[R-sig-ME] glmmADMB troubles

[Ben Bolker]

On 13-02-28 01:15 PM, Ross Boylan wrote:
> On 2/27/2013 8:05 PM, Ben Bolker wrote:
>> Ross Boylan <ross at ...> writes:
>>
>>> It seems it's one thing after another.  Ben suggested glmmADMB for
>>> poisson--actually for truncated poisson, but for now I'm just trying to
>>> get anything going.  Some of my count variables have 1, not 0 as a
>>> minimum, and some have a maximum too, e.g., all values >10 are reported
>>> as 10.
>>    If you have enough data to make it worthwhile, you might try the
>> 'ordinal' package ...
> Thanks for the pointer.  Does it make the proportional odds assumption?
>>
>>> I was able to install it from r-forge, with a warning that it was build
>>> for 2.15.3.  But ...
>>>

  [snip]

>>> Figuring that its missing value handling might be off,

  Yes. I might be able to fix the NA-handling, but given that I am
fairly sure that this error means an NA problem, I have taken the lazy
way out and advised the user that this means they have to deal with NAs
themselves.

>> I tried
>>> removing the
>> missing values:
>>>> r <- glmmadmb(sexActs~(1|id), sexpartner[!is.na(sexpartner$sexActs),])
>>> Error in system(cmd, intern = intern, wait = wait | intern,
>> show.output.on.console = wait,  :
>>>     'C:/Program' not found
>>>> traceback()
>>> 4: system(cmd, intern = intern, wait = wait | intern,
>>> show.output.on.console =
>> wait,
>>>          ...)
>>> 3: shell(cmd, invisible = TRUE, intern = !verbose)
>>> 2: run_bin(platform, bin_loc, file_name, cmdoptions, run, rm_binary =
>> !use_tmp_dir,
>>>          debug = debug, verbose = verbose)
>>> 1: glmmadmb(sexActs ~ (1 | id), sexpartner[!is.na(sexpartner$sexActs),
>>>          ])
>>     Hmmm.  Can you give
>>
>> * the results of sessionInfo()
>> * the results of trying your command with debug=TRUE ?
>> * the results of glmmADMB:::get_bin_loc() ?
>>
>>   Ben Bolker
>>
>>
> I wasn't sure which command you wanted trace, and so I did both:
> 
>> library(glmmADMB)
> Loading required package: MASS
> Loading required package: R2admb
> 
> Attaching package: 'glmmADMB'
> 
> The following object(s) are masked from 'package:MASS':
> 
>     stepAIC
> 
> The following object(s) are masked from 'package:lme4':
> 
>     fixef, ranef
> 
> The following object(s) are masked from 'package:stats':
> 
>     step
> 
> Warning message:
> package 'glmmADMB' was built under R version 2.15.3
>> sessionInfo()
> R version 2.15.2 (2012-10-26)
> Platform: i386-w64-mingw32/i386 (32-bit)
> 
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] glmmADMB_0.7.4  R2admb_0.7.5.3  MASS_7.3-22     lme4_0.999999-0
> [5] Matrix_1.0-10   lattice_0.20-10
> 
> loaded via a namespace (and not attached):
>  [1] colorspace_1.2-0   compiler_2.15.2    dichromat_1.2-4    digest_0.6.0
>  [5] ggplot2_0.9.3      grid_2.15.2        gtable_0.1.2       labeling_0.1
>  [9] munsell_0.4        nlme_3.1-106       plyr_1.8           proto_0.3-10
> [13] RColorBrewer_1.0-5 reshape2_1.2.2     scales_0.2.3       stats4_2.15.2
> [17] stringr_0.6.2      tools_2.15.2

  [snip: not including version without NAs removed, since we already
know what the issue is there]

>> r <- glmmadmb(sexActs~(1|id), sexpartner[!is.na(sexpartner$sexActs),],
>> debug=TRUE)
> platform: windows 32
> executable name: glmmadmb.exe
> bin_loc:
> c:/Users/rdboylan/Documents/R/R-2.15.2/site-library/glmmADMB/bin/windows32/glmmadmb.exe
> 
> using temp directory
> C:\Users\rdboylan\AppData\Local\Temp\Rtmpy2JsMY\glmmADMB17085c19f4d
> creating temp directory
> changed working directory to
> C:/Users/rdboylan/AppData/Local/Temp/Rtmpy2JsMY/glmmADMB17085c19f4d
> Command line:
> "c:/Users/rdboylan/Documents/R/R-2.15.2/site-library/glmmADMB/bin/windows32/glmmadmb.exe"
> -maxfn 500 -maxph 5 -noinit -shess
> Error in system(cmd, intern = intern, wait = wait | intern,
> show.output.on.console = wait,  :
>   'C:/Program' not found

  I'm a little bit baffled here.  What happens if you use save.dir to
save the input files to a temporary directory and run

"c:/Users/rdboylan/Documents/R/R-2.15.2/site-library/glmmADMB/bin/windows32/glmmadmb.exe"
-maxfn 500 -maxph 5 -noinit -shess

from the command line?

 What is the result of .Platform (and .Platform$OS in particular)

 It looks conceivably like R is misdiagnosing your system as *not* being
windows, as that's the only way system() should be running.  Are you
running under Cygwin (you say it's installed below) ...  ?

> changed working directory to i:/LAMOC/Ross
> removed temp directory
> C:\Users\rdboylan\AppData\Local\Temp\Rtmpy2JsMY\glmmADMB17085c19f4d
>> glmmADMB:::get_bin_loc()
> $bin_loc
> [1]
> "c:/Users/rdboylan/Documents/R/R-2.15.2/site-library/glmmADMB/bin/windows32/glmmadmb.exe"
> 
> 
> $platform
> [1] "windows"
> 
> P.S. about lme4; I don't have a build environment and so trying the
> github version will not be my first move.
> Although perhaps lack of a build environment is why the second version
> is failing.  I do have cygwin installed, althoughI would not expect R to
> know how to find it.

  lme4 should be installable from lme4.r-forge.r-project.org/repos now,
as stated in a message earlier today.