Thursday 27 April 2017

Biodiverse now works on Macs



Thanks to some sterling work by Jason Mumbulla we now have a native version of Biodiverse for Macintosh computers.

Installation is by dmg file, so follows the same approach as most mac installations.

The interface is somewhat "old school" (think 1998), but all the functionality is in place and works (see screenshots below).

Download links are at https://purl.org/biodiverse/wiki/Downloads (at the time of writing there is only a development release), with installation instructions at https://purl.org/biodiverse/wiki/Installation.








Shawn Laffan
27-Apr-2017


For more details about Biodiverse, see http://purl.org/biodiverse 

For the full list of changes in the 1.99 series (leading to version 2) see https://purl.org/biodiverse/wiki/ReleaseNotes (for all issues addressed or being targeted to fix for version 2, see https://github.com/shawnlaffan/biodiverse/milestone/4 ).

To see what else Biodiverse has been used for, see https://purl.org/biodiverse/wiki/PublicationsList


You can also join the Biodiverse-users mailing list at http://groups.google.com/group/Biodiverse-users

Wednesday 26 April 2017

Biodiverse now exports tree branch colours

Biodiverse version 2 will allow you to export the tree branch colours.  This means you can now get your tree colours to the point that you are happy with them, and export them to another program such as FigTree to generate figures for a publication.

Colours can be exported with the Nexus and tabular Tree formats.  If you use the tabular format then there will be a column in the output table called Colour.  For the Nexus format, the colours are stored in the comments block for each branch.

Click on the "Export colours" checkbox to export the colours in a Nexus file. 

A few examples are below.

View labels tab with a set of labels highlighted on the tree.


The selection colours displayed in FigTree.

A cluster analysis with six clusters coloured.

The tree in FigTree with the six clusters coloured.  

A user defined selection.

The same user defined selection in FigTree.

The colouring works for anything that is applied to the tree, so you can also export continuous palettes when you have calculations per node (branch).

PD calculated for each cluster node (branch).

And the same PD colouring now in FigTree.

Kudos to Luke Fitzpatrick for getting it working.

Shawn Laffan
26-Apr-2017


For more details about Biodiverse, see http://purl.org/biodiverse 

For the full list of changes in the 1.99 series (leading to version 2) see https://purl.org/biodiverse/wiki/ReleaseNotes (for all issues addressed or being targeted to fix for version 2, see https://github.com/shawnlaffan/biodiverse/milestone/4 ).

To see what else Biodiverse has been used for, see https://purl.org/biodiverse/wiki/PublicationsList


You can also join the Biodiverse-users mailing list at http://groups.google.com/group/Biodiverse-users

Matching spatial, tree, matrix and property data is now easier

One of the biggest bugbears when using Biodiverse has been matching the names between the spatial data and any tree, matrices, group properties and label properties.

Biodiverse uses an exact matching scheme to link tree branch names with Basedata labels (e.g. species).  If there is even a single character different then the two sets will not match, and analyses either do not run or are incomplete.

The standard approach used in Biodiverse to ensure the data match is for users to provide a remap table that "maps" labels from one data set to another (e.g. make the tree names match the basedata).  However, experience suggest that users are often unsure what columns should be used for what (and sometimes how many), and that generation of the remap file is more difficult than desired.

Biodiverse version 2 has a greatly simplified remap process that can generate possible matches automatically.  Any object can have its element names remapped at import, as before, but now there are also options under the Basedata, Tree and Matrix menus.  Better yet, there is also a centralised interface that can be accessed under the file menu.


In the centralised remap interface, one can match any object to any other object in the project, as well as to names loaded from a file.  If an object is chosen then Biodiverse will search the sets of names in each object to find possible matches.  The User defined from file is the conventional process, where the file needs to define the set of input and remapped columns.  The Auto from file allows users to load a list of names which will be searched to find possible matches, in the same way as it searches other objects.

The search process uses a fuzzy text matching scheme, as well as searching for differences purely in punctuation or in quoting characters.  The minimum acceptable distance option allows control over how different possible matches can be.  If a very large value is used then anything can match anything else, which is unlikely to be useful.

The interface for the automatic remaps is as below.  There are panes listing exact matches, non-matches (i.e. differences were too great), punctuation matches and possible typos.  Users can choose to ignore any of these sets, and also select subsets within the sets if, for example, there are false matches.

The menus for Basedata, Matrices and Trees all have remap options, but there is also a centralised system under the File menu.


Any object can be matched with any other object, as well as loading remaps from files.

The Maximum acceptable distance controls how different names can be before they are no longer considered as possible matches.
Users can control the level of remapping used within the match categories.  



Users can also choose to export the remap to a file to re-use later on (or inspect for possible problems) using the Export remap to file button.  A copy of the remap can also be sent to the clipboard for direct use in spreadsheets, text editors and the like.



Remapping of BaseData objects is not permitted if they have existing outputs, as that would potentially wreak havoc with the matches between the BaseData and the outputs.




The system will also warn if you try to map an object to itself (but it will let you try if you are determined to do so).




Kudos to Luke Fitzpatrick who got it all working.


Shawn Laffan
26-Apr-2017


For more details about Biodiverse, see http://purl.org/biodiverse 

For the full list of changes in the 1.99 series (leading to version 2) see https://purl.org/biodiverse/wiki/ReleaseNotes (for all issues addressed or being targeted to fix for version 2, see https://github.com/shawnlaffan/biodiverse/milestone/4 ).

To see what else Biodiverse has been used for, see https://purl.org/biodiverse/wiki/PublicationsList


You can also join the Biodiverse-users mailing list at http://groups.google.com/group/Biodiverse-users


Constrain the extent of your exported results

This one is a short post.

Following a suggestion by Chris Barratt, Biodiverse version 2 will allow users to use a definition query when exporting spatial outputs.  This means you can run your analysis for a large data set, but limit the set of exported groups to a subset.

If the analysis itself used a definition query then the export windows will set that by default.  Just delete it to export all records.

Users can specify a definition query when exporting their data.  In this case the analysis also used a definition query so it is specified by default. 

The exported data only contain those groups (cells) that passed the definition query.  In this screenshot, no-data cells are in light grey to indicate the full extent of the exported data set.  

Shawn Laffan
26-Apr-2017


For more details about Biodiverse, see http://purl.org/biodiverse 

For the full list of changes in the 1.99 series (leading to version 2) see https://purl.org/biodiverse/wiki/ReleaseNotes (for all issues addressed or being targeted to fix for version 2, see https://github.com/shawnlaffan/biodiverse/milestone/4 ).

To see what else Biodiverse has been used for, see https://purl.org/biodiverse/wiki/PublicationsList


You can also join the Biodiverse-users mailing list at http://groups.google.com/group/Biodiverse-users