Re: ASM Patch 3 nearing completion; hdf5 question

[Marcus G. Daniels]

>>>>> "PJ" == Paul E Johnson <address@hidden> writes:

PJ> I understand these are telling me it is ignoring my "deep" objects
PJ> with this shallow save.  Other than that, they don't do any harm,
PJ> do they?

No.  Btw, in Java, these can be avoided by remove `public' from the objects
you don't wanted saved.

PJ> what I see is one R object for each time the data was saved.  I
PJ> have no idea how to put all the times into a single data frame,
PJ> but I expect I can figure that out if needed.  Here is what I want
PJ> to know. Should I redesign my output so that the hdf5 data set is
PJ> like a data frame from the start

If you do that the problem is then you have to store them in a List,
and that List could exhaust memory if you are running for a long enough time.

One alternative is to store fixed size (shallow) lists of agents,
dropping the lists after each epoch.  Otherwise, you'll need to write
some R code to convert the data from the (deep) lists of lists into a
data frame.  For simple data streams of one variable, I'd suggest
using the HDF5 support in EZGraph, which avoids these issues.

PJ> I personally prefer to save data in raw ASCII format, for reasons of
PJ> portability and permanence of access. 

ASCII doesn't mean data is portable.  For example, floating point
conversions using printf & scanf will give you different decodings and
encodings on different platforms.  For example, this could lead to
subtle changes in initial conditions when you change platforms.  HDF5
stores the precise binary representation and precise metadata about
the representation, as well as handling the conversions when
necessary.  Some environments such as Common Lisp expect implementors
to go to extreme lengths to provide predictable encoding and decoding
of floating point data, but most environments do not.


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