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

[damian.collins at dpi.nsw.gov.au]

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   

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