<html><body><div style="color:#000; background-color:#fff; font-family:arial, helvetica, sans-serif;font-size:12pt"><div style="font-size: 12pt; font-family: arial, helvetica, sans-serif; "><span>Thank you for the speedy replies Ben and Dave,</span></div><div style="font-size: 12pt; font-family: arial, helvetica, sans-serif; "><span><br></span></div><div><span style="font-family: arial, helvetica, sans-serif; font-size: 12pt; ">I've since retried my models with the suggested changes to the extra arguments for models that returned the error "Function Maximizer Failed" . Adding ", </span><span class="Apple-style-span" style="font-size: 12pt; font-family: 'times new roman', 'new york', times, serif; ">admb.opts = admbControl(shess = FALSE, noinit = FALSE)" seems to have done the trick. </span></div><div><span class="Apple-style-span" style="font-size: 12pt; font-family: 'times new roman', 'new york', times, serif;
"><br></span></div><div><span class="Apple-style-span" style="font-size: 12pt; font-family: 'times new roman', 'new york', times, serif; ">Thanks again,</span></div><div style="font-size: 12pt; "><span class="Apple-style-span"><br></span></div><div style="font-size: 12pt; font-family: arial, helvetica, sans-serif; ">Andrew Harbicht<br><br></div><div style="font-size: 12pt; font-family: arial, helvetica, sans-serif; "><div style="font-size: 12pt; font-family: 'times new roman', 'new york', times, serif; "><b><br></b>On 11-12-09 08:16 PM, dave fournier wrote:<br>> Try running it from outside R. It appears to work for me that way.<br>> Of course I'm not saddled with a MAC.<br><br>Ben wrote:<br> The problem is apparently with some of the extra arguments that we<br>decided to use in glmmADMB, in particular -shess -noinit. If you<br>turn these off by adding admb.opts=admbControl(shess=FALSE,noinit=FALSE)<br>then glmmADMB gets all the way
through, albeit with some warnings in<br>one case.<br><br> On the other hand, you get almost the same answer by averaging the<br>Admix value by lake (which is fairly reasonable since the predictor<br>variables are constant per lake) and running a quasibinomial model<br>(which is a quick/cheesy way to get a variance proportional to p*(1-p)<br>and a logistic curve with respect to the predictors) ...<br><br> Watch out for bogus line breaks below.<br><br>adat <- read.table("admix_small_data.txt",header=TRUE, na.strings="na")<br>library(MASS)<br>library(glmmADMB)<br><br>adat <- transform(adat,Lake=reorder(Lake,Admix))<br>library(reshape)<br>am <- melt(adat,id.var=c("Lake","Admix"))<br>library(ggplot2)<br>g1 <-<br>ggplot(am,aes(x=value,y=Admix,colour=Lake))+facet_grid(.~variable,scale="free")+<br> geom_smooth(aes(group=1),method="glm",family="binomial")+theme_bw()+<br>
scale_colour_manual(breaks=levels(am$Lake),<br><br>value=colorRampPalette(colors=c("red","blue"))(length(levels(am$Lake))))<br><br>g1 + geom_boxplot()<br>g1 + stat_summary(fun.data="mean_cl_boot")<br><br>glmm4<-glmmadmb(formula = Admix ~ SDI + (1|Lake), data = adat, family =<br>"beta",<br> admb.opts=admbControl(shess=FALSE,noinit=FALSE))<br><br>glmm4<-glmmadmb(formula = Admix ~ SDI + (1|Lake), data = adat, family =<br>"beta",<br> save.dir="gtmp",admb.opts=admbControl(run=FALSE))<br>glmm4B <- glmmadmb(formula = Admix ~ SDI + (1|Lake), data = adat, family<br>= "beta",<br> save.dir="gtmp",admb.opts=admbControl(run=FALSE))<br><br><br>glmm8<-glmmadmb(formula = Admix ~ pH + (1|Lake), data = adat, family =<br>"beta")<br><br>glmm8 <- glmmadmb(formula = Admix ~ pH + (1|Lake), data =
adat, family =<br>"beta",<br> admb.opts=admbControl(shess=FALSE,noinit=FALSE))<br>## warnings but finishes<br>glmm15<-glmmadmb(formula = Admix ~ StMonth + (1|Lake), data = adat,<br>family = "beta",<br> admb.opts=admbControl(shess=FALSE,noinit=FALSE))<br><br><br>glmmnew <-glmmadmb(formula = Admix ~ pH+ StMonth + SDI + (1|Lake), data<br>= adat, family = "beta",<br> admb.opts=admbControl(shess=FALSE,noinit=FALSE))<br><br>mdat <- ddply(adat,.(Lake),<br> function(x) { with(x,<br> data.frame(Lake=Lake[1],<br>
pH=pH[1],<br> StMonth=StMonth[1],<br>SDI=SDI[1], Admix=mean(Admix)))})<br><br>m2 <- glm(Admix~pH+StMonth+SDI,data=mdat,family=quasibinomial())<br><br>library(betareg)<br>m4 <- betareg(Admix~pH+StMonth+SDI,data=mdat) ## hmmm.<br><br>library(coefplot2)<br>coefplot2(list(glmmnew,m2))<br>_______________________________________________<br>Users mailing list<br><a ymailto="mailto:Users@admb-project.org" href="mailto:Users@admb-project.org">Users@admb-project.org</a><br><a href="http://lists.admb-project.org/mailman/listinfo/users" target="_blank">http://lists.admb-project.org/mailman/listinfo/users</a><br><br><br> </div> </div> </div></body></html>