[Babase] RE: FW: LAH has a naughty focal point sample
Niki Learn
nlearn at princeton.edu
Mon Mar 8 11:33:37 EST 2010
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://eeblistserv.Princeton.EDU/pipermail/babase/attachments/20100308/7b224fda/attachment-0001.html
More information about the Babase
mailing list