[R-sig-ME] monitoring convergence in gamm4 (with the new lmer-1.0-4 modular functionality)

[Steve Walker]

Hi Damian,

I'm pretty sure you've found a bug, which I've reported here:

https://github.com/lme4/lme4/issues/135

Steve

On 2013-09-25 3:30 AM, damian.collins at dpi.nsw.gov.au wrote:
> Dear all,
>
> Can someone tell me how I can monitor the convergence of a gamm4 run using the new lmer-1.04 modular functions and the iprint or verbose arguments?
> (I wish to debug a warning message re: "failure to converge in 10,000 iterations".)
>
> In the past, I successfully used "options(verbose=T)" to turn on monitoring. But now that option appears to have no effect.
>
> After examining the documentation/code for gamm4,  glFormula/updateGlmerDevfun, lmerControl and Nelder_Mead, I tried (using the example from gamm4 helpfile):
>
> lr.fit0 <- gamm4(y~s(x0)+s(x1)+s(x2), family=binomial, data=dat, control=lmerControl(optCtrl=list(iprint=20)))
>
> and got an error:
>
> Error in updateGlmerDevfun(devfun, b$reTrms, ...) :
>    unused argument (control = list(optimizer = "Nelder_Mead", restart_edge = TRUE, checkControl = list(check.nobs.vs.rankZ = "warningSmall", check.nobs.vs.nlev = "stop", check.nlev.gtreq.5 = "ignore", check.nlev.gtr.1 = "stop"), optCtrl = list(iprint = 20)))
> In addition: Warning message:
> In (function (npt = min(n + 2L, 2L * n), rhobeg = NA, rhoend = NA,  :
>    unused control arguments ignored
>
> Similar attempts, using more or less nesting in the control= option, led to similar error messages.
>
> I am using R-3.0.1, mgcv 1.7-26, gamm4 0.2-1, lmer 1.04, Matrix 1.0-12 on a Fedora 18 x64 laptop.
>
> Transcript copied/pasted below
>
> Damian Collins | Biometrician | Primary Industries
> Industry & Investment NSW | Elizabeth Macarthur Agricultural Institute | Woodbridge Rd, Menangle NSW 2568 | Private Bag 4008, NARELLAN NSW 2567
> T: 02 4640 6451 | F: 02 4640 6300 | M: 0410 271 144 |  E: damian.collins at industry.nsw.gov.au
>
>
>
> ----- Transcript (non-essential lines removed ...)  - run on Fedora 18 x64 machine  -----
>
> R version 3.0.1 (2013-05-16) -- "Good Sport"
> Copyright (C) 2013 The R Foundation for Statistical Computing
> Platform: x86_64-redhat-linux-gnu (64-bit)
> ...
>>> assignInNamespace(".help.ESS", help, ns=asNamespace("base"))
>> options(STERM='iESS', str.dendrogram.last="'", editor='emacsclient', show.error.locations=TRUE)
>> library(gamm4)
> Loading required package: Matrix
> Loading required package: lattice
> Loading required package: lme4
> Loading required package: mgcv
> Loading required package: nlme
>
> Attaching package: ‘nlme’
>
> The following object is masked from ‘package:lme4’:
>
>      lmList
>
> This is mgcv 1.7-26. For overview type 'help("mgcv-package")'.
> This is gamm4 0.2-1
>> dat <- gamSim(1,n=600,dist="binary",scale=.33)
> Gu & Wahba 4 term additive model
>> lr.fit0 <- gamm4(y~s(x0)+s(x1)+s(x2),family=binomial,data=dat)
>> options(verbose=T)
>> lr.fit0 <- gamm4(y~s(x0)+s(x1)+s(x2),family=binomial,data=dat)
>> lr.fit0 <- gamm4(y~s(x0)+s(x1)+s(x2),family=binomial,data=dat,control
> =lmerControl(optCtrl=list(iprint=20)))
> Error in updateGlmerDevfun(devfun, b$reTrms, ...) :
>    unused argument (control = list(optimizer = "Nelder_Mead", restart_edge = TRUE, checkControl = list(check.nobs.vs.rankZ = "warningSmall", check.nobs.vs.nlev = "stop", check.nlev.gtreq.5 = "ignore", check.nlev.gtr.1 = "stop"), optCtrl = list(iprint = 20)))
> In addition: Warning message:
> In (function (npt = min(n + 2L, 2L * n), rhobeg = NA, rhoend = NA,  :
>    unused control arguments ignored
>> packageDescription("lme4",fields=c("Version","Date"))
> Version: 1.0-4
> Date: 2013-09-08
>> packageDescription("Matrix",fields=c("Version","Date"))
> Version: 1.0-12
> Date: 2013-03-26
>> packageDescription("nlme",fields=c("Version","Date"))
> Version: 3.1-109
> Date: 2013-03-21
>> sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-redhat-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=C                 LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] gamm4_0.2-1     mgcv_1.7-26     nlme_3.1-109    lme4_1.0-4
>
> [5] Matrix_1.0-12   lattice_0.20-15
>
> loaded via a namespace (and not attached):
> [1] compiler_3.0.1 grid_3.0.1     MASS_7.3-26    minqa_1.2.1    Rcpp_0.10.4
> [6] splines_3.0.1  tools_3.0.1
>
> This message is intended for the addressee named and may...{{dropped:8}}
>
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