Tuesday, 24 March 2020

Publications using Biodiverse in 2019

2020 is now in full swing, so here is a list of publications from 2019 that used Biodiverse. 

If you want to see the full list (111 at the time of writing), then go to https://github.com/shawnlaffan/biodiverse/wiki/PublicationsList 

For more details about Biodiverse, see http://shawnlaffan.github.io/biodiverse/ 

Shawn Laffan
24-Mar-2020



Allen, J.M., Germain-Aubrey, C.C., Barve, N., Neubig, K., Majure, L.C., Laffan, S.W., Mishler, B.D., Owens, H.L., Smith, S.A., Whitten, W.M., Abbott, J.R., Soltis, D.E., Guralnick, R. and Soltis, P.S. (2019) Spatial phylogenetics of Florida vascular plants: The effects of calibration and uncertainty on diversity estimates. iScience, 11, 57-70.

Crouch, N.M.A., Capurucho, J.M.G., Hackett, S.J. and Bates, J.M. (2019) Evaluating the contribution of dispersal to community structure in Neotropical passerine birds. Ecography, 42, 390-399.
Dagallier, L.-P.M.J., Janssens, S.B., Dauby, G., Blach-Overgaard, A., Mackinder, B.A., Droissart, V., Svenning, J.-C., Sosef, M.S.M., Stévart, T., Harris, D.J., Sonké, B., Wieringa, J.J., Hardy, O.J. and Couvreur, T.L.P. (2019) Cradles and museums of generic plant diversity across tropical Africa. New Phytologist.

Daru, B.H., le Roux, P.C., Gopalraj, J., Park, D.S., Holt, B.G. and Greve, M. (2019) Spatial overlaps between the global protected areas network and terrestrial hotspots of evolutionary diversity. Global Ecology and Biogeography, 28, 757-766.

Fuentes-Castillo, T., Scherson, R.A., Marquet, P.A., Fajardo, P., Corcoran, D., Román, M.J. and Pliscoff, P. (2019) Modelling the current and future biodiversity distribution in the Chilean Mediterranean hotspot. The role of protected areas network in a warmer future. Diversity and Distributions, 25, 1897-1909.

Gallien, L., Thornhill, A.H., Zurell, D., Miller, J.T., and Richardson, D.M. (2019) Global predictors of alien plant establishment success: combining niche and trait proxies. Proceedings of the Royal Society B, 286, 20182477.

Garcia–R, J.C., Gonzalez-Orozco, C.E. and Trewick, S.A. (2019) Contrasting patterns of diversification in a bird family (Aves: Gruiformes: Rallidae) are revealed by analysis of geospatial distribution of species and phylogenetic diversity. Ecography, 42, 500-510.

Greenlon, A., Chang, P.L., Damtew, Z.M., et al. (2019) Global-level population genomics reveals differential effects of geography and phylogeny on horizontal gene transfer in soil bacteria. Proceedings of the National Academy of Sciences, 201900056.

Lam-Gordillo, O. and Ardisson, P-L. (2019) The global distribution and richness of frog crabs (Raninoidea). Crustaceana, 92, 1-31.

López-Aguirre, C., Hand, S.J., Laffan, S.W., & Archer, M. (2019) Zoogeographical regions and geospatial patterns of phylogenetic diversity and endemism of New World bats. Ecography, 42, 1188-1199.

McDonald-Spicer, C., Knerr, N.J., Encinas-Viso, F. and Schmidt-Lebuhn, A.N. (2019) Big data for a large clade: Bioregionalization and ancestral range estimation in the daisy family (Asteraceae). Journal of Biogeography, 46, 255-267.

Mekala, S., Donoghue, M.J., Farjon, A., Filer, D., Mathews, S., Jetz, W. and Leslie, A.B. (2019) Accumulation over evolutionary time as a major cause of biodiversity hotspots in conifers. Proceedings of the Royal Society B, 286, 20191887.

Shelley, J.J., Dempster, T., Le Feuvre, M.C., Unmack, P.J., Laffan, S.W. & Swearer, S.E. (2019) A revision of the bioregionalisation of freshwater fish communities in the Australian Monsoonal Tropics. Ecology and Evolution, 9, 4568-4588.

Tolley, K.A., da Silva, J.M. & Jansen van Vuuren, B. (2019) South African National Biodiversity Assessment 2018 Technical Report Volume 7: Genetic Diversity. South African National Biodiversity Institute, Pretoria. http://hdl.handle.net/20.500.12143/6376

Friday, 13 March 2020

Biodiverse version 3.1 has now been released

Biodiverse version 3.1 has now been released



Versions for Windows, Mac and Linux are available and can be downloaded from https://github.com/shawnlaffan/biodiverse/wiki/Downloads

Installation instructions are at https://github.com/shawnlaffan/biodiverse/wiki/Installation


Version 3.1 represents 7 issues closed across since version 3.00 was released.

Highlights of the changes since version 3.00 are at https://github.com/shawnlaffan/biodiverse/wiki/ReleaseNotes#version-31

A more detailed listing of the closed issues is at https://github.com/shawnlaffan/biodiverse/milestone/16?closed=1


The main changes of note are that the View Labels lists now sort properly again (see issues #744 and #747), and that the Select and Pan buttons work again on Mac binary releases.



Shawn Laffan
13-March-2020


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For more details about Biodiverse, see http://shawnlaffan.github.io/biodiverse


To see what Biodiverse has been used for, see https://github.com/shawnlaffan/biodiverse/wiki/PublicationsList



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

Tuesday, 3 September 2019

Biodiverse version 3.00 has now been released

Biodiverse version 3.00 has now been released


Versions for Windows, Mac and Linux are available and can be downloaded from https://github.com/shawnlaffan/biodiverse/wiki/Downloads

Installation instructions are at https://github.com/shawnlaffan/biodiverse/wiki/Installation


Version 3.00 represents 44 issues closed across 350 source code commits.  187 files have been changed, with 13,623 insertions and 10,486 deletions.

Highlights of the changes since version 2.1 are at https://github.com/shawnlaffan/biodiverse/wiki/ReleaseNotes#version-300, and the related blog posts can be accessed via https://biodiverse-analysis-software.blogspot.com/search/label/Version3

A more detailed listing of the closed issues is at https://github.com/shawnlaffan/biodiverse/milestone/15?closed=1


The only change of note since the most recent development release (version 2.99_005) is to address issue #742.  The internal index used for matrices now uses the C locale for numeric values. Incorrect values could otherwise be returned in some locales where the comma is used as the radix character. Biodiverse now throws an exception when it encounters indexes with commas in the values, recommending that the matrix be rebuilt.



Shawn Laffan
03-September-2019


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For more details about Biodiverse, see http://shawnlaffan.github.io/biodiverse


To see what Biodiverse has been used for, see https://github.com/shawnlaffan/biodiverse/wiki/PublicationsList



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

Monday, 12 August 2019

Version 2.99_005 released, Version 3 is next

The final development release in the 2.99 series has now been released (2.99_005).

Barring any major issues, this will be the final development release before Version 3 is released.


The main update in this version (from 2.99_004) is that the spatial patterns of cluster and region grower analysis outputs can now be exported to shapefile format, with each branch getting its own polygon or point features.  This means you can now use the polygon or point geometries for any branch in the tree for further analysis and/or display.  More details are in the blog post:  https://biodiverse-analysis-software.blogspot.com/2019/08/export-cluster-analyses-to-shapefiles.html


The more detailed summary of changes in the 2.99 series is at https://github.com/shawnlaffan/biodiverse/wiki/ReleaseNotes#version-299, and the related blog posts can be accessed via https://biodiverse-analysis-software.blogspot.com/search/label/Version3


This version can be downloaded from links on the downloads page at https://github.com/shawnlaffan/biodiverse/wiki/Downloads


Shawn Laffan
12-August-2019


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For more details about Biodiverse, see http://shawnlaffan.github.io/biodiverse


To see what Biodiverse has been used for, see https://github.com/shawnlaffan/biodiverse/wiki/PublicationsList



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

Export cluster analyses to shapefiles

In Version 3 of Biodiverse it is possible to export your cluster and region grower analyses to shapefile formats.

This makes it easier to use the regions in geospatial analyses, for example as conditions in spatial analyses in Biodiverse.  Perhaps the best example is that you can generate a regionalisation using one data set, and then assess its values for one or more other data sets.  See for example González-Orozco et al. (2013, 2014a and 2014b).

The option is available via the export menu for cluster and region grower analyses.  The options are all the usual ones, although that is not many in this case.


The option is chosen from the export menu for a cluster (or region grower) analysis.  


There are not that many choices, but Shape type can be exported as POLYGON or POINT geometries (shapes).  You can attach lists of results, or choose to only export the geometries themselves.


You might need to run a selection to highlight the branch you are interested in.  This example is branch 120___, which corresponds to the red cluster in the first screenshot above.  You might also choose to use a Definition Query (ArcGIS) or Layer Subset (QGIS) to filter out the geometries you are not interested in.  


And here the component polygons that form the polygons for branch 120___ are highlighted in red.



There are three points to watch for.

1.  If you export a list with the data, then each polygon or point feature is repeated for each item in the list.  This is due to shapefile field names being limited to 11 characters, which is far too short for many of the list entries in Biodiverse.  (Support for the GeoPackage format is in the works to obviate this issue).

2.  The exported features (geometries) are multipolygon or multipoint.  This means that each geometry comprises one or more geometries, with each internal branch including all polygons of its terminal branches.  The internal boundaries between polygons are not dissolved, so you will see all the component polygons, but any GIS will support a dissolve operation.  If you are wondering what multipolygons and multipoints are, then Wikipedia has a decent explanation as part of the Well Known Text entry.

3.  Remember that Biodiverse knows nothing about coordinate systems and map projections (agnostic might be a better way of putting it).  You will need to define the coordinate system of the output file yourself using a GIS or other geospatial tool.



Shawn Laffan
12-August-2019

If you want to try this out before version 3 is released then the 2.99_005 development release can be accessed through the downloads page at https://github.com/shawnlaffan/biodiverse/wiki/Downloads


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For more details about Biodiverse, see http://shawnlaffan.github.io/biodiverse


To see what Biodiverse has been used for, see https://github.com/shawnlaffan/biodiverse/wiki/PublicationsList



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

Tuesday, 21 May 2019

Reproduce spatial plots with the same colours in GIS software

Biodiverse version 3 will allow users to export GeoTIFFs of the display colours for spatial outputs that have been displayed in the GUI.

The format used is RGBA (red, green, blue with a fourth Alpha channel for transparency).  This is a standard image format and is supported by many GIS packages.

This one is best demonstrated with pictures.  The GIS used is QGIS, but the general process is the same in ArcGIS.


The Acacia PD data displayed using a log scale with the default colour scheme. 

The RGB export is in the exports menu, with all the other exports.

The file selection is the usual process.  

And now in the GIS, the file is selected using the normal process.  Note that the file name is updated like the GeoTIFF exports, but with _rgb appended to the main part of the name. 

Biodiverse knows nothing about coordinate systems, so it is up to the user to choose the correct one for their data.  

The default display has all the colours, but the background is black.  To fix that you need to set the fourth band as the transparency layer.

As per the previous image caption, choose band 4 as the transparency layer.  The same general process is needed in ArcGIS (set the alpha channel to be band 4). 

And here is the data with some Open Street Map data in the background.  


And as a bonus, the RGB GeoTIFFs can be exported at the same time as a standard GeoTIFF export using the "Generate RGB Rasters" option.

As the tooltip states, the RGB files are only generated for indices that have been displayed, so you don't get huge numbers of exports if you have not displayed them.   



Shawn Laffan
20-May-2019

If you want to try this out before version 3 is released then the 2.99_004 (or later) development release can be accessed through the downloads page at https://github.com/shawnlaffan/biodiverse/wiki/Downloads

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For more details about Biodiverse, see http://shawnlaffan.github.io/biodiverse


To see what Biodiverse has been used for, see https://github.com/shawnlaffan/biodiverse/wiki/PublicationsList




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

Drop label and group axes

On occasion one might load a data set where the labels consist of several levels of the Linnean hierarchy, e.g. the name of a label will be made up of order, family, genus, species and subspecies.  Or you might have packed in extra information for debugging, or you have population ID included.

However, sometimes you want to simplify the records and use them at an different level.  For example, you might want to collapse your genus:species data to the genus level, or remove population and family details.

You might also have generated group names using geographic coordinates, plus additional details about time or region (see Stephenson  et al. 2015 and Laffan et al. 2013 for examples of those), but then want to remove the region or time axes.


One approach is to export the data (labels or groups) and then reimport them using only the axes you need, but this can be tedious as it involved several steps.  You could also use the rename interface with a remap table, but setting up the table can also be tedious.

From Version 3 it can be done directly within Biodiverse.

Some screenshots are probably the best way to explain it.  See captions for details.

The data in this case were used in Cassis et al. (2017) and consist of details downloaded from the Atlas of Living Australia .  Each label comprises the family, genus, scientific name and taxonomic level, joined using a colon (the standard join character used in Biodiverse).  This last column (axis) made it easier to remove records that were not at the species level, but is not needed for many analyses.  All these columns also make it hard to link the data to phylogenies.  (Note that they have no effect on indices like taxon endemism, rarity and richness, as those only need to work with unique identifiers).



Each label comprises four axes of information.  This can be useful, but not for everything.  

The process is done through one of the duplication options.  There is no undo, so it is safer to generate a new data set.



Unsurprisingly, the new basedata needs a name.

The system can work with either groups or labels.  If you need to trim axes from both then run it twice, once for groups and once for labels.  

Select which axes you wish to drop.  In this case only the scientific name will be retained.  Note that the axes are numbered from zero, which is common for many programming languages (but not for R).  

And here are the data with simplified labels.  Note that if, two or more labels collapse down to the same name then their sample counts are merged.  


And that's pretty much it.

The same process applies to groups so there are no screenshots provided for them.

Shawn Laffan
20-May-2019

If you want to try this out before version 3 is released then the 2.99_004 (or later) development release can be accessed through the downloads page at https://github.com/shawnlaffan/biodiverse/wiki/Downloads

--------

For more details about Biodiverse, see http://shawnlaffan.github.io/biodiverse


To see what Biodiverse has been used for, see https://github.com/shawnlaffan/biodiverse/wiki/PublicationsList


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