<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>I didn't reply on the thread because the ADMB users list prefers to not get questions that are specific to glmmadmb and not ADMB. So I'm trying to first check if the problem is specific to R or mixed models before we get the ADMB people involved.</div><div><br></div><div><div><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); 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; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: 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; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Mollie Brooks<br>Postdoctoral Researcher, Ponciano Lab<br>Biology Department, University of Florida<br><a href="http://people.biology.ufl.edu/mbrooks">http://people.biology.ufl.edu/mbrooks</a><br><br></div></span></span>
</div>
<br><div><div>On 4 Sep 2012, at 12:59 PM, Nathan Svoboda wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">
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<div dir="ltr"><font color="#000000" size="2" face="Arial">Hi Mollie,</font></div>
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<div dir="ltr"><font size="2" face="Arial">Wow, thanks for your fast reply!! If I am not responding to this properly please let me know as I am not exactly sure how to reply to the thread.</font></div>
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<div dir="ltr"><font size="2" face="Arial">Here is the output you requested. Please know that this is a very, very small portion of my data (2%). My entire data set is extremely large and must be ran on a "super computer". Sorry I didn't make that clear in my previous post. Thanks. In additon, you will notice in this output there are a number of other variables that were not used in the model. As suggested by others, I tried running a very simple model first (1 parameter [D_ROADS]). The data is also centered and standardized.</font></div>
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<div dir="ltr"><font size="2" face="Arial"><span style="widows: 2; text-transform: none; background-color: rgb(225, 226, 229); text-indent: 0px; letter-spacing: normal; border-collapse: separate; font: normal normal normal 13px/15px 'Lucida Console'; white-space: pre-wrap; orphans: 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; " class="Apple-style-span"><pre style="BORDER-BOTTOM-STYLE: none; LINE-HEIGHT: 1.2; MARGIN: 0px; OUTLINE-STYLE: none; OUTLINE-COLOR: ; BORDER-LEFT-STYLE: none; FONT-FAMILY: 'Lucida Console'; WHITE-SPACE: pre-wrap !important; BORDER-TOP-STYLE: none; BORDER-RIGHT-STYLE: none; FONT-SIZE: 10pt !important" class="GDXA2EVBEAB" tabindex="0"><span style="WHITE-SPACE: pre; COLOR: blue" class="GDXA2EVBHAB ace_keyword">> </span><span style="COLOR: blue" class="GDXA2EVBL5 ace_keyword">head(FAWNS)
</span> GRID LOCS ID SEASON YEAR LCOVER D_ROADS D_WATER D_EDGE D_CROPS D_GRASS D_PASTURE C_D_ROADS St_D_ROADS C_D_WATER
1 423504 0 F052 1 B 4 256.4013 1196.771 125.404 1048.366 339.9444 189.5776 -126.9503 -0.3887686 676.4331
2 423504 0 F100 1 C 4 256.4013 1196.771 125.404 1048.366 339.9444 189.5776 -126.9503 -0.3887686 676.4331
3 423504 0 F002 1 A 4 256.4013 1196.771 125.404 1048.366 339.9444 189.5776 -126.9503 -0.3887686 676.4331
4 423504 0 F096 1 C 4 256.4013 1196.771 125.404 1048.366 339.9444 189.5776 -126.9503 -0.3887686 676.4331
5 423504 0 F056 1 B 4 256.4013 1196.771 125.404 1048.366 339.9444 189.5776 -126.9503 -0.3887686 676.4331
6 423504 0 F004 1 A 4 256.4013 1196.771 125.404 1048.366 339.9444 189.5776 -126.9503 -0.3887686 676.4331
St_D_WATER C_D_EDGE St_D_EDGE C_D_CROPS St_D_CROPS C_D_GRASS St_D_GRASS C_D_PASTURE St_D_PASTURE
1 1.551042 58.35901 0.6745019 -567.5301 -0.4225448 -235.4515 -0.4788633 -1472.005 -0.8576336
2 1.551042 58.35901 0.6745019 -567.5301 -0.4225448 -235.4515 -0.4788633 -1472.005 -0.8576336
3 1.551042 58.35901 0.6745019 -567.5301 -0.4225448 -235.4515 -0.4788633 -1472.005 -0.8576336
4 1.551042 58.35901 0.6745019 -567.5301 -0.4225448 -235.4515 -0.4788633 -1472.005 -0.8576336
5 1.551042 58.35901 0.6745019 -567.5301 -0.4225448 -235.4515 -0.4788633 -1472.005 -0.8576336
6 1.551042 58.35901 0.6745019 -567.5301 -0.4225448 -235.4515 -0.4788633 -1472.005 -0.8576336
<span style="WHITE-SPACE: pre; COLOR: blue" class="GDXA2EVBHAB ace_keyword">> </span><span style="COLOR: blue" class="GDXA2EVBL5 ace_keyword">summary(FAWNS)
</span> GRID LOCS ID SEASON YEAR LCOVER D_ROADS
Min. : 423504 Min. :0.0000000 F001 : 95538 Min. :1 A:573228 Min. :1.000 Min. : 0.0018
1st Qu.: 715519 1st Qu.:0.0000000 F002 : 95538 1st Qu.:1 B:573228 1st Qu.:3.000 1st Qu.: 135.5950
Median : 827524 Median :0.0000000 F003 : 95538 Median :1 C:573228 Median :4.000 Median : 298.2452
Mean : 813639 Mean :0.0001483 F004 : 95538 Mean :1 Mean :3.571 Mean : 383.3516
3rd Qu.: 947406 3rd Qu.:0.0000000 F005 : 95538 3rd Qu.:1 3rd Qu.:4.000 3rd Qu.: 535.0293
Max. :1075786 Max. :3.0000000 F006 : 95538 Max. :1 Max. :9.000 Max. :1880.4748
(Other):1146456
D_WATER D_EDGE D_CROPS D_GRASS D_PASTURE C_D_ROADS St_D_ROADS
Min. : 0.0027 Min. : 0.00 Min. : 0.0 Min. : 0.0 Min. : 0.0 Min. :-383.35 Min. :-1.1740
1st Qu.: 180.2651 1st Qu.: 12.56 1st Qu.: 556.6 1st Qu.: 223.3 1st Qu.: 256.8 1st Qu.:-247.76 1st Qu.:-0.7587
Median : 407.5491 Median : 33.88 Median :1228.0 Median : 441.5 Median :1039.2 Median : -85.11 Median :-0.2606
Mean : 520.3377 Mean : 67.05 Mean :1615.9 Mean : 575.4 Mean :1661.6 Mean : 0.00 Mean : 0.0000
3rd Qu.: 748.8116 3rd Qu.: 85.71 3rd Qu.:2394.4 3rd Qu.: 790.4 3rd Qu.:2669.7 3rd Qu.: 151.68 3rd Qu.: 0.4645
Max. :2561.0986 Max. :782.55 Max. :6939.0 Max. :3153.1 Max. :7620.8 Max. :1497.12 Max. : 4.5847
C_D_WATER St_D_WATER C_D_EDGE St_D_EDGE C_D_CROPS St_D_CROPS C_D_GRASS
Min. :-520.3 Min. :-1.1931 Min. :-67.05 Min. :-0.7749 Min. :-1615.9 Min. :-1.2031 Min. :-575.4
1st Qu.:-340.1 1st Qu.:-0.7798 1st Qu.:-54.48 1st Qu.:-0.6297 1st Qu.:-1059.3 1st Qu.:-0.7887 1st Qu.:-352.1
Median :-112.8 Median :-0.2586 Median :-33.16 Median :-0.3833 Median : -387.9 Median :-0.2888 Median :-133.9
Mean : 0.0 Mean : 0.0000 Mean : 0.00 Mean : 0.0000 Mean : 0.0 Mean : 0.0000 Mean : 0.0
3rd Qu.: 228.5 3rd Qu.: 0.5239 3rd Qu.: 18.67 3rd Qu.: 0.2158 3rd Qu.: 778.6 3rd Qu.: 0.5797 3rd Qu.: 215.0
Max. :2040.8 Max. : 4.6794 Max. :715.51 Max. : 8.2697 Max. : 5323.1 Max. : 3.9633 Max. :2577.7
St_D_GRASS C_D_PASTURE St_D_PASTURE
Min. :-1.1702 Min. :-1661.6 Min. :-0.9681
1st Qu.:-0.7161 1st Qu.:-1404.8 1st Qu.:-0.8185
Median :-0.2724 Median : -622.4 Median :-0.3626
Mean : 0.0000 Mean : 0.0 Mean : 0.0000
3rd Qu.: 0.4373 3rd Qu.: 1008.1 3rd Qu.: 0.5874
Max. : 5.2425 Max. : 5959.2 Max. : 3.4720 </pre></span></font></div>
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<div>I added the "Verbose=TRUE" and "mcmc=FALSE" statements and received an error.</div>
<div>Code:<span style="widows: 2; text-transform: none; background-color: rgb(225, 226, 229); text-indent: 0px; letter-spacing: normal; border-collapse: separate; font: normal normal normal 13px/15px 'Lucida Console'; white-space: pre-wrap; orphans: 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; " class="Apple-style-span"><pre style="BORDER-BOTTOM-STYLE: none; LINE-HEIGHT: 1.2; MARGIN: 0px; OUTLINE-STYLE: none; OUTLINE-COLOR: ; BORDER-LEFT-STYLE: none; FONT-FAMILY: 'Lucida Console'; WHITE-SPACE: pre-wrap !important; BORDER-TOP-STYLE: none; BORDER-RIGHT-STYLE: none; FONT-SIZE: 10pt !important" class="GDXA2EVBEAB" tabindex="0"><span style="COLOR: blue" class="GDXA2EVBL5 ace_keyword">fit_zipoiss <- glmmadmb(LOCS~D_ROADS + (1|YEAR) , data=FAWNS, zeroInflation=TRUE, family="poisson", Verbose=TRUE, mcmc=FALSE)</span></pre></span></div>
<div> </div>
<div>Error: <span style="widows: 2; text-transform: none; background-color: rgb(225, 226, 229); text-indent: 0px; letter-spacing: normal; border-collapse: separate; font: normal normal normal 13px/15px 'Lucida Console'; white-space: pre-wrap; orphans: 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; " class="Apple-style-span"><pre style="BORDER-BOTTOM-STYLE: none; LINE-HEIGHT: 1.2; MARGIN: 0px; OUTLINE-STYLE: none; OUTLINE-COLOR: ; BORDER-LEFT-STYLE: none; FONT-FAMILY: 'Lucida Console'; WHITE-SPACE: pre-wrap !important; BORDER-TOP-STYLE: none; BORDER-RIGHT-STYLE: none; FONT-SIZE: 10pt !important" class="GDXA2EVBEAB" tabindex="0"><span class="GDXA2EVBP5">Error in glmmadmb(LOCS ~ D_ROADS + (1 | YEAR), data = FAWNS, zeroInflation = TRUE, :
unused argument(s) (Verbose = TRUE)</span></pre></span></div>
<div><font color="#000000" size="2" face="Arial"></font> </div>
<div><font color="#000000" size="2" face="Arial">Thank you!!</font></div>
<div><font size="2" face="Arial"></font> </div>
<div><font size="2" face="Arial">Nate</font></div>
<div><font size="2" face="Arial"></font> </div>
<div><font color="#000000" size="2" face="Arial"></font> </div>
<div><font color="#000000" size="2" face="Arial">Nathan Svoboda</font></div>
<div><font size="2" face="Arial">Graduate Research Assistant</font></div>
<div><font size="2" face="Arial">Mississippi State University</font></div>
<div><font size="2" face="Arial"></font> </div>
<div> </div>
<div><font size="2" face="Arial">Carnivore Ecology Lab</font></div>
<div><font size="2" face="Arial">Mississippi State University</font></div>
<div><font size="2" face="Arial">College of Forest Resources </font></div>
<div><font size="2" face="Arial">775 Stone Blvd</font></div>
<div><font size="2" face="Arial">251 Thompson Hall Box 9690</font></div>
<div><font size="2" face="Arial">Mississippi State, MS 39762<br>Cell: (231) 350-1397<br>Fax: (662) 325-8750 </font></div>
<div><font size="2" face="Arial">Email: <a href="mailto:nsvoboda@cfr.msstate.edu">nsvoboda@cfr.msstate.edu</a></font></div>
<div><font size="2" face="Arial"></font> </div>
<div><font size="2" face="Arial">Project Website: <a href="http://www.fwrc.msstate.edu/carnivore/predatorprey/index.asp"><font color="#0000ff">http://www.fwrc.msstate.edu/carnivore/predatorprey/index.asp</font></a></font></div>
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<font size="2" face="Tahoma"><b>From:</b> Mollie Brooks [mailto:mbrooks@ufl.edu]<br><b>Sent:</b> Tue 9/4/2012 11:48 AM<br><b>To:</b> Nathan Svoboda<br><b>Subject:</b> Re: [ADMB Users] ADMB error- function maximizer failed (couldnt find STD file)<br></font><br></div>
<div>Hi Nate,
<div>
<div>Could you provide the output from head(FAWNS) and/or summary(FAWNS)?</div>
<div><br></div>
<div>Also, run the model with verbose=TRUE and mcmc=FALSE and provide the output.</div>
<div>thanks,</div>
<div>Mollie</div>
<div><br></div>
<div>
<div><span style="widows: 2; text-transform: none; text-indent: 0px; letter-spacing: normal; border-collapse: separate; font: normal normal normal medium/normal Helvetica; white-space: normal; orphans: 2; word-spacing: 0px; " class="Apple-style-span"><span style="widows: 2; text-transform: none; text-indent: 0px; letter-spacing: normal; border-collapse: separate; font: normal normal normal medium/normal Helvetica; white-space: normal; orphans: 2; word-spacing: 0px; " class="Apple-style-span">
<div style="WORD-WRAP: break-word">Mollie Brooks<br>Postdoctoral Researcher, Ponciano Lab<br>Biology Department, University of Florida<br><a href="http://people.biology.ufl.edu/mbrooks">http://people.biology.ufl.edu/mbrooks</a><br><br></div></span></span></div><br>
<div>
<div>On 4 Sep 2012, at 12:32 PM, Nathan Svoboda wrote:</div><br class="Apple-interchange-newline">
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<div dir="ltr"><font color="#000000" size="2" face="Arial">Greetings glmmADMB users,</font></div>
<div dir="ltr"><font size="2" face="Arial"></font> </div>
<div dir="ltr"><font size="2" face="Arial">I am trying to run a series of models using the glmmADMB function with several different distribution families (e.g., poisson, negbinom). I am using a Optiplex 790 PC with Windows 7, 16.0 GB of RAM and a 64-bit operating system. I am running R version 2.15.0 and started out using the most recent version of glmmADMB (I believe version 7.2.15). My data is zero inflated count data that is overdispersed. When I ran the following code for either a zero inflated poisson (family="poisson") or a neg binomial (i.e., family="nbinom"):</font></div>
<div dir="ltr"><font size="2">fit_zipoiss1 <- glmmadmb(LOCS~D_ROADS + (1|YEAR) , data=FAWNS, zeroInflation=TRUE, family="poisson", mcmc=TRUE)</font></div>
<div dir="ltr"><font color="#000000" size="2" face="Arial">I get the error: <span style="WIDOWS: 2; TEXT-TRANSFORM: none; BACKGROUND-COLOR: rgb(225,226,229); TEXT-INDENT: 0px; LETTER-SPACING: normal; BORDER-COLLAPSE: separate; FONT: 13px/15px 'Lucida Console'; WHITE-SPACE: pre-wrap; ORPHANS: 2; WORD-SPACING: 0px" class="Apple-style-span"><pre style="BORDER-BOTTOM-STYLE: none; LINE-HEIGHT: 1.2; MARGIN: 0px; OUTLINE-STYLE: none; BORDER-LEFT-STYLE: none; FONT-FAMILY: 'Lucida Console'; WHITE-SPACE: pre-wrap; BORDER-TOP-STYLE: none; BORDER-RIGHT-STYLE: none; FONT-SIZE: 10pt" class="GDXA2EVBEAB" tabindex="0"><span class="GDXA2EVBP5">Error in glmmadmb(LOCS ~ D_ROADS + (1 | YEAR), data = FAWNS, zeroInflation = TRUE, :</span></pre></span><span style="WIDOWS: 2; TEXT-TRANSFORM: none; BACKGROUND-COLOR: rgb(225,226,229); TEXT-INDENT: 0px; LETTER-SPACING: normal; BORDER-COLLAPSE: separate; FONT: 13px/15px 'Lucida Console'; WHITE-SPACE: pre-wrap; ORPHANS: 2; WORD-SPACING: 0px" class="Apple-style-span"><pre style="BORDER-BOTTOM-STYLE: none; LINE-HEIGHT: 1.2; MARGIN: 0px; OUTLINE-STYLE: none; BORDER-LEFT-STYLE: none; FONT-FAMILY: 'Lucida Console'; WHITE-SPACE: pre-wrap; BORDER-TOP-STYLE: none; BORDER-RIGHT-STYLE: none; FONT-SIZE: 10pt" class="GDXA2EVBEAB" tabindex="0"><span class="GDXA2EVBP5">The function maximizer failed (couldn't find STD file)</span></pre></span></font></div>
<div dir="ltr"><font size="2" face="Arial"></font> </div>
<div dir="ltr"><font size="2" face="Arial">I tried setting the number of mcmc iterations by running the following code: <span style="WIDOWS: 2; TEXT-TRANSFORM: none; BACKGROUND-COLOR: rgb(225,226,229); TEXT-INDENT: 0px; LETTER-SPACING: normal; BORDER-COLLAPSE: separate; FONT: 13px/15px 'Lucida Console'; WHITE-SPACE: pre-wrap; ORPHANS: 2; WORD-SPACING: 0px" class="Apple-style-span"><span style="COLOR: blue" class="GDXA2EVBL5 ace_keyword"><span style="WIDOWS: 2; TEXT-TRANSFORM: none; BACKGROUND-COLOR: rgb(225,226,229); TEXT-INDENT: 0px; LETTER-SPACING: normal; BORDER-COLLAPSE: separate; FONT: 13px/15px 'Lucida Console'; WHITE-SPACE: pre-wrap; ORPHANS: 2; WORD-SPACING: 0px" class="Apple-style-span"><pre style="BORDER-BOTTOM-STYLE: none; LINE-HEIGHT: 1.2; MARGIN: 0px; OUTLINE-STYLE: none; BORDER-LEFT-STYLE: none; FONT-FAMILY: 'Lucida Console'; WHITE-SPACE: pre-wrap; BORDER-TOP-STYLE: none; BORDER-RIGHT-STYLE: none; FONT-SIZE: 10pt" class="GDXA2EVBEAB" tabindex="0"><span style="COLOR: blue" class="GDXA2EVBL5 ace_keyword">fit_zipoiss <- glmmadmb(LOCS~D_ROADS + (1|YEAR) , data=FAWNS, zeroInflation=TRUE, </span></pre><pre style="BORDER-BOTTOM-STYLE: none; LINE-HEIGHT: 1.2; MARGIN: 0px; OUTLINE-STYLE: none; BORDER-LEFT-STYLE: none; FONT-FAMILY: 'Lucida Console'; WHITE-SPACE: pre-wrap; BORDER-TOP-STYLE: none; BORDER-RIGHT-STYLE: none; FONT-SIZE: 10pt" class="GDXA2EVBEAB" tabindex="0"><span style="COLOR: blue" class="GDXA2EVBL5 ace_keyword">family="poisson", mcmc=TRUE, mcmc.opts=mcmcControl(mcmc=50000))</span></pre></span></span></span></font><font size="2" face="Arial">but again received the same "Function maximizer...." error. </font></div>
<div dir="ltr"><font size="2" face="Arial"></font> </div>
<div dir="ltr"><font size="2" face="Arial">As suggested by previous users (specifically Ben Bolker) I downloaded an earlier version of glmmADMB ("glmmADMB_0.7.tar.gz") and re-ran the same models (e.g., poisson and neg. binomial) and received the same error. A</font><font size="2" face="Arial">s suggested by Mr. Bolker and others I also tried running both a poisson and neg. binomial model with "admb.opts=admbControl(shess=FALSE,noinit=FALSE) " and received the same error.</font></div>
<div dir="ltr"><font size="2" face="Arial"></font> </div>
<div dir="ltr"><font size="2" face="Arial">I am not sure if an even older version of glmmADMB (i.e., glmmADMB v. 0.6.5) would work as it seems to have worked for others but I am unsure of where I can find this version?</font></div>
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<div dir="ltr"><font size="2" face="Arial">Any suggestions would be very much appreciated. Thank you for your time.</font></div>
<div dir="ltr"> </div>
<div dir="ltr"><font size="2" face="Arial">Nate Svoboda</font> </div></div>
<div dir="ltr" id="idSignature690">
<div> </div>
<div><font size="2" face="Arial"></font> </div>
<div><font size="2" face="Arial">Nathan Svoboda</font></div>
<div><font size="2" face="Arial">Graduate Research Assistant</font></div>
<div><font size="2" face="Arial">Mississippi State University</font></div>
<div><font size="2" face="Arial"></font> </div>
<div> </div>
<div><font size="2" face="Arial">Carnivore Ecology Lab</font></div>
<div><font size="2" face="Arial">Mississippi State University</font></div>
<div><font size="2" face="Arial">College of Forest Resources </font></div>
<div><font size="2" face="Arial">775 Stone Blvd</font></div>
<div><font size="2" face="Arial">251 Thompson Hall Box 9690</font></div>
<div><font size="2" face="Arial">Mississippi State, MS 39762<br>Cell: (231) 350-1397<br>Fax: (662) 325-8750 </font></div>
<div><font size="2" face="Arial">Email: <a href="mailto:nsvoboda@cfr.msstate.edu">nsvoboda@cfr.msstate.edu</a></font></div>
<div><font size="2" face="Arial"></font> </div>
<div><font size="2" face="Arial">Project Website: <a href="http://www.fwrc.msstate.edu/carnivore/predatorprey/index.asp"><font color="#0000ff">http://www.fwrc.msstate.edu/carnivore/predatorprey/index.asp</font></a></font></div>
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