working with pairlists imported from HDF5, converting to data frames?
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 at 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