[Babase] Conversion of interaction and point sample data, also rank validation question

Susan Alberts alberts at duke.edu
Tue Aug 29 17:31:52 EDT 2006


This is great, by the way. Thanks, looking forward to seeing you soon.

Susan

On Aug 26, 2006, at 8:48 PM, Karl O. Pinc wrote:

> Hi,
>
> I've finished with the data validation on the
> social interaction part of the database.
> This leaves the sexual cycle stuff.  And it
> now occurs to me that it also leaves the ranks
> table.  (See following email.)
>
> This is mostly for Leah, but everyone will want to
> read through this, especially the last part.
>
> I've checked all the interaction
> and point sample data by running the
> data through the conversion.  This means
> there's now data errors to go through.  There's
> almost certainly still bugs in the code, so let me
> know when you find one.
>
> I've divided the errors into two parts, neighbors,
> female point samples, and allmiscs and everything else.
> (In two parts because I was able to not "start over"
> and reconvert interactions when I had to fix bugs
> later on in the process.)
>
> This time, I've made a directory where I've put the files:
> papio:/biology/groups/babase/errors/
>
> The everything else errors are:
> errors.interact
> And the corresponding data file is:
> loadscript.interact
>
> There are about 1,700 errors, some of them 'cascading' --
> resulting from previous errors.
>
> The neighbors, female point samples, allmiscs related errors are in:
> errors.neighbors
> And the corresponding data file is:
> loadscript.neighbors
>
> There are about 3,000 of these, I'd say at least half
> due to previous errors.
>
> I believe the reason there's so many problems with
> the neighbors may be that at various times various codes have
> had different meanings.  For example, at some point in time
> it was perfectly ok to have 2 different neighbors
> be the same individual.  Later on, the same codes
> were used but each neighbor was expected to be
> unique.  A neighbor code in Babase (NCODES)
> determines whether or not the neighbor must be
> unique.  You _could_ use the same code for unique
> and non-unique data, but then neither would get
> checked for uniqueness.  That'd be silly.
> The thing to do is to use a different code, and if
> it's necessary to combine the two codes during
> analysis we can have another column on the NCODES
> table that says the two codes "go together".
> We've done this already on the ACTS table with
> respect to agonisims, the AS and AO agonisims are
> all "A" type agonisims.
>
> (The female point samples in particular seem to
> have a lot of errors where one of the neighbors
> is the focal of the point sample.)
>
> All in all not bad for half a million interactions
> and 30,000 point samples (10 times that many
> individual points and 400,000 neighbors.)
>
> If it matters, the result of the conversion is
> in babase_test.  Note that there is no sexual
> cycle related data in this database.
>
> Karl <kop at meme.com>
> Free Software:  "You don't pay back, you pay forward."
>                  -- Robert A. Heinlein
>
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-----------------------------------------------
Susan Alberts, Dept. Biology, Duke University, Durham NC 27708. Phone  
919-660-7272, Fax 919-660-7293. alberts at duke.edu





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