[Babase] Reproductive cycling info
Karl O. Pinc
babase@www.eco.princeton.edu
Sun, 30 Jan 2005 08:35:42 +0000
Hi,
Here's what I've got so far. I'm stopping now because
questions keep coming up, particulary regards the 'seed'
dates. They were supposed to inform the system regards
post menarche females who come under observation after
reaching menarche. But I'm starting to have questions
about periods when there's big observational gaps (war, etc.)
Also, I've not tried to incorporate the 'guessed' M dates
or made any other changes to the CYCSTATS doc here. (I've
got notes on the T date guess when there's a D date.)
The SEED table docs are incomplete and fuzzy.
REPSTATS is worth looking at.
Probably best to wait until I show up to discuss things.
I have ideas (TM). I don't think we're that far
off.
Karl <kop@meme.com>
Free Software: "You don't pay back, you pay forward."
-- Robert A. Heinlein
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REPSTATS
(REProductive STATus) Contains one row per female per day from post
menarche date, when menarche is observed, through date of death
(inclusive). When menarche is unobserved then REPSTATS rows begin on
a 'seed' date supplied by the user. (See SEEDS.) While the
individual is alive the last date is either the statdate or the last
recorded sexual cycle endpoint, which ever is later. End of cycle
dates are T (turgesence onset) date or end-of-pregnancy date. The
day-by-day nature of this table makes it easy to correlate sexual
cycle information with other events.
Note that because of gaps in the observational record some sexual
cycles may not be recorded, or may be partially recorded. Therefore
the Din and Dr column values cannot be accepted without critical
examination because they reflect recorded values and so may indicate
over-long cycle times when the information in the database is
incomplete.
See CYCSTATS for more fertility detail.
Data Entry Rules
This table is not maintainable by the user. The system constructs
this table automatically from the data values recorded in the CYCLES
table, the BIOGRAPH.Status and BIOGRAPH.Statdate columns, and the
SEEDS table.
Data Element Descriptions
Rid
A unique number which serves to identify the row.
Date
The row records a female's reproductive state on this day.
Sname
The Sname identifying the female whose reproductive state is recorded.
(See BIOGRAPH.)
State
General reproductive state of the female on the Date given. The legal
values are: P (pregnant), from the D (deturgesence onset) date through
the end-of-pregnancy date (inclusive of endpoints). C (cycling), from
(including) the T (turgesence onset) date up to (but not including)
the T date of the following cycle, or in the case of pregnancy, up to
(but not including) the D date. L (lactating), from (but not
including) the end-of-pregnancy date to (but not including) the next
T date. Note that post menopausal individuals have a state of C, or
possibly L if the last cycle resulted in a pregnancy.
Dins (NULL allowed)
(Days INto State) The number of days since the state started. The
first day of the state has a value of 1, the next a value of 2, etc.
This column is NULL when the system cannot determine when the state
began. This occurs when the starting date of a female's cycle is
obtained from the SEEDS table.
See the table description above for caveats regarding the accuracy of
this column.
Dr (NULL allowed)
(Days Remaining) The number of days remaining in the state. The last
day of the state has a value of 0, the next to last day a value of 1,
etc. Note that the sum of Dins and Dr is always the total number of
days the cycle spent in the state.
This column is NULL when the system cannot determine when the state
ends because data remains to be entered. This occurs under the
following conditions: When there is a record of the start of a
pregnancy but no record of the pregnancy's end. (Birth, death of the
mother, abortion, etc. end the pregnancy.) When the end of the state
is set based upon BIOGRAPH.Statdate and BIOGRAPH.Status indicates the
individual is still alive.
See the table description above for caveats regarding the accuracy of
this column.
Cids
(Census IDentifier at Start of cycle) The Cid of the CENSUS row which
records the beginning of the cycle. (See CENSUS table.)
Cide (NULL allowed)
(Census IDentifier at End of cycle) The Cid of the CENSUS row which
records the end of the cycle. NULL for the last cycle of an
individual. Note that a NULL does not necessarily mean the individual
is post-menopausal, it may simply indicate that the individual has had
no further data entry performed.
Pid
(Pregnancy IDentifier) The Pid of the pregnancy associated with the
state. This value must be present when the state is P or L. There is
also a Pid value for those C cycles that result in pregnancy. (See
PREGS table.)
CYCSTATS
(fertility CYCle STATus) Contains one row per female per day, for
those days in REPSTATS where the REPSTATS Status is C (cycling.) This
is a day-by-day record of the details of the females' fertile
cycles. Where data on a portion of the female's cycles is missing
there will be "gaps" where there are no rows for a female for a
sequence of dates. Missing Mdate, Tdate, or Ddate values in CYCLES
cause gaps. When there is no data on entire cycles, .i.e. some cycles
are not recorded in CYCLES rows, there will not be a gap, but there
will be long cycles that span the entire interval.
Data Entry Rules
This table is not maintainable by the user. The system constructs
this table automatically from the data values recorded in the CYCLES
table, the BIOGRAPH.Status and BIOGRAPH.Statdate columns, and the
SEEDS table.
Data Element Descriptions
Csid
A unique number which serves to identify the row.
Date
The row records a female's reproductive state on this day.
Sname
The Sname identifying the female whose reproductive state is recorded.
(See BIOGRAPH.)
State
Categorizes the period within the reproductive cycle. Legal values
are: F (follicular), the T (turgesence onset) date through 6 days
before the D (deturgesence onset) date (inclusive of endpoints.) O
(ovulating), from 5 days before the D date through the day before the
D date (inclusive of endpoints.) L (luetal), from the D date through
the day before the T date (inclusive of endpoints.) Note that
post-menopausal individuals' final cycles will have a status of L and
a long duration, with the individual's date of death being the last
day of the cycle.
Dins
(Days INto State) The number of days since the state started. The
first day of the state has a value of 1, the next a value of 2, etc.
Dr
(Days Remaining) The number of days remaining in the state. The last
day of the state has a value of 0, the next to last day a value of 1,
etc. Note that the sum of Dins and Dr is always the total number of
days the cycle spent in the state.
Cids
(Census IDentifier at Start of cycle) The Cid of the CENSUS row which
records the beginning of the cycle. (See CENSUS table.)
Cide
(Census IDentifier at End of cycle) The Cid of the CENSUS row which
records the end of the cycle. 0 (empty) for the last cycle of an
individual. Note that a 0 does not necessarily mean the individual is
post-menopausal, it may simply indicate that the individual has had no
further data entry performed.
SEEDS (sexual cycle SEED data)
This table contains one row for every female that is post menarche but
who's menarche was not observed and recorded. It is used to provide
estimates of menarche date.
(Comment: Why don't we use a female's BIOGRAPH.Matured date (now
MATUREDATES.Matured in the new design)
instead? If we do use MATUREDATES.Matured, how will we tell when a
discrepancy between that date and the first CYCLES.Mdate is an error
and when it means that there's missing CYCLES? Perhaps we put an
additional flag on the MATUREDATES table to indicate we want the date
used to begin REPSTATS cycling? IIRC, the answer is that we don't
want REPSTATS all the way from MATUREDATES.Matured when the individual
is old when we start observations, because there could be lots of
pregnancies, etc. We just want the REPSTATS state as of the start of
observations so we can guess at the initial start of that state.
What about long periods of 'gaps' in observation, where there may be
several pregnancies, etc.? That's when we have "blank" CYCLES. Right
now that means that the REPSTATS spanning these 'blank' CYCLES have
'over long' lactation times. (As there's no other cycle data
lactation runs from birth to next pregnancy, right? Do we need to
adjust the design or did we figure this was ok? Not a problem at the
beginning of _any_ observation (no REPSTATS at all) but a problem when
there's gaps after observation starts.) Beginning of pregnancy and
end of pregnancy have 'markers' and so we do get correct (estimated)
REPSTATS times for the pregnancy itself.)
This table exists so that REPSTATS can be populated from the date of
menarche when CYCLES has no row recording menarche.
Data Entry Rules
There are no custom programs used in the maintenance of this table.
Data Element Descriptions
Hid (system generated)
A unique number which serves to identify the row.
Date
Estimated date of menarche.
Sname
Sname of female.
Stae
(STate At Entry??)