monitoring convergence in gamm4 (with the new lmer-1.0-4 modular functionality)

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}}