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| <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"><html><head> <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> <meta name="Author" content="Peter E. Midford"> <meta name="Description" content="Info page for the PDAP/PDTree module."> <title>PDAP</title></head><body bgcolor="#AFEEEE"> <table BORDER=4 CELLSPACING=2 CELLPADDING=0 ><tr><td><img src="splash.gif" alt="PDAP/PDTree splash icon" height=64 width=164></td><td BGCOLOR="#0000FF"><h2><font color="#FFFAFA">PDAP:PDTREE</font><font color="#00FF00">: A translation of the PDTREE module of Garland et al.'s Phenotypic Diversity Analysis Programs</font></h2></td></tr></table><h4>Peter E. Midford, Theodore Garland Jr., and Wayne Maddison</h4>August 2009<p>This package of modules and library classes was brought over from version5.0 of PDAP. PDAP was originally described in Garland, Dickerman,Janis, and Jones (1993), but several functions pertaining to reconstructed root values were added later (see Garland, T., Jr., P. E. Midford, and A. R. Ives. 1999. An introduction to phylogenetically based statistical methods, with a new method for confidence intervals on ancestral values. <i>American Zoologist</i> 39:374-388.; Garland, T., Jr., and A. R. Ives. 2000. Using the past to predict the present: confidence intervals for regression equations in phylogenetic comparative methods. <i>American Naturalist</i> 155:346-364. and the documentation for PDAP, PDINSTRW.DOC). Current functionality includes what is in PDTREE, i.e., computation of independent contrasts, diagnostic screens to check adequacy of branch lengths, transformations of branch lengths, and some conventional statistical analyses. Other components of PDAP, suchas simulation functionality, will be added soon. News and the latest update for thispackage are available <a href="http://mesquiteproject.org/pdap_mesquite/">here</a>.<ul><li><a href="#overview">Overview</a></li><li><a href="#installation">Installation</a></li><li><a href="#examples">Examples</a></li><li><a href="#citation">Citation</a></li><li><a href="#contact">Contact</a></li><li><a href="#acknowledgments">Acknowledgments</a></li></ul><h3><a NAME="overview"></a>Overview</h3>The translation of PDAP currently includes:<ul><li><B>Import and Export of .PDI files, including name conversion as needed.</B></li><li><B>Exporting of Nexus tree and character information to .PDI files. </B></li><li><B>Dignostic Screens and Statistics</B> These are available once a PDAP diagnostic window is opened.<ul><li>Absolute values of standardized contrasts vs. their standard deviation</li><li>Absolute values of standardized contrasts vs. the (corrected) height oftheir base node</li><li>Absolute values of standardized contrasts vs. the estimated character valueat their base node</li><li>(Corrected) height of internal nodes vs. their estimated character values</li><li>Contrast vs. contrast plots</li><li>Contrast residuals vs. X value and base node height</li><li>Statistics pertaining to reconstructed root values (Garland, Midford, andIves, 1999).</li><li> Generation of .FIC files. These have been tested with recent versions of Microsoft Excel.</li></ul><li><B>Branch length transformations and estimates</B> These are available in the tree window.<ul><li>Log base 10 transform of branch lengths</li><li>Exponential transform of branch lengths</li><li>Transform branch lengths by Grafen's (1989) rho</li><li>Set all branch lengths to a constant (1.0)</li><li>Set branch lengths according to a method of Grafen (1989)</li><li>Set branch lengths according to a method of Pagel (1992)</li><li>Set branch lengths according to a method suggested by S. Nee (cited inPurvis 1995)</li></ul></li><li><B>Character (tip) data manipulations</B> These are available in the character matrix editor.<ul><li>Log base 10 transform character values</li><li>Base 10 antilog transform character values</li><li>Exponential transform of character values</li><li>Raise character values to a power</li><li>Divide one character value by another</li></ul></li><li><b>Export of distance matrix files equivalent to the DOS PDDIST application</b><ul><li>(1)Pairwise differences of tip data values from character matrix (for a specified character)</li><li>(2)Patristic distance</li><li>(3)Node count along path between tips (speciation patristic)</li><li>(4)Shared proportional history distance</li><li>(5)Shared history distances. This is the DSC matrix of PDDIST (C matrix of Garland and Ives 2000), i.e., the phylogenetic variance-covariance matrix as would be used for PGLS analyses.</li></ul></li></ul><hr><h3><a NAME="installation"></a>Installation</h3>The compressed file you download will contain a directory (folder) called pdap_mes. This will, in turn, contain two directories, one titled PDAP and one titled examples. To install the PDAP modules, the "PDAP" directory must be installed in the "mesquite" directory within the directory titled"Mesquite_Folder".<br><hr><h3><a NAME="examples"></a>Examples</h3>A demo which includes examples based on the 49lbr and appamg91 trees distributedwith DOS PDAP is included. The examples include a navigation window that allows the user to scroll through the examples in order. The example set starts with the file Part1.nex. There are additional examples including an updated versionof the 49lbr tree with full species and character names.<hr><h3><a NAME="citation"></a>Citation</h3>Midford, P. E., T. Garland Jr. & W. Maddison. 2009. PDAP:PDTREE package for Mesquite, version 1.15. http://mesquiteproject.org/pdap_mesquite/<p>Citations for the Turbo Pascal implementationof PDAP may be found in its accompanying documentation (PDINSTRW.DOC),which is available from Ted Garland (tgarland@ucr.edu).<hr><h3><a NAME="contact"></a>Contact</h3>For questions regarding this module, please contact Peter Midfordat <a href="mailto:peteremidford@yahoo.com">peteremidford@yahoo.com</a>and put PDAP in the subject line.<hr><h3><a NAME="acknowledgements"></a>Acknowledgements</h3><hr><p>© Peter E. Midford, Theodore Garland Jr., and Wayne Maddison, 2002-2009<br> </body></html> |