Version 1.02 BIODIVERSITY INFORMATIC APPLICATION Virtual Reality of the Niche Theory Niche Analyst User Guide 1 BIODIVERSITY INFORMATIC APPLICATION Niche Analyst Huijie Qiao, Jorge Soberón, Lindsay Campbell & A. Townsend Peterson mailto:[email protected] Biodiversity Institute, University of Kansas 1345 Jayhawk Blvd. Lawrence, KS, 66045-7593 USA Key Laboratory of Animal Ecology and Conservation Biology, Chinese Academy of Sciences 1 Beichen West Road, Chaoyang District, Beijing 100101, P.R.China October 3, 2012 ----------------------------------------- FOREWORD ----------------------------------------- The Niche Analyst (NicheA) User Guide provides a detailed overview of NicheA, the application in ecological niche analysis. It was thought as a comprehensive, fully-searchable, self-contained, annotatable manual. Its latest version can always be obtained from a website (a website). The source files are available through a subversion version control repository at svn://mmweb.animal.net.cn/nichea/trunk. Given NicheA’s heavy development this guide will always remain incomplete. All NicheA users and developers are encouraged to contribute to the NicheA documentation resources. Table of Contents 1. INTRODUCTION TO NICHEA ................................................................................................................................ 1 1.1 WHAT’S NICHEA ............................................................................................................................................................. 1 1.2 SUPPORTED PLATFORMS ................................................................................................................................................. 5 1.3 REQUIREMENTS ............................................................................................................................................................... 7 2. INSTALLATION ......................................................................................................................................................... 7 2.1 INSTALLING ON WINDOWS .............................................................................................................................................. 8 2.2 INSTALLING ON MAC OS X ............................................................................................................................................. 8 2.3 INSTALLING ON LINUX .................................................................................................................................................... 9 3. RUNNING NICHEA .................................................................................................................................................. 10 3.1 LAUNCH NICHEA FOR THE FIRST TIME .......................................................................................................................... 10 3.2 THE GRAPHICAL USER INTERFACE ................................................................................................................................ 11 Main Menu: ..................................................................................................................................................................... 11 Widget: ............................................................................................................................................................................ 11 3.3 CREATING YOUR FIRST BACKGROUND CLOUD ............................................................................................................... 12 Definition ......................................................................................................................................................................... 12 Creating a BC .................................................................................................................................................................. 12 3.4 PLAYING WITH SDS ....................................................................................................................................................... 16 Definition ......................................................................................................................................................................... 16 Creating a SDS ................................................................................................................................................................ 17 Displaying a SDS ............................................................................................................................................................ 18 Designing barrier ............................................................................................................................................................ 21 3.5 INTERACTING WITH OTHER ENMS ................................................................................................................................ 23 4. FUNCTION LIST ...................................................................................................................................................... 24 1. Generating principal components ............................................................................................................................... 24 2. Quantifying niche similarity ........................................................................................................................................ 24 3. ES viewer and widgets ................................................................................................................................................. 24 4. Generating a SDS ........................................................................................................................................................ 25 5. GS viewer .................................................................................................................................................................... 25 6. Conversion tool ........................................................................................................................................................... 25 7. Interacting with other ENMs ....................................................................................................................................... 25 5. FAQ ............................................................................................................................................................................. 25 6. CITING NICHEA ...................................................................................................................................................... 25 7. REFERENCES ........................................................................................................................................................... 25 8. SUPPORTED FORMATS IN NICHEA .................................................................................................................. 27 9. ACKNOWLEDGEMENTS ....................................................................................................................................... 28 hanks for using NicheA! At present, this software should be considered an alpha release – some bits aren’t meant to be used yet, and it hasn’t been extensively user-proofed yet. It’s still entirely possible to tell the software to do things that it shouldn’t do, which will produce nonsense results (Robbed from ENMTools. *_^). 1. Introduction to NicheA 1.1 What’s NicheA Niche Analyst (NicheA; https://sourceforge.net/p/nichea/) is an open-source, cross-platform application released under a GNU Public License (GPL). NicheA is written in Java, combining several toolkits, such as R (R Development Core Team 2011), Weka (Hall 2009), JAMA (Hicklin et al. 2012), GDAL (GDAL Development Team 2011) and QuickHull3D (Lloyd 2012; Fig. 1). The platform is a window-based, user-friendly application that executes on most common operating systems, including Microsoft Windows, Mac OS X, and some Linux releases, such as Ubuntu. Users can use NicheA (1) to re-orient and re-cast environmental variables through principal component analysis (PCA), (2) visualize species’ distributions in linked E and G spaces, (3) design barriers to dispersal in G, (4) estimate and display Grinnellian niches in E, and (5) map objects between G and E. Fig. 2 shows functions and feasible action flows in NicheA. NicheA can also import and display results of widely-used ENMs, and export SDSs in formats compatible with various ENM platforms. The unique functionality in NicheA, not available in other software programs, is that of estimating Grinnellian niches of species based on environmental variables and occurrence records, but with a clear focus on fundamental ecological niches. We have implemented two algorithms, a minimum volume ellipsoid (MVE; Van Aelst & Rousseeuw 2009) and a convex hull (Lloyd 2012), both designed to approximate the full dimensions of fundamental niches via approximation of convex shapes in multivariate environmental spaces. NicheA can display ecological niches; calculate their shape, density, location, and other attributes; and quantify similarity among multiple niches based on MVE overlap. A few studies have used convex hulls to 1 estimate niches (Rissler & Apodaca 2007; Monahan & Tingley 2012), but this approach has not been implemented easily owing to the complexity of its formulas. Fig. 1. The software architecture of NicheA.