[Babase] Social interaction documents 2nd draft

Susan Alberts alberts at duke.edu
Sat Feb 4 17:59:51 EST 2006


Thanks Karl, my comments below. I am trying your proposed method of 
inserting them into text of the email. Tell me how it works.

>
>1. Introduction

Looks good, no comments

>
>    Other Resources
>2. Babase System Architecture
>
>     Table Overview
>       (Descriptions of tables below.)

Fix this:

Anyone working with Babase will require a

familiarity

  with  the database's tables. An understanding of the entity each row 
represents is critical when working with a table. The remainder  of 
this section provides short definitions of the entities each  table 
holds in its rows.

I don't understand the following warning,

Use views in place of tables with names ending in  "_DATA" to ensure 
compatiblity with future Babase  releases.

I suggest you replace it with some sentences that have you further 
down in the doc under "Views", as follows. It is OK to repeat this in 
two places:
Tables which  have names ending in "_DATA" should not be used,  there 
is always a view of the data in these tables that may be  used in 
their place. Tables ending in "_DATA" may change in future Babase 
minor releases, breaking queries  and programs which use the table. 
Use of the corresponding  views will ensure compatibility with future 
Babase  releases.

In table 2.3, fix this:

problem in identifying neighbor of focal during point sampling
[DELETE "all occurrences" from this sentence]

>     Entity-Relationship Diagrams
>       (All the tables and views below.)


Looks good, no comments.

>     Views
>       (Intro text and descriptions of
>        views below.)


A spelling error: menstruation not menstration
>
>3. Baboon Data: Primary Source Material
>
>     INTERACT_DATA (Interactions)


IN the following section I don't think you need the first sentence. 
Put the parentheticals in the next two sentences and delete the 
first, it will be clearer:

There are certain lower limits as to when mount (ACTS.Class of  M), 
consortship (ACTS. Class of  C), and ejaculation (ACTS. Class of  E) 
interactions may occur.[49] 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.

I suggest  the following :

Many rules surrounding INTERACT_DATA's values are closely  tied to 
the project's data collection protocols. There are two  general sorts 
of data on behavioral events:  all-occurrences data and  ad-libitum 
data. All occurrences data  are

collected during focal animal samples. They are

data on all the occurrences of a particular behavior or  interaction 
during a given time interval and/or involving a  participating focal 
individual.[50]

I suggest the following:

Although consortship and  mount[51] information is collected

as all-occurrences data during focal  samples

that information, along with ejaculation information,

does not appear in INTERACT_DATA with an SID associated with it. This 
is because our protocol requires that consortships be recorded with a 
duration, and the palmtop data collection protocol does not 
accomodate this. Hence, all consortship, mounts and ejactulations are 
to be collected on paper via  ad libitum sampling and so,

presumably, there will  always be a INTERACT_DATA row for the 
consortship, mount, or  ejaculation from the ad-libitum sample data 
collection.

I suggest:

It is expected that  ad-libitum data

are

  entered with a 1 minute precision.[52] Consequently the seconds 
portion of the time value  must always be 0 when Sid is NULL. 
All-occurrences interaction data (Sid is not NULL)

do

  contain seconds.[53]

Karl: do global changes on the following:

"Data is" should be changed to "data are", "data was" to "data were", 
"data does" to "data do", "data has" to "data have", "this data" to 
"these data", "data that does" to "data that do". I will try to think 
of others.

>     PARTS (Participants in interactions)


Looks good.

>     SAMPLES (focal point Sample set)


I suggest the following change:

One row for every

focal animal sample, i.e., one row for every

continuous period of time during which  data is collected at regular 
intervals on a specific focal  individual. Although the field 
protocols center around  collecting data primarily stored in the 
POINT_DATA table, other information, normally  collected during 
ad-libitum data collection, may be collected as  well and are also 
associated with the sample set. Further, a  sample is allowed to 
contain no

information identifying the focal animal.[54]

Each SAMPLES row contains the information  pertaining to all the data 
collected during the sample

including the identity of the focal animal.

I suggest the following change. Instead of:

The date of the sample set.[56] This column may not be  NULL.

how about:

The date of the focal animal sample.[56] This column may not be  NULL.

>     POINT_DATA (focal Point sample data)


I suggest in th3e table description:

One row for every point observation collected on a focal  individual during a

focal animal sample.

>     FPOINTS (focal Point sample data on Females)


Looks good.

>     NEIGHBORS (focal point sample data on Neighbors)


Looks good

>     ADLIBS (Adlib focal point sample data)


You changed the name of this table to All_miscs..

Change the following:

The data that

do

  not conform to the design of INTERACT_DATA and POINT_DATA

are

  kept in the ALLMISC table.

Change the following:

Consortships recorded as ad-libitum data during focal point  sampling 
are not stored on INTERACT_DATA  because INTERACT_DATA requires that 
consortships have a starting and an ending time and data  collected 
during focal point sampling

are

  without duration.  Such consortship data

are

  stored as an ALLMISCS row.


Karl, you note:

Babase does the same thing with ejaculations recorded on  the 
palmtops as it does with mounts: it records them in ALLMISCS rather 
than INTERACT_DATA. However, the protocol says nothing  about 
ejaculations occurring during all-occurrences sampling.  Anyone 
researching ejaculations will need to investigate this  further.

This is just an oversight in the protocol. Ejaculations are treated 
exactly the same way as mounts and this should be reflected in your 
document throughout.

That's as far as I got today, I will continue with support tables and 
views etc tomorrow.


Susan


>
>6. Support Tables
>
>     FOODCODES (Food item Codes)
>     FOODTYPES (Food Types)
>     KIDCONTACTS (spacial relationship between female and infant)
>     SUCKLES (infant suckling activity)
>     ACTS (Interaction Types)
>     ACTIVITIES
>     NCODES (Neighbor classifications)
>     POSTURES
>     UNKSNAMES (problem in identifying focal's neighbor)
>     OBSERVERS (Field Data Collection Staff)
>     PALMTOPS (the Palmtop handheld data collection units)
>     PROGRAMIDS (Program versions used on the palmtop)
>    SETUPIDS (Setup files used on the palmtop)
>
>7. The Babase Views
>
>     INTERACT (INTERACT_DATA, with enhanced dates and times)
>     POINTS (POINT_DATA, with enhanced times)
>     ACTOR_ACTEES (Complete social interactions, INTERACT extended
>                   twice with PARTS)
>
>10. Babase PROGRAMS
>
>     Useful Programs and Functions
>      (Somehow I've lost these from the table of contents,
>       you'll have to use the "next" link.)
>      spm
>      spm_to
>
>A. Manipulating Date and Time Values
>
>C. Changes to Babase between 1.0 and 2.0
>     Changes JPSAMPS and FPSAMPS (and POINT_DATA and FPOINTS)
>     Changes to Time Representation
>     Changes to the All-Occurrences and Ad-Lib Focal Point Data
>
>
>
>
>Karl <kop at meme.com>
>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, Associate Professor 
Department of Biology, Duke University, Box 90338, Durham NC 27708 
phone 919-660-7272  fax 919-660-7293


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