Program "JOLLYAGE" : User Instructions (DRAFT)
by
James E. Hines
U. S. Fish and Wildlife Service
Patuxent Wildlife Research Center
Laurel, Maryland 20708
This program is used to compute survival rate, population
size, and birth/immigration estimates for an age-stratified
capture-recapture data set using a stochastic model developed
by S. L. Stokes. The program assumes the population to be
stratified onto young (who remain young for one sampling period)
and adult. The adult estimates of survival rate, population
size, and birth/immigration, and young estimates of survival
rate are computed for each sampling period.
Definition of variables:
| N(i) |
- Number of adults in the population just before
the i-th sample |
| M(i) |
- Number of marked adults in the i-th sample |
| B(i) |
- Number of adults caught before the i-th sample
which are not caught in the i-th sample, but are caught
later before and after sample i |
| R(i) |
- Number of marked adults which are released from
the i-th sample which are subsequently recaptured |
| R'(i) |
- Number of marked young which are released from
the i-th sample which are subsequently recaptured |
| Phi(i) |
- Survival rate of adults from samples i to i+1 |
| Phi'(i) |
- Survival rate of young from samples i to i+1 |
| p(i) |
- Capture probability of adults in sample i year
adults |
Data input:
The input file for program JOLLYAGE must contain some
control records, followed by the data records. The control
records are used to tell the program the title of the data,
number of capture periods, and data type. The format of
the control records is:
PARAMETER=value
Only one program parameter may be set on each record,
and the equal sign is required. No spaces may be entered
on the right of the equal sign except in the TITLE record.
The following are example control records:
TITLE=Sample data for program JOLLYAGE
NUMBER OF PERIODS=12
FIRST=1966
DATA TYPE=TOTALS
The data records may be in one of three forms. The default
is capture- history record format type. The other types
of input data are "CAP/REL HISTORY RECORDS" and "TOTALS".
Capture history records are strings of digits which indicate
the status of each animal in each time period. One record
is entered for each animal banded in the experiment.
Each column contains a one (1) if the animal was captured
and released in the sampling period. If the animal was not
captured in the period, a zero (0) is entered in the column
corresponding to that period.
Occasionally, animals are killed in the traps and not
released back into the population. In this case, a two (2)
is entered in the column to indicate capture but not released.
If an animal is resighted between two sampling periods,
codes three (3) or four (4) are used. Code three (3) indicates
that the animal was not captured in the current period,
but was resighted before the next sampling period. Code
four (4) indicates that an animal was captured in the current
sample and was resighted before the next sample.
To reduce the amount of input, a weighting variable is
read in at the end of each capture-history record. This
variable indicates the number of animals which the capture-history
represents. IMPORTANT: Even if you do not enter anything
for this weighting variable, it must be accounted for in
the format! (ie. If you have x time periods, the format
must allow for:
x+2 variables under capture-history record format,
or 2x+2 variables under cap/rel-history record format.)
Example 1 (Capture-history record format):
The following is an example of an experiment with 5 time-periods:
CARD |________________________________________________________
- !TITLE=Example data set for JOLLYAGE user instructions
- !PERIODS=5
- !FIRST=1971
- !DATA TYPE=CAPTURE HISTORY RECORDS
- !ADULT=1
- !YOUNG=2
- !FORMAT=(6X,A1,1X,5I2,1X,I2)
- ! 1 1 1 0 2 0 2
- ! 1 1 0 0 0 0 15
- ! 1 0 1 1 1 1 7
- ! 2 1 1 0 1 1 21
- ! 2 1 1 0 3 4 1
- ! 2 0 2 0 0 0 1
- ! 0 1 1 1 0 0 1
- Explanation:
- Card 1: identifies the data set.
Card 2: contains the number of time-periods in the
experiment.
Card 3:sets the number of the first time period to
1971.
Card 4: indicates that the data type will be capture
history records. (0=not captured, 1=captured & released,
2=captured & not released)
Card 5: sets the adult age code = 1 (instead of 'A').
Card 6: sets the young age code = 2 (instead of 'Y').
Card 7: contains the FORTRAN format of the data records.
Age-code is in column 7, the status codes will start
in column 10 and the number of occurrences will be in
column 21.
Card 8: is the first recapture record. This recapture
record contains:
Age-code in column 7 (age=1 - adult),
Status in period 1 (1 - captured and released),
Status in period 2 (1 - captured and released),
Status in period 3 (0 - not captured),
Status in period 4 (2 - captured and not released),
Status in period 5 (0 - not captured),
Number of occurrences of this capture-history = 2.
Card 9: is the second recapture record. These 15 animals
are adults and were captured and released in period
1 only.
Card 10 : 7 adults, captured and released in periods
2,3,4,5,6,8.
Card 11 : 21 young, captured and released in periods
1,2,4,5,7,8.
Card 12 :
1 young, captured and released in periods
1 and 2,
sighted between periods 4 and 5,
captured in period 5, and
sighted after period 5.
Card 13 : 1 young, captured but not released from period
2.
Card 14 : 1 unknown age at first capture. This record
would be ignored.
Summary totals format:
Program JOLLYAGE can read the summary statistics instead
of the capture history records of each individual. This
is done by setting the data type to TOTALS. In this case,
the program will read 8 variables from the next n cards
(where n is the number of time-periods).
Example
RECORD |__________________________________________________
- |TITLE=CANADA GOOSE TRAPPING DATA, TENN. (FROM CROMER
1978)
- |PERIODS=10
- |TYPE=TOTALS
- |FORMAT=(8F5.0)
- | 0 88 98 88 98 68 63 0
- | 111 126 78 126 78 106 59 20
- | 144 168 121 168 121 126 74 41
- | 158 196 143 196 143 171 116 83
- | 305 327 302 327 290 232 235 65
- | 442 515 286 515 230 415 201 90
- | 615 721 305 721 257 527 224 91
- | 722 840 307 840 86 606 53 120
- | 644 834 395 834 95 529 71 135
- | 735 1149 828 1149 436 0 0 0
Card 1 : Title
Card 2 : Number of trapping periods
Card 3 : Summary totals read in
Card 4 : 8 variables per record, 5 cols. each
Card 4 : Summary totals for time-period 1.
Variables are: m(1) : Number marked adults caught
in period 1
n(1) : Number adults caught in period 1
n'(1) : Number young caught in period 1
R(1) : Number adults released in period 1
R'(1) : Number young released in period 1
r(1) : Number adults caught in period 1 which were also
caught after period 1
r'(1) : Number young caught in period 1 which were also
caught after period 1
b(1) : Number adults caught before period 1 which were not
caught in period 1 and were caught after period 1
Cards 5-13 : Summary totals for time-periods 2-10.
Program Output:
Output from the program consists of:
- A page of definitions(optional),
- Input summary statistics,
- Estimates of the parameters for model A2,
- Variances and covariances(optional),
- Likelihood-ratio test of the single-age Jolly-Seber
model
- vs. the age-stratified model, and
- Goodness-of-fit test of the age-stratified model (A2),
- Estimates for reduced parameter models (B2 & D2),
- Likelihood ratio tests and goodness-of-fit tests for
A2,B2 & D2.
All of the parameters contained in the printout are defined
in the page of definitions. However, there may be some confusion
about the standard error of the estimates. There are two standard
errors printed out for some parameters. One standard error
is computed using the full multinomial variance, which includes
both error of estimation or sampling variation and binomial
variation associated with the actual survival process. The
other standard error omits the binomial variation and can
be thought of as reflecting only sampling variation associated
with the estimation process.
- Restrictions:
-
- The number of trapping periods must be less than
or equal to 50.
- The FORTRAN format which describes the recapture
records must specify the data to be of type INTEGER
- The FORTRAN format which describes values in the
TOTALS table must specify the data to be of type REAL.
- Note:
Error number 3023 indicates that a carriage return
and/or linefeed character is missing at the end of the
input file. Use your word- processor to check the input
file.
If you have questions, problems or comments with this
program please contact:
Jim Hines
U. S. Fish & Wildlife Service
Patuxent Wildlife Research Center
Laurel, Md. 20708
Phone:(301)498-0389
FTS 937-7389
e-mail: hinesj@mail.fws.gov
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