Monday, 8 April 2019

Reduce the spatial resolution of your data

A longstanding wish-list item for Biodiverse is the ability to decrease the resolution of the cells (groups).  For example, you might have imported your data at a 50 km resolution but want to see what happens to the analysis results when the data are aggregated to 100 km.

This has just been implemented for version 3.  If you are impatient then you can try it in the 2.99_003 development release.  The download link is at the end of this post (and please provide feedback if you do try it).

Some screenshots will probably help explain things.  A few more details follow them.

The original data (100,000 units on a side) with some lines from a shapefile overlaid. 

The interface is accessed through the BaseData menu, and generates a new BaseData object

The interface allows control over the new name, the new resolution and the new origin.

In this example, the new cells will be 200,000 units on each side, with the cells aligning with an origin coordinate at (100,000, 100,000).  For these data it means that, if the cells span the coordinate (0,0) then it will be the centre of a cell.

And the new data with the reduced resolutions (200,000 units on a side), again with the lines so they can be cross-referenced with the original data.  Note how the sample counts for each label are the same, but the variety scores (number of groups each label is found in) are now smaller.    

There is nothing stopping rectangular groups, except perhaps a cultural preference for square cells.  

A few extra details:

The cell sizes can only ever be increments of the current cell sizes.  The data used in Biodiverse are commonly observations that have been aggregated to the groups (cells), and the original ditribution are not kept.  There is no good way of disaggregating the data to restore the original distributions.  This means you can aggregate to coarser units, but not go the other way.

The origins are also increments of the cell sizes, for the same reason.

The GUI will snap any values to increments of the cell size if users try to enter different values.

Text axes cannot be aggregated (although it could be done if there were a need and a good way of doing so).

Axes with zero cellsizes, e.g. where data are used as points, can be aggregated to any coarser resolution.  The system generates a default for each axis using the extent of that axis divided by 20 (so it will result in 20 cells along each axis by default).

Shawn Laffan

If you want to try this out before version 3 is released then the 2.99_003 release can be accessed through the downloads page at


For more details about Biodiverse, see

To see what Biodiverse has been used for, see

You can also join the Biodiverse-users mailing list at or follow the google plus page:

Tuesday, 2 April 2019

Publications using Biodiverse in 2018

We are well into 2019, so here is a list of publications that used Biodiverse in 2018. 

If you want to see the full list (100 at the time of writing), then go to 

For more details about Biodiverse, see 

Shawn Laffan

Bloomfield, N.J., Knerr, N. and Encinas-Viso, F. (2018) A comparison of network and clustering methods to detect biogeographical regions. Ecography, 41, 1-10.

Carta, A., Pierini, B., Roma-Marzio, F., Bedini, G. and Peruzzi, L. (2018) Phylogenetic measures of biodiversity uncover pteridophyte centres of diversity and hotspots in Tuscany. Plant Biosystems, 152, 831-839.

Dalrymple, R.L., Kemp, D.J., Laffan, S.W., White, T.E., Flores-Moreno, H., Hemmings, F.A., Hitchcock, T.D., & Moles, A.T. (2018) Abiotic and biotic predictors of macroecological patterns in bird and butterfly coloration. Ecological Monographs, 88, 204-224.

Di Virgilio, G., Wardell-Johnson, G.W., Robinson, T.P., Temple-Smith, D., Hesforde, J. (2018) Characterising fine-scale variation in plant species richness and endemism across topographically complex, semi-arid landscapes. Journal of Arid Environments, 156, 59-68.

Elliott, M.J., Knerr, N.J. and Schmidt-Lebuhn, A.N. (2018) Choice between phylogram and chronogram can have a dramatic impact on the location of phylogenetic diversity hotspots. Journal of Biogeography, 45, 2190-2201.

Guedes, T.B., Sawaya, R.J., Zizka, A., Laffan, S.W., Faurby, S., Pyron, A., Bérnils, R.S., Jansen, M., Passos, P., Prudente, A.L.C., Cisneros-Heredia, D.F., Braz, H.B., Nogueira, C.d.C., & Antonelli, A. (2018) Patterns, biases and prospects in the distribution and diversity of Neotropical snakes. Global Ecology and Biogeography, 27, 14-21.

Laffan, S.W. (2018). Phylogeny-based measurements at global and regional scales. In R. Scherson & D. Faith (Eds.), Phylogenetic Diversity: Applications and Challenges in Biodiversity Science (pp. 111-129): Springer.

Link-Pérez, M.A. and Laffan, S.W. (2018) Fern and lycophyte diversity in the Pacific Northwest: Patterns and predictors. Journal of Systematics and Evolution, 56, 498-522.

López-Aguirre, C., Archer, M., Hand, S.J. and Laffan, S.W. (2018) Phylogenetic diversity, types of endemism and the evolutionary history of New World bats. Ecography, 41, 1955-1966.

Miu, I.V., Chisamera, G.B., Popescu, V.D., Iosif R., Nita, A., Manolache, S., Gavril, V.D., Cobzaru, I. and Rozylowicz, L. (2018) Conservation priorities for terrestrial mammals in Dobrogea Region, Romania. ZooKeys, 792, 133-158.

Montaño-Arias, G., Luna-Vega, I., Morrone, J.J., Espinosa, D. (2018) Biogeographical identity of the Mesoamerican dominion with emphasis on seasonally dry tropical forests. Phytotaxa, 376, 277-290.

Orsenigo, S. et al. (2018) Red Listing plants under full national responsibility: Extinction risk and threats in the vascular flora endemic to Italy. Biological Conservation, 224, 213-222.

Sosa, V., De-Nova, J.A. and Vásquez-Cruz, M. (2018) Evolutionary history of the flora of Mexico: Dry forests cradles and museums of endemism. Journal of Systematics and Evolution, 56, 523-536.

Spalink, D., Pender, J., Escudero, M., Hipp, A.L., Roalson, E.H., Starr, J.R., Waterway, M.J., Bohs, L. and Sytsma, K.J. (2018) The spatial structure of phylogenetic and functional diversity in the United States and Canada: An example using the sedge family (Cyperaceae). Journal of Systematics and Evolution, 56, 449-465.

Spalink, D. et al. (2018) Spatial phylogenetics reveals evolutionary constraints on the assembly of a large regional flora. American Journal of Botany, 105, 1938-1950.

Yap, J-YS., Rossetto, M., Costion, C., et al. (2018) Filters of floristic exchange: How traits and climate shape the rain forest invasion of Sahul from Sunda. Journal of Biogeography, 25, 838-847.

Zhang, H., Bonser, S. P., Chen, S.-C., Hitchcock, T. and Moles, A. T. (2018) Is the proportion of clonal species higher at higher latitudes in Australia? Austral Ecology, 43, 69-75.