List Of Programs

In this page, I list programs that I used for my analyses. Many of them are written in Matlab. Others are in C. To run these programs, you need Matlab and a C compiler. Whenever possible, I try to create executable programs for Windows. You can download these programs and run them on your Wiondow's computer. All programs are designed to run on my computers, so some tweeking are necessary befor you can use them on your computer. If you need assisstance, please let me know.

1. MATLAB programs and functions
   • caraGubbins.m: This program creates sighting histories of Cara Gubbins's data. It uses two input files: 1. SCCG.txt and 2. caraGubbins.txt. SCCG.txt has two columns: 1. central ID catalog numbersand 2. corresponding Cara's ID numbers. caraGubbins.txt already has sighting histories for each individual. This program adds the central ID number and eliminate histories of individuals that are not in the central catalog.
   • create01data.m: This program creates capture history (01 data) from historyXX.txt files. For each study location, this program will create a table of capture histories. Rows represent individuals, columns represent sampling days. Table contains zeros and ones. Input file should be capture history data, where first column is central ID numbers, second column is local ID numbers and the subsequent columns are resighting data in month/day/year format. These files are named historyXX.txt, where XX are initials of researchers.
   • date2jul1.m: This function converts date in yyyymmdd to julian days.
   • date2jul2.m: This function converts date in dd.mmyy to julian days and julian dates.
   • ericZolman.m: This program creates a capture history file for Eric Zolman's data. This is a rather pooly written program without many comments. I'll try to fix it in the near future (6/15/2001).
   • marthaJane.m: This program creates a capture history file for Marthajane Caldwell's data.
   • richMallonday.m: This program creates a capture history data for Rich Mallonday's data. Another poorly written program with a few comments. Need some additional work (6/15/2001).
   • robustEstimatesP2.m: This function reads a 01 data file and computes estimated total capture probability for the dataset by using the robust-design closed model. In the robust-design model, the abundance within a primary time period is assumed to be constant. The time period is moved through the dataset. The number of recaptures during a secondary sampling period is distributed binomial with parameters Q_j and p, where Q_j = total number of animals caught before the j-th sampling, p is the capture probability, and j = the index for secondary sampling periods. The joint likelihood for a primay sampling period is then: Pr[m1, m2, ..., mk] = BIN(sum(Q_j), p). This p is estimated using a Bayesian analysis. For more detailed explanations of the method, please take a look at this brief summary.
   • summaryDataRY.m: This program creates a capture history file for Rob Young's data. Yet another example of bad programming. Not enough annotations.
   • summaryWilmington.m: This program converts wilmingtonID.txt file to sorted file. Data for Wilmington are in columns (date, sighting#, and id#). This program converts that to rows (id#, dates).
   • theDolphinProject.m: This program makes sighting histories for The Dolphin Project's data. It uses two input files: 1. theDolphinProject.txt and 2. GADPnew.txt. GADPnew.txt has two columns: 1. central ID catalog numbers and 2. corresponding local ID numbers. theDolphinProject.txt has 4 columns: 1. Local Id numbers, 2. Month, 3. Date, and 4. Year.
   • Here is a link to a folder that contains all functions and a program that were used to compute posterior distributions in my dissertation. I cleaned these programs so they are better documented than when I used them for myself. You will need all these functions to run the main program (bayesMarkRecap.m). I included the original c functions as well as compiled dll files. If you need to recompile these c functions, use the mex function in MATLAB. And Yes, you will need Matlab to run this program. If you have any questions please feel free to email me.
2. C programs
• readData.c: This program reads resighting data of bottlenose dolphins from Kieth Rittmaster and converts them into mark-resight history matrix. The output matrix contains all individuals in the first column and other columns indicate sampling dates. An example of how NOT to write a program. Need more comments!
• dec2hex.c: This program converts a decimal integer to a hexadecimal value. For a compiled Windows version, download dec2hex.exe. Also, using Matlab, I created the same function with graphic user interface (GUI). To download, follow this link.
• hex2dec.c: This program converts a hexadecimal value to an integer. For a compiled Windows version, download hex2dec.exe.
• listdir.exe: A program to list all jpg files in a directory.

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