Re: [R] working with pairlists imported from HDF5, converting to data frames?

From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
Date: Thu 17 Mar 2005 - 07:27:02 EST

Does do.call("data.frame", effective) work? I think it ought to. If not, as.data.frame(as.list(effective)) would appear to. In fact almost anything you do to a pairlist will turn it into a list, e.g. effective[].

This is really a bug in the hdf5 package, one that you should raise with the authors. The help says that groups map to lists, not pairlists, and pairlist -> list is easy at C level via PairToVectorList.

On Wed, 16 Mar 2005, Paul Johnson wrote:

> I've used the HDF5 library to bring some data into R. THe verbose output
> looks like this:
>
>> hdf5load("hdfGraphWed_Mar_16_13_33_37_2005.hdf",load=T,verbosity=1,tidy=T)
> Processing object: cprSeats ...... which is a Group
> Processing object: Seats 0 ...... its a dataset......Finished dataset
> Processing object: Seats 1 ...... its a dataset......Finished dataset
> Processing object: Seats 2 ...... its a dataset......Finished dataset
> Processing object: Seats 3 ...... its a dataset......Finished dataset
> Processing object: Seats 4 ...... its a dataset......Finished dataset
> ... Done group cprSeats
> Processing object: effective ...... which is a Group
> Processing object: AggComp ...... its a dataset......Finished dataset
> Processing object: AggNonComp ...... its a dataset......Finished dataset
> Processing object: CPR ...... its a dataset......Finished dataset
> Processing object: PR ...... its a dataset......Finished dataset
> Processing object: SMD ...... its a dataset......Finished dataset
> ... Done group effective
>
>
> Each item inside the group "effective" is a vector of numbers. I want to
> convert effective into a data frame or matrix for use with matplot.
>
> However, R sees effective not as a collection of vectors, but as a pairlist.
> I'm not a Lisp programmer, so don't understand the significance of the list
> help page's comment about dotted lists.
>
>> class(effective)
> [1] "pairlist"
>> attributes(effective)
> $names
> [1] "SMD" "PR" "CPR" "AggNonComp" "AggComp"
>
> I can access the elements in effective as list elements, either with
> effective$SMD or effective[[1]], as in:
>
>> effective[[1]]
> [1] 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000
> [9] 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000
> [17] 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000
> [25] 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 4.761905 4.668534
> [33] 4.743833 4.743833 4.694836 4.672897 4.612546 4.612546 4.612546 4.950495
> [41] 4.766444 4.761905 4.329004 4.990020 4.930966 4.906771 4.378284 4.686036
> [49] 4.935834 4.793864 4.793864 4.541326 4.849661 4.730369 4.960317 4.159734
>
>
> But I can't force it into a data frame
>
>> as.data.frame(effective)
> Error in as.data.frame.default(effective) :
> can't coerce pairlist into a data.frame
>
>
> But I can manually build the dataframe
>
>>
> data.frame(effective$SMD,effective$PR,effective$CPR,effective$AggNonComp,effective$AggComp)
>
> But that is a bit frustrating for every individual dataset coming in.
>
> Is there a short cut?

-- 
Brian D. Ripley,                  ripley@stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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Received on Thu Mar 17 07:35:00 2005

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