Biodiverse now calculates the CANAPE super class

Since version 4.3, Biodiverse has calculated and plotted the CANAPE results when the relevant calculations have been run. 

However, it did not calculate the super class when first implemented. Now it does.

From version 5, Biodiverse calculates all CANAPE classes when a randomisation is run for an analysis that includes phylogenetic endemism and relative phylogenetic endemism.    

Note that the CANAPE classed are only updated after at least one randomisation iteration has been run.  If you have an existing randomisation then you can run one more iteration to trigger the calculation.  Otherwise you can run a new randomisation with the same settings.  This should not take long for most analyses, assuming they are consistent with the sizes of data sets in existing publications.     

If you are wondering why it was not plotted in the first place, it was largely because the plotting system needed some re-engineering to allow for additional legend labels.  This was done when the z-score and p-rank plotting was implemented, a little while after the initial CANAPE plotting.  

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Shawn Laffan

02-Dec-2023

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

For a list of some of the analyses Biodiverse has been used for, see https://github.com/shawnlaffan/biodiverse/wiki/PublicationsList 

You can also join the Biodiverse-users mailing list at https://groups.google.com/group/Biodiverse-users or start a discussion at https://github.com/shawnlaffan/biodiverse/discussions 

Biodiverse 4.3 has been released

 

Biodiverse version 4.3 has now been released.  

Versions for Windows, Mac and Linux (Ubuntu) are available and can be accessed via https://github.com/shawnlaffan/biodiverse/wiki/Downloads

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

This release contains a small number of bug fixes and improved functionality. 

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.

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Shawn Laffan

01-May-2023

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

For a list of some of the analyses Biodiverse has been used for, see https://github.com/shawnlaffan/biodiverse/wiki/PublicationsList 

You can also join the Biodiverse-users mailing list at https://groups.google.com/group/Biodiverse-users or start a discussion at https://github.com/shawnlaffan/biodiverse/discussions 

Changes to randomisation results - the p-rank data

 

Randomisations in Biodiverse produce a range of outputs.  These are kept in a range of lists, differing by name (see the help system).  

One of the lists that is generated in the p-ranks.  This is essentially the same as the P_ values in the main randomisation lists but where the low values account for ties so one can be sure the values represent the relative ranking of the observed value against those generated from the randomised data.  For example, the significance of a low value should account for any ties.

The p-ranks were implemented a few years versions ago and are detailed in this blog post.  Due to how the plotting was set up at the time, only values in the outer 10% of the distribution were retained. This helped understand which groups contained significant results without a major update to the display system but in the end was probably confusing.  Now that the z-score plotting has been implemented the system has the infrastructure to handle the full range of values.  

So what has changed?  

Two things: the calculation of values and how they are plotted.  

Note that the set of cells that can be regarded as significant using the standard alpha threshold of 0.05 for high or low values is unchanged.  All that has changed is the number of cells with defined values and how they are displayed in the GUI.  

The calculation   

Put simply, all values are now retained.  Any "P_" value less than 0.5 accounts to the number of ties.  Expressed as pseudocode it is:

if P_index > 0.5

  p_rank = P_index 

else 

  p_rank = ((C_index + T_index) / Q_index)  

where "index" is whichever index is being compared at the time.  

This makes post-hoc calculation of compound indices like CANAPE easier (although remember that Biodiverse now does that for you).  

The display

The addition of the z-score plotting means that the infrastructure for the plotting is in place so it was not too difficult to re-use it to instead display percentile classes.  This is applied to the p-score lists by default.  

Compare the two plots below and consider which is easier to work with.  

The p-rank plotting in Biodiverse version 4.2 and earlier works, but it is difficult to see which cells are in specific percentile bands.  For example which of these cells is in the outer 5%?  

Indices in the p-rank lists are now plotted as percentile classes.  Compare with the plot above.   

As with other plots, the coloured cells can be exported as RGB geotiffs to display in a GIS or other plotting system.  

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Shawn Laffan

27-Apr-2023

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

For a list of some of the analyses Biodiverse has been used for, see https://github.com/shawnlaffan/biodiverse/wiki/PublicationsList 

You can also join the Biodiverse-users mailing list at https://groups.google.com/group/Biodiverse-users or start a discussion at https://github.com/shawnlaffan/biodiverse/discussions 

Publications using Biodiverse in 2022

2023 is now in full swing, so here is a list of publications from 2022 that used Biodiverse.

If you want to see the full list (183 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/

• Amaral, D.T., Bonatelli, I.A.S., Romeiro-Brito, M., Moraes, E.M. and Franco, F.F. (2022) Spatial patterns of evolutionary diversity in Cactaceae show low ecological representation within protected areas. Biological Conservation, 273, 109677.

• Ávila-González, H., González-Gallegos, J.G., Munguía-Lino, G. & Castro-Castro, A. (2022) The genus Sisyrinchium (Iridaceae) in Sierra Madre Occidental, Mexico: A new species, richness and distribution. Systematic Botany, 47, 319-334.

• Carter, B. E., Misiewicz, T. M. & Mishler, B. D. (2022). Spatial phylogenetic patterns in the North American moss flora are shaped by history and climate. Journal of Biogeography, 49, 1327-1338.

• Chen, K., Khine, P.K., Yang, Z. and Schneider, H. (2022) Historical plant records enlighten the conservation efforts of ferns and Lycophytes’ diversity in tropical China, Journal for Nature Conservation, 68, 126197.

• Contreras-Medina, R., García-Martínez, A. I., Ramírez-Martínez, J. C., Espinosa, D., Balam-Narváez, R., and Luna-Vega, I. (2021). Biogeographic analysis of ferns and lycophytes in Oaxaca: A Mexican beta-diverse area. Botanical Sciences, 100, 204-222.

• Fernandes, N.B.G., de Menezes Yazbeck, G. & Milward-de-Azevedo, M.A. (2022) Taxonomic diversity of Passifloraceae sensu stricto along altitudinal gradient and on Serra dos Órgãos mountain slopes in southeastern Brazil. Rodriguésia, 73, e00702021.

• Gosper C.R., Percy-Bower J.M., Byrne M., Llorens T.M. & Yates C.J. (2022) Distribution, Biogeography and Characteristics of the Threatened and Data-Deficient Flora in the Southwest Australian Floristic Region. Diversity, 14, 493.

• Griffiths, D. (2022). Do the drivers and levels of isolation in fish faunas differ across Atlantic and Pacific drainages in the Americas? Journal of Biogeography, 49, 930-941.

• Gutiérrez-Rodríguez, B.E., Guevara, R., Angulo, D.F. et al. (2022) Ecological niches, endemism and conservation of the species in Selenicereus (Hylocereeae, Cactaceae). Brazilian Journal of Botany, 45, pages 1149–1160.

• Gutiérrez–Rodríguez, B.E., Vásquez–Cruz, M. and Sosa, V. (2022) Phylogenetic endemism of the orchids of Megamexico reveals complementary areas for conservation. Plant Diversity, 44, 351-359.

• Kong, H., Condamine, F.L., Yang, L., Harris, A.J., Feng, C., Wen, F. and Kang, M. (in press) Phylogenomic and macroevolutionary evidence for an explosive radiation of a plant genus in the Miocene. Systematic Biology, 71, 589–609.

• Moreira-Muñoz, A, Palchetti, V.A., Morales-Fierro, V., Duval, V.S., Allesch-Villalobos, R., & González-Orozco, C.E. (2022) Diversity and Conservation Gap Analysis of the Solanaceae of Southern South America. Frontiers in Plant Science, 13.

• Murillo-Pérez, G., Rodríguez, A., Sánchez-Carbajal, D., Ruiz-Sanchez, E., Carrillo-Reyes, P., Munguía-Lino, G. (2022) Spatial distribution of species richness and endemism of Solanum (Solanaceae) in Mexico. Phytotaxa 558, 147–177

• Olivares-Juárez, M.I., Burgos-Hernández, M. and Santiago-Alvarádo, M. (2022) Patterns of Species Richness and Distribution of the Genus Laelia s.l. vs. Laelia s.s. (Laeliinae: Epidendroideae: Orchidaceae) in Mexico: Taxonomic Contribution and Conservation Implications. Plants, 11:2742.

• Paz, A., Silva, A.S. & Carnaval, A. (2022) A framework for near-real time monitoring of diversity patterns based on indirect remote sensing, with an application in the Brazilian Atlantic rainforest. PeerJ, 10:e13534.

• Rivera-Martínez, R., Ramírez-Morillo, I.M., De-Nova, José A., Carnevali, G., Pinzón, J.P., Romero-Soler, K.J. & Raigoza, N. (2022) Spatial phylogenetics in Hechtioideae (Bromeliaceae) reveals recent diversification and dispersal. Botanical Sciences, 100, 692-709.

• Silva, D.C., Oliveira, H.F.M., Zangrandi, P.L. and Domingos, F.M.C.B. (2022) Flying Over Amazonian Waters: The Role of Rivers on the Distribution and Endemism Patterns of Neotropical Bats. Frontiers in Ecology and Evolution, 10:774083.

• Wang, Q., Huang, J., Zang, R., Li, Z. and El-Kassaby, Y. A. (2022). Centres of neo- and paleo-endemism for Chinese woody flora and their environmental features. Biological Conservation, 276, 109817.

• Yang, X., Qin, F., Xue, T., Xia, C., Gadagkar, S. R., & Yu, S. (2022). Insights into plant biodiversity conservation in large river valleys in China: A spatial analysis of species and phylogenetic diversity. Ecology and Evolution, 12, e8940.

• Yang, X., Zhang, W., Qin, F., et al. (2022). Biodiversity priority areas and conservation strategies for seed plants in China. Frontiers in Plant Science, 13, 962609.

• Zhang, W., Bussmann, R.W., Li, J., Liu, B., Xue, T., Yang, X., Qin, F., Liu, H. and Yu, S. (2022) Biodiversity hotspots and conservation efficiency of a large drainage basin: Distribution patterns of species richness and conservation gaps analysis in the Yangtze River Basin, China. Conservation Science and Practice, 4, e12653.

• Zhang, Y., Qian, L., Chen, X., Sun, L., Sun, H. and Chen, J. (2022) Diversity patterns of cushion plants on the Qinghai-Tibet Plateau: a basic study for future conservation efforts on alpine ecosystems. Plant Diversity, 44, 231-242.

• Zhang, X.X, Ye, J.F., Laffan, S.W., Mishler, B.D., Thornhill, A.H., Lu, L.M. et al. (2022) Spatial phylogenetics of the Chinese angiosperm flora provides insights into endemism and conservation. Journal of Integrative Plant Biology, 64, 105-117.

• Zhao, R., Xu, S., Song, P., Zhou, X, Zhang, Y. and Yuan, Y. (2022) Distribution patterns of medicinal plant diversity and their conservation in the Qinghai-Tibet Plateau. Biodiversity Science, 30, 21385.

Shawn Laffan

02-Apr-2023

 

Biodiverse version 4.2 has been released

 

Biodiverse version 4.2 has now been released.  

Versions for Windows, Mac and Linux (Ubuntu) are available and can be accessed via https://github.com/shawnlaffan/biodiverse/wiki/Downloads

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

This release contains a small number of bug fixes and improved functionality. 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.

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Shawn Laffan

29-Mar-2023

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

For a list of some of the analyses Biodiverse has been used for, see https://github.com/shawnlaffan/biodiverse/wiki/PublicationsList 

You can also join the Biodiverse-users mailing list at https://groups.google.com/group/Biodiverse-users or start a discussion at https://github.com/shawnlaffan/biodiverse/discussions 

Biodiverse version 4.1 has been released

 

We are pleased to announce the release of Biodiverse version 4.1.  

Versions for Windows, Mac and Linux (Ubuntu) are available and can be accessed via https://github.com/shawnlaffan/biodiverse/wiki/Downloads

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

Version 4.1 represents five issues closed across 96 source code commits.

Highlights of the changes since version 4.0 are at https://github.com/shawnlaffan/biodiverse/wiki/ReleaseNotes#version-41, and the related blog posts can be accessed via https://biodiverse-analysis-software.blogspot.com/search/label/Version41

A more detailed listing of the closed issues is at https://github.com/shawnlaffan/biodiverse/milestone/19?closed=1

The main user visible change is that z-score indices are now plotted using a divergent colour scale using z-score significance thresholds.  More details are in this blog post. 

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Shawn Laffan

07-Feb-2023

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

For a list of some of the analyses Biodiverse has been used for, see https://github.com/shawnlaffan/biodiverse/wiki/PublicationsList 

You can also join the Biodiverse-users mailing list at https://groups.google.com/group/Biodiverse-users or start a discussion at https://github.com/shawnlaffan/biodiverse/discussions 

Plotting z-score indices and randomisation results

From version 4.1, Biodiverse will plot indices it knows are z-scores using a divergent colour scheme, with values classified into intervals (adapted from the ArcGIS implementation).  This makes it much easier to see which locations are potentially significant given the expected values.

This process applies to indices like the Net Relatedness Index and Net Taxon Index, all of the Gi* indices such as for group properties and label properties (more on such analyses here), as well as the z-scores generated by randomisation analyses.  It also applies to branches of a cluster dendrogram when indices have been calculated for each node/branch.  

You can export the coloured images to geotiff in the same way as for any data set.

There is not much more to it than that, so here are some images of what it looks like for a spatial analysis using the Acacia data set of Mishler et al. (2014).  

The Net Relatedness Index

Z-scores for Phylogenetic Diversity after a spatial randomisation process

Net Relatedness Index calculated for the groups (cells) under each branch of a cluster analysis. Coloured cells are associated with the dendrogram branches that intersect the blue slider bar.

The spatial distribution of PD significance (left) with branches occurring in a cell in south-west Western Australia (black dot) coloured by clade score significance against the same randomisation process.

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Shawn Laffan

07-Feb-2023

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

For a list of some of the analyses Biodiverse has been used for, see https://github.com/shawnlaffan/biodiverse/wiki/PublicationsList 

You can also join the Biodiverse-users mailing list at https://groups.google.com/group/Biodiverse-users or start a discussion at https://github.com/shawnlaffan/biodiverse/discussions