[R-sig-ME] Bug in afex, pbkrtest or lme4 in parametric bootstrapping?

[Tom Wenseleers]

Oh yes, and FYI the traceback() was
10: stop(gettextf("unable to find an inherited method for function %s for signature %s", 
        sQuote(fdef at generic), sQuote(cnames)), domain = NA)
9: (function (classes, fdef, mtable) 
   {
       methods <- .findInheritedMethods(classes, fdef, mtable)
       if (length(methods) == 1L) 
           return(methods[[1L]])
       else if (length(methods) == 0L) {
           cnames <- paste0("\"", sapply(classes, as.character), 
               "\"", collapse = ", ")
           stop(gettextf("unable to find an inherited method for function %s for signature %s", 
               sQuote(fdef at generic), sQuote(cnames)), domain = NA)
       }
       else stop("Internal error in finding inherited methods; didn't return a unique method", 
           domain = NA)
   })(list("glmerMod"), function (object, newdata, ...) 
   standardGeneric("refit"), <environment>)
8: refit(sm, newresp = yyy)
7: .getref(largeModel, smallModel, nsim = nsim, seed = seed)
6: PBrefdist.merMod(largeModel, smallModel, nsim = nsim, cl = cl, 
       details = details)
5: PBrefdist(largeModel, smallModel, nsim = nsim, cl = cl, details = details)
4: PBmodcomp.merMod(largeModel = <S4 object of class "glmerMod">, 
       smallModel = <S4 object of class "glmerMod">, nsim = 10)
3: (function (largeModel, smallModel, nsim = 1000, ref = NULL, cl = NULL, 
       details = 0) 
   {
       UseMethod("PBmodcomp")
   })(largeModel = <S4 object of class "glmerMod">, smallModel = <S4 object of class "glmerMod">, 
       nsim = 10)
2: do.call(PBmodcomp, args = c(largeModel = full.model, smallModel = fits[[c]], 
       args.test))
1: mixed(use ~ age + I(age^2) + urban + livch + (1 | district), 
       family = binomial, data = Contraception, args.test = list(nsim = 10), 
       method = "PB")

So I gather the error might have to do something with the lme4 function not currently working with glmerMod classes perhaps? Is that right?

Cheers,
Tom

-----Original Message-----
From: r-sig-mixed-models-bounces at r-project.org [mailto:r-sig-mixed-models-bounces at r-project.org] On Behalf Of Tom Wenseleers
Sent: 21 August 2013 19:47
To: sorenh at mail.dk; henrik.singmann at psychologie.uni-freiburg.de; Ben Bolker (bbolker at gmail.com); r-sig-mixed-models at r-project.org
Subject: [R-sig-ME] Bug in afex, pbkrtest or lme4 in parametric bootstrapping?

Dear all,
I was just trying to use parametric bootstrapping to calculate significance levels in a Poisson mixed model using afex/pbkrtest. Using the data in attachment and the code

data_alates=read.csv("alates_raw_FINAL3.csv", header=TRUE, fill=TRUE) mixed(ALATES~ANT_TENDED*MELEZITOSE+NR_START+(1|CLONES)+(1|PLANT)+(1|REPLICATE),type=3,family=poisson,method="PB",args.test = list(nsim = 10),data=data_alates)

I get the following error message though:
Fitting 6 lmer() models:
[......]
Obtaining 5 p-values:
[
Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function 'refit' for signature '"glmerMod"'
In addition: Warning message:
In mixed(ALATES ~ ANT_TENDED * MELEZITOSE + NR_START + (1 | CLONES) +  :
  Numerical variables NOT centered on 0 (i.e., likely bogus results if in interactions): NR_START

Any thoughts perhaps what might be wrong, and what workaround I could perhaps use to make this work?

Cheers,
Tom

PS I was using the following package versions:


sessionInfo()

R version 3.0.0 (2013-04-03)

Platform: x86_64-w64-mingw32/x64 (64-bit)



locale:

[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252    LC_MONETARY=English_United Kingdom.1252

[4] LC_NUMERIC=C                            LC_TIME=English_United Kingdom.1252



attached base packages:

 [1] grid      stats4    splines   parallel  stats     graphics  grDevices utils     datasets  methods   base



other attached packages:

 [1] lsmeans_1.10-00   plyr_1.8          effects_2.2-4     colorspace_1.2-2  nlme_3.1-109      afex_0.6-77       stringr_0.6.2     reshape2_1.2.2

 [9] car_2.0-16        nnet_7.3-6        coin_1.0-22       modeltools_0.2-19 mvtnorm_0.9-9994  survival_2.37-4   pbkrtest_0.3-5.1  lme4_1.1-0

[17] Matrix_1.0-12     lattice_0.20-15   glmmADMB_0.7.7    R2admb_0.7.5.3    MASS_7.3-26       devtools_1.2



loaded via a namespace (and not attached):

[1] digest_0.6.3    evaluate_0.4.3  httr_0.2        memoise_0.1     minqa_1.2.1     multcomp_1.2-18 RCurl_1.95-4.1  tools_3.0.0     whisker_0.3-2