This extension has been archived. With the introduction of the Universal Cohort Library, age-only succession is not compatible with LANDIS-II v8 and is therefore being depricated.

Changes to this extension are governed by the Repository Rules from the Technical Advisory Committee. Robert Scheller is the Custodian of this repository.

Welcome to the source code repository for Extension-Age-Only-Succession, a LANDIS-II succession extension.

Extension-Age-Only-Succession defines cohort succession as a function of cohort reproduction, cohort ageing, and cohort mortality. The onset of cohort reproduction requires three prior events:

1. a propagule must exist, either through seeding, resprouting, or planting;
2. there must be adequate light; and
3. the probability of species establishment must exceed a random number. Disturbance, seed dispersal, and amount of shade all affect cohort reproduction. Extension-Age-Only-Succession uses the seed dispersal algorithm described in the white paper provided on the LANDIS-II web site (www.landis-ii.org/documentation) by Ward et al. (2005).

The science powering the LANDIS-II model ultimately resides in .cs files, written in the C# programming language. The collection of .cs files associated with the LANDIS-II Core Model or with any LANDIS-II extension is the so-called source code. Using the source code and the .NET Framework, the actual libraries (.dll files) and executables (.exe files) of the LANDIS-II model are constructed. The LANDIS-II model then uses various sets of libraries and executables to produce process-based output.

The .NET Framework provides the runtime environment needed for executing C# source code. Executing C# source code means that the source code is compiled to produce an assembly, either a library (.dll file) or an executable (.exe file). The C# code in .cs files cannot be independently executed; the use of the .NET Framework is required because the C# programming language is so-called 'managed code'.

Integrated development environments (IDEs) are used to assist in compiling .cs files into assemblies. Visual Studio and MonoDevelop are two useful IDEs for the C# programming language. To help with tracking the set of .cs files that are to be compiled, Visual Studio creates 'container' files called 'projects' and 'solutions'. A 'project' is the collection of source code files that the C# compiler will combine to produce a single output (an assembly). A Visual Studio project file is designated with a .csproj extension. A 'solution' is a set of one or more .csproj files. A Visual Studio solution file is designated with a .sln extension.

The process of building 'the science' into 'the model' is done via a LANDIS-II extension. The process looks like this:

• a set of .cs files is created or modified that translates process-based science into algorithms, and from the algorithms, into C# source code (script)
• a .csproj file is created that links the various .cs files together within an IDE
• the IDE takes the set of .cs files plus the .NET Framework and 'builds' the requisite assemblies: libraries (.dll files) and executables (.exe files). LANDIS-II extensions consist ONLY of libraries.
• the newly-built assemblies constitute 'the extension' and are packaged into a Windows-based installer (a Wizard)
• LANDIS-II users run the Wizard which installs the extension (a set of assemblies into the following directory: C:\Program Files\LANDIS-II-v7\extensions

• It is recommended that you use Git for version control and change tracking. This means cloning the Extension-Base-Harvest repository to your local machine. Help with Git functionality can be found in the ProGit Manual (freely available) as a .pdf (https://git-scm.com/book/). A very straighforward Windows/Git interface is "git BASH" (available at https://git-for-windows.github.io/)

• Should you want the LANDiS-II Foundation to consider your changes for inclusion in the LANDIS-II Foundation's main GitHub repository https://github.com/LANDIS-II-Foundation/) you will need to submit a Pull request.

• Visual Studio (VS) may mark references to some libraries as "unavailable" until the solution is actually (re)built. During the build process, VS will automatically retrieve any requisite libraries (assmeblies) from the Support-Library-Dlls repository, located at https://github.com/LANDIS-II-Foundation/Support-Library-Dlls-v7. Retrieval of requisite libraries is done by running the script,
  
  

The following steps use both a Git command-line interface (GitBASH for Windows; see above) and the menu-driven options available in Visual Studio (VS).

The example given below is a specific one and uses the extension,"Extension-Base-Harvest". The repo for this extension is available at https://github.com/LANDIS-II-Foundation/Extension-Base-Harvest.

Substitute, as appropriate, for your extension of interest.

===== STEP1. Clone and .git track a local version of an extension repository ================

a. Clone the extension repository (repo) of interest to your machine.
a1. The COPY of the extension repo on your machine is the LOCAL repo;
    the SOURCE of the cloned repo is the REMOTE repo

$ git clone https://github.com/LANDIS-II-Foundation/Extension-Base-Harvest.git Cloning into 'Extension-Base-Harvest'... remote: Counting objects: 429, done. remote: Compressing objects: 100% (17/17), done. remote: Total 429 (delta 6), reused 0 (delta 0), pack-reused 410 Receiving objects: 100% (429/429), 2.54 MiB | 1.09 MiB/s, done. Resolving deltas: 100% (263/263), done.

$ git remote -v origin https://github.com/LANDIS-II-Foundation/Extension-Base-Harvest.git (fetch) origin https://github.com/LANDIS-II-Foundation/Extension-Base-Harvest.git (push)

• Visual Studio 2017 with installation of
  • .NET Core cross-platform development
  • GitHub Extension for Visual Studio (optional)
• Inno Setup - required for creating a Windows installer
  • Install latest version from http://jrsoftware.org/isdl.php
    
    

git clone https://github.com/LANDIS-II-Foundation/Extension-Base-Harvest.git

1. Open .csproj file in src folder with Visual Studio 2017.
2. In the Solution Explorer find /lib/support_libs_download.ps1 file.
3. Right click the file name and click Open with PowerShell ISE
4. Click Run Script (breen arrow) button or press F5 key. The script download dependencies from GitHub.
5. Close PowerShell ISE.
6. Build the application

Notes:

• LANDIS-II Core libralies are on MyGet landis-ii-v7 feed
• LANDIS-II Support libraries are on GitHub LANDIS-II-Foundation repository

1. Change Configuration from Debug to Release in Visual Studio and Build the extension application. DLLs are created in src\bin\Release\netstandard2.0 folder.
2. Go to .\deploy folder.
3. Edit text file name and information.
4. Open .iss file.
5. Edit extension information and compile.