[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
>
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--
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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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