Data input:

Program "JOLLYAGE" : User Instructions

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 |________________________________________________________
  1  !TITLE=Example data set for JOLLYAGE user instructions
  2  !PERIODS=5
  3  !FIRST=1971
  4  !DATA TYPE=CAPTURE HISTORY RECORDS
  5  !ADULT=1
  6  !YOUNG=2
  7  !FORMAT=(6X,A1,1X,5I2,1X,I2)
  8  !      1  1 1 0 2 0  2
  9  !      1  1 0 0 0 0 15
 10  !      1  0 1 1 1 1  7
 11  !      2  1 1 0 1 1 21
 12  !      2  1 1 0 3 4  1
 13  !      2  0 2 0 0 0  1
 14  !      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 |__________________________________________________
   1   |TITLE=CANADA GOOSE TRAPPING DATA, TENN. (FROM CROMER 1978)
   2   |PERIODS=10
   3   |TYPE=TOTALS
   4   |FORMAT=(8F5.0)
   5   |    0   88   98   88   98   68   63    0
   6   |  111  126   78  126   78  106   59   20
   7   |  144  168  121  168  121  126   74   41
   8   |  158  196  143  196  143  171  116   83
   9   |  305  327  302  327  290  232  235   65
  10   |  442  515  286  515  230  415  201   90
  11   |  615  721  305  721  257  527  224   91
  12   |  722  840  307  840   86  606   53  120
  13   |  644  834  395  834   95  529   71  135
  14   |  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,
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
BRD - USGS
11510 American Holly Dr. #201
Patuxent Wildlife Research Center
Laurel, Md. 20708

Phone:(301)497-5661
email: Jim_Hines%40usgs.gov