PASSaGE 2 Release Notes: Version 2.0.11.

6 (June 3, 2011) ------------------------------* Updated * Official publication details * If the OS will allow it (64-bit or specially modified 32-bit), PASSaGE c an now use more than the standard 2Gb of RAM allocated for programs * Fixed * Bug in command-line version of second-order analysis which would cause a crash when performing randomization tests under certain conditions * Bug when importing a file containing a single column of data with a colu mn header Version 2.0.10.18 (January 7, 2011) ----------------------------------* First official non-beta release * New * All missing batch commands have been added * Added SE calculations to point-line analysis * Added PASSaGE citation to About/Help * Fixed * Moving Split Window analysis would sporadically fail to record the positions of the windows * Second Order Analysis randomization tests gave an incorrect confidence inter val when the coordinates were latitude/longitude and used spherical distances (Euclid ean distance-based intervals were fine) * Second Order Analysis now allows fractional designation of maximal distance * Mantel Correlograms and Mantel Bearing Correlograms could be run without spe cifying all required matrices * Typos in output of command line version * Error in echoing output when creating connection matrices * Slight bug in the way certain drop down menus worked in the ribbon bar of th e GUI Version 2.0.9.24 (October 29, 2009) ---------------------------------* New * You can use the delete key to remove selected matrices from memory * New polar plot from Angular Wavelet output * A help file is now included and integrated into the software (although some of the help entries are still incomplete) * Fixed * Missing batch commands: MergePoly * Bug where PASSaGE failed to read Excel files written by Excel2007, even when saved as Excel 97-2003 XLS format. * A number of issues which would cause PASSaGE to crash when setting distance class boundaries * Cleaned up popup menu in data monitor * Data distances could be run without selecting a distance measure * Data distances: Crash when calculating scaled Euclidean distances

* Added a second analysis tab and moved some of the methods to this second tab ; this should help avoid a problem where some analyses were not running (no reaction from PASSaGE) when the menu was compressed * Drawing connections de novo did not enable general map options. * Could not edit color gradient when drawing closed tessellations and polygons * Export to GoogleEarth is only available if mapped data is represented by lat itude and longitude * Occasional crash in second order analysis with bivariate/multivariate option ; should improve memory efficiency as well * Memory leaks in Second Order analysis (bivariate group names; randomization tests [major leak]) * Memory leak in Angular Wavelet analysis * Memory leak after canceling distance/angle creation from coordinates * Point-polygon options were not enabling/disabling properly * Incorrect error message when trying to run agglomerative clustering on scatt ered data * Some of the text output was missing from Bearing analysis * The graphical output of Bearing analysis was not indicating significance cor rectly * Mislabeled box in GUI conversion of polygons to coordinates * Combining binary matrix GUI background color of black was lost * Draw Tessellation form was not enabling ok button when choosing a tessellati on * Creating Connections from Distance Classes * De/Select All buttons were not enabling * If there was only one DC in memory, the class list was not auto-loading * The Ok Button was not enabling when classes were checked Version 2.0.8.20 (January 8, 2009) ---------------------------------* New * A 64-bit Windows command line version (experimental) * Added a 2D Sombrero Wavelet (experimental) * Fixed * The Morlet wavelet was being calculated in a way that wasn t providing accurat e estimates of the scale of pattern (Note: there may still be problems with this wavelet; u se at your own risk) * Memory leak when exiting the program with a matrix view window open * Minor bug in enabling/disabling options for 2nd order analysis * Join Count analysis based on a connection matrix, but making use of non-bina ry, distance-based weights was crashing * Correlogram analysis was not checking for matrix size compatibility correctl y in all circumstances * Fixed a bug preventing command line versions of the program from reading sha pe files * Fixed a bug which would sometimes cause line and polygon shape files to impo rt with stray lines or to crash * There was no default matrix name if the imported file had no file extension * The Echo for wavelet and bivariate wavelets was producing an invalid paramet er * Batch Commands * The last version had broken the ability to correctly parse lists of data c

ontained within {}s * A number of batch commands that included a column list and an All option whe re All was the default, were always analyzing as if All was chosen, regardless of the actual input p arameter. This included the LoadData, DataDistances, DescribeData, AngularCorrelation, and SplitWi ndow commands. * LoadData command had incorrect matrix type as default (should have been re ctangular matrix) * Variogram batch command was defaulting to Save = Yes rather than Save = No , and the error message involving a missing value for the parameter SaveName was mistakenly listing the parameter as Name * Wavelet, bivariate wavelet, and spectral batch commands were not processin g requests to analyze rows, only columns * Changed * The style of the basic GUI interface has been completely changed * Updated and began standardizing many error messages * The Edit matrices option from the View mode has currently been disabled; it is currently incompatible with some internal changes that were deemed more critical * A number of (presumably transparent) major and minor internal changes Version 2.0.7.29 (May 1, 2008) -----------------------------* New * Analyses * Bearing correlograms * Mantel bearing correlograms * Windrose correlograms * Mantel windrose correlograms * Moving Split-Window distances for boundary detection of 1D/transect data * Wombling: categorical and continuous for both raster/surfaces and scattere d data * Agglomerative clustering * Dispersion Indices * Point-Polygon relationships * Data * Polygons and Lines now have coordinate systems in the same manner as point data (xy, lon/lat, or UTM) * Coordinate study plots based on polygons are now specified by attaching a polygon matrix rather than as a list of coordinates. This should allow more compl icated study plot shapes as well as making import of a study boundary easier. * New data matrix type: Boundaries these represent specific types of data a s produced by methods such as Wombling * Data within boundary matrices can be extracted to other data types * Polygons or lines from different matrices can be merged into a single matr ix * Polygon and lines can now be exported to text and spreadsheet formats * Miscellaneous * Added squared Euclidean distances as a distance measure for data * Added function for constructing a set of coordinates which represent the p ositions of a set of polygons

* Graphics * When graphing continuous variables using a color gradient (e.g., for point s, polygons, or tessellations), one can now optionally use the ranks of the variable ra ther than the raw values * When graphing line sets, you can now use colored variation, thickness, and style, based on an external variable in the same manner one can already use to differen tiate between points and polygons * Draw/map boundaries and/or add boundaries to other plots. Can also displa y boundaries as individual elements, vectors (for continuous wombling), or as connected subboundaries. Individual elements/vectors can also be color coded to represent the magni tude of change associated with the boundary element. * Surface maps can now be plotted alongside other map elements. * Fixed * Added error checking and generally cleaned up the point-line relationship an alysis * Added batch commands for converting connections/tessellations to polygons/li nes, point/line relationships, angular wavelets, and LISAs * Missing error message for invalid values of Lambda when calculating Minkowsk i distances * Conversion of connection matrices to line matrices was creating each individ ual line twice * Bug in copying the study plot correctly when a coordinate matrix was copied * Values associated with lines can now be represented by different line styles when mapped * In Windows Vista, Aero effects such as taskbar preview and window scroll sho uld now be enabled * Changed * Some minor font changes * Split the analysis toolbar into multiple smaller toolbars * Removed * Option for plotting background maps; this became unnecessary when polygons w ere added as a data type Version 2.0.6.17 (February 15, 2008) -----------------------------------* Fixed * JoinCount analyses were generating an error when used with a connection matr ix * Modified t-test for correlation * Computational bug in estimate of covariance & CRH correction; with large n umbers of points, the error was subtle/minor, but with small data sets the error could be ve ry large * No longer generates error if a column of data contains no numeric values * Mantel tests * Computational problem with partial Mantel tests consisting of 4 or more ma trices (classic 3 matrix partial Mantel tests unaffected), involving improper matrix multipl ication

* Memory leak in partial Mantel tests consisting of 4 or more matrices * Memory leak in any partial Mantel test which included permutation tests * Replaced approach for storing data for the permutation tests of wavelet anal ysis; the new approach has substantially lower memory requirements (~95% reduction in memory usage) * Added some file error checking when importing images * Changed one last stray reference of alpha version to beta version * New * Added LISA/Getis-Ord analysis * Note: No graphical output at this time * Note: Batch command is not yet active * Added option for turning on a timestamp that will record the date/time of th e beginning and end of analyses in the output, as well as the computational time * Coordinates can now be directly saved in ArcInfo shapefile format * Added initial support for polygons and polylines as data types * Import/export as ArcInfo Shapefiles * Import/export as PASSaGE format * Import/export polygons (only) as Surfer BLN files * Mapping/drawing in plots * Connections and tessellations can be converted to lines and/or polygons (as appropriate) * Note: Batch command is not yet active * Added preliminary method for analyzing point-line distances * Note: Batch command is not yet active * Added ability to plot/map lines, polygons, tessellations, and connections wi thout first plotting points * Removed * Export to Arc/Info Shapefile option * This would export coordinates, tessellations, or connections to shapefiles . It is no longer necessary since coordinates can be directly saved as shapefiles and tessellations an d connections can be converted to lines/polygons which can be saved as shapefiles * Note: The addition of polygons and lines as data types will eventually lead t o a number of changes which are not completely implemented yet. This includes * Replacing the limited polygon style study plot with a formal and full polygon data type * Removing the background map option from plotted points (and similar data). Since these background maps were essentially just specialized polygon files and polygons can now be loaded as data and mapped, it makes more sense to just use polygons for that purpose rather than sending them through a special conversion process for PASSaGE. Version 2.0.5.14 (November 9, 2007) ----------------------------------* Fixed * First public release was marked as "Alpha" when it should have been "Beta" * Fake error generated when "Arrange" was chosen from Windows menu * JoinCount and Correlogram would not correctly allow/use nonbinary weighting with a connections matrix * JoinCount Analysis * GUI was not properly checking for correct choices before enabling the OK b utton * The # of pairs per class was being reported as double the actual number * Potential major computational error in counting and identifying the class

memberships in Join Count analysis; could effect counts within and across class types * Distance class creation * Reporting the wrong count for points within a class for the smallest class (1 too many) and the largest class (1 too few) * Fixed two errors in distance class creation when manually editing class bo undaries * Error in importing Multipoint, MultiPointZ, and MultiPointM shapes from Arc/ Info shape files * Spectral analysis * Spectral analysis now automatically chooses first column when a data matri x is specified * Error generated by canceling a spectral analysis * New * Added function for creating a connection matrix from a set of distance and d istance classes * Coordinate matrices, tessellations, and connection matrices can now be expor ted to Arc/Info shape files * Added batch command for spectral analysis * Added marker for nonsignificant values in correlogram (and similar) plots * Correlograms: when plotting data added option to specify alpha significance and option for plotting confidence intervals * Randomization test for spectral analysis * Added an option for outputting a table of nearest neighbor distances; this o ption has been in version 1 but had not been included in version 2 Version 2.0.5.1 (August 30, 2007) ---------------------------------* First public beta release of PASSaGE 2