June 2, 2006

PATN v3.1 released! The changes include-

  • PATN can now import a lower symmetric association matrix for objects or variables (File | Import | Row (or column) Lower Symmetric Association matrix). This matrix can be either be formatted as an unlabelled CSV file or as a file in the identical format as exported from PATN. A classification and ordination can be performed on this matrix by selecting Association = “None” in the Data Analysis Window. All subsequent evaluations (e.g. ANOSIM, displaying association on the ordination plot etc) will use the imported association matrix.
  • A Print Preview button has been added to the standard button bar.
  • A Print button has been added to the standard button bar.
  • A new option has been added to the Data menu that will create one new extrinsic variable for each variable group. This option is called “Create new variables from variable groups”. The new variable for each variable group is the mean of the values in each of the variables within the group. For example, the new variable Group 1 will contain N rows that will be the mean of each variable in variable group 1. This option helps to reduce noise on datasets with a large number of variables. The method produces new variables which are groups of original variables.
  • The export of column (variable) group statistics has been added to the File | Export Evaluation Data menu. Export group statistics has been renamed Export Row Group statistics.
  • Two-step association for column association replaces Bray and Curtis where it appears that the variables are species and the matrix is sparse.
  • The time required for each step in an analysis is now added to the log file.
  • A non-hierarchical classification (rows only) will now produce a correct two-way table. The ordering of rows within the groups is arbitrary, but a user-defined ordering of the rows within the table can be imported (see next item).
  • The ordering of rows or columns in dendrograms can now be imported as a CSV file (File | Import | Row (or Column) Dendrogram Order. Imported ordering will be used for displaying dendrograms and two-way tables. It is possible to produce an ordering of the dendrogram which, given the classification, is impossible to display correctly. If an ‘illegal’ ordering is imported, PATN will still try and display a dendrogram but it may look a mess! If a legal ordering is used, the dendrogram will display correctly.
  • The row and column dendrogram ordering is appended to data table on export (if they are available).
  • PATN will now detect duplicate rows in the Data Table (Data | Delete duplicate rows) and allow for deletion of duplicates.
  • The default ‘Visible Stats’ tab will now display ‘Num > 0’ instead of ‘mean’ by default. The display can be changed using Tools | Options.
  • The missing data value is now set to “-9999.9999” when a random Data Table is generated in PATN.
  • The labeling of the ANOSIM output has been corrected. The values output were correct, but the labeling wasn’t.
  • The layout of the dendrogram window has been improved to scale better.
  • The ordination plot legend is now generated to a scrollable region. The text and symbol size can be controlled in that window as with other PATN windows.
  • Page-Up and Page-Down keys now control symbol size on the Ordination Plot and the scatter plot. Try it. Neat!
  • Multiple monitors will not work with PATN’s Ordination Plot – but PATN won’t fall in a heap either.
  • Unhide of a row or column will work when any adjacent row or column is selected and unhide is activated.
  • Transposition will now reset extrinsics and hidden rows and columns.
  • Improved capture and display of BMP ad EMF images.
  • Eliminated PATN’s prompt for saving the project file when no changes had been made to it.
  • A long Project Comment will now automatically wrap in the text box.
  • Status bar is updated faster when changes are made to the number of rows or columns in the Data Table.
  • Importing ordination coordinates will update the Ordination Plot.
  • View | Ordination was cross-linked to View | ANOSIM – now corrected.
  • Corrected overflow when applying Box and Whisker plots to a large number of objects.
  • Sparse data in ‘relational’ format can now be imported into PATN. Data with >50% zeros is often stored in the form ‘species label, site label, abundance value’.
  • Imported ordination coordinates can be used in the 3d-display even if an ordination had not been previously run.
  • An error in the display of a-priori centroid labels in the 3d-plot has been corrected.
  • An error in the display of the lengths of the ordination axes has been corrected. In v3.01-3.03, the ordination axes were displayed with unit length.
  • The ‘depth’ (z-axis) of the 3d ordination display has been increased to improve its 3d properties.
  • Ordination ‘spheres’ have been rendered with a finer mesh to improve the view.
  • 3d-plot legend now uses scrollbars as required.
  • ANOSIM has a new option that can use either PATN generated groups or an a-priori grouping (defined externally to PATN).
  • Box and Whisker plots have a new option to use either PATN-generated groups or a-priori groups
  • A Zoom toggle has been added to the 3d-plot
  • Selected points in the Scatter Plot will now be highlighted in the Data Table in the same way as with the ordination plot.

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