<html><head><base href="x-msg://18/"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Emma,<div>There are a few possibilities that come to mind...</div><div><br></div><div>Your formula is a bit complicated, maybe too complicated for your data. I recommend thinking carefully about what your really want to include. Do you have 10-20 data points per parameter? </div><div><br></div><div>Also, it is important to recognize that species*btrees*built includes all of the following terms: species+btrees+built+species:btrees+species:built+btrees:built+species:btrees:built (where ":" indicates an interaction). So your formula is redundant.</div><div><br></div><div>Season can only be included as a fixed effect because it has 2 levels (minimum 5 or 6 needed for estimating std of a random effect). Class is on the borderline. </div><div> </div><div>You may want to check <a href="http://glmm.wikidot.com/faq">http://glmm.wikidot.com/faq</a> for a general reference.</div><div><br></div><div>cheers,</div><div>Mollie</div><div><br></div><div><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-variant: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; ">Mollie Brooks<br>Ph.D. Candidate<br>NSF IGERT Fellow<br>Biology Department<br>University of Florida<br><a href="mailto:mbrooks@ufl.edu">mbrooks@ufl.edu</a><br>http://people.biology.ufl.edu/mbrooks<br><br><br><br></span>
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<br><div><div>On 14 Oct 2011, at 6:23 AM, Emma Rosenfeld wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div lang="EN-GB" link="blue" vlink="purple"><div class="Section1" style="page: Section1; "><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 12pt; ">Dear all,<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 12pt; ">I am having some problems trying to run a<span class="Apple-converted-space"> </span></span><span style="font-size: 12pt; ">GLMM<span class="Apple-converted-space"> </span></span><span style="font-size: 12pt; ">model<span class="Apple-converted-space"> </span></span><span style="font-size: 12pt; ">with zero-inflation</span><span style="font-size: 12pt; "><span class="Apple-converted-space"> </span>using the alpha version of glmmADMB (0.6.4) using R (2.13.1) in Windows and I would greatly appreciate some help.<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 12pt; ">My count response variable (number of birds: count) fits a negative binomial distribution and the explanatory variables are both continuous and categorical (species= 17). The three random effects are site (68 of them), season (1 or 2) and land class (1 to 6). Ideally I would also like to build in a variance structure to allow a different spread per land class. This is the model I'm trying to run:<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 10pt; font-family: 'Lucida Console'; ">(fm<-glmmadmb(count~species*btrees+species*built+species*btrees*built+(1|season)+(1|landclass)+(1|site), data=srp12, famil="nbinom", zeroInflation=TRUE))</span><span style="font-size: 10pt; font-family: 'Lucida Console'; "><o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; ">I have read most of the supporting documents to<span class="Apple-converted-space"> </span><span style="font-size: 12pt; ">glmmADMB and studied the examples but am still struggling to make headway.<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 12pt; "><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 12pt; ">This is the error message I get;<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 9pt; font-family: 'Lucida Console'; "><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 10pt; font-family: 'Lucida Console'; ">Memory allocation error -- Perhaps you are trying to allocate too much memory in your program<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 10pt; font-family: 'Lucida Console'; ">Warning: running command 'C:\Windows\system32\cmd.exe /c "C:/R-2.13.1/library/glmmADMB/bin/windows32/glmmadmb.exe" -maxfn 500' had status 1<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 10pt; font-family: 'Lucida Console'; ">Warning in shell(cmd, invisible = TRUE) :<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 10pt; font-family: 'Lucida Console'; "> '"C:/R-2.13.1/library/glmmADMB/bin/windows32/glmmadmb.exe" -maxfn 500' execution failed with error code 1<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 10pt; font-family: 'Lucida Console'; ">Error in glmmadmb(count ~ species * btrees + species * built + species * :<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 10pt; font-family: 'Lucida Console'; "> The function maximizer failed<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 12pt; "><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 12pt; ">I noticed the discussion entitled ‘</span><span style="font-size: 12pt; ">help with glmmADMB 0.6.4 - function maximizer failed’ with Rafael Mares discusses similar problems. I have tried some of the suggested solutions, none of which have been recognised as code in R for some reaason.<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 12pt; "><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 12pt; ">I have also run:<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 12pt; "><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 10pt; font-family: 'Lucida Console'; ">> summary(fm)<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 12pt; "><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 12pt; ">Which results in:<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 12pt; "><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 10pt; font-family: 'Lucida Console'; ">Error in summary(fm) : object 'fm' not found<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 12pt; "><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 12pt; ">This has happened however the equation is labelled.<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 12pt; "><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 12pt; ">Perhaps there is a more appropriate package that I should be using (MCMCglmm)?<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 12pt; ">I am quite new to R, so it is quite possible that I am missing something, so any help would be most appreciated.<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 12pt; "><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 12pt; ">Apologies for the long message!<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 12pt; "><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 12pt; ">Many thanks,<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 12pt; "><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 12pt; ">Emma Rosenfeld<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 12pt; ">PhD student,<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 12pt; ">School of Geography, Earth and Environmental Sciences,<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 12pt; ">University of Birmingham<o:p></o:p></span></div><p class="MsoNormal" style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 10pt; margin-left: 0cm; line-height: 17px; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></p></div>_______________________________________________<br>Users mailing list<br><a href="mailto:Users@admb-project.org" style="color: blue; text-decoration: underline; ">Users@admb-project.org</a><br><a href="http://lists.admb-project.org/mailman/listinfo/users" style="color: blue; text-decoration: underline; ">http://lists.admb-project.org/mailman/listinfo/users</a><br></div></span></blockquote></div><br></div></body></html>