[Babase] RE: FW: LAH has a naughty focal point sample

Susan Alberts alberts at duke.edu
Mon Mar 8 21:18:14 EST 2010


Hi all,

Yes in principle the definition of an adult female for purposes of  
point samples should be the same as for M&C. In practice we relax the  
criterion because (1) they add females to the adult roster the month  
they are going to turn four, in anticipation,  this is easier than  
adding them as a consequence of menarche, which is not a thing that  
happens at a given time., and (2) the team makes mistakes about when  
females switch status but we don't want to lose the data.

Hope this helps clarify why the rules are different for point samples.
S

On Mar 8, 2010, at 12:13 PM, Niki Learn wrote:

> This is all it says – it doesn’t say why it was done that way…
>
> Females may have juvenile (Stype=J) SAMPLES rows until their first  
> conception. Males (or those of unknown sex) may have juvenile  
> (Stype=J) SAMPLES rows for up to but not including 1 year after  
> maturity (MATUREDATES.Matured).
> Only females may have female samples (Stype=F). Females may not have  
> female samples more than 1 year before maturity (MATUREDATES.Matured).
> It seems to me that it should match the mounts and consorts rule, no?
>
> A female may not participate in a mount, consortship, or ejaculation  
> interaction before menarche (MATUREDATES.Matured). A male may not  
> participate in a mount, consortship, or ejaculation interaction  
> before 4 years of age.
>
> From: babase-bounces at eeblistserv.Princeton.EDU [mailto:babase-bounces at eeblistserv.Princeton.EDU 
> ] On Behalf Of Niki Learn
> Sent: Monday, March 08, 2010 11:34 AM
> To: 'The Baboon Database Project'
> Subject: [Babase] RE: FW: LAH has a naughty focal point sample
>
> That seems odd…  What should be happening is menarche gets recorded  
> when Jeanne does her sexskin scoring, which always occurs with the  
> demography update.  Either the baboon is cycling or not – we really  
> couldn’t miss it.  And we have to do the demography update before  
> you do the interaction and focal point data because otherwise you’d  
> get all kinds of errors for animals that didn’t exist (in babase)  
> yet.  I guess maybe there could be a case occasionally where a  
> female might start cycling before the team starts observing them  
> specifically to look for signs of cycling but obviously they  
> wouldn’t do adult focal points until they noticed that she was  
> cycling so the assignment of a mature date and the first appearance  
> of adult point data should still be in the same update period.   
> I’ll see if the docs say anything, per Karl’s suggestion.  If I  
> don’t send another email then it says nothing relevant.
>
> From: Lacey Maryott Roerish [mailto:lroerish4 at gmail.com]
> Sent: Monday, March 08, 2010 11:20 AM
> To: Niki Learn
> Cc: Karl O. Pinc
> Subject: Re: FW: LAH has a naughty focal point sample
>
> Its allowed exactly because female maturedates are often added after  
> the fact I think... It only has the maturedate to check against, and  
> if there isn't one at all, it won't kick it out in case the team  
> just knows more than the database does at that time... I Think.
>
> We have errors for Juv after menarche and males after maturity, but  
> nothing for kids sampled as adults, just because those markers can  
> be decided upon so much later.
>
> L
>
> On Mon, Mar 8, 2010 at 10:55 AM, Niki Learn <nlearn at princeton.edu>  
> wrote:
> One more little puzzle for you, Karl.  I’m just wondering.  It  
> seems like adult female point data would never be collected for a  
> female that has not undergone puberty so I’m wondering why you can  
> enter adult data for a prepubescent female in the first place.  It  
> seems like it would make more sense to have babase reject adult  
> interactions for juveniles than to have this funny maturedates  
> error, which wouldn’t even have caught the error if it had occurred  
> a month or two later.
>
> Thanks, Niki
>
> From: Lacey Maryott Roerish [mailto:lroerish4 at gmail.com]
> Sent: Friday, March 05, 2010 9:16 PM
> To: Niki Learn
> Subject: Re: LAH has a naughty focal point sample
>
> Hey,
>
>   Unfortunately, this whole sample will have to be deleted. This is  
> just a mistake the team sometimes makes, however, since different  
> types of data are collected for J vs F points, these get deleted. I  
> will take care of this next week.
>
> Lacey
>
> On Thu, Mar 4, 2010 at 11:19 AM, Niki Learn <nlearn at princeton.edu>  
> wrote:
> Lacey,
> I am running the 09b demography update in babase_test.  I hit the  
> following error when trying to upload the female maturity dates:
>
> Line 2: ERROR: LAH: MATUREDATES.Matured more than 1 year after the  
> date of an (adult) female point sample
>
> I’m not really sure why that is the way babase is checking this.   
> It seems like it should be that they can’t have an adult point  
> sample if they don’t have a maturedate, no?  Prepubescent females  
> are never sampled as adults, are they?
>
> Anyway, I don’t have copies of the original data for that year so I  
> cannot be sure what is going on.  I tracked down the offending  
> record and tried to change the stype from F to J but babase said I  
> couldn’t because it had related fpoints.  So I did some more  
> tracking and found the records below related to the naughty samples  
> record.  The psion record sheets do say LAH was sampled that day by  
> RSM and it looks like the only activity she was recorded as doing is  
> feeding so it seems likely that it is a real record for LAH and it  
> was just accidentally coded as F instead of J somewhere along the  
> line, but I cannot be sure without seeing the data, especially since  
> I am not really familiar with these tables.
>
> So that I can continue trying out the upload in test I have gone  
> ahead and deleted the fpoints in babase_test and changed the stype  
> to J.  Please let me know if this is what I should do in real babase  
> or if something else is required.
>
> Hope you are healing up!
>
> Thanks,
> Niki
>
> select * from biograph where sname = 'LAH';
>
> bioid ¦ sname ¦ name  ¦ pid  ¦ birth      ¦ bstatus ¦ sex ¦  
> matgrp ¦ statdate   ¦ status ¦ dcause
> −−−−−−+−−−−−−−+−−−−−−−+−− 
> −−−−+−−−−−−−−−−−−+−−−−−− 
> −−−+−−−−−+−−−−−−−−+−−−−−− 
> −−−−−−+−−−−−−−−+−−−−−−−
>
>
>  1183 ¦ LAH   ¦ LAHAI ¦ LOL2 ¦ 2004-09-16 ¦       0 ¦ F   ¦    
> 2.10 ¦ 2009-06-29 ¦      0 ¦      0
> 1 row(s)
>
> select * from samples where sname = 'LAH' and date = '2008-09-25';
>
>   sid ¦ date       ¦    stime ¦ observer ¦ stype ¦  grp ¦ sname  
> ¦ mins ¦ minsis ¦ programid ¦ setupid ¦ palmtop
> −−−−−−+−−−−−−−−−−−−+−−−− 
> −−−−−−+−−−−−−−−−−+−−−−−− 
> −+−−−−−−+−−−−−−−+−−−−−−+−− 
> −−−−−−+−−−−−−−−−−−+−−−−− 
> −−−−+−−−−−−−−
> 55273 ¦ 2008-09-25 ¦ 17:54:00 ¦ RSM      ¦ F     ¦ 2.10 ¦ LAH    
> ¦   10 ¦      5 ¦         2 ¦       4 ¦       5
> 1 row(s)
>
> select * from point_data where sid = 55273;
>
>  pntid ¦   sid ¦ min ¦ activity ¦ posture ¦ foodcode ¦    ptime
> −−−−−−−+−−−−−−−+−−−−−+−−− 
> −−−−−−−+−−−−−−−−−+−−−−−− 
> −−−−+−−−−−−−−−
> 565064 ¦ 55273 ¦   6 ¦ F        ¦ 2       ¦ GRC      ¦ 18:00:02
> 565065 ¦ 55273 ¦   7 ¦ F        ¦ 2       ¦ GRC      ¦ 18:01:03
> 565066 ¦ 55273 ¦   8 ¦ F        ¦ 2       ¦ GRC      ¦ 18:02:12
> 565067 ¦ 55273 ¦   9 ¦ F        ¦ 2       ¦ GRC      ¦ 18:03:10
> 565068 ¦ 55273 ¦  10 ¦ F        ¦ 2       ¦ GRC      ¦ 18:04:09
> 5 row(s)
>
> select * from fpoints where pntid = 565064;
>
>  pntid ¦ kidcontact ¦ kidsuckle
> −−−−−−−+−−−−−−−−−−−−+−−− 
> −−−−−−−
> 565064 ¦ A          ¦ N
> 1 row(s)
>
> select * from fpoints where pntid = 565065;
>
>  pntid ¦ kidcontact ¦ kidsuckle
> −−−−−−−+−−−−−−−−−−−−+−−− 
> −−−−−−−
> 565065 ¦ A          ¦ N
> 1 row(s)
>
> select * from fpoints where pntid = 565066;
>
>  pntid ¦ kidcontact ¦ kidsuckle
> −−−−−−−+−−−−−−−−−−−−+−−− 
> −−−−−−−
> 565066 ¦ A          ¦ N
> 1 row(s)
>
> select * from fpoints where pntid = 565067;
>
>  pntid ¦ kidcontact ¦ kidsuckle
> −−−−−−−+−−−−−−−−−−−−+−−− 
> −−−−−−−
> 565067 ¦ A          ¦ N
> 1 row(s)
>
> select * from fpoints where pntid = 565068;
>
>  pntid ¦ kidcontact ¦ kidsuckle
> −−−−−−−+−−−−−−−−−−−−+−−− 
> −−−−−−−
> 565068 ¦ A          ¦ N
> 1 row(s)
>
> Total runtime: 33.675 ms
>
>
>
>
>
> -- 
> - -
> Lacey K. Maryott Roerish
> Alberts Lab
> Department of Biology
> Duke University
> ph: 919-660-7306
> fax: 919-660-7293
> Lacey.Maryott at duke.edu
>
>
>
> -- 
> - -
> Lacey K. Maryott Roerish
> Alberts Lab
> Department of Biology
> Duke University
> ph: 919-660-7306
> fax: 919-660-7293
> Lacey.Maryott at duke.edu
> _______________________________________________
> 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, 919-660-7272 (Ph), 919-660-7293 (Fax)







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