inSTREAM Version 5.0
Readme file revised 28 August 2014, SF Railsback

***inSTREAM V. 5.0 updated 28 August 2014 to fix a bug in how cells identify neighbor cells. This bug could cause significant errors (not identifying all neighbor cells, thereby restricting habitat selection by small fish) when habitat cells were laid out in the old approach of transects with rectangular cells (which was used in versions 4 and earlier of inSTREAM).***

***inSTREAM V. 5.0 updated 31 July 2014 to fix a bug in the aquatic predation survival functions, which previously eliminated the effect of piscivorous fish density on predation survival.***

Version 5.0 of inSTREAM is largely a major software update, with few changes in model formulation. The model formulation remains as described in the documentation for version 4.2 (Railsback, S. F., B. C. Harvey, S. K. Jackson, and R. H. Lamberson. 2009. InSTREAM: the individual-based stream trout research and environmental assessment model. PSW-GTR-218, USDA Forest Service, Pacific Southwest Research Station, Albany, California. Available at: http://www.fs.fed.us/psw/publications/documents/psw_gtr218/psw_gtr218.pdf). Changes in model formulation are:

1) Habitat is represented as one or more reaches of polygonal cells, instead of rectangular cells. Cells can have any number of sites. This allow fully two-dimensional representation of habitat. This is the first version that supports multiple two-dimensional reaches.

2) Barriers to upstream movement are not represented in version 5.0. This change is simply because barriers are not trivial to define with the two-dimensional habitat. 

3) The method for calculating distance from a cell to the reach's end is modified to accomodate the two-dimensional habitat representation. This method is used by fish in determining which cells in other reaches are potential movement destinations.

Software changes include:

1) inSTREAM is now packaged with a graphical user interface for Windows users. This GUI supports assembly and checking of input sets, setup of simulation experiments, and automated sensitivity ("limiting factors") analysis.

2) The MinGW compiler is used to produce a Windows executable of the model. Hence, using inSTREAM no longer requires installation of Swarm on Windows computers. Installing the model either as a stand-alone executable or within the GUI requires only copying the necessary directories and files.

3) A new approach is used by the HabitatSpace class to identify cells within a specified distance (its method getNeighborsWithin: aRange). This method uses the KD-Tree data structure instead of simply calculating the distance to each cell, and should provide faster execution. 

4) Almost all input files (except Setup files) can now be in .CSV format, facilitating their preparation in Excel or other spreadsheet and statistical software. The EcoSwarm TimeSeriesInput manager was modified to read input files with values separated either by commas or white space.

5) The EcoSwarm BreakoutReporter that writes output files was modified to (a) produce output in .CSV format, and (b) write output in a format with fewer columns that is more convenient for analysis via Excel's "PivotTables" and statistical software.

6) Optional output is now controlled via (optional) parameters in the Model.Setup file instead of by code statements. Hence, optional output can be turned on and off without re-compiling the software.

7) A new optional output reports the state of each individual fish.

8) A number of cleanups such as reorganizing the setup files to better separate observer and model parameters, and a thorough search for memory leaks.

9) Four digital documents (available as PDF and HTML Help files) provide documentation of (a) the model formulation, (b) the model software, (c) the graphical user interface, and (d) the "Limiting Factors Tool" built into the GUI. These documents are included as help files in the GUI.

Production of inSTREAM version 5.0 was funded via the project "Adaptation of inSTREAM for Steelhead" conducted by Lang, Railsback & Associates for Earth Systems Institute, with funding from the U.S. Forest Service. 

Many of the software improvements in inSTREAM 5.0 were original made for the project "Improvement of Salmon Life-Cycle Framework Model (inSALMO)", Contract R09PS20027, conducted by Lang, Railsback & Associates and USDA Forest Service Redwood Sciences Lab, Arcata CA, for U. S. Bureau of Reclamation,  Mid-Pacific Regional Office. 

inSTREAM 5.0 was developed by Steven Railsback and Bret Harvey, and software development was by Colin Sheppard, Steve Jackson, and Charles Sharpsteen.


For information and assistance contact:
	Steve Railsback
	Lang, Railsback & Assoc.
	Arcata, CA, USA 95521
	info@LangRailsback.com

 or:

	Bret Harvey
	USDA Forest Service
	Redwood Sciences Laboratory
	Arcata, CA, USA 95521
	http://www.fs.fed.us/psw/rsl/

inSTREAM software and its documentation are copyright 2011 by Lang, Railsback & Associates, and distributed as free software under the GNU General Public License (see file LICENSE).