[R-sig-ME] glmmADMB troubles

[Ross Boylan]

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 ...
>>
>>> r <- glmmadmb(sexActs~(1|id), sexpartner)
>> Error in II[, ii] = II[, ii] + REmat$codes[[i]] :
>>     number of items to replace is not a multiple of replacement length
>> In addition: Warning messages:
>> 1: In glmmadmb(sexActs ~ (1 | id), sexpartner) :
>>     NAs removed in constructing fixed-effect model frame: you should probably
> remove them manually, e.g.
>> with na.omit()
>> 2: In II[, ii] + REmat$codes[[i]] :
>>     longer object length is not a multiple of shorter object length
>>
>> Figuring that its missing value handling might be off, 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
> r <- glmmadmb(sexActs~(1|id), sexpartner, 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\glmmADMB1708678a587a
creating temp directory
changed working directory to C:/Users/rdboylan/AppData/Local/Temp/Rtmpy2JsMY/glmmADMB1708678a587a
Error in II[, ii] = II[, ii] + REmat$codes[[i]] :
   number of items to replace is not a multiple of replacement length
In addition: Warning messages:
1: In glmmadmb(sexActs ~ (1 | id), sexpartner, debug = TRUE) :
   NAs removed in constructing fixed-effect model frame: you should probably remove them manually, e.g. with na.omit()
2: In II[, ii] + REmat$codes[[i]] :
   longer object length is not a multiple of shorter object length
# The previous message suggests to me that the NA was not systematically removed from the data, so
# different columns have different lengths
changed working directory to i:/LAMOC/Ross
removed temp directory C:\Users\rdboylan\AppData\Local\Temp\Rtmpy2JsMY\glmmADMB1708678a587a
> 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
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.