A summary of the paternity analysis. Contains one row for each offspring having a paternity analysis.
The Kid value must be unique
-- there can be at most 1 row on DAD_DATA per offspring. The
BIOGRAPH row related to the Kid must have a
non-NULL Birth
-- the offspring must be born.
There can be information as to whether the mother has
been genetically sampled (there can be a
non-NULL Mom_sampled) if and only if the mother is
known (BIOGRAPH.Pid of the Kid
is non-NULL). The system will report an
error when this is not the case. The system will not allow
changes to Mom_sampled that violate
this rule but does allow changes to BIOGRAPH.Pid that
violate this rule. It is assumed that any inconsistencies
introduced in this fashion are only temporary and will be
fixed soon when the related Mom_sampled value is updated.
There can be information as to whether the father has
been genetically sampled (there can be a
non-NULL Dad_sampled) if and only if the father is
known (Dad_consensus is not
NULL).
The number of potential dads genotyped (Pdads_typed) must not be larger than the
number of potential dads (Pdads_considered).
This number must be 1 or larger when Dad_sampled is TRUE --
when the Dad_consensus has been
genotyped -- and otherwise must be
0 or larger.
The columns identifying potential dads, Dad_excl, Dad_1perr, Dad_5perr, Dad_allmales, and Dad_consensus are subject to a number of data integrity checks, as follows: The individual must be male. If the mother is known he must be alive during the mother's fertile period -- the male's BIOGRAPH.Statdate must be on or after the mother's Zdate minus the 5 day fertile period, minus an additional 14 days to allow for interpolation if the male is alive. If the mother is known the male must be mature before the the conception date -- the male must have a row in MATUREDATES and MATUREDATES.Matured must be before the Zdate. The system will report a warning if the male is not in the mother's supergroup at any time during the fertile period.
The Loci_excl column must be
NULL if the Dad_excl column is
NULL. Otherwise Loci_excl must be
non-NULL.
The Conf_1perr column must be
NULL if the Dad_1perr column is
NULL. Otherwise Conf_1perr must be
non-NULL.
The Conf_5perr column must be
NULL if the Dad_5perr column is
NULL. Otherwise Conf_5perr must be
non-NULL.
The Conf_allmales column must
be NULL if the Dad_allmales column is
NULL. Otherwise Conf_allmales must be
non-NULL.
The Date must be on or after the offspring's BIOGRAPH.Birth date.
A unique integer which identifies the DAD_DATA row.
This column is automatically maintained by the
database, cannot be changed, and must not be
NULL.
The individual on which the paternity analysis was
done. A three-letter code which uniquely identifies an
individual (an Sname) in BIOGRAPH. There must always be a row in BIOGRAPH for the individual identified
here. This column must not be
NULL.
TRUE when there is a genetic sample
of the mother on file, FALSE when there
is not. This column must not be
NULL.
TRUE when there is a genetic sample
of the father on file (the Dad_consensus),
FALSE when there is not. This column must
not be NULL.
The father chosen based on an exclusion analysis of locus matches between the offspring and all potential fathers for which genetic data were available (note that potential fathers are by definition fathers that were in the group in which the infant was conceived during the 5 days prior to the Zdate). A three-letter code which uniquely identifies an individual (an Sname) in BIOGRAPH. There must always be a row in BIOGRAPH for the individual identified here. Field observations of physical proximity, social interaction, etc., are not part of this analysis.
This column may be NULL when the
exclusion analysis yields no father.
The number of loci at which the offspring and father, the Dad_excl, do not match.
The value of this column, when
non-NULL, must be between
0 and
40, inclusive.
Total number of potential dads considered. The primary factors leading to inclusion in the pool of potential fathers are maturity as of the Zdate and membership in the mother's social group during the 5 days prior to the Zdate.[165]
The POTENTIAL_DADS view may be used to produce a list of potential fathers that are currently considered to be members of the mother's group at the time of conception.
This column must not be NULL and
must be between 0 and
50,
inclusive.
The number of potential dads, those which Pdads_considered counts, for which there are genetic data.
This column must not be NULL.
The father chosen by the analysis software from among potential fathers (those present in the mother's social group during the 5 days prior to the Zdate) under the assumption of a 1% error rate in the determination of the genotype at the loci. A three-letter code which uniquely identifies an individual (an Sname) in BIOGRAPH. There must always be a row in BIOGRAPH for the individual identified here.
This column is NULL when the
automated analysis yields no father given an 80% confidence
level.
The percent confidence in the Dad_1perr result. Values must be
NULL or integers between
0 and
1, inclusive.
The father chosen by the analysis software from among potential fathers (those present in the mother's social group during the 5 days prior to the Zdate) under the assumption of a 5% error rate in determining the genotype at the loci. A three-letter code which uniquely identifies an individual (a Sname) in BIOGRAPH. There must always be a row in BIOGRAPH for the individual identified here.
This column is NULL when the
automated analysis yields no father given an 80% confidence
level.
The percent confidence in the Dad_5perr result. Values must be
NULL or integers between
0 and
1, inclusive.
The father chosen by the analysis software considering all males in the population under the assumption of a 1% error rate in determining the genotype at the loci. A three letter code which uniquely identifies an individual (a Sname) in BIOGRAPH. There must always be a row in BIOGRAPH for the individual identified here.
This column is NULL when the
automated analysis yields no father given an 80% confidence
level.
The percent confidence in the Dad_allmales result. Values must be
integers between 0 and
1, inclusive. This
column must not be NULL.
The father chosen taking all factors into account. A three-letter code which uniquely identifies an individual (an Sname) in BIOGRAPH. There must always be a row in BIOGRAPH for the individual identified here.
This column may be NULL if there is
no consensus dad.
Code for the software used[166] in the genetic paternity analysis. The legal values of this column are defined by the DAD_SOFTWARE support table.
The group membership table. This table records which group each animal is in on which date, excepting fetal losses (individuals with no Sname). There is a row in MEMBERS for every individual for every day between Birth and Statdate, inclusive, including periods during which the whereabouts of an individual are either recorded as being unknown or assumed unknown by the interpolation procedure. (See: the unknown group.) Some living individuals have MEMBERS rows after their Statdate, for more information see the section: Interpolation at the Statdate. MEMBERS is most useful when one is interested in an individual's location on a particular date. Simply check MEMBERS for the individual on that date. To find all the individuals in a group on a date, look at all the rows in the table on that date for the group.
MEMBERS is a single
population-wide table created and updated automatically using
information from CENSUS, BIOGRAPH, and DEMOG. The method used to do this is
called interpolation and is described fully in a
section below. Briefly, interpolation guesses which
group an individual is likely to be in when there is no
observational data. The MEMBERS rows which are the result of
guessing have an I as their
Origin value.
Babase requires that an animal be located in exactly one group on any particular day, the combination of Sname and Date should be unique. The intent of this table is to record the location of each animal at the start of each day. See other documents for further information on how the actual practice of data acquisition and entry impacts this goal.
Babase populates this table automatically, users cannot directly manipulate the table's data.
A unique integer which identifies the MEMBERS row.
This column is automatically maintained by the
database, cannot be changed, and must not be
NULL.
The individual whose location is being recorded. The three-letter code that identifies the individual's row in the BIOGRAPH table. There will always be a row in BIOGRAPH for the individual identified here.
This column may not be NULL.
The group where the individual is located. This is a Gid value from GROUPS. This field should contain the most specific sub-grouping available -- subject to the constraints of the data entry protocol, of course. Aggregation into larger groupings is accomplished by retrieving the associated Supergroup from GROUPS and/or use of the supergroup() function.
This column may not be NULL.
Usage exception: For the years 1989-1991, inclusive, the group recorded for the sub-groups of Alto's group do not necessarily reflect the actual groupings of the animals on a particular day, but are instead indications of the group-splitting process. See Jeanne Altmann and the Data Management Manual for a further explanation.
A one letter code indicating the source of the
location information. This information is derived from,
and has the same values as, the Status column of CENSUS, with the exceptions that
MEMBERS.Origin contains the
I (interpolated) value
not found in CENSUS, and
does not contain the A
(absent) value. The codes are as follows:
C (CENSUS) values represent census
data points, I
(interpolated) values are derived from the census data
points, D (demography) values
represent demography notes not present in the census
sheets, M and
N (manual) values
represent census data points due to operator intervention
in CENSUS . The
S, E,
F, B,
G, T,
L, and R
codes are derived from analysis of historical data. See
the CENSUS section for
further information.
This column may not be NULL.
The time interval, in days, from the date in which
an individual was previously observed to be in a group
(censused or born into group -- automatic placement in
the unknown group does not count) to the date of the
MEMBERS row. So the value
is 0 on those days on which the
individuals are censused (and on the individuals' birth
dates), 1 on those (non-census) days
immediately before or after the census days, etc. For
those MEMBERS rows in which
the interpolation procedure has associated an individual
with the unknown group, for lack of a better place to
put them, the Interp column is the number of days
“distant” from the interpolating CENSUS row, or the birth date,
that determined the group membership. Note that the CENSUS row that determined that
the MEMBERS.Grp should be
unknown may record an absence.
The Interp value is not meaningful over intervals
that contain census rows that are themselves the result
of an analysis. Over these intervals Interp is
NULL. For more information see Interpolation, Data are not Re-Analyzed.
This column many be NULL.
The ranking of individuals within groups. This table contains a row for every month for every ranked individual for every type of rank assigned to the individual. When the ranking has not been done for a type of rank in a month, there are no rows for members of that group for that month with that type of rank.
Rankings are determined via a manual process that considers both quantitative information, such as the outcome of agonism interactions within a particular month, and some qualitative judgments such as other observed behavior during and surrounding the month in question. As such the rankings are somewhat smoothed and are not strictly dependent upon observations made within a single 1 month time interval. For further information please consult your local Babase scientist.
The system will report a warning when a ranking of some Rnktype has been done on a group and there are individuals (returned by the RNKTYPES.Query) who have not been ranked.
The above warning has not yet been implemented.
Rankings may be based on irregular observations of a group before the long-term study began, or before it became an "official" study group. Either way, the ranks for such a group will likely be before any of the individuals' Entrydates. Because of this, the system will allow but issue a warning when an individual's Rnkdate is before the first of the month of the individual's Entrydate.
The combination of Sname, Rnkdate, Grp, and Rnktype must be unique.
Ranks are assigned within groups, so all individuals must be in the group ranked at some point during the month. Specifically, MEMBERS must record that the ranked individual is a member of some sub-group[167]of the ranked group's Supergroup, as determined by the supergroup() function given MEMBERS.Grp and MEMBERS.Date, during the ranked month.
Be careful when changing group membership or group rankings; the rank will almost certainly change if an individual's group is changed.
A number of possibilities exist for ranking, and coding the groups, during a period of group fission. Individuals may be simultaneously ranked within all temporary sub-groups and in the original group, the supergroup, regardless of which individuals are censused in which sub-groups. The censuses of the sub-groups and the records of the temporary sub-groups may be retained forever, even if the sub-groups never become groups in their own right. The only caveat is that once a group becomes a permanent group (GROUPS.Permanent) it is no longer a sub-group of the group from which it fissioned, at which point an individual must be censused in both the original group and the sub-group in order to be ranked in both.
A unique integer which identifies the RANKS row.
This column is automatically maintained by the
database, cannot be changed, and must not be
NULL.
The individual whose rank is being recorded. The
three-letter code which uniquely identifies an individual
(in Sname) in BIOGRAPH. There must always be a
row in BIOGRAPH for the
individual identified here. This column must not be
NULL.
A date that falls on the first day of a month,
representing The year and month of the ranking. The year
must be between 1940
and 2040,
inclusive. This column must not be
NULL.
Use the rnkdate() function to obtain the first day of the month when writing queries.
The kind of rank assigned to the individual, a
Rnktype value from the RNKTYPES table. This column may
not be NULL. Examples of various
rankings are: Adult Females, All Females, etc., as defined
in the RNKTYPES
table.
This is the ranking among all the animals of the
Rnktype in the group over the Rnkdate period. The most
dominant individual is given a rank of
1, the next most dominant a rank of
2, etc. This information is updated
through the ranking program and as a rule need not be
manually updated. This column must not be
NULL. The rank values must be
contiguous and start with 1.[168]
[165] Group membership on the Zdate does not include a male in the set of potential fathers.
[166] Or other basis of analysis.
[167] Including the supergroup itself, as a supergroup is a sub-group of itself.
[168] Note that the requirement that ranks be contiguous means that in order to change an existing ranking the ranks must first be deleted, from highest numbered rank to lowest, and then the new ranking re-created, from lowest numbered rank to highest.