Software
Please find here links to all the simulation models and R scripts developed by our workgroup.
[img_assist|nid=202|title=|desc=|link=url|url=http://www.botany.ut.ee/~meelis/bgsim_intro.htm|align=right|width=360|height=183]
BGSIMweb - online simulation of biogeograhpy
BGSIMweb is a web-based simulation of biogeography programmed by prof. Meelis Pärtel. It allows to create islands and continents, change species traits and to follow changes in biodiversity in ecological and evolutionary time-scales. BGSIMweb is aimed for students and anyone who wishes to find a better understanding of biogeographical processes.
[img_assist|nid=228|title=|desc=|link=url|url=http://www.botany.ut.ee/dispersal/|align=right|width=360|height=200]
dispeRsal - R script for predicting seed dispersal distances
dispeRsal is a function and accompanying data set to be used in the statistical software R that predicts seed dispersal distances for a set of species supplied by the user. dispeRsal uses statistical modeling to predict the dispersal distances from a number of dispersal related plant traits. In the current version, these traits comprise growth form, dispersal mode, seed mass, plant height and seed terminal velocity. The user needs to supply data for at least a subset of these traits together with the species list.
[img_assist|nid=366|title=|desc=|link=url|url=http://onlinelibrary.wiley.com/store/10.1111/jvs.12052/asset/supinfo/jvs12052-sup-0001-AppendixS1-S5.pdf?v=1&s=da9f6bfd4c0bd8fda04f3fb3bf8617ecde7ce620|align=right|width=360|height=200]
Modified MPD – R script for modified MPD (considering species´ abundances, independent of number of species)
A modified version of the function ´mpd´ (mean pair-wise distance) in package ´picante´ (v. 1.5-2) in R with the option ´abundance.weighted = TRUE´. The original function includes the diagonal in the dissimilarity matrix between species (which is always 0), and is hence dependent of the number of species in the matrix. Our modified version does not include the diagonal, and is intrinsically independent of the number of species. When using this function, please refer to the Appendix 2 (which includes the script) in the following paper:
Gerhold P, Price JN, Püssa K, Kalamees R, Aher K, Kaasik A & Pärtel M (2013) Functional and phylogenetic community assembly linked to changes in species diversity in a long-term resource manipulation experiment. Journal of Vegetation Science 24:843-852
Please find here links to all the simulation models and R scripts developed by our workgroup.
[img_assist|nid=202|title=|desc=|link=url|url=http://www.botany.ut.ee/~meelis/bgsim_intro.htm|align=right|width=360|height=183]
BGSIMweb - online simulation of biogeograhpy
BGSIMweb is a web-based simulation of biogeography programmed by prof. Meelis Pärtel. It allows to create islands and continents, change species traits and to follow changes in biodiversity in ecological and evolutionary time-scales. BGSIMweb is aimed for students and anyone who wishes to find a better understanding of biogeographical processes.
[img_assist|nid=228|title=|desc=|link=url|url=http://www.botany.ut.ee/dispersal/|align=right|width=360|height=200]
dispeRsal - R script for predicting seed dispersal distances
dispeRsal is a function and accompanying data set to be used in the statistical software R that predicts seed dispersal distances for a set of species supplied by the user. dispeRsal uses statistical modeling to predict the dispersal distances from a number of dispersal related plant traits. In the current version, these traits comprise growth form, dispersal mode, seed mass, plant height and seed terminal velocity. The user needs to supply data for at least a subset of these traits together with the species list.
[img_assist|nid=366|title=|desc=|link=url|url=http://onlinelibrary.wiley.com/store/10.1111/jvs.12052/asset/supinfo/jvs12052-sup-0001-AppendixS1-S5.pdf?v=1&s=da9f6bfd4c0bd8fda04f3fb3bf8617ecde7ce620|align=right|width=360|height=200]
Modified MPD – R script for modified MPD (considering species´ abundances, independent of number of species)
A modified version of the function ´mpd´ (mean pair-wise distance) in package ´picante´ (v. 1.5-2) in R with the option ´abundance.weighted = TRUE´. The original function includes the diagonal in the dissimilarity matrix between species (which is always 0), and is hence dependent of the number of species in the matrix. Our modified version does not include the diagonal, and is intrinsically independent of the number of species. When using this function, please refer to the Appendix 2 (which includes the script) in the following paper:
Gerhold P, Price JN, Püssa K, Kalamees R, Aher K, Kaasik A & Pärtel M (2013) Functional and phylogenetic community assembly linked to changes in species diversity in a long-term resource manipulation experiment. Journal of Vegetation Science 24:843-852