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