<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Lisa,<div>It looks like you have the syntax wrong. You may want to try</div><div><blockquote type="cite"><div><div style="line-height: normal; margin-top: 0cm; margin-right: 0cm; margin-bottom: 0pt; margin-left: 0cm; "><span style="font-family: 'Courier New'; ">model2<-glmm.admb(aabundm2~babundm2+tramplingf*litterf,random=~1,group="block", data=exp, family='nbinom')</span></div></div></blockquote><div>This wil give each block a random intercept. </div><div><br></div><div>There's a new version coming out soon which has a syntax more familiar to R users.They just need to get the binaries built. See <a href="http://glmmadmb.r-forge.r-project.org/">http://glmmadmb.r-forge.r-project.org/</a> for updates.</div><div>best,</div><div>Mollie</div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: 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; "><div><span class="Apple-style-span" style="font-size: 12px; "><div>Mollie Brooks</div><div>Ph.D. Candidate</div><div>NSF IGERT Fellow</div><div>Biology Department</div><div>University of Florida</div><div><a href="mailto:mbrooks@ufl.edu">mbrooks@ufl.edu</a></div><div><a href="http://www.zoology.ufl.edu/mbrooks">www.zoology.ufl.edu/mbrooks</a></div><div><br></div></span></div></span><br class="Apple-interchange-newline">
</div>
<br><div><div>On 2 Aug 2011, at 3:18 AM, Lisa Denmead wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div><font face="courier new,monospace">Hi,</font></div>
<div><font face="courier new,monospace"></font> </div>
<div><font face="courier new,monospace">Up until earlier today I have been using glmmADMB with no real issues, but now every model I try and run comes up with the error below, even though I have run it with this data before. I have been in contact with some other students using this and they seem to be having the same problem, yet none of us can figure out where we are going wrong. Any advice would be greatly appreciated!</font></div>
<div> </div>
<div><div style="line-height: normal; margin-top: 0cm; margin-right: 0cm; margin-bottom: 0pt; margin-left: 0cm; "><span style="FONT-FAMILY: 'Courier New'">> model2<-glmm.admb(aabundm2~babundm2+tramplingf*litterf,random=~1|block,group="group", data=exp, family='nbinom')</span></div><div style="line-height: normal; margin-top: 0cm; margin-right: 0cm; margin-bottom: 0pt; margin-left: 0cm; "><span style="FONT-FAMILY: 'Courier New'"><span style="mso-spacerun: yes"> </span>1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1</span></div><p style="LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Courier New'"> </span></p><div style="line-height: normal; margin-top: 0cm; margin-right: 0cm; margin-bottom: 0pt; margin-left: 0cm; "><span style="FONT-FAMILY: 'Courier New'"><span style="mso-spacerun: yes"> </span>- final statistics:</span></div><div style="line-height: normal; margin-top: 0cm; margin-right: 0cm; margin-bottom: 0pt; margin-left: 0cm; "><span style="FONT-FAMILY: 'Courier New'">13 variables; iteration 0; function evaluation 0</span></div><div style="line-height: normal; margin-top: 0cm; margin-right: 0cm; margin-bottom: 0pt; margin-left: 0cm; "><span style="FONT-FAMILY: 'Courier New'">Function value -1.#INDe+000; maximum gradient component mag -1.#INDe+000</span></div><div style="line-height: normal; margin-top: 0cm; margin-right: 0cm; margin-bottom: 0pt; margin-left: 0cm; "><span style="FONT-FAMILY: 'Courier New'">Exit code = 0;<span style="mso-spacerun: yes"> </span>converg criter<span style="mso-spacerun: yes"> </span>1.0000e-004</span></div><div style="line-height: normal; margin-top: 0cm; margin-right: 0cm; margin-bottom: 0pt; margin-left: 0cm; "><span style="FONT-FAMILY: 'Courier New'">Var<span style="mso-spacerun: yes"> </span>Value<span style="mso-spacerun: yes"> </span>Gradient<span style="mso-spacerun: yes"> </span>|Var<span style="mso-spacerun: yes"> </span>Value<span style="mso-spacerun: yes"> </span>Gradient<span style="mso-spacerun: yes"> </span>|Var<span style="mso-spacerun: yes"> </span>Value<span style="mso-spacerun: yes"> </span>Gradient<span style="mso-spacerun: yes"> </span></span></div><div style="line-height: normal; margin-top: 0cm; margin-right: 0cm; margin-bottom: 0pt; margin-left: 0cm; "><span style="FONT-FAMILY: 'Courier New'"><span style="mso-spacerun: yes"> </span>1<span style="mso-spacerun: yes"> </span>0.0000 -1.#INDe+000 |<span style="mso-spacerun: yes"> </span>2<span style="mso-spacerun: yes"> </span>0.0000 -1.#INDe+000 |<span style="mso-spacerun: yes"> </span>3<span style="mso-spacerun: yes"> </span>0.0000 -1.#INDe+000</span></div><div style="line-height: normal; margin-top: 0cm; margin-right: 0cm; margin-bottom: 0pt; margin-left: 0cm; "><span style="FONT-FAMILY: 'Courier New'"><span style="mso-spacerun: yes"> </span>4<span style="mso-spacerun: yes"> </span>0.0000 -1.#INDe+000 |<span style="mso-spacerun: yes"> </span>5<span style="mso-spacerun: yes"> </span>0.0000 -1.#INDe+000 |<span style="mso-spacerun: yes"> </span>6<span style="mso-spacerun: yes"> </span>0.0000 -1.#INDe+000</span></div><div style="line-height: normal; margin-top: 0cm; margin-right: 0cm; margin-bottom: 0pt; margin-left: 0cm; "><span style="FONT-FAMILY: 'Courier New'"><span style="mso-spacerun: yes"> </span>7<span style="mso-spacerun: yes"> </span>0.0000 -1.#INDe+000 |<span style="mso-spacerun: yes"> </span>8<span style="mso-spacerun: yes"> </span>0.0000 -1.#INDe+000 |<span style="mso-spacerun: yes"> </span>9<span style="mso-spacerun: yes"> </span>0.0000 -1.#INDe+000</span></div><div style="line-height: normal; margin-top: 0cm; margin-right: 0cm; margin-bottom: 0pt; margin-left: 0cm; "><span style="FONT-FAMILY: 'Courier New'"><span style="mso-spacerun: yes"> </span>10<span style="mso-spacerun: yes"> </span>0.0000 -1.#INDe+000 | 11<span style="mso-spacerun: yes"> </span>0.0000 -1.#INDe+000 | 12<span style="mso-spacerun: yes"> </span>0.0000 -1.#INDe+000</span></div><div style="line-height: normal; margin-top: 0cm; margin-right: 0cm; margin-bottom: 0pt; margin-left: 0cm; "><span style="FONT-FAMILY: 'Courier New'"><span style="mso-spacerun: yes"> </span>13<span style="mso-spacerun: yes"> </span>0.0000 -1.#INDe+000 |</span></div><p style="LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Courier New'"> </span></p><div style="line-height: normal; margin-top: 0cm; margin-right: 0cm; margin-bottom: 0pt; margin-left: 0cm; "><span style="FONT-FAMILY: 'Courier New'"><span style="mso-spacerun: yes"> </span>- final statistics:</span></div><div style="line-height: normal; margin-top: 0cm; margin-right: 0cm; margin-bottom: 0pt; margin-left: 0cm; "><span style="FONT-FAMILY: 'Courier New'">13 variables; iteration 0; function evaluation 0</span></div><div style="line-height: normal; margin-top: 0cm; margin-right: 0cm; margin-bottom: 0pt; margin-left: 0cm; "><span style="FONT-FAMILY: 'Courier New'">Function value -1.#INDe+000; maximum gradient component mag -1.#INDe+000</span></div><div style="line-height: normal; margin-top: 0cm; margin-right: 0cm; margin-bottom: 0pt; margin-left: 0cm; "><span style="FONT-FAMILY: 'Courier New'">Exit code = 0;<span style="mso-spacerun: yes"> </span>converg criter<span style="mso-spacerun: yes"> </span>1.0000e-004</span></div><div style="line-height: normal; margin-top: 0cm; margin-right: 0cm; margin-bottom: 0pt; margin-left: 0cm; "><span style="FONT-FAMILY: 'Courier New'">Var<span style="mso-spacerun: yes"> </span>Value<span style="mso-spacerun: yes"> </span>Gradient<span style="mso-spacerun: yes"> </span>|Var<span style="mso-spacerun: yes"> </span>Value<span style="mso-spacerun: yes"> </span>Gradient<span style="mso-spacerun: yes"> </span>|Var<span style="mso-spacerun: yes"> </span>Value<span style="mso-spacerun: yes"> </span>Gradient<span style="mso-spacerun: yes"> </span></span></div><div style="line-height: normal; margin-top: 0cm; margin-right: 0cm; margin-bottom: 0pt; margin-left: 0cm; "><span style="FONT-FAMILY: 'Courier New'"><span style="mso-spacerun: yes"> </span>1<span style="mso-spacerun: yes"> </span>0.0000 -1.#INDe+000 |<span style="mso-spacerun: yes"> </span>2<span style="mso-spacerun: yes"> </span>0.0000 -1.#INDe+000 |<span style="mso-spacerun: yes"> </span>3<span style="mso-spacerun: yes"> </span>0.0000 -1.#INDe+000</span></div><div style="line-height: normal; margin-top: 0cm; margin-right: 0cm; margin-bottom: 0pt; margin-left: 0cm; "><span style="FONT-FAMILY: 'Courier New'"><span style="mso-spacerun: yes"> </span>4<span style="mso-spacerun: yes"> </span>0.0000 -1.#INDe+000 |<span style="mso-spacerun: yes"> </span>5<span style="mso-spacerun: yes"> </span>0.0000 -1.#INDe+000 |<span style="mso-spacerun: yes"> </span>6<span style="mso-spacerun: yes"> </span>0.0000 -1.#INDe+000</span></div><div style="line-height: normal; margin-top: 0cm; margin-right: 0cm; margin-bottom: 0pt; margin-left: 0cm; "><span style="FONT-FAMILY: 'Courier New'"><span style="mso-spacerun: yes"> </span>7<span style="mso-spacerun: yes"> </span>0.0000 -1.#INDe+000 |<span style="mso-spacerun: yes"> </span>8<span style="mso-spacerun: yes"> </span>0.0000 -1.#INDe+000 |<span style="mso-spacerun: yes"> </span>9<span style="mso-spacerun: yes"> </span>0.0000 -1.#INDe+000</span></div><div style="line-height: normal; margin-top: 0cm; margin-right: 0cm; margin-bottom: 0pt; margin-left: 0cm; "><span style="FONT-FAMILY: 'Courier New'"><span style="mso-spacerun: yes"> </span>10<span style="mso-spacerun: yes"> </span>0.0000 -1.#INDe+000 | 11<span style="mso-spacerun: yes"> </span>0.0000 -1.#INDe+000 | 12<span style="mso-spacerun: yes"> </span>0.0000 -1.#INDe+000</span></div><div style="line-height: normal; margin-top: 0cm; margin-right: 0cm; margin-bottom: 0pt; margin-left: 0cm; "><span style="FONT-FAMILY: 'Courier New'"><span style="mso-spacerun: yes"> </span>13<span style="mso-spacerun: yes"> </span>0.0000 -1.#INDe+000 |</span></div><div style="line-height: normal; margin-top: 0cm; margin-right: 0cm; margin-bottom: 0pt; margin-left: 0cm; "><span style="FONT-FAMILY: 'Courier New'"><span style="mso-spacerun: yes"> </span>inner maxg = -1.#IO<span style="mso-spacerun: yes"> </span>Inner f = -1.#IO</span></div><div style="line-height: normal; margin-top: 0cm; margin-right: 0cm; margin-bottom: 0pt; margin-left: 0cm; "><span style="FONT-FAMILY: 'Courier New'"><span style="mso-spacerun: yes"> </span>f = -1.#IND max g = 1.#QNAN</span></div><div style="line-height: normal; margin-top: 0cm; margin-right: 0cm; margin-bottom: 0pt; margin-left: 0cm; "><span style="FONT-FAMILY: 'Courier New'">Newton raphson 1<span style="mso-spacerun: yes"> </span>Error in matrix inverse -- matrix singular in inv(dmatrix)</span></div><div style="line-height: normal; margin-top: 0cm; margin-right: 0cm; margin-bottom: 0pt; margin-left: 0cm; "><span style="FONT-FAMILY: 'Courier New'">Error in matrix inverse -- matrix singular in inv(dmatrix)</span></div><div style="line-height: normal; margin-top: 0cm; margin-right: 0cm; margin-bottom: 0pt; margin-left: 0cm; "><span style="FONT-FAMILY: 'Courier New'">Error in glmm.admb(aabundm2 ~ babundm2 + tramplingf * litterf, random = ~1 |<span style="mso-spacerun: yes"> </span>: </span></div><div style="line-height: normal; margin-top: 0cm; margin-right: 0cm; margin-bottom: 0pt; margin-left: 0cm; "><span style="FONT-FAMILY: 'Courier New'"><span style="mso-spacerun: yes"> </span>The function maximizer failed</span></div><div style="line-height: normal; margin-top: 0cm; margin-right: 0cm; margin-bottom: 0pt; margin-left: 0cm; "><span style="FONT-FAMILY: 'Courier New'">In addition: Warning messages:</span></div><div style="line-height: normal; margin-top: 0cm; margin-right: 0cm; margin-bottom: 0pt; margin-left: 0cm; "><span style="FONT-FAMILY: 'Courier New'">1: running command 'C:\Windows\system32\cmd.exe /c "C:/Users/20731259/Documents/R/win-library/2.13/glmmADMB/bin/windows/nbmm.exe" -maxfn 500 ' had status 1 </span></div><div style="line-height: normal; margin-top: 0cm; margin-right: 0cm; margin-bottom: 0pt; margin-left: 0cm; "><span style="FONT-FAMILY: 'Courier New'">2: In shell(cmd, invisible = TRUE) :</span></div><div style="line-height: normal; margin-top: 0cm; margin-right: 0cm; margin-bottom: 0pt; margin-left: 0cm; "><span style="FONT-FAMILY: 'Courier New'"><span style="mso-spacerun: yes"> </span>'"C:/Users/20731259/Documents/R/win-library/2.13/glmmADMB/bin/windows/nbmm.exe" -maxfn 500 ' execution failed with error code 1</span></div><p style="LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Courier New'"></span> </p><div style="line-height: normal; margin-top: 0cm; margin-right: 0cm; margin-bottom: 0pt; margin-left: 0cm; "><span style="FONT-FAMILY: 'Courier New'">Thanks,Lisa</span></div></div>
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