Bug in afex, pbkrtest or lme4 in parametric bootstrapping?
Fair enough. I haven't checked PBmodcomp carefully -- but errors in fitting particular PB replicates are not surprising to me, especially with relatively small data sets. I don't know if PBmodcomp is designed to be robust to these types of failures, but it probably should be ... That said, I'm sure there is also room for improvement in the robustness of lme4.
On 13-08-21 05:32 PM, Henrik Singmann wrote:
Although I also see myself out of the discussion on how to solve the
bigger issue, I want to make one point clear, the problem is not related
with the somewhat controversial way of how afex construes the model. It
rather seems to be a problem of model and/or data.
By using method = "LRT" (which is only available in the development
version from r-forge) we can get only the models and see that PBmodcomp
fails for all models, also the unproblematic ones (the p-values are then
taken from anova(full.model, lower.model) which does not fail):
require(afex)
data_alates <- read.csv("alates_raw_FINAL3.csv", header=TRUE, fill=TRUE)
t1 <-
mixed(ALATES~ANT_TENDED*MELEZITOSE+NR_START+(1|CLONES)+(1|PLANT)+(1|REPLICATE),
family=poisson, method="LRT", data=data_alates)
## Fitting 6 lmer() models:
## [......]
## 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
# full model versus model without NR_START (has only main effect)
PBmodcomp(t1$full.model, t1$restricted.models[[4]])
## Error: pwrssUpdate did not converge in 30 iterations
## In addition: Warning messages:
## 1: In pwrssUpdate(pp, resp, tolPwrss, GQmat, compDev, fac, verbose) :
## Cholmod warning 'not positive definite' at
file:../Cholesky/t_cholmod_rowfac.c, line 431
## 2: In pwrssUpdate(pp, resp, tolPwrss, GQmat, compDev, fac, verbose) :
## Cholmod warning 'not positive definite' at
file:../Cholesky/t_cholmod_rowfac.c, line 431
# full model versus model without interaction
PBmodcomp(t1$full.model, t1$restricted.models[[5]])
## Error in pwrssUpdate(pp, resp, tolPwrss, GQmat, compDev, fac, verbose) :
## Downdated VtV is not positive definite
Note furthermore that the exact error message varies. The "Downdated
VtV" can be replaced with the "did not converge in 30 iterations" for
the second comparison and the extra warnings appear from time to time.
However, even when running multiple times, I don't obtain a working
solution (although I haven't put it in a while loop with tryCatch).
Cheers,
Henrik
Ben Bolker schrieb:
This takes care of the proximal problem but I still have a problem
with this example with the latest versions of everything --
data_alates=read.csv("alates_raw_FINAL3.csv", header=TRUE, fill=TRUE)
## devel pbkrtest from:
## http://people.math.aau.dk/~sorenh/software/pbkrtest/devel/
## devel afex from r-forge
## devel lme4 from github
library(afex)
sapply(c("afex","lme4","pbkrtest"),function(x)
paste(packageVersion(x),collapse="."))
## afex lme4 pbkrtest
## "0.6.77" "1.1.0" "0.3.5.1"
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)
## Fitting 6 lmer() models:
## [......]
## Obtaining 5 p-values:
## [Error in pwrssUpdate(pp, resp, tolPwrss, GQmat, compDev, fac,
verbose) :
## Downdated VtV is not positive definite
## 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
It seems to fail on the first submodel, which is the model without an
intercept (a pretty weird model, if you ask me ...)
mm <- model.matrix(mm1)
form <- reformulate(c("-1",
colnames(mm)[-1],"(1|CLONES)","(1|PLANT)","(1|REPLICATE)"),response="ALATES")
newdat <- data.frame(list(model.matrix(mm1)[,-1],
getME(mm1,"flist"),
model.frame(mm1)["ALATES"]),check.names=FALSE)
mm2 <- update(mm1,formula=form,data=newdat)
confint(mm2,method="boot",nsim=20)
## 14/20 bootstrap runs failed
I don't know whether it is better to devote effort to fixing this on
the lme4 level (i.e. making the optimization more robust), or the
PBmodcomp level (i.e. making it handle fit failures better)
On 13-08-21 02:34 PM, S?ren H?jsgaard wrote:
Please use the lme4 version on github; that should fix the problem,
otherwise please report back to me.
Best regards
S?ren
-----Original Message-----
From: Tom Wenseleers [mailto:Tom.Wenseleers at bio.kuleuven.be]
Sent: 21. august 2013 20:20
To: Tom Wenseleers; 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: RE: [R-sig-ME] Bug in afex, pbkrtest or lme4 in parametric
bootstrapping?
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