[Babase] RE: biograph question

nlearn at princeton.edu nlearn at princeton.edu
Fri Dec 4 14:40:53 EST 2009


  BODY { font-family:Arial, Helvetica, sans-serif;font-size:12px; }
 99 it is.  I will discuss documentation further with Karl as needed
once I've had a look at it.  Thanks for the input!
 On Fri 04/12/09  9:57 AM , Susan Alberts alberts at duke.edu sent:
 Yes, agreed, the purpose of having a "censored" category is that we 

 don't want the animal to be alive, but we also don't want them to be
 
 dead. It's a third category. A dcause of 99 makes sense to me --  
 something that stands out from the rest of the list.
 S
 On Dec 3, 2009, at 10:06 PM, Niki Learn wrote:
 > Right, the purpose of censoring the males is so they won't be  
 > recognized as
 > "alive" (i.e., cannot have data entered after their statdates).   
 > Since we
 > need to have a nonzero dcause for all animals not "alive" (status
=  
 > 0), we
 > will definitely need to add a dcause to go with the censored
status.
 > Currently the dcauses go from 0 to 8 (0 being alive and all others
 
 > some form
 > of dead).  Shall we use 9 for censored?  Or would a more removed  
 > number
 > (like 99?) be preferred to make it more obvious that the animal
isn't
 > necessarily dead, yet is not recognized as "alive"?
 >
 > I will look over the alive and dead documentation when I have a  
 > chance and
 > see what may need to be changed.  Thanks, Karl.
 >
 > Niki
 >
 > -----Original Message-----
 > From: Karl O. Pinc [kop at meme.com [1]]
 > Sent: Wednesday, November 25, 2009 4:35 PM
 > To: Niki Learn; babase at eeblistserv.Princeton.EDU [2]
 > Subject: Re: biograph question
 >
 > On 11/25/2009 02:17:51 PM, Niki Learn wrote:
 >> Karl,
 >>
 >>
 >>
 >> So I was trying to implement this change to biograph where we
censor
 >> the old
 >> animals and the males that have left the study groups and haven't
 >> been
 >> seen
 >> for at least one update period.and I hit a snag.  I added the new
 >> status
 >> code to the statuses table - 2 for Censored.  But then if I try
to
 >> change an
 >> individual to censored, I get this error message:
 >>
 >>
 >>
 >> SQL error:
 >>
 >> ERROR:  new row for relation "biograph" violates check constraint
 >> "Dcause
 >> for live animal, or no dcause for dead animal"
 >>
 >> In statement:
 >> UPDATE "biograph" SET "bioid"='1386', "sname"='BAK',
"name"='BAKARI',
 >> "pid"=NULL, "birth"='1999-10-01', "bstatus"='1', "sex"='M',
 >> "matgrp"='9.00',
 >> "statdate"='2007-11-23', "status"='2', "dcause"='0' WHERE
 >> "bioid"='1386'
 >>
 >>
 >>
 >> It looks like there is a check in biograph that says you can't
have a
 >> dcause
 >> for an animal with status 1 and you can't have an animal that is
not
 >> "live"
 >> (where live is only status 1) that does not have a dcause and
since
 >> the new
 >> status of 2 does not have a dcause associated with it, babase
doesn't
 >> like
 >> it.  Even the one appearance of code 4 has a dcause of 7
(unknown)
 >> even
 >> though that individual isn't necessarily dead.
 >
 > Yes, Babase requires that a BIOGRAPH.Status of 0 (0 not 1) be the
 > only status where the individual is alive.  (See the "Special
Values"
 > section in the docs on the STATUSES table:
 > https://papio.biology.duke.edu/babase_system_html/ch06s02.html
 > )
 >
 > Anybody who's not alive needs a dcause.
 >
 >>
 >>
 >>
 >> So I guess that means either I should invent a dcause that's not
 >> really a
 >> dcause but a "censor cause" to go with the censored status or we
need
 >> to
 >> revise the checks somehow.  What do you advise?  Can we make
status 2
 >> count
 >> as live for the purposes of this check so it won't be violated or
 >> would that
 >> muck up other things?
 >
 > I don't think we want a status of 2 to be alive -- in other words
I
 > think we need to refine the definition of what "alive", Status
code
 > 0, means.  IIRC what Status 0 means to the system is that you can
 > put in data after the Statdate and the Statdate will then  
 > automatically
 > update to the newer date.  We probably don't want this behavior
 > for censored individuals and so don't want to classify them as
 > "alive" in this sense.  Do we?  IIRC anybody that's dead has
 > a "Statdate that sticks", one that does not change and one
 > that does not allow anything to happen to the individual
 > after the Statdate.  It seems right to have this sort of behavior
 > for censored individuals but I want to hear what everybody
 > else says.
 >
 > "Alive" isn't really "alive in real life", it's "an individual
 > on which new data is continuing to be collected".
 >
 > So I'd go for adding a censored "cause of death" and using that
 > along with the censored status value.
 >
 > We also need to update the Babase system documentation to make
 > all of this more clear; to document exactly what 'alive' means.
 > It's in the documentation now but spread out in various places
 > where it says what alive or dead individuals can or can't do.
 >
 > We may want to search the documentation for the words 'alive'
 > and 'dead' and see what comes up.  (Via the "everything on
 > one page version" would be easiest.)  If you guys want me
 > to do the work I can search the validation code for everyplace
 > the status is tested for aliveness and come up with a list
 > that way.  This will give us a precise idea of exactly what
 > alive means.
 >
 > What does everybody else think and what should the above
 > referenced documentation say about what it means to babase
 > for an individual to be alive?  What about the DCAUSES
 > documentation.  Should it say more?
 >
 >
 > Karl 
 > Free Software:  "You don't pay back, you pay forward."
 >                 -- Robert A. Heinlein
 >
 >
 > _______________________________________________
 > Babase mailing list
 > Babase at www.eco.princeton.edu
 > http://www.eco.princeton.edu/mailman/listinfo/babase
 ------------------------------------------------------------
 Susan Alberts, Dept of Biology, Duke University, Box 90338, Durham
NC  
 27708. Phone 919-660-7272, FAX 919-660-7293
 _______________________________________________
 Babase mailing list
 Babase at www.eco.princeton.edu
 http://www.eco.princeton.edu/mailman/listinfo/babase
 

Links:
------
[1] mailto:kop at meme.com
[2] mailto:babase at eeblistserv.Princeton.EDU
[3] mailto:kop at meme.com
[4] http://www.eco.princeton.edu
[5] http://www.eco.princeton.edu
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://eeblistserv.Princeton.EDU/pipermail/babase/attachments/20091204/aa35b839/attachment.html


More information about the Babase mailing list