! I was using the function pvals.fnc from package 'languageR' until April. I do not know which version. Yesterday I updated all my packages and tried to run my loop again. Now I get the following error message: error in pvals.fnc(mm, nsim = 1000) : MCMC sampling is not yet implemented in lme4_0.999375-27 for models with random correlation parameters I guess it?s because of

Hi. I get an error message about not converging when I try and use the pvals.fnc from the languageR library. The LMER analysis worked fine (See below). I am not an expert so I don't understand why the LMER worked but not the pvals.fnc Any help gratefully received. - Mike AIC BIC logLik MLdeviance REMLdeviance -7324 -7254 3673 -7451 -7346 Random effects: Groups

Dear folks (or Dear Professor Bates), I'm quite confused as to the current status of some of the available functions applicable to lmer objects. Following the examples in Baayen, Davidson, Bates (2006), my plan is to run mcmcsamp on a random effect model created by lmer in package lme4, then use the (perhaps outdated) pvals to estimate p-value. But then I couldn't find pvals anywhere.

Dear R list, I have a recurring problem with the languageR package, specifically the aovlmer.fnc function. When I try to run the following code (from R. H. Baayen's textbook): # Example 1: library(languageR) latinsquare.lmer <- lmer(RT ~ SOA + (1 | Word) + (1 | Subject), data = latinsquare) x <- pvals.fnc(latinsquare.lmer,

Hi Everyone, I am using R 2.10.1. lmer function works properly, however pvals.fnc () does not despite the fact that I uploaded: - library(lme4) - library(coda) - library(languageR) This is the error message I get pvals.fnc(lexdec3.lmerE2, nsim=10000)$fixed Error in pvals.fnc(lexdec3.lmerE2, nsim = 10000) : MCMC sampling is not yet implemented in lme4_0.999375 for models with random

Dear R-help: I've been trying to run pvals.fnc in the newest version of R (2.13.0). The function lmer worked fine, but when I tried to use pvals.fnc on the lmer object, I got the following error: "Error in pvals.fnc(elogr.subj.dys.sum.3x3.p, nsim = 10000) : trying to get slot "coefs" from an object (class "summaryDefault") that is not an S4 object." How can I

Dear r-helpers, Following up on http://finzi.psych.upenn.edu/R/Rhelp02a/archive/ 81159.html where Douglas Bates gives a helpful application of lmer() to data(sleepstudy, package = 'lme4'), I need a bit more help in order to plot the correct confidence intervals of a designed experiment such as: > data(ratdrink, package = 'faraway') I follow the steps Douglas took in

(To the list moderator: I just subscribed to the list. Apologies for not having done so longer before trying to post.) Hi all, I am currently using lmer to analyze data from an experiment with a single fixed factor (treatment, 6 levels) and a single random factor (block). I've been trying to follow the online guidance for estimating p-values for parameter estimates on these and other

Hola buenas noches, tengo un problema bastante gordo. ¿A alguno le ha dejado de funcionar las funciones pamer.fnc y mcp.fnc con la nueva versión de R? La semana pasada formatee el ordenador y ahora scripts antiguos no funcionan. La cuestión es que me precupa que no funcione el ejemplo de tutorial del autor. Os dejo un script que debería de funcionar y no lo hace

Hola buenas tras meses investigando como hacer anovas para factores con efectos fijos y efectos aleatorios, he encontrado una serie de funciones que satisfacen mis pretensiones y creo correctas en cierta medida. Me gustaría compartirlas con vosotros con doble intención, la primera es compartirla para que si otro se encuentra en esta situación que tenga el trabajo hecho y la segunda es que sean

Hace unos meses os escribir para comunicaros que había un fallo en esta función. Como os prometí os comento la respuesta por si alguno está interesado en utilizar el paquete LMERconvenientsfucntions Dear Javier, The package has been updated and should work for you fine now. Note that function mcp.fnc does not return the fourth plot (dffits) anymore. We still have to figure out a way to compute

Hello All, I am learning mixed effects logistic regression (lmer in lme4), and I am having problems deciphering the goodness of fit function plot.logistic.fit.fnc (languageR package). The only information I can find is that this function plots observed proportions against mean predicted probabilities for some binning of the data. I have explored this function with several datasets, and have had

The object is a mcmc sample from lmer. I am using R v2.7.1. Please let me know what additional information I can provide, hopefully I am just making a simple mistake. Thanks in advance! > data(ratdrink, package = 'faraway') > rd.er <- lmer(wt ~ weeks*treat + (1 | subject), data = ratdrink) > rd.mc <- mcmcsamp(rd.er, 10000) > library(coda) Loading required package:

Hi, I have been using the library languageR in R2.6.0 for some while. I now would like to use new functions of this library (especially plotLMER.fnc) and have downloaded R 2.8.0. Error messages appear when I load the languageR library (I have tried several times on different computers but this doesn't help.: Attachement du package : 'Matrix' The following object(s)

Hello, I can not get the function plot.logistic.fit.fnc() working....it returns "Error: could not find function "plot.logistic.fit.fnc"". Do I need to upload as specific package first? I am trying to check the fit of a mixed logistic model. Also, any advice for checking the assumption of independence in a mixed logistic model? Many thanks in advance, Sarah Foster

Dear R users I am trying to obtain p-values for (quasi)poisson lmer models, including Markov-chain Monte Carlo sampling and the command summary. > > My problems is that p values derived from both these methods are totally different. My question is (1) there a bug in my code and > (2) How can I proceed, left with these uncertainties in the estimations of > the p-values? > > Below

Estimado Javier Villacampa Gonzáles Si una persona se toma el trabajo de desarrollar y compartir, como es el caso de R, seguramente conoce de problemas que tuvo que decidir mientras escibía el código, y estará agradecido porque hay gente que utiliza su aporte, su trabajo no fué a la nada, todo lo contrario. En mi caso un solo autor tuvo una respuesta negativa para con migo. Javier Marcuzzi

This evening I ran into the problem Chuck Clifton referred to in message 86 of Volume 71 Issue 9 of this list. That is, objects created by lmer change after calling pvals.fnc on that lmer object when using lme4 version 0.999375-16 and 0.999375-28. This is somewhat troublesome. The bug tracker on R-Forge (

Hola, Lo primero muchas gracias a todos por vuesta habitual ayuda. Llevo meses con las funciones lmer, pero tengo un problema no se como plantear unas comparaciones multiples una vez demostrado que el factor tiene diferencias significativas. Tengo multiples opciones, Solución A: una es hacer un bonferroni a saco (pero eso me chirria ya que tego muchos datos) Solución B: Otra es utilizar glht,

Gracias a todos por las recomendaciones. Ya me he puesto en contacto con el autor y le explicado donde esta el error. Es tan fácil como que han cambiado la estructura de los objetos tipos lmer desde la versión 2.15.3 con lo que su paquete dejo de funcionar. Por suerte la nueva estructura conserva por lo menos la parte necesaria para hacer sus funciones. Se localizar el fallo y como arreglarlo, lo