[Babase] RE: FW: LAH has a naughty focal point sample
Susan Alberts
alberts at duke.edu
Mon Mar 8 21:41:05 EST 2010
Oh right, I forgot that the criterion is indeed the first swelling not
the fourth bd. But, I think that a lot of the samples taken
incorrectly are actually mistakes, and we decided that we don't want
to lose the data. Anyway thanks for checking.
Susan
On Mar 8, 2010, at 1:31 PM, Niki Learn wrote:
> Jeanne just gave a good example. Occasionally the first "cycle"
> will be very small with a maximum T of only 1 or so. The team might
> start counting that baboon as an adult for focal sampling because
> they see that she has started to swell but then when Jeanne scores
> she wouldn't count that as the first cycle because it is so tiny. A
> year is still a big gap but okay. Thanks for filling me in.
>
> -----Original Message-----
> From: babase-bounces at eeblistserv.Princeton.EDU [mailto:babase-bounces at eeblistserv.Princeton.EDU
> ] On Behalf Of Susan Alberts
> Sent: Monday, March 08, 2010 9:18 PM
> To: The Baboon Database Project
> Subject: Re: [Babase] RE: FW: LAH has a naughty focal point sample
>
> 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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>
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--------------------------------------------------------
Susan Alberts, Dept of Biology, Duke University, Box 90338, Durham NC
27708, 919-660-7272 (Ph), 919-660-7293 (Fax)
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