[R] Odp: Observed responses in 'augPred' data frame - Wrong order ?

[Petr PIKAL]

Hi

I had similar problem before and I ended with some ordering of groups 
before making grouped data object but it was data specific so I can not 
give you definite clue.

Regards
Petr


r-help-bounces at r-project.org napsal dne 08.10.2008 19:30:07:

> Dea-R community.
> 
> I'd like to draw your attention to an issue I have recently
> encountered while doing my current data analysis.
> 
> I've got an unexpected (to me) result from the command:
> 
> > augPred(lmList(my.object)),
> 
> 'my.object' being a grouped data frame of class:
> 
> > class(my.object)
> [1] "nfnGroupedData" "nfGroupedData"  "groupedData"    "data.frame"
> 
> The problem is more easily explained by showing these two to Trellis
> plot:
> 
> > plot(my.object,some_options)
> > plot(augPred(lmList(my.object)),some_options)
> 
> [link to output: http://www.palug.net/Members/jabba ]
> 
> Clearly the problem is that the predictions are correct, but the
> responses in the ``original'' part of the augPred data frame are in the
> wrong order, i.e. the response order does not match the grouping
> factor order (not sure this is in correct English, sorry).
> 
> Debugging the function 'augPred.lmList' I've managed to understand that
> the problem resides in the following function calls:
> 
> > debug(nlme:::augPred.lmList)
> > fm1.lis <- lmList(my.object)
> > augPred(fm1.lis)
> debugging in: augPred.lmList(fm1.lis)
> debug: {
>     .....
>     primary <- getCovariate(data)
>     .....
>     groups <- getGroups(object)
>     .....
>     orig <- data.frame(primary,groups, getResponse(object))
>     .....
> }
> 
> This approach works well on other datasets, such us the Orthodont data,
> but not for mine because, i guess, my rows are not first ordered by
> subject (subject is my grouping factor). In fact:
> 
> > getGroups(fm1.lis)[1:5]
> [1] CBT.1 CBT.2 CBT.3 CBT.4 CBT.5
> 34 Levels: CBT.14 < CBT.2 < CBT.11 < CBT.13 < CBT.12 < CBT.5 < ... < V.6
> > getResponse(fm1.lis)[1:5]
> CBT.1 CBT.1 CBT.1 CBT.1 CBT.2 
>    34    32    29    27    28 
> 
> My question: 
> is there a simple way to get the proper result (modify the dataset or
> modify the function)? RTFM responses are welcomed.
> 
> My (humble?) opinion:
> Neither Pinheiro-Bates (2000) nor online documentation, report the
> need for a particular row order in the costruction of grouped data
> objects, and i think it should be better do not rely on it. Or, at
> least, to document it somewhere.
> 
> 
> I want to thank the R-core team and the entire R community for this
> amazingly efficient and versatile software, and i am very proud that the
> (not only) statistical state-of-the-art software have a ``gpl
> distribution'' (which have many desirable properties ;-) ).
> 
> Cheers.
> 
> +---------------------------+
> |Relevant system information|
> +---------------------------+
> 
> > R.version
>                _ 
> platform       i486-pc-linux-gnu 
> arch           i486 
> os             linux-gnu 
> system         i486, linux-gnu 
> status 
> major          2 
> minor          7.2 
> year           2008 
> month          08 
> day            25 
> svn rev        46428 
> language       R 
> version.string R version 2.7.2 (2008-08-25)
> 
> > sessionInfo()
> R version 2.7.2 (2008-08-25) 
> i486-pc-linux-gnu 
> 
> locale:
> 
LC_CTYPE=it_IT;LC_NUMERIC=C;LC_TIME=it_IT;LC_COLLATE=it_IT;LC_MONETARY=C;LC_MESSAGES=it_IT;LC_PAPER=it_IT;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=it_IT;LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods
> base 
> 
> other attached packages:
> [1] MASS_7.2-44     lattice_0.17-15 nlme_3.1-89 
> 
> loaded via a namespace (and not attached):
> [1] grid_2.7.2  tools_2.7.2
> 
> 
> -- 
>   Marco Barbàra
> 
> - Undergraduate student in Statistics 
>   at the University of Palermo (Italy)
> 
> - Only free-as-in-freedom software user
> 
> - Emacs lover
> 
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