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File Date Author Commit
 Containers 2016-06-17 sviscido sviscido [8b7432] Signed-off-by: sviscido <viscidost@...>
 Environment 2016-06-20 sviscido sviscido [38eff9] Signed-off-by: sviscido <viscidost@...>
 Functions 2016-06-20 sviscido sviscido [38eff9] Signed-off-by: sviscido <viscidost@...>
 Organisms 2016-06-20 sviscido sviscido [38eff9] Signed-off-by: sviscido <viscidost@...>
 Recorders 2018-06-13 Viscido Viscido [a792d5] New code for generating summary data across models
 Scripts 2018-06-13 Viscido Viscido [a792d5] New code for generating summary data across models
 UserInterface 2018-06-13 Viscido Viscido [a792d5] New code for generating summary data across models
 Utility 2016-06-27 sviscido sviscido [fe6fe7] Signed-off-by: sviscido <viscidost@...>
 WORK 2016-06-16 sviscido sviscido [352047] Signed-off-by: sviscido <viscidost@...>
 BookKeeper.m 2016-06-27 sviscido sviscido [fe6fe7] Signed-off-by: sviscido <viscidost@...>
 Contents.m 2016-06-20 sviscido sviscido [38eff9] Signed-off-by: sviscido <viscidost@...>
 Readme.m 2014-03-06 sviscido sviscido [6af6d1] Added summary statistics and made some cosmetic...
 changelog.m 2016-06-27 sviscido sviscido [fe6fe7] Signed-off-by: sviscido <viscidost@...>
 dlm.m 2013-09-16 sviscido sviscido [c0a557] Updated the way Habitat objects are stored (sav...

Read Me

% Documentation file for the Dynamic Linkage toolbox
%
% This file contains basic documentation on the Dynamic Linkage toolbox.
% It is not intended for users, but is intended for developers and
% programmers.  It is also not intended to be comprehensive. A more
% comprehensive PDF document will be provided for both developers and end
% users at the time of software release.
%
% Contents of this file:
% 1. Directory Structure
% 2. Contents of the directories
% 3. Naming conventions
%
% README
% 1.Directory Structure
%   The Dynamic Linkage toolbox is arranged into directories (folders) to
%   help keep things organized. Directories and their associated files are
%   listed below:
%
%   DynamicLinkage  This is the main directory
%   Containers      Classes that contain other objects
%   Environment     Classes pertaining to the physical environment
%   Organisms       The Organism class and all sub-classes
%   Utility         Objects that execute useful methods
%   UserInterface   Objects for the various parts of the UI
%   Recorders       Objects that record data stored on other objects
%   Work            The default folder for storing temporary data
%
% 2. Contents of the directories
%   Below, the contents of each directory will be explained. See the
%   Contents.m file for a complete list of files, and the Programmer's
%   Reference Guide for more details.
%
%   DynamicLinkage
%   This is the main, or parent, directory for the toolbox.  It contains
%   the subdirectories (subfolders) that store the various class definition
%   files and scripts for the program.  It also stores certain basic
%   documentation files (changelog, Contents.m, etc.) and the basic
%   executables and class definition files for starting the program.
%
%   Containers
%   This folder contains the class definition files for the 'pure
%   container' objects. Pure containers are objects that hold other
%   objects, but do not have any existence independent of those objects.
%   For example, a Pack object holds the members of a wolf pack. If you
%   took the members out, the pack would not exist as an entity. 
%   Container classes in this directory include:
%   Graveyard
%   Pack
%   Population
%   Group
%
%   Environment
%   This folder contains class definition files for objects related to the
%   non-living (physical) environment. This includes the overall Habitat
%   object, as well as the PhysicalCharacteristics object. Note that the
%   Habitat object is a container as well as an entity (it exists
%   independent of what it contains, unlike a wolf Pack, which cannot exist
%   without wolvers).
%   Environment classes in this directory include:
%   Habitat
%   PhysicalCharacteristics
%   
%   Organisms
%   This folder contains class definition files for the different types of
%   organisms. It also contains subfolders for the larger subclasses, such
%   as predators.
%
%   Utility
%   This folder contains objects that perform utility functions not
%   assocated with any one particular object. For example, an object that
%   does unit conversions (radians to degress, feet to cm) might go here.
%
%   Recorders
%   This folder contains objects whos job is to act as data loggers for
%   other objects. For example, the "RadioTransmitter" object is generated
%   for each animal in the simulation. It stores the historical position,
%   speed, NGDR, and other statistical data (the animal itself only stores
%   current-time-step data).  This allows us to separate the animal object
%   from the recorded data, and mimics what happens in the field (such as
%   when a tracking device is attached to an animal's leg).
%
%   UserInterface
%   This is a folder holds class definition files and scripts for executing
%   the GUI. The folder contains subfolders, each named for one menu item
%   on the UI. For example, all the objects pertaining to the File Menu
%   (saving, loading, exporting) can be found in the File directory.  Note:
%   all comprehensive documentation files are found in the Help folder
%   within this directory.
%
%   Work
%   This directory contains temporary data files used by the program. All
%   changes to all data are stored here, rather than in RAM, so that in the
%   event of a crash, the data can be restored from this folder.
%
% 3. Naming Conventions
%   The project uses the following naming conventions.
%   * All DIRECTORIES (folders) begin with an Upper Case letter and are
%   otherwise Lower case
%
%   * All files, folders, and variables must be named using a combination
%   of uppper and lower case letters and numerals.  No special characters
%   (e.g., ^,%,$,*) or spaces may be used when naming things.
%
%   * Names for NUMERIC variables should start with the letter "n",
%   followed by a captial letter and then lower case. For example, nCount.
%
%   * Names for all ARRAY variables should be named with in ALL CAPS. For
%   example, POPULATION.
%   
%   * Names for objects should start with a lower-case "o." For example,
%   oFish would be a fish object; oPop would be a population object.
%
%   * Names for all structures will be all lower case. For example,
%   population.
%
%   * Names for Classes and Objects will begin with an upper case letter
%   and otherwise be all lowercase. For example, Population.
%
%   * Names for object properties should be descriptive, and if the name
%   represents more than one word, each word after the first should be
%   capitalized. Captilization of the first word in the name is optional.
%   For example, either MetabolicRate, or metabolicRate is acceptable.
%
%   * Names for all methods will be written as phrases describing
%   what the function does, with words of the phrase capitalized.
%   Capitalization of the first letter is optional. For example, either
%   DetectPrey or detectPrey is acceptable.
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