03 Feb 05:30

b56b8da

Version 4.99_002 (development release) Pre-release

Pre-release

Summary

This is a development release, leading towards version 5.0.

Executables/Binaries

Executables/Binaries are available below for Windows and Macintosh. Linux (Ubuntu) files can be made available if needed.

You might need to expand the "Assets" section below to see them (click on the triangle).

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

Known issues

The binaries are not signed.
The tree displays flicker on Macs. This is perhaps due to the canvas library.
There are some copy-paste oddities on Macs that are yet to be diagnosed.

Changes

For the full list of issues and changes leading to the 5.0 release, see https://github.com/shawnlaffan/biodiverse/milestone/18

Main changes:

Data import
- Spreadsheet imports from XLSX files are now substantially faster. Details are in Issue 882.
- Shapefile imports are now slightly faster. Details are in Issue 885.
Indices:
- The CANAPE super class is now calculated and plotted. Issue 890 Blog post
- Indices for the Hurlbert species richness estimator are now available. The set of sample numbers may be changed or made more flexible in the future. Implementation is under issue 871.
- The phylogenetic and range weighted turnover indices are now faster, particularly when used in pairwise mode such as when building a cluster matrix.
GUI
- A basedata can be trimmed using another basedata (previously only matrices and trees could be used). The basedata trimming interface has been streamlined as part of this process. Issue 880. Blog post
- The tree being displayed in any of the visualisation tabs can now be exported. Issue 902.
- Trees can be plotted by depth across all visualisation tabs. Issue 906.
- The tree plot control menu options are now a separate submenu. Issue 905. Blog post
- Better colour schemes are now used by default when plotting indices that are zero-centred divergent and ratio based. Issue 820 Blog post pending.
- Spatial tab
  - Tree branches can be coloured using list indices from any spatial output in the project. Issue 833. Blog post

Assets 5

27 Apr 04:42

shawnlaffan

r4.3

c956edb

Version 4.3 Latest

Latest

UPDATE 2023-11-17.

A bug in one of the dependencies was causing crashes under some circumstances. That has been fixed. Please use the 4.3.1 downloads.

Summary

This is a minor bug fix release with some new functionality.

Executables/Binaries

Executables/Binaries are available below for Windows, Macintosh and Linux (Ubuntu). Unlike 4.0, there is currently only a Mac variant for the M1 chip. A release for Intel-based Macs is pending further development of dependencies.

You might need to expand the "Assets" section below to see them (click on the triangle).

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

Changes

For the full list of issues and changes leading to the 4.3 release, see https://github.com/shawnlaffan/biodiverse/milestone/21

Main changes:

GUI:
- z-score plotting has been fixed (colours were reversed). Issue 857.
Randomisations
- The p-rank calculations now generate ranks for all defined values. The GUI also now colours the values, similar to the z-scores. Issue 856. More details in the blog post.
Spatial conditions
- The sp_points_in_same_poly_shape condition is now faster when any points do not intersect any polygons. See commit 3ca2703.

Assets 7

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29 Mar 00:56

shawnlaffan

r4.2

ebef082

Version 4.2

This is a minor bug fix release with some new functionality.

Executables/Binaries

You might need to expand the "Assets" section below to see them (click on the triangle).

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

Changes

For the full list of issues and changes leading to the 4.2 release, see https://github.com/shawnlaffan/biodiverse/milestone/20

Main changes:

GUI
- Branch highlighting in the View Labels tab works again. This was broken in version 4.1. Issue #850.
Data imports
- Raster imports now include the band labels if defined in multiband files. Issue #852.
- Importing a raster now works when the nodata value is NaN. Issue #851.

Assets 6

07 Feb 04:32

shawnlaffan

r4.1

d70b531

Version 4.1

This is a minor release containing some new functionality and bug fixes.

Executables/Binaries

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

Changes

For the full list of issues and changes leading to the 4.1 release, see https://github.com/shawnlaffan/biodiverse/milestone/19

Main changes:

GUI
- Z-score indices are now plotted using a five class divergent colour scheme to more clearly indicate which locations are in the outer 10%, 5% and 1% of the expected distribution. Issue 841. See also this blog post
Indices
- A bug in the NRI, NTI and Net VPD indices meant undefined results were obtained the second time a tree was used, and when only one of NRI/NTI or VPD were calculated the first time. Issue 842.
- The phylogenetic endemism indices have been further optimised. (There is no associated issue).
Imports
- An issue with raster imports being offset has been fixed. Issue 845

Assets 5

25 Nov 09:09

shawnlaffan

r4.0

90e58e9

Version 4.0

Executables/Binaries

Executables/Binaries are available below for Windows, Macintosh and Linux (Ubuntu). There are two Mac variants. If you are using a Mac with an M1 chip then download the mac_arm zip file. If you are using a Mac with an Intel chip then download the mac_intel zip file.

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

Changes

For the full list of issues and changes leading to the 4.0 release, see https://github.com/shawnlaffan/biodiverse/milestone/17

A series of blog posts goes into more detail about several of the changes: http://biodiverse-analysis-software.blogspot.com/search/label/Version4

General
- As of 3.99_005 the Windows executable files are digitally signed. This will avoid OS warnings when files are downloaded.
Analyses
- CANAPE
  - Biodiverse now automatically generates and plots CANAPE results for any analysis that contains the phylogenetic endemism and relative phylogenetic endemism indices. Issue 819. More details are in this blog post.
  - The PE and RPE calculations have been sped up. PR 831.
- Cluster analyses
  - Cluster analyses will now lump all zero distance matrix pairs in an initial pass where possible. This avoids needless tie-breaker calculations when data sets have large sets of groups with the same label assemblages. Issue 760
  - Cluster and Region Grower analyses are no longer rebuilt by default under the randomisations, speeding up any randomisations that include them. Comparison of per-node calculations is still done, though, as this does not use the rebuilt tree. There is a user visible option in the GUI to enable the previous behaviour if it is needed. Issue 765
  - Cluster and region grower analyses now warn and provide an informative error message when there is only a single group in the basedata. Issue 782
- Randomisations
  - Randomisations now also generate z-scores of the observed values against the random distribution. Issue 764. More details are in the blog post.
  - The Independent Swaps algorithm is now implemented. Issue 772. More details are in the blog post.
Calculations
- A local PD calculation, "Phylogenetic Diversity (local)", now allows the calculation of PD and PD_P to the last common ancestor, as opposed to the root node. Issue 762
- A new calculation, "Last shared ancestor properties", provides details about the last shared ancestor for a set of labels, for example the length from its tipwards end to the root node. Issue 763
- MPD, MNTD, NRI & NTI: The MPD and MNTD calculations are now substantially faster. The NRI and, for ultrametric trees, NTI calculations are orders of magnitude faster as they use expected values calculated using the exact methods described in Tsirogiannis et al. (2012) and Tsiriogiannis et al. (2014). There is also no longer a performance penalty under the randomisations for outputs containing NRI and NTI indices when richness scores are held constant (which is the default). This is because the expected values for a given tree are re-used across analyses. Issue 786, Issue 789, Issue 790. More details are in the blog post.
- The taxonomic distinctness calculations have been moved to the BiodiverseX namespace and so are not available in the GUI by default. Issue 751.
- The calculation of median and percentile values for the element properties have changed. Issue #798. More details in the blog post.
- The phylogenetic distincness variance (VPD) is now calculated with the mean and other related statistics. The net VPD and its component indoces can also be calculated to assess significance of the net VPD against random resampling. Issue #811 See blog post
Spatial Conditions
- New condition sp_richness_greater_than() allows the neighbour set to be defined as the set of groups with a richness exceeding a threshold. Issue 783.
- New condition sp_redundancy_greater_than() allows the neighbour set to be defined as the set of groups with a sample redundancy exceeding a threshold.
- New conditions sp_point_in_cluster() and sp_points_in_same_cluster() that can be used to model polygons from clusters in a Cluster or RegionGrower analysis without first needing to export them to a shapefile and any subsequent processing to extract the relevant parts. Issue 803. More details in the blog post.
Imports
- Group properties can now be directly imported from rasters. This makes it much easier to analyse environmental patterns in relation to taxonomic and/or phylogenetic ones. Issue 761. More details are in the blog post
Exports
- Cluster and RegionGrower analyses can be exported to shapefile format in a grouped form. This models the cluster display where multiple sub-clusters are coloured. The output file is somewhat awkward and needs further processing, which is why the sp_points_in_same_cluster() spatial condition was developed (see above). Issue 757. More details are in the blog post
Trees
- A new option has been added to merge only-child ("knuckle") nodes with their parents. This is probably most useful after trimming a tree but can be applied to any tree. Issue 814. More details are in the blog post

Assets 6

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24 Oct 06:38

shawnlaffan

r3.99_005

ad034c1

r3.99_005 Pre-release

Pre-release

Development release 3.99_005. Fifth in the 3.99 series, leading to the v4 release.

A list of changes is at https://github.com/shawnlaffan/biodiverse/wiki/ReleaseNotes#version-399-dev-series

See also the related blog posts: https://biodiverse-analysis-software.blogspot.com/search/label/Version4

The most notable changes from 3.99_004 are that the exe file is now digitally signed on Windows and that the CANAPE indices are automatically calculated for output objects if PE and RPE2 have been calculated and a randomisation analysis has been run. To see the CANAPE results, choose the list below the map that looks like "rand_name>>CANAPE>>".

Binaries are available for Windows and Mac.

The Mac is not signed so will need permissions to run (see the Mac binary installation instructions).

If you are using an M1 Mac then download Biodiverse-3.99_005-2.dmg.

If you are using a Mac with an Intel chip then download Biodiverse-3.99_005-intel.dmg.

Click on the Assets link below if you cannot see the files.

Assets 5