[Babase] Censoring + Alto's split

Susan Alberts alberts at duke.edu
Thu Oct 22 17:38:33 EDT 2009


Thank you, and YES, this sounds very good to me.
Susan

On Oct 20, 2009, at 11:02 AM, Niki Learn wrote:

> Sorry, I guess I'm the only one steeped in these biograph dates and  
> a little more explanation is required.
>
> The statdate for any given animal presently is either (1) the  
> assigned deathdate (which, unless the date of death is actually  
> known, is calculated by taking the midpoint between the last date  
> the animal was seen alive and the first date the animal was recorded  
> absent) or (2) the last date the animal appears in the census  
> record.  In terms of animals with old, dangling statdates, the  
> second case is true for both males that disappear from a group (but  
> are assumed to have emigrated rather than to have died) and the  
> animals from groups that we stopped monitoring like Proton's and  
> Lodge's (unless they showed up again sometime later in an other  
> group census or by immigrating into a study group).  We also have to  
> assign a statdate when entering births and new immigrant males (in  
> this case it is the same as the bithdate or date of entry to the  
> group); the statdate then gets updated automatically by babase when  
> census data is entered.
>
> To assign animals to a status of censored, I have to link the status  
> change to a date, just like I would when changing animals to dead;  
> hence the censordate.  Babase will not allow any data to be entered  
> after a statdate linked to a status other than alive.  So I am  
> proposing that (1) males who emigrate out of a study group (and  
> therefore have both a date last present and a date first absent from  
> the group) get a censordate that is the midpoint between the date  
> last seen and the date first not seen (just like we would calculate  
> the deathdate) and that (2) animals from groups that we are no  
> longer studying or who stop showing up in other group censuses for a  
> peripherally monitored group and therefore have no date when they  
> were first recorded absent (at least not one that's anywhere near  
> the last date they were recorded present...) be assigned a  
> censordate the day after they last appeared in the census record  
> (since we know they were there that last day but don't know what ha!
> ppened to them after that).
>
> This will produce a database with three possible meanings of  
> statdate instead of two.  Only animals seen alive in the last update  
> will have a statdate equal to the last date they were censused.  All  
> others will have a statdate equal to either their real or estimated  
> deathdate or their newly assigned censordate.  I will have to update  
> that part of the data management protocol and repost on the wiki  
> once it is implemented.  Hmm...actually it looks like it's not even  
> on the wiki (only the babase 1.0 version of Princeton's protocol is  
> there) - not sure why that is.  I'll put getting that up on my list  
> of things to do.
>
> Is this an agreeable protocol for assigning censordates?
>
> Thanks,
> Niki
>
> -----Original Message-----
> From: babase-bounces at eeblistserv.Princeton.EDU [mailto:babase-bounces at eeblistserv.Princeton.EDU 
> ] On Behalf Of Susan Alberts
> Sent: Monday, October 19, 2009 8:54 PM
> To: The Baboon Database Project
> Subject: Re: [Babase] Censoring + Alto's split
>
> I am not completely sure what the censordate is -- are you referring
> to the statdate for an animal that has "censored" as its status? Just
> clarifying.
>
> With respect to calculating what the date should be, it sounds like
> you are saying that the statdate is calculated differently in the
> following two cases:
> 1. The animal is known or strongly suspected to have died, so you give
> it a death in status, versus
> 2. The animal suddenly disappears, not enough evidence to assign
> death, the animal just has an unknown fate, as in a male that leaves
> and may have emigrated and we don't know where he goes, and until know
> you would have given him a status of "alive" sometime near the last
> date he was seen.
>
> Am I correct that you calculate these two types of statdates
> differently?  There is no information in the babase tech specs about
> this, so I'm not sure.
>
> If so, then I think maybe we should revisit this, as I am not sure
> there is a reason to calculate them differently. And, if you do them
> differently, it probably makes most sense now to calculate the date of
> censoring the same way you calculate a death date.  Jeanne?
>
> Susan
>
>
> On Oct 16, 2009, at 4:21 PM, Niki Learn wrote:
>
>> That's fine.  I wasn't sure initially how far off the other data was
>> in coming but Lacey called me earlier and said it could be a while
>> yet.  I'll go ahead and censor them all and we'll worry about
>> updating the censordates when the other data is ready.
>>
>> I guess the best date to use as the censordate is a) the midpoint
>> between when an animal was last seen and when it was first absent
>> (as with the deathdate) or b) in these Alto's cases (and any others
>> where animals were rarely censused and have not been seen or in any
>> way marked absent in some time), the day after an animal last
>> appears in the census record.  Does that make sense to everyone?
>>
>> Thanks,
>> Niki
>>
>> -----Original Message-----
>> From: babase-bounces at eeblistserv.Princeton.EDU [mailto:babase-bounces at eeblistserv.Princeton.EDU
>> ] On Behalf Of Susan Alberts
>> Sent: Friday, October 16, 2009 3:26 PM
>> To: The Baboon Database Project
>> Subject: Re: [Babase] Censoring + Alto's split
>>
>> Right, thanks for clarifying your concern. I still think it makes  
>> most
>> sense to change all the alives to censoreds, and deal with the
>> statdate changes at the time they come up. I say this because I think
>> it is likely that we will need to use the data in analysis before we
>> update the census info for Proton's group, and it will be confusing  
>> to
>> have those animals alive  -- does this make sense to you? YOu have
>> more experience with uploading data than I do...
>> Susan
>>
>> On Oct 16, 2009, at 3:00 PM, Niki Learn wrote:
>>
>>> Susan,
>>>
>>> When I "kill" a baboon in babase the statdate changes to the
>>> deathdate.  This would work the same way with censoring them.  So
>>> the reason I was thinking it would be tricky to censor the baboons
>>> in Proton's, for example, is that the census data for them currently
>>> ends at a totally random point and if the later data is to be added,
>>> yes the individuals would still end up censored but not on the same
>>> date.  I could go ahead and censor all of them now with the best
>>> dates available in the database but we would have to remember to
>>> change the censor date before uploading any missing data that fell
>>> after that date; otherwise babase will yell at us.
>>>
>>> I'm happy to try to help sort out Proton's group too.  Puzzles are
>>> fun :)
>>>
>>> Niki
>>>
>>> -----Original Message-----
>>> From: babase-bounces at eeblistserv.Princeton.EDU [mailto:babase-bounces at eeblistserv.Princeton.EDU
>>> ] On Behalf Of Susan Alberts
>>> Sent: Friday, October 16, 2009 2:46 PM
>>> To: The Baboon Database Project
>>> Subject: Re: [Babase] Censoring + Alto's split
>>>
>>> Hi Niki and Lacey,
>>>
>>> I thought I should jump in here to comment.
>>>
>>> First, with respect to the censored/alive/dead codes in biograph (I
>>> think this is what you are asking about when you say "I think we
>>> should skip censoring any Alto's animals...") I think you should
>>> still
>>> change ALIVE to CENSORED for any case in which the statdate is not
>>> the
>>> date of your most recent update (i.e. where statdate is earlier than
>>> Jun 2009). The status (censored, alive, dead) for those animals
>>> mostly
>>> won't change after the data are uploaded as actual census data (they
>>> will still mostly be censored), although the statdate might change  
>>> in
>>> biograph. In other words, implement the censoring code in biograph
>>> without skipping any periods for any groups. I think you should be
>>> able to apply the rule for all cases without producing any errors.
>>> Does this make sense?
>>>
>>> Second, unfortunately I think that there will always be a lot of
>>> confusion about Proton's group in the early 1990's. The messy nature
>>> of the data accurately reflects what happens when you gradually,
>>> rather than suddenly, stop monitoring a group. The uploading of the
>>> census data that Lacey has on her list will probably not clear many
>>> of
>>> these things up and in fact will probably raise some sticky
>>> questions,
>>> like how do we deal with the fact Scion clearly had a infant whose
>>> birth was entirely missed (I am guessing that we will just censor
>>> Scion at an earlier age than we actually know she lived to, just as
>>> we
>>> do now). The virtue of the current database, frustrating as it can
>>> be,
>>> is that it simply skirts these issues. We will have to deal with  
>>> them
>>> at some point but I am quite sure that when we go to enter the data
>>> we
>>> will raise more questions, initially, than we will resolve.
>>>
>>> And, before we can enter the data we still need to work through some
>>> details about how to capture the fission information -- it will
>>> require at least one and possibly two new groups to be created in  
>>> the
>>> database I think, because commonly during fissions the animals are  
>>> in
>>> "groups" that don't currently exist (for instance, some animals from
>>> what eventually became Nyayo's might have spent some days with some
>>> animals from what eventually became Dotty's group, while the rest
>>> were
>>> in another subgroup that has no name). To capture this information,
>>> these groups will have to be given a group identity (presumably
>>> something like "temporary fission group") before the data can be
>>> entered. I don't think we are quite there yet.
>>>
>>> Thanks for the offer of helping with catch up on the lagging parts  
>>> of
>>> Alto's. I think this would be great;  now that we have extra hands  
>>> in
>>> our lab, we are still finding that the amount of old data we are
>>> entering is huge (old darting data, old juv point samples data, old
>>> predation data, old demog notes)), and also we have been hindered in
>>> the census data by the design issues I raised above.
>>>
>>> I also have some comments on your email about Allison's infants  
>>> but I
>>> will do that separately; I hope this helps as a start, let me know  
>>> if
>>> you have other questions about the status codes.
>>>
>>> Susan
>>>
>>>
>>>
>>>
>>>
>>>
>>> On Oct 16, 2009, at 11:12 AM, Niki Learn wrote:
>>>
>>>> Lacey,
>>>>
>>>> Is the census (other than demog notes you mentioned you are waiting
>>>> on), biograph (births, immigrations, and deaths), and pregnancy/
>>>> cycling (upon which births rely) data ready to be uploaded?
>>>>
>>>> If so, what if you go ahead and send those to me for upload.  We  
>>>> can
>>>> fill in the demog notes later since those are less likely to impact
>>>> the statdate.  And then I guess you will have interaction data to
>>>> upload too (and eventually we’ll do ranks for the years/groups
>>>> with
>>>> sufficient data?).  Even if only some of the years/subgroups are
>>>> ready it could be worth going ahead with what we’ve got for now.
>>>>
>>>> If the census/biograph data is not ready, I guess we should skip
>>>> censoring any Alto’s animals whose statdates fall within that
>>>> period since we would just have to uncensor most of them later to
>>>> upload the missing data.  I could go ahead and censor animals like
>>>> Scion who were seen after that period though.  Presumably most
>>>> members of Nyayo’s and Dotty’s would fall into this category.
>>>>
>>>>
>>>> The censoring is something I think I can implement in early
>>>> November, even if I have to skip that period of Alto’s for now.
>>>> Possibly next year I can help catch up the lagging parts of  
>>>> Alto’s
>>>> if there is still a lack of undergraduates?  Demog notes are, after
>>>> all, much more interesting to enter than old sexskin swelling sizes
>>>> and PCS colors – that I would gladly yield to undergrads.
>>>>
>>>> Thanks,
>>>> Niki
>>>>
>>>> From: Lacey Roerish [mailto:lroerish4 at gmail.com]
>>>> Sent: Tuesday, October 13, 2009 8:12 PM
>>>> To: Niki Learn
>>>> Subject: Re: wounds and pathologies question (white monkeys) + that
>>>> crazy Alto's split (and Cocoa, another white monkey)
>>>>
>>>> Just my little input on the part of this that is pertinent to me...
>>>> The Alto's Census backfill and demog notes backfill are both on my
>>>> list of things to do. I'm getting there. As for how to deal with  
>>>> the
>>>> fission of Alto's Group, this is also on our list, and has already
>>>> been looked at once.. we have all of the notes. Am just waiting to
>>>> put an undergrad on fishing through demog notes.
>>>>
>>>> So its all in the works! :)
>>>> We'll keep you posted
>>>> Lacey
>>>>
>>>> On Tue, Oct 13, 2009 at 4:30 PM, Niki Learn <nlearn at princeton.edu>
>>>> wrote:
>>>> I've attached a sheet that began as Alison's infants of interests
>>>> file.  Most of the infants and a handful of others were used in her
>>>> final analysis.  I've added the others she used and a couple others
>>>> that she maybe could have used but did not.  I am not sure how she
>>>> concluded that several of them could have had white monkey syndrome
>>>> (particularly WAU, LOW, and ENE, all of whom were less than two
>>>> months old and died of unrelated causes, and PAW seems to me to  
>>>> have
>>>> had something different).
>>>>
>>>> Alison did locate all the infants with wound sheets indicating they
>>>> had white fur (except CAC who was only slightly whitish) and those
>>>> indicating a stiff walk (coded as either 10 or 14).  She flagged
>>>> some early in the process who had code 7 but only ended up using
>>>> TOF, HAV, and CYC, none of which I am very confident had the
>>>> syndrome (TOF at least is reported to have had weak feet, though  
>>>> his
>>>> arms were primarily affected by whatever he had; the other two seem
>>>> like unseen injuries to me).  None of these have demography notes
>>>> indicating any additional useful information (other than to confirm
>>>> the dcauses that demonstrate that the questionable infants WAU,  
>>>> LOW,
>>>> and ENE did not die because they were sick).
>>>>
>>>> Code 7 - Limp, no wound visible
>>>> Code 10 - Malaise, weakness, stiffness in absence of wound
>>>> Code 14 - Other pathology
>>>>
>>>> I would not advise using code 7 for the stiff walk.  This is the
>>>> most frequently used code and it already has some irregularities
>>>> that should probably be addressed.  [Essentially, limp has changed
>>>> from time to time on the datasheets, sometimes being listed simply
>>>> as limp or even as limp from wound but usually as "limp, no wound
>>>> visible" - sometimes it is marked along with wounds that could
>>>> obviously be causing a limp, particularly in older data where the
>>>> name may not match up with the code's name.  Recent data (2000
>>>> onward) is fairly consistent in not checking code 7 if there is a
>>>> limp-causing wound.  This is fine because there is also the column
>>>> for checking whether the wound "impairs locomotion" which SHOULD
>>>> always be checked when code 7 is used and whenever a limp-causing
>>>> wound is evident.  It also often marked with code 10 when the
>>>> stiffness or weakness impairs locomotion.]
>>>>
>>>> Code 10 is mostly used in the following cases:  To indicate slowing
>>>> by older baboons (rheumatism, stiffness, slowing down, etc.), to
>>>> indicate infants that are not thriving (can't cling, etc.), and for
>>>> cases where a baboon has been badly wounded or is very sick and so
>>>> is weak/in a state of malaise.  The large outbreak of Coxsackie
>>>> mentioned earlier was coded as 10, as are two cases that seem
>>>> similar where 3 or 4 baboons simultaneously had stiff walks/stiff
>>>> sacral regions for a short period of time.
>>>>
>>>> Code 14 is mostly used for really bizarre things that nobody knows
>>>> where else to put and for more extreme cases where baboons become
>>>> very thin (I found several cases of thinning that were flagged "low
>>>> body weight" in the notes - I similarly flagged Liberty and can  
>>>> flag
>>>> any other individuals that I actually get wounds & pathologies
>>>> sheets for).
>>>>
>>>> That said it sounds like 10 is the best existing code to use.
>>>> Possibly if we think they are white monkey cases we could flag them
>>>> "possible white monkey syndrome" in the notes?  Of course, right  
>>>> now
>>>> there are four tables, three of which have notes.  I'll have to see
>>>> how Karl wants to arrange everything in babase since these sheets
>>>> were designed with a different database system in mind; babase
>>>> usually designated ids but these have predesignated ids (with many
>>>> gaps) to allow the information in the four tables to be aligned  
>>>> with
>>>> each other.
>>>>
>>>> It appears that wounds and pathologies mentioned solely in
>>>> demography notes (of which I think there are many) do not appear in
>>>> the existing wounds and pathologies tables.  For example, surely
>>>> there were cases of white monkey syndrome before 2003 but they were
>>>> not given wounds sheets and so cannot be easily located.  Is this
>>>> something we need to remedy?
>>>>
>>>> On a related note, Catherine mentioned a white monkey case she has
>>>> been discussing with you that she discovered in Proton's group in a
>>>> demography note for darting of his mother, Scion, on 14 May 1994.
>>>> While investigating the case, more and more questions were raised.
>>>> The infant is Cocoa who is not in babase (but is on the list of
>>>> snames not in babase).  I came to find a few problems:
>>>>
>>>> The demography note indicates that Cocoa was about 9 months old and
>>>> then determines (and this data matches what is in the notebook
>>>> elsewhere) that the infant would have been born in August 1993.   
>>>> But
>>>> this demography note is not in babase, nor is any of the Proton's
>>>> data contained in this notebook, which includes census and related
>>>> data from Feb 1994 to 2 Sep 1999 (admittedly with a decreasing
>>>> amount of information over time as fewer individuals became
>>>> identifiable).  Records for all of SCI's infants last known to be
>>>> living end on 11 June 1993, which is also when SCI's census record
>>>> ends, save for a single demog note entry in August 2001.  In fact,
>>>> the census records for SCI and others in Proton's group (and from
>>>> what I can tell all of Alto's fission groups) are not actually in
>>>> babase.  Instead there is some kind of interpolated data (more like
>>>> you would see in the members table) that begins on the split date
>>>> (1/1/1989) and goes (for Proton's anyway) through 11 June 1993 and
>>>> was apparently carried over from another database system - Scion is
>>>> listed as R - "(result of Alto's breakup) The datum is S, E, F, B,
>>>> G, T, or L datum which has had locations which were changed from  
>>>> 1.0
>>>> to the group in which the animal was censused on 15/4/92. This
>>>> change left all R rows as part of a contiguous series of days  
>>>> during
>>>> which the animals are located in the Alto's sub-group as censused  
>>>> on
>>>> 15/4/92, and the time-adjacent locations were not 1.0." and her
>>>> slightly older kid Cake, for example, as L (even though he has a
>>>> birthdate in babase) - "(lineage) The group is from the Matgrp on
>>>> the old CYCTOT database, either because the animal did not appear  
>>>> in
>>>> the DISPERSE database, or because the first location for the animal
>>>> in the old DISPERSE database had a Datein and this Datein was after
>>>> the birth date of the animal.".  Proton's then was not monitored
>>>> again until Feb 1994 (maybe they were in Tanzania?).
>>>>
>>>> Catherine said she recalled at some point that this census data was
>>>> supposed to be fixed.  She thought by Lacey?  Is this still in
>>>> progress somewhere?  On the backburner?  Forgotten?  Should this be
>>>> brought back from the dead?
>>>>
>>>> In addition to the lost census information there is clearly other
>>>> useful information that can be gleaned from these data, such as
>>>> presence of white infants).  This wonky split/database conversion
>>>> combination also led to inclusion of a bunch of pretty much useless
>>>> data in babase.
>>>>
>>>> Furthermore, it is clear from the darting/white infant demography
>>>> note and the dates that Cocoa is SCI5, but SCI5 is the one case
>>>> listed as "pregnancy with undetermined outcome" (status 4).  Given
>>>> the demography note, I'm not sure why that code was invented but
>>>> perhaps the demography note was forgotten since it was not in
>>>> babase?  There may be other cases where this code should be used,
>>>> particularly among the data from 1996 - 1999 that has not been
>>>> entered into babase and where information becomes increasingly
>>>> sketchy over time.
>>>>
>>>> The demography note [with comments]:
>>>> "14 Mar 94  1330 - Scion darted, fitted with radio collar (channel
>>>> 6), released at 1700, rejoined group.  NOTE: Scion has an infant,
>>>> named Cocoa, ~9 months old, that looks unwell.  Coat is extremely
>>>> pale, almost white and kid spent most of morning riding lying
>>>> dorsal.  After Scion was darted, it joined other kids and played,
>>>> continued after Scion returned to group.
>>>>
>>>> "There is no record of this kid's birth or sex.  RSM/SNS have been
>>>> assuming it was Cake (born Jun92) but this is not possible.  We
>>>> looked at reproductive records; decided that it was likely to have
>>>> been conceived in Feb 93 (she's scored as cycling in Feb and Jan93,
>>>> then as PPA [flat and black, actually] in Mar) and born Aug93.  She
>>>> was seen only once, Jun93, in the interim [no data collected in
>>>> April or May] and scored P/B at that time, but this was not noted  
>>>> on
>>>> the reproductive records in the field notebook [not sure what this
>>>> means - she is marked P/B on the sexskin sheet in the 1993 notebook
>>>> - 11 June was the only census date that month].  No census of
>>>> Proton's done, June93-Jan94.  The new infant has been called Cake
>>>> since Mar94 [but Cake and other juveniles, aside from infants seen
>>>> with their mothers, was not marked present on 1994 census sheets -
>>>> Cocoa was, beginning in May, where he is marked as male - he is
>>>> sporadically marked present for the rest of 2004 but then either
>>>> died or joined the older juveniles in the realm of the
>>>> nonidentifiable]; not known if Cake present.
>>>>
>>>> "Note: Something similar may have happened with Voi, less likely
>>>> with Vera, Sunbird."
>>>>
>>>> Scion's kids:
>>>> bioid ¦ sname ¦ name  ¦ pid  ¦ birth      ¦ bstatus ¦ sex ¦
>>>> matgrp ¦ statdate   ¦ status ¦ dcause
>>>> −−−−−−+−−−−−−−+−−−−−−−+−
>>>>>>>> −−−−+−−−−−−−−−−−−+−−−−− 
>>>>>>>> −−−+−−−−−+−−−−−−−−+−−−−−
>>>>>>>> −−−−−−+−−−−−−−−+−−−−−−−
>>>> 67 ¦ CAS   ¦ CASEY ¦ SCI1 ¦ 1988-02-05 ¦       0 ¦ F   ¦
>>>> 1.00 ¦ 1993-06-11 ¦      0 ¦      0
>>>> 74 ¦ CHO   ¦ CHOMA ¦ SCI2 ¦ 1989-10-23 ¦       0 ¦ M   ¦
>>>> 1.00 ¦ 1989-11-26 ¦      1 ¦      1
>>>> 68 ¦ CAT   ¦ CATE  ¦ SCI3 ¦ 1990-11-01 ¦       0 ¦ F   ¦
>>>> 1.30 ¦ 1993-06-11 ¦      0 ¦      0
>>>> 63 ¦ CAK   ¦ CAKE  ¦ SCI4 ¦ 1992-06-05 ¦       0 ¦ M   ¦
>>>> 1.30 ¦ 1993-06-11 ¦      0 ¦      0
>>>> 1015 ¦       ¦       ¦ SCI5 ¦ 1993-06-11 ¦       1 ¦ U   ¦
>>>> 1.30 ¦ 1993-06-11 ¦      4 ¦      7
>>>>
>>>>
>>>>
>>>> -----Original Message-----
>>>> From: Susan Alberts [mailto:alberts at duke.edu]
>>>> Sent: Saturday, October 10, 2009 11:01 AM
>>>> To: Jeanne Altmann
>>>> Cc: Niki H. Learn
>>>> Subject: Re: JA input needed - wounds and pathologies question
>>>>
>>>> OK, so we're agreed on 2 codes, one for the walk and one for the
>>>> white
>>>> fur. I don't think it is feasible to have a "stiff walk" code that
>>>> is
>>>> specific to this particular pathology, simply because our judgment
>>>> won't always be right -- we're not making a clinical assessment,
>>>> just
>>>> an observational one. I think it makes sense to just class it with
>>>> other instances of "stiff walk."
>>>>
>>>> It does seem to me that it will be useful to track down Alison's
>>>> work
>>>> and compare it to what you have found, Niki. I don't know whether
>>>> you'll be able to do that before Jeanne gets home, but it seems  
>>>> like
>>>> the next step in the process of figuring out what to do.
>>>>
>>>> Susan
>>>>
>>>> On Oct 10, 2009, at 4:05 AM, Jeanne Altmann wrote:
>>>>
>>>>> Sorry for the delay.
>>>>> Thanks for the analysis and thoughtful input Niki.
>>>>>
>>>>> I agree that we should have 2 codes, 1 for the walk, the other for
>>>> the
>>>>> white fur and that infants exhibiting both should get both. I am
>>>>> not
>>>>> clear whether we need a new code for stiff walk or can use the
>>>>> existing
>>>>> one for locomotor problem? However, Susan rightly raised the
>>>> potential
>>>>> confusion when we have a localized locomotor problem that seems to
>>>> be
>>>>> from a fall or wound (e.g. thorn or other injury of that sort).
>>>>>
>>>>> It would be good to see whether Alison caught all of the candidate
>>>>> infants--multiple-limb, non-injury stiff walk or white fur.
>>>>>
>>>>> jeanne
>>>>>
>>>>> -----Original Message-----
>>>>> From: Niki Learn [mailto:nlearn at princeton.edu]
>>>>> Sent: Friday, October 09, 2009 1:48 PM
>>>>> To: 'Jeanne Altmann'
>>>>> Subject: FW: JA input needed - wounds and pathologies question
>>>>>
>>>>> Jeanne,
>>>>>
>>>>> Have you had an opportunity to look at this?
>>>>>
>>>>> Currently the "stiff walk" associated with white monkey syndrome
>>>>> has
>>>>> been
>>>>> listed using two or three different codes (malaise/weakness, other
>>>>> pathology, etc.).  I had suggested combining it with the code for
>>>>> white
>>>>> fur
>>>>> but Susan thought it would be better to give the stiff walk its  
>>>>> own
>>>>> code,
>>>>> which is fine too.  I think we then should just mark the rare
>>>>> individual
>>>>> with both white fur and the stiff walk with both codes.
>>>>>
>>>>> Thanks,
>>>>> Niki
>>>>>
>>>>> -----Original Message-----
>>>>> From: Susan Alberts [mailto:alberts at duke.edu]
>>>>> Sent: Tuesday, September 29, 2009 8:55 AM
>>>>> To: Jeanne Altmann
>>>>> Cc: Niki H. Learn; Lacey Maryott
>>>>> Subject: Re: JA input needed - wounds and pathologies question
>>>>>
>>>>> I think there is no hurry or urgency on this at all -- it can
>>>> wait. I
>>>>> just wanted to make sure that you knew it will need your input.
>>>>>
>>>>> Susan
>>>>>
>>>>>
>>>>> On Sep 29, 2009, at 8:07 AM, Jeanne Altmann wrote:
>>>>>
>>>>>> Hi niki & susan,
>>>>>> You'll need to give me a few more days to get back to you on  
>>>>>> this,
>>>>>> Sorry,
>>>>>> jeanne
>>>>>>
>>>>>> -----Original Message-----
>>>>>> From: Susan Alberts [mailto:alberts at duke.edu]
>>>>>> Sent: Monday, September 28, 2009 3:54 PM
>>>>>> To: Niki H. Learn
>>>>>> Cc: 'Jeanne Altmann'; 'Lacey Maryott'
>>>>>> Subject: Re: JA input needed - wounds and pathologies question
>>>>>>
>>>>>> Hi, see below.
>>>>>>
>>>>>>
>>>>>>> Adding another code for the stiff walking makes a lot of sense.
>>>>>>> Since none
>>>>>>> of the older cases appear to have received wounds & pathologies
>>>>>>> sheets there
>>>>>>> are only cases from 2004 onward then in the record so far.   
>>>>>>> Would
>>>>>>> previous
>>>>>>> cases have been noted in demography notes or something?  (There
>>>> are
>>>>>>> a few
>>>>>>> recent cases where wounds and illnesses mentioned in demog notes
>>>>>>> that did
>>>>>>> not have wounds sheets were added to the database but I don't
>>>> think
>>>>>>> this was
>>>>>>> done for older data and maybe not consistently for the newer
>>>> data.)
>>>>>>
>>>>>> I think Jeanne needs to give input on this. I believe she had an
>>>>>> undergrad working on this at one point, and there was an issue of
>>>>>> finding these cases if I recall correctly. I think it turned out
>>>> that
>>>>>> they had not been consistently recorded. But, I also seem to
>>>>>> recall
>>>>>> that the undergrad scoured the data and found whatever there
>>>>>> was. I
>>>>>> certainly do feel like there have been cases before 2004 but I
>>>> don't
>>>>>> remember.
>>>>>>
>>>>>>> I think
>>>>>>> Rhus is the only one that displayed both symptoms during the
>>>> 2004-6
>>>>>>> period
>>>>>>> and Rhus currently has two codes for the one illness.  We could
>>>>>>> easily have
>>>>>>> the two symptoms separate and just assign both to any  
>>>>>>> individuals
>>>>>>> that
>>>>>>> display both symptoms.
>>>>>>>
>>>>>>> What about the Coxsackie?  Is that something that has shown up
>>>> again
>>>>>>> since
>>>>>>> 1987?  Should that have a code of its own if the team is readily
>>>>>>> able to
>>>>>>> identify it?  Or is it really only obvious that it's Coxsackie
>>>> if a
>>>>>>> bunch of
>>>>>>> animals are seen with it at once like in 1987?
>>>>>>
>>>>>> I don't know. I suspect that the team would not name it. I don't
>>>>>> think
>>>>>> we've had any outbreaks of multiple individuals since 1987, but  
>>>>>> we
>>>>>> may
>>>>>> have had single cases, and I don't think we would necessarily  
>>>>>> know
>>>>>> from the wounds sheets.
>>>>>>
>>>>>> Susan
>>>>>>
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Niki
>>>>>>>
>>>>>>> -----Original Message-----
>>>>>>> From: Susan Alberts [mailto:alberts at duke.edu]
>>>>>>> Sent: Monday, September 28, 2009 3:17 PM
>>>>>>> To: Niki Learn
>>>>>>> Cc: 'Jeanne Altmann'; 'Lacey Maryott'
>>>>>>> Subject: Re: wounds and pathologies question
>>>>>>>
>>>>>>> Hi Niki,
>>>>>>>
>>>>>>> Thanks for the detailed input.
>>>>>>>
>>>>>>> The 1987 outbreak was a different pathology, as far as we know,
>>>> from
>>>>>>> white monkey syndrome (I am the SA that took the notes with RSM
>>>> -- I
>>>>>>> didn't know I ever used just SA!). We think this is so because,
>>>>>>> unlike
>>>>>>> white monkey syndrome, which develops somewhat gradually, the
>>>>>>> 1987
>>>>>>> cases came on very suddenly and resolved fairly quickly and
>>>> affected
>>>>>>> all age classes, not just infants. And, there was no white fur.
>>>>>>> It
>>>>>>> behaved like a previous outbreak of Coxsackie virus (a water-
>>>>>>> borne
>>>>>>> virus) that Jeanne and Stuart identified in the 1960's. I
>>>> guessed at
>>>>>>> the time that it was Coxsackie, but have no real way of knowing.
>>>>>>> But,
>>>>>>> it wasn't the same as the syndrome that the little kids get.  
>>>>>>> It's
>>>>>>> true
>>>>>>> that the stiffness of the walk is similar, but the onset and
>>>>>>> termination were so much more rapid, and other things so
>>>> different,
>>>>>>> that I think it's a reasonable assumption.
>>>>>>>
>>>>>>> Regarding how to record it when it seems to be what we are
>>>>>>> calling
>>>>>>> white monkey syndrome, I would almost favor creating a new
>>>> category
>>>>>>> just for that (combination of white fur and stiff walking OR
>>>>>>> stiff
>>>>>>> walking in an infant that appears to be consistent with white
>>>> monkey
>>>>>>> syndrome). This would potentially create errors if we categorize
>>>> the
>>>>>>> disease wrong but would have the advantage of making it a lot
>>>> easier
>>>>>>> to find these cases. I think using 10 is way to nonspecific  
>>>>>>> given
>>>>>>> what
>>>>>>> we know about the disease.
>>>>>>>
>>>>>>> How does this sound?
>>>>>>>
>>>>>>> SUsan
>>>>>>>
>>>>>>>
>>>>>>> On Sep 28, 2009, at 2:52 PM, Niki Learn wrote:
>>>>>>>
>>>>>>>> There is a sheet of observations from 2006 that specifically
>>>> deals
>>>>>>>> with
>>>>>>>> identified and possible white monkey infants.  This refers to
>>>>>>>> the
>>>>>>>> stiff walk
>>>>>>>> as a "walking problem with the back legs".  In the regular
>>>>>>>> wounds
>>>>>>>> and
>>>>>>>> pathologies sheets I found references to white-furred and  
>>>>>>>> stiff-
>>>>>>>> walking
>>>>>>>> baboons between 2004 and 2006 - I guess there was a bit of an
>>>>>>>> outbreak then.
>>>>>>>> For these years the wounds and pathologies sheets almost always
>>>>>>>> call
>>>>>>>> it
>>>>>>>> the/that "stiff walk".  Sometimes when white fur is mentioned
>>>>>>>> the
>>>>>>>> team
>>>>>>>> specifically noted that no stiff walk was noticeable.  Rhus had
>>>>>>>> both
>>>>>>>> white
>>>>>>>> fur and the stiff walk.  Rhus is marked with both codes 15
>>>>>>>> (white
>>>>>>>> fur) and
>>>>>>>> 10 (malaise, weakness, stiffness in absence of wound).   
>>>>>>>> Little's
>>>>>>>> note
>>>>>>>> referred directly to this case: "She is beginning to have that
>>>>>>>> stiff
>>>>>>>> walk
>>>>>>>> like Rhus".  This is one of the ones marked with a 14 (other
>>>>>>>> pathology)
>>>>>>>> during the more recent data entry effort.
>>>>>>>>
>>>>>>>> It appears there was another outbreak in 1987 where 31 animals
>>>> were
>>>>>>>> given
>>>>>>>> pathology sheets on the same day with the same symptoms.  They
>>>> were
>>>>>>>> all
>>>>>>>> reported on one sheet by SA and RSM with the following note
>>>>>>>> "Partial
>>>>>>>> hind
>>>>>>>> limb paralysis with stiff, not fully extended legs seen in many
>>>>>>>> baboons of
>>>>>>>> Alto group on this same day".  These are marked with pathology
>>>> code
>>>>>>>> 10
>>>>>>>> (malaise, weakness, stiffness in absence of wound).  There is  
>>>>>>>> no
>>>>>>>> mention of
>>>>>>>> white fur in these notes.  Strangely the symptoms were gone  
>>>>>>>> five
>>>>>>>> days later
>>>>>>>> and the original datasheet mentions that "this bout of  
>>>>>>>> paralysis
>>>>>>>> was
>>>>>>>> very
>>>>>>>> brief relative to bouts of paralysis in the past".  I have not
>>>> yet
>>>>>>>> found any
>>>>>>>> prior references though - perhaps they were not previously
>>>> recorded
>>>>>>>> on
>>>>>>>> wounds sheets?  There are no cases of white fur recorded back
>>>> then
>>>>>>>> either -
>>>>>>>> the first record of it (in wounds and pathologies) appears to
>>>> be in
>>>>>>>> 2004.
>>>>>>>>
>>>>>>>> Sometimes stiff or stiffly is used when referring to walking or
>>>>>>>> general
>>>>>>>> movement of other baboons but "stiff walk" is not used and it  
>>>>>>>> is
>>>>>>>> pretty
>>>>>>>> clear from the notes that the baboon is wounded, has stiffness
>>>>>>>> restricted to
>>>>>>>> one limb though no wound is visible, is sick in some other way,
>>>> or
>>>>>>>> is just
>>>>>>>> plain getting old (this last often includes mention of being
>>>>>>>> hunched).
>>>>>>>> There are very few cases where "stiff walk" or the above note
>>>>>>>> for
>>>>>>>> Alto's
>>>>>>>> group was not used that cannot be quickly recognized as being
>>>> cause
>>>>>>>> by one
>>>>>>>> of these other causes.
>>>>>>>>
>>>>>>>> I would definitely say we need to change the ones that are
>>>>>>>> listed
>>>>>>>> as
>>>>>>>> 14 - we
>>>>>>>> could go with 10, as in the 1987 cases and even Rhus' case, or
>>>>>>>> expand 15 to
>>>>>>>> include the stiff walk along with white fur under the umbrella
>>>>>>>> of
>>>>>>>> white
>>>>>>>> monkey syndrome.
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Niki
>>>>>>>>
>>>>>>>> -----Original Message-----
>>>>>>>> From: Susan Alberts [mailto:alberts at duke.edu]
>>>>>>>> Sent: Saturday, September 26, 2009 10:14 AM
>>>>>>>> To: Niki Learn
>>>>>>>> Cc: 'Jeanne Altmann'
>>>>>>>> Subject: Re: wounds and pathologies question
>>>>>>>>
>>>>>>>> Thanks Niki,
>>>>>>>>
>>>>>>>> It might be helpful if you could compile a list of the  
>>>>>>>> different
>>>>>>>> ways
>>>>>>>> the white monkey syndrome has been recorded in the past, as you
>>>>>>>> alluded to below. Then Jeanne and you and I and Lacey can
>>>> consider
>>>>>>>> options better.
>>>>>>>>
>>>>>>>> Susan
>>>>>>>>
>>>>>>>> On Sep 25, 2009, at 1:53 PM, Niki Learn wrote:
>>>>>>>>
>>>>>>>>> Sure, we'll see what Jeanne says.  All the instances I've seen
>>>> so
>>>>>>>>> far refer
>>>>>>>>> to it as "that stiff walk" or "the stiff walking" so it seems
>>>> like
>>>>>>>>> the team
>>>>>>>>> has a specific way they refer to it.
>>>>>>>>>
>>>>>>>>> Also I found a case this morning where one individual was at
>>>> first
>>>>>>>>> noted to
>>>>>>>>> have white fur and then developed the stiff walk.  The team
>>>> wrote
>>>>>>>>> up a
>>>>>>>>> separate wounds sheet for the stiff walking but noted that it
>>>>>>>>> was a
>>>>>>>>> continuation of the other note.  In the wounds database this
>>>>>>>>> was
>>>>>>>>> combined as
>>>>>>>>> one note but given two wounds/pathologies codes, 15 for the
>>>> white
>>>>>>>>> fur and 10
>>>>>>>>> for "Malaise, weakness, stiffness in absence of wound", which
>>>>>>>>> seems
>>>>>>>>> more
>>>>>>>>> appropriate than the 14 (other pathology) that Tabby used
>>>> anyway,
>>>>>>>>> if
>>>>>>>>> we want
>>>>>>>>> to keep the stiff walk separate (a code I suspect will get
>>>> used a
>>>>>>>>> lot in
>>>>>>>>> this year's wounds & pathologies entries for those slipping
>>>>>>>>> away
>>>>>>>>> due
>>>>>>>>> to the
>>>>>>>>> drought).  One of the cases I found yesterday even referred to
>>>>>>>>> this
>>>>>>>>> individual's case, as in "so and so is developing that stiff
>>>> walk
>>>>>>>>> like
>>>>>>>>> Rhus".
>>>>>>>>>
>>>>>>>>> In any case there seems to have been some inconsistency in how
>>>> the
>>>>>>>>> stiff
>>>>>>>>> walk has been recorded under different data people.  I also
>>>> found
>>>>>>>>> that
>>>>>>>>> sometimes body part code 44 (over entire body) is entered for
>>>>>>>>> cases
>>>>>>>>> of white
>>>>>>>>> fur and in other cases there is no entry for body part (as is
>>>> the
>>>>>>>>> case with
>>>>>>>>> the stiff walk and "limping, no wound visible" if no body part
>>>> was
>>>>>>>>> specified
>>>>>>>>> by the team).  So I will wait to see what the consensus is and
>>>>>>>>> then
>>>>>>>>> implement a uniform policy for it.
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>> Niki
>>>>>>>>>
>>>>>>>>> -----Original Message-----
>>>>>>>>> From: Susan Alberts [mailto:alberts at duke.edu]
>>>>>>>>> Sent: Friday, September 25, 2009 1:35 PM
>>>>>>>>> To: Niki Learn
>>>>>>>>> Cc: 'Jeanne Altmann'
>>>>>>>>> Subject: Re: wounds and pathologies question
>>>>>>>>>
>>>>>>>>> Thanks Niki,
>>>>>>>>>
>>>>>>>>> I like your idea of modifying the description to read "white
>>>>>>>>> monkey
>>>>>>>>> syndrome, symptoms = white fur and/or stiff walk". In  
>>>>>>>>> practice,
>>>>>>>>> these
>>>>>>>>> two symptoms are different, but we do seem to be converging on
>>>> the
>>>>>>>>> idea that they are indicating the same thing. And, it is very
>>>>>>>>> likely
>>>>>>>>> that the team essentially treats them as two different
>>>>>>>>> manifestations
>>>>>>>>> of the same thing. That is, it seems possible that both would
>>>>>>>>> occur
>>>>>>>>> but they would record only one at a time, and not refer to an
>>>>>>>>> individual with stiff walking already having had white fur,
>>>>>>>>> especially
>>>>>>>>> if they did a "white fur" sheet a couple of months prior.
>>>>>>>>>
>>>>>>>>> I think the risk is that stiff walking could come from other
>>>>>>>>> things,
>>>>>>>>> so we run the risk of attributing some stiff walking to white
>>>>>>>>> monkey
>>>>>>>>> syndrome when it's not really that.
>>>>>>>>>
>>>>>>>>> I'd like to hear Jeanne's thoughts. Also she might recall the
>>>>>>>>> discussion when Tabby changed them to 14.
>>>>>>>>>
>>>>>>>>> Susan
>>>>>>>>>
>>>>>>>>> On Sep 25, 2009, at 9:13 AM, Niki Learn wrote:
>>>>>>>>>
>>>>>>>>>> Jeanne and Susan,
>>>>>>>>>>
>>>>>>>>>> I've been sifting through the wounds and pathologies tables
>>>>>>>>>> figuring
>>>>>>>>>> out
>>>>>>>>>> where things left off, how this or that was assigned, and
>>>>>>>>>> investigating
>>>>>>>>>> bizarre notes, etc.  I found two notes from Linda's 2006
>>>>>>>>>> wounds
>>>>>>>>>> where young
>>>>>>>>>> baboons developed "that stiff walk that some Viola's  
>>>>>>>>>> juveniles
>>>>>>>>>> get".
>>>>>>>>>> Both
>>>>>>>>>> were followed for several months and the stiff walk did not  
>>>>>>>>>> go
>>>>>>>>>> away
>>>>>>>>>> during
>>>>>>>>>> that time.  These were originally marked with a pathology
>>>> code of
>>>>>>>>>> 15
>>>>>>>>>> (white
>>>>>>>>>> fur) and Tabby changed them to 14 (other pathology).  I don't
>>>>>>>>>> know
>>>>>>>>>> who
>>>>>>>>>> entered them originally but I remember from Alison's
>>>> presentation
>>>>>>>>>> at
>>>>>>>>>> the
>>>>>>>>>> joint meeting that this stiff walk was also a symptom of  
>>>>>>>>>> white
>>>>>>>>>> monkey
>>>>>>>>>> syndrome, just like the white fur and that baboons often
>>>>>>>>>> displayed
>>>>>>>>>> only one
>>>>>>>>>> of the two symptoms.  So wouldn't the original code of 15 be
>>>>>>>>>> correct
>>>>>>>>>> here?
>>>>>>>>>> Perhaps the code description should be updated to read
>>>> something
>>>>>>>>>> like "White
>>>>>>>>>> monkey syndrome, symptoms = white fur and/or stiff walk"?
>>>>>>>>>>
>>>>>>>>>> Thanks,
>>>>>>>>>> Niki
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --------------------------------------------------------
>>>>>>>>> Susan Alberts, Dept of Biology, Duke University, Box 90338,
>>>> Durham
>>>>>>>>> NC
>>>>>>>>> 27708, 919-660-7272 (Ph), 919-660-7293 (Fax)
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>> --------------------------------------------------------
>>>>>>>> Susan Alberts, Dept of Biology, Duke University, Box 90338,
>>>> Durham
>>>>>>>> NC
>>>>>>>> 27708, 919-660-7272 (Ph), 919-660-7293 (Fax)
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>> --------------------------------------------------------
>>>>>>> Susan Alberts, Dept of Biology, Duke University, Box 90338,
>>>>>>> Durham
>>>>>>> NC
>>>>>>> 27708, 919-660-7272 (Ph), 919-660-7293 (Fax)
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>> --------------------------------------------------------
>>>>>> Susan Alberts, Dept of Biology, Duke University, Box 90338,
>>>> Durham NC
>>>>>> 27708, 919-660-7272 (Ph), 919-660-7293 (Fax)
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>> --------------------------------------------------------
>>>>> Susan Alberts, Dept of Biology, Duke University, Box 90338, Durham
>>>> NC
>>>>> 27708, 919-660-7272 (Ph), 919-660-7293 (Fax)
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>> --------------------------------------------------------
>>>> Susan Alberts, Dept of Biology, Duke University, Box 90338, Durham
>>>> NC
>>>> 27708, 919-660-7272 (Ph), 919-660-7293 (Fax)
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> -- 
>>>> - -
>>>> 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)
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Babase mailing list
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>>>
>>>
>>> _______________________________________________
>>> Babase mailing list
>>> Babase at www.eco.princeton.edu
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>>
>> --------------------------------------------------------
>> Susan Alberts, Dept of Biology, Duke University, Box 90338, Durham NC
>> 27708, 919-660-7272 (Ph), 919-660-7293 (Fax)
>>
>>
>>
>>
>>
>> _______________________________________________
>> Babase mailing list
>> Babase at www.eco.princeton.edu
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>>
>> _______________________________________________
>> Babase mailing list
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>
> --------------------------------------------------------
> Susan Alberts, Dept of Biology, Duke University, Box 90338, Durham NC
> 27708, 919-660-7272 (Ph), 919-660-7293 (Fax)
>
>
>
>
>
> _______________________________________________
> Babase mailing list
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------------------------------------------------------------
Susan Alberts, Dept of Biology, Duke University, Box 90338, Durham NC  
27708. Phone 919-660-7272, FAX 919-660-7293






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