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Biodiverse Changelog

What's new in Biodiverse 0.16 Beta

Feb 17, 2012
  • General:
  • Groups and spatial outputs can now be exported direct to DIVAGIS raster formats. Issue #220
  • GUI:
  • Matrices generated by cluster analyses are now added to the project and can be visualised as a spatial plot. Click on an element (cell) in the plot to see its dissimilarity with every other element used in the matrix (the index element is coloured grey). This is very useful when used in conjunction with tools like Generalised Dissimilarity Modelling and when interpreting correlograms of species turnover. Issue #199
  • Grey scale shading is now supported. Issue #32
  • Users can now switch between tabs using control-tab and shift-control-tab keys. Issue #196
  • The colour of the shapefile overlay can be changed. Issue #75
  • Outputs tab - the output type is listed next to each output. Issue #201
  • Colour stretches can be adjusted using percentile values (2.5, 5, 95, 97.5). Issue #244
  • View labels tab
  • Element properties with a value of nodata are displayed as -99999. Issue #189
  • System no longer intermittently hangs when control clicking. Issue #194
  • Labels list is now stable when sorting by a column with tied values. Issue #246
  • Label and group axes can be re-ordered after import. This is useful when you have forgotten to reorder them at import and, for example, your data file contains a field for latitude before longitude. Issue #188
  • Analyses:
  • New analysis type of RegionGrower. It is an extension to the cluster analyses that uses any scalar metric that lumps two neighbour sets together when calculated. One can also merge those pairs that either maximise or minimise the selected index. When used with indices like richness it is effectively a one-pass complementarity analysis. (Its matrices can also be displayed spatially since it is just a variant on the cluster analyses - see issue #199 ). Issue #204
  • Cluster matrices can be written to file as they are built. These are not added to the GUI, thus saving memory and allowing extremely large matrices to be built for use in external applications. Issue #186
  • More efficient cluster matrix construction and use. Issue #185 , Issue #210 , Issue #234
  • Better handling of empty groups. Issue #180 , Issue #181 , Issue #228 , Issue #234
  • Calculations and indices:
  • NEST_RESULTANT index is now correctly calculated. Issue #182
  • Added phylogenetic nearest taxon distance indices. Issue #225
  • Indices for phylogenetic dissimilarity are now available. Issue #215 . Issue #240
  • Added AED, BED and related indices. Issue #206
  • Added indices for numeric label dissimilarity. Issue #223
  • Spatial conditions:
  • sp_select_sequence() now works as a definition query. Issue #190
  • sp_is_left_of(), sp_is_right_of() and sp_in_line_with() identify if the element is to one side of a vector or on it. Issue #202
  • sp_select_block () for block subsampling. Issue #218
  • sp_point_in_polygon(). Issue #221
  • sp_group_not_empty() - does the group have any labels? See Issue #234

New in Biodiverse 0.15 (Feb 17, 2012)

  • Calculations and Indices:
  • The PD node list has been moved to its own calculation ( issue #130 )
  • The Phylogenetic Endemism (PE) lists have been moved to their own sub ( issue #131 )
  • Exporting data:
  • Exporting groups to raster formats now works properly ( issue #129 )
  • Exporting matrices from a cluster analyses now works ( issue #142 )
  • Exporting to ER-Mapper files now works properly, with some caveats (see issue #135 and the FAQ)
  • Importing data:
  • Column numbers are now displayed when importing data ( issue #128 )
  • Tree imports now use the same quotes character as BaseData imports ( issue #152 )
  • Spatial Conditions:
  • sp_ellipse() works properly now ( issue #150 )
  • Randomisations:
  • Ties are now counted ( issue #146 )
  • Visualisation:
  • User defined properties are now displayed in the view labels tab ( issue #155 ).
  • Under the bonnet:
  • User defined properties are now imported properly in the GUI ( issue #154 )
  • Neighbour set recycling works properly now ( issue #127 & issue #145 )
  • Module Statistics::Descriptive2 is now deprecated. It has been replaced by Biodiverse::Statistics which depends explicitly on Statistics::Descriptive ( issue #139 )

New in Biodiverse 0.14 (Feb 17, 2012)

  • GUI (and general):
  • The naming errors with saving basedata, tree, and matrix files to the biodiverse native format have been corrected. ( Issue #104 )
  • Reading a tree file from biodiverse format works again. ( Issue #105 )
  • The GUI now recognises R style tables for import (as exported using the write.table() function in R). ( Issue #20 )
  • Tree and matrix objects can be renamed. ( Issue #72 )
  • Users can now describe the selected basedata, tree and matrix. Results are printed to both a popup and to the log window (from where they can be more easily copied). ( Issue #93 )
  • The parameters sections of the Spatial and Cluster tabs can be hidden to free up real estate when selecting calculations to run. Click on the Parameters button at the top left of the tab to apply it. ( Issue #68 )
  • Trees and matrices embedded in basedata objects can be added to the project. ( Issue #71 )
  • Labels in a basedata object can be deleted using the nodes/elements in the selected tree or matrix. The converse can also be done, where those BaseData labels not in the matrix or tree are deleted. ( issue #74 ).
  • Calculations and indices:
  • The count calculations have each been seperated into one calculation for the lists and one for the summary stats. This applies to the local ranges, local sample counts and element lists.
  • Metadata for the indices now includes formulae. These are displayed in the online help, but are not displayed in the GUI. http://code.google.com/p/biodiverse/wiki/Indices
  • Added new index, NEST_RESULTANT (nestedness-resultant, Indices#Nestedness-resultant) from Baselga (2010) Glob Ecol Biogeog. http://dx.doi.org/10.1111/j.1466-8238.2009.00490.x ( issue #92 )
  • Added binary and sample weighted taxonomic distinctness and variation from Clarke & Warwick (2001) Mar Ecol Progr Ser. http://dx.doi.org/10.3354/meps216265 (note that these are beta level implemenations and need user testing) ( issue #102 )
  • The Endemism and Rarity calculations are now listed under their own headings.
  • Added new list calculations to enable hierarchical partitioning of the endemism results (the ENDC_HPART_ and ENDW_HPART_ lists). ( Issue #99 )
  • The Bray-Curtis calculation (Indices#Bray-Curtis_non-metric) now also returns the A, B and W values used in the calculations. ( Issue #124 )
  • Added new calculation for Bray-Curtis values normalised by the neighbourhood group counts (Indices#Bray-Curtis_non-metric,_group_count_normalised). Resultant indices are the BRAY_CURTIS_NORM and associated A, B and W values. ( Issue #126 )
  • Spatial Conditions
  • New condition sp_match_regex which allows the user to match using arbitrary regular expressions. For example, to match any group where the neighbour's third axis starts with the processing group's third axis, use sp_match_regex (re => qr/^$coord[2]/, axis => 2, type => 'nbr'). ( Issue #101 )
  • Randomisations
  • The randomisations now compare against all lists, not just those in SPATIAL_RESULTS. One consequence of this is that the resulting list names have changed. To enable users to keep track of the results across multiple lists, the results are now named using the randomisation name, followed by >>, followed by the original list name. For example, for a randomisation called Rand1, one could have resulting lists called Rand1>>SPATIAL_RESULTS and Rand1>>ENDC_WTLIST. The naming scheme for the list contents has not changed (see AnalysisTypes#Randomisations). The code is not backwards compatible, so previously run randomisations cannot be extended cleanly using this method. This is because the SPATIAL_RESULTS comparisons will be divided across two lists in an output, e.g. Rand1 and Rand1>>SPATIAL_RESULTS. Re-running the randomisation from scratch is recommended. Alternately, one can manually sum the C_ and Q_ values across the two result sets and from them calculate the updated P_ values. ( Issue 100 )
  • The swapping algorithm has been rewritten so it converges more efficiently for large data sets. (Swapping is used to reach richness targets in the rand_structured randomisation). A consequence of this is that structured randomisations will not produce the same result between versions 0.13 and 0.14 if the seed value is specified. This is because the random values are used in a different order and so will produce different results if given the same sequence of random values. As with the previous change, the simple solution to this is to start any randomisations afresh after upgrading rather than continuing any existing randomisations. Continuing randomisations created in BaseData objects prior to version 0.14 will result in mixed algorithms, thus making reproduction of results difficult. ( Issue #103 )
  • The comparison algorithm used when comparing spatial analyses now uses recycled results, resulting in a smaller memory footprint. Recycling occurs when results are the same across the neighbourhood, as occurs with block and zone type spatial conditions. In these cases one can generate one set of results and apply them across the neighbourhood rather than having multiple sets of identical results. ( Issue #107 )
  • Under the bonnet
  • Several optimisations have been added where the system can use recycled results (those where the results are the same for all groups in a neighbourhood).

New in Biodiverse 0.13 (Mar 1, 2010)

  • Analyses, Calculations and Indices:
  • The use of the term "analyses" in the documentation is now clearer. Analyses can be one of Cluster, Spatial or Randomisation. The term "calculation" is now used to describe the collection of indices that are calculated together, e.g. for the groups under a cluster node or within a spatial neighbourhood. An analysis can apply several calculations to generate some number of indices.
  • The endemism calculations have been subdivided. The list indices are now in their own calculations, and need to be called explicitly if needed.
  • Two new rarity calculations have been added to generate the lists of weights and sample counts for each label used, as per the endemism calculations.
  • View labels tab:
  • The view labels lists now have additional columns to allow sorting based on the selections (i.e. to promote the selected set to the top of the list). Note that the list order changes dynamically according to the sort options. This means that the list will be reordered if the label selection is changed and there is a sort in place using one or both of these columns.
  • The second view labels list is only shown if there is a selected matrix. This is because it is used to show the matrix column selection and control their sort order.
  • The map legend is now shown in the view labels map pane. This allows easier interpretation of the mapped values.
  • Trees:
  • Nexus file import is now more flexible in the characters it accepts in names (anything that has no special meaning in nexus files), and also numeric formats used for lengths.
  • Newick files are now supported for import (see issue #79 ).
  • When displaying the cluster dendrogram, the user can choose not to use the slider bar to select nodes to plot on the map (access via the dendrogram Options menu).
  • Group coordinates can be specified as Degree, Minutes, Seconds within a single column. (Note: this is currently a beta level implementation). See issue #61 .
  • The system now warns if the user attempts to create a new output, or rename an existing output, using a name that is already in use for that output type (see issue #62 ).
  • The randomisation list results are now accessible (see issue #45 ).