[Babase] Repstats / Cycstats document changes
Karl O. Pinc
babase@www.eco.princeton.edu
Thu, 10 Feb 2005 17:56:06 +0000
FYI,
Here's the last set of changes.
The big clarification is that the cycling state on REPSTATS
counts from the starting of cycling up to the next pregnancy,
individual cycles don't "restart" the counting.
Karl <kop@meme.com>
Free Software: "You don't pay back, you pay forward."
-- Robert A. Heinlein
--- orig/doc/BabaseSystem.txt
+++ mod/doc/BabaseSystem.txt
@@ -580,14 +580,14 @@
Pid
The contents of this column uniquely identifies the pregnancy record.
-The Pid is the mothers Sname followed by the parity. Because the Pid
-is only used to identify the record, it is not necessary to change the
-Pid just because the parity of the pregnancy is found to have changed.
-In general, once a unique Pid is established, it should not be
-changed. When retrieving data from this table the safe approach is to
-assume nothing about the contents of this column except that it will
-uniquely identify a pregnancy. Although it is true that the
-non-numeric portion of the PID is the mother's Sname, care must be
+The Pid is the mothers Sname followed by the probable parity. Because
+the Pid is only used to identify the record, it is not necessary to
+change the Pid just because the parity of the pregnancy is found to
+have changed. In general, once a unique Pid is established, it should
+not be changed. When retrieving data from this table the safe
+approach is to assume nothing about the contents of this column except
+that it will uniquely identify a pregnancy. Although it is true that
+the non-numeric portion of the PID is the mother's Sname, care must be
taken because, for instance, an Sname may (and at least one does) end
with a space. The safe way to obtain the bearer of the pregnancy is
to find the female associated with the ovulation by joining PREGS.
@@ -609,7 +609,7 @@
initiated the pregnancy. This is the Cid of a CYCLES row of the
mother. The associated CYCLES row should contain a Ddate value to
record the date of conception. The dates of the associated CYCLES
-record, when dates are present, should be should be between the sexual
+record, when dates are present, should be between the sexual
maturity date and the death date of the mother. This column should
contain a unique datum.
@@ -707,7 +707,7 @@
continuous series of observations that, presumably, have produce a
complete record all the female's sexual transition events which
occurred throughout the observation period. When a female first comes
-under observe ration her CYCLES rows have a Series value of 1. If the
+under observation her CYCLES rows have a Series value of 1. If the
female can no longer be observed the series ends. When observation of
the female resumes the Series number is incremented and the female's
subsequent CYCLES rows are given a Series value of 2. Additional
@@ -866,13 +866,21 @@
State (NULL allowed)
The state of the female's sexual cycle on the given date. Valid
-values are: 'M', menses, follicular phase 1 -- Mdate (inclusive) to
-Tdate (exclusive); 'S', swelling, follicular phase 2 -- Tdate
-(inclusive) to 6 days prior to Ddate (inclusive); 'O', ovulating -- 5
-days prior to Ddate (inclusive) to Ddate (exclusive); 'D',
-deturgesence, luteal -- Ddate (inclusive) to Mdate (exclusive); 'P'
-pregnant -- Ddate (inclusive) to birth (exclusive); 'L', lactating --
-birth (inclusive) to Mdate (exclusive).
+values are:
+
+'M', menses-follicular, Mdate (inclusive) to Tdate (exclusive)
+
+'S', swelling-follicular, Tdate (inclusive) to 5 days prior to Ddate
+(exclusive)
+
+'O', ovulating -- 5 days prior to Ddate (inclusive) to Ddate
+(exclusive)
+
+'D', deturgesence, luteal -- Ddate (inclusive) to Mdate (exclusive)
+
+'P' pregnant -- Ddate (inclusive) to birth (exclusive)
+
+'L', lactating -- birth (inclusive) to Mdate (exclusive).
Must not be NULL when Code is 'S' or 'P', must be NULL when code is
'E'. See discussion in the table description above.
@@ -959,6 +967,12 @@
or have starting and ending dates that are marked with a Period of S
and E respectively.
+Note: There are plans afoot to automatically fill in the early and
+late dates. The early dates would include the immediately prior
+census date, the late date would be the day before the immediately
+following census date. There must also be a mechanism for manually
+overriding the automatic dates.
+
Data Entry Rules
We'll figure something out.
@@ -1464,15 +1478,21 @@
State
General reproductive state of the female on the given Date. The legal
-values are: 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. P
-(Pregnant), from (including) the D (deturgesence onset) date up to
+values are:
+
+C (cycling), from (including) the T (turgesence onset)
+up to (but not including) the D date of the onset of pregnancy.
+
+P (Pregnant), from (including) the D (deturgesence onset) date up to
(but not including) the end-of-pregnancy date, date of birth,
-abortion, or death. L (lactating), from (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.
+abortion, or death.
+
+L (lactating), from (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.
+
+Any of the above states may start late or end early in the event
+of gaps in observation. (See GAPS.)
Dins (NULL allowed)
@@ -1514,24 +1534,26 @@
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.
The day-by-day nature of this table makes it easy to correlate sexual
-cycle information with other events. 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.
+cycle information with other events.
+
+Rows exist only when there is information on a female's sexual cycle,
+or enough information to estimate sexual cycle transition dates. (See
+CYCLES.) There are no CYCSTATS rows when a female is pregnant or
+lactating. Likewise there are no CYCSTATS rows when there are gaps in
+the observational record. (See GAPS.) See the description of the Din
+and Dr columns below for further information on how sexual cycles are
+recorded when there missing sexual cycle transition markers.
Note that post-menopausal individuals' final cycles will have a State
of D and a long duration, with the individual's date of death being
the last day of the cycle.
-When the end of S (swelling, follicular phase 2) cycle state is not
-known, that is Dr (days remaining in state) is NULL, some of the
-computed Din (days into state) values may be skewed as the end of the
-state is counted backward from the beginning of the D date, the next
-observed transition marker. See the information on the calculation of
-the O (ovulatory) state below.
+When the end of S (swelling, follicular) cycle state is not known,
+that is Dr (days remaining in state) is NULL, some of the computed Din
+(days into state) values may be skewed as the end of the state is
+counted backward from the beginning of the D date, the next observed
+transition marker. See the information on the calculation of the O
+(ovulatory) state below.
Data Entry Rules
@@ -1557,13 +1579,19 @@
State
Categorizes the period within the reproductive cycle. Legal values
-are: M (menses, follicular phase 1), the M (onset of menses) date to
-the day before the T (turgesence onset) date (inclusive of endpoints);
-S (swelling, follicular phase 2), the T 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); D (deturgesing, luteal), from the D date
-through the day before the M date (inclusive of endpoints).
+are:
+
+M (menses, follicular), the M (onset of menses) date to the day before
+the T (turgesence onset) date (inclusive of endpoints)
+
+S (swelling, follicular), the T 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)
+
+D (deturgesence, luteal), from the D date through the day before the M
+date (inclusive of endpoints).
Dins (NULL allowed)