LOLASURVIV (ver 1.0)

User's Manual

by

James E. Hines
Biological Resources Div., USGS
12100 Beech Forest Rd. #206
Patuxent Wildlife Research Center
Laurel, MD 20708-4017

email: jim_hines%40usgs.gov

Introduction

    Program LOLASURVIV  (Unknown-sex  SURVIVal analysis) computes "open-model"
    parameter  estimates  of  survival  and capture  probabilities.  Actually,
    LOLASURVIV  is a specially  modified  version of SURVIV  written by Dr. G.
    White. With this program and it's  companion  program,  CNVLOLA, users are
    able  to  get   parameter   estimates   for  these  complex   models  from
    capture-history data without having to specify the cell probabilities.

    LOLASURVIV  is  intended  to be  used in a  situation  where  the sex of a
    captured animal is not known at each capture occasion.

    Output from LOLASURVIV  includes survival  probability  estimates, capture
    probability estimates, goodness-of-fit tests, and likelihood-ratio tests.

    The  data-conversion  program  CNVLOLA,  will  allow the user to  generate
    models  with   time-constant   or   time-specific   survival  and  capture
    probabilities, as well as sex-proportion estimtes. If necessary, users may
    examine these models to generate statements for their own models.

    The  experimental  situation to which this program applies is one in which
    animals are initially marked with a unique tag, and released. This process
    is repeated for each of the sampling  periods.  Information used to assign
    the animal to the proper stratum (eg. sex, weight, age, capture  location,
    ...) is recorded  for each  capture of each animal.  Using these data, the
    capture-history of each animal is generated consisting of codes indicating
    the status of the animal at each  capture  period. For  example, if a male
    animal was captured in time 1 and the  biologist was able to determine the
    sex at that time, but was not able to determine sex on the next capture at
    time 4, the capture history would be: "M00U".

    Input to LOLASURVIV  consists of statements  which define the capture data
    and  statements  defining the selected model  structure. The format of the
    input file is similar to the input for program MARK. Statements  which set
    parameters equal to other parameters define model structure.

Step 1: Getting the data in the proper format

    Capture-history  data must be in a format  acceptable to the program.  The
    format is as follows:
    
    COHORT=R1 /* 1st captured in time 1*/;
    AAAA N1;
    BBBB N2;
    CCCC N3;
      :  :
      :  :
    COHORT=R2 /* 1st captured in time 2*/;
    0AAA N4;
    0BBB N5;
    0CCC N6;
      :  :
      :  :
      
    Where R1,R2,... are the number of animals which were initially captured in
    time 1,2,...
    
          N1,N2,...   are  the   number  of  animals   which   exhibited   the
          corresponding capture-history (AAAA,BBBB,...).
          
    This format is very  similar to the  widely-used  program MARK except that
    the number of animals  initially  captured at each  occasion is needed and
    the data  must be sorted by time of  initial  capture.  If the data are in
    MARK format, the  conversion  program,  CNVLOLA,  will sort and insert the
    necessary  COHORT   statements.  The  program  will  also  generate  model
    statements  to build  various  models. 

Step 2: Running the program.

    CNVLOLA is a Windows  program  which reads the  MARK-style  input file and
    generates an output file to be used with LOLASURVIV. The program is fairly
    simple to run and is similar to many Windows programs. Once the program is
    launched,  Select "Open" from the "File" menu, then select the  MARK-style
    input file. Next, use the "Model" menu to select the parameters  which are
    to be constant or  time-specific.  Finally,  select "Save" from the "File"
    menu to save the file. The output file will be named "CNVLOLA.OUT" and can
    be run with LOLASURVIV from the "Run" menu or in a DOS window.

    To  run   LOLASURVIV,   open  a  DOS  (or  CMD)  window,   change  to  the
    directory/folder where the LOLASURVIV program resides, and type:
    
    lolasurviv i=cnvlola.out l=myoutput.txt
    
    If there are many input records and/or many  time-periods, the program may
    take a long time to run.  Progress  messages are printed while the program
    runs to let the user know it is actually doing something.
    
    When the program finishes, the output file  (myoutput.txt in this example)
    can be viewed with the Windows  Notepad, or any editor.  After viewing the
    output, more models may be desired,  which can be run by  modifying a copy
    of the first input file,  CNVLOLA.OUT,  and running the modified file with
    LOLASURVIV.