[ADMB Users] ADMB error- function maximizer failed (couldnt find STD file)
Mollie Brooks
mbrooks at ufl.edu
Tue Sep 4 10:07:26 PDT 2012
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.
Mollie Brooks
Postdoctoral Researcher, Ponciano Lab
Biology Department, University of Florida
http://people.biology.ufl.edu/mbrooks
On 4 Sep 2012, at 12:59 PM, Nathan Svoboda wrote:
> Hi Mollie,
>
> 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.
>
> 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.
>
> > head(FAWNS)
> 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
> > summary(FAWNS)
> 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
>
> I added the "Verbose=TRUE" and "mcmc=FALSE" statements and received an error.
> Code:
> fit_zipoiss <- glmmadmb(LOCS~D_ROADS + (1|YEAR) , data=FAWNS, zeroInflation=TRUE, family="poisson", Verbose=TRUE, mcmc=FALSE)
>
> Error:
> Error in glmmadmb(LOCS ~ D_ROADS + (1 | YEAR), data = FAWNS, zeroInflation = TRUE, :
> unused argument(s) (Verbose = TRUE)
>
> Thank you!!
>
> Nate
>
>
> Nathan Svoboda
> Graduate Research Assistant
> Mississippi State University
>
>
> Carnivore Ecology Lab
> Mississippi State University
> College of Forest Resources
> 775 Stone Blvd
> 251 Thompson Hall Box 9690
> Mississippi State, MS 39762
> Cell: (231) 350-1397
> Fax: (662) 325-8750
> Email: nsvoboda at cfr.msstate.edu
>
> Project Website: http://www.fwrc.msstate.edu/carnivore/predatorprey/index.asp
>
>
> From: Mollie Brooks [mailto:mbrooks at ufl.edu]
> Sent: Tue 9/4/2012 11:48 AM
> To: Nathan Svoboda
> Subject: Re: [ADMB Users] ADMB error- function maximizer failed (couldnt find STD file)
>
> Hi Nate,
> Could you provide the output from head(FAWNS) and/or summary(FAWNS)?
>
> Also, run the model with verbose=TRUE and mcmc=FALSE and provide the output.
> thanks,
> Mollie
>
> Mollie Brooks
> Postdoctoral Researcher, Ponciano Lab
> Biology Department, University of Florida
> http://people.biology.ufl.edu/mbrooks
>
>
> On 4 Sep 2012, at 12:32 PM, Nathan Svoboda wrote:
>
>> Greetings glmmADMB users,
>>
>> 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"):
>> fit_zipoiss1 <- glmmadmb(LOCS~D_ROADS + (1|YEAR) , data=FAWNS, zeroInflation=TRUE, family="poisson", mcmc=TRUE)
>> I get the error:
>> Error in glmmadmb(LOCS ~ D_ROADS + (1 | YEAR), data = FAWNS, zeroInflation = TRUE, :
>> The function maximizer failed (couldn't find STD file)
>>
>> I tried setting the number of mcmc iterations by running the following code:
>> fit_zipoiss <- glmmadmb(LOCS~D_ROADS + (1|YEAR) , data=FAWNS, zeroInflation=TRUE,
>> family="poisson", mcmc=TRUE, mcmc.opts=mcmcControl(mcmc=50000))
>> but again received the same "Function maximizer...." error.
>>
>> 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. As 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.
>>
>> 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?
>>
>> Any suggestions would be very much appreciated. Thank you for your time.
>>
>> Nate Svoboda
>>
>>
>> Nathan Svoboda
>> Graduate Research Assistant
>> Mississippi State University
>>
>>
>> Carnivore Ecology Lab
>> Mississippi State University
>> College of Forest Resources
>> 775 Stone Blvd
>> 251 Thompson Hall Box 9690
>> Mississippi State, MS 39762
>> Cell: (231) 350-1397
>> Fax: (662) 325-8750
>> Email: nsvoboda at cfr.msstate.edu
>>
>> Project Website: http://www.fwrc.msstate.edu/carnivore/predatorprey/index.asp
>>
>> _______________________________________________
>> Users mailing list
>> Users at admb-project.org
>> http://lists.admb-project.org/mailman/listinfo/users
>
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