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
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