Given a phylogenetic tree and a presence/absence matrix this script calculates phylogenetic diversity of a group of species across a given set of grid cells or locations. The library "ape" is required to read the tree in R. Command is "read.tree" or "read.nexus".Options of type:"P" is a normalized mearure of … See more Calculate all phylogenetic diversity measures listed in Schweiger et al., 2008 (see full reference below). See more This function returns a list of phylogenetic diversity values for each of the grid cells in the presence/absence matrix See more Schweiger, O., S. Klotz, W. Durka and I. Kuhn. 2008. A comparative test of phylogenetic diversity indices. Oecologia, 157, 485-495. Pio, D.V., O. Broennimann, … See more WebMay 11, 2014 · The method to calculate pairwise and nearest neigbor measures for functional traits is same as those for phylogenetic diversity. For FD, we need to decide to use the dendrogram or the raw distance matrix as input. If using dendrogram, we need change it into a distance matrix first cophenetic (my.dendro) which may will lose …
Phylogenetic dispersion and diversity in regional assemblages of ... - PNAS
WebMay 6, 2011 · The caper package provides a set of functions to conduct comparative analyses using both independent contrasts and phylogenetic generalised least squares … WebMeasures of diversity Diversity in the ecological sense is intuitively understood as the complexity of a community of organisms. There are many ways to quantify this complexity so that we can compare communities objectively. The two main categories of methods are known as alpha diversity and beta diversity (Whittaker 1960). blend food processor recipe
Diversity statistics - GitHub Pages
WebMar 14, 2024 · Abstract. Although dengue is typically considered an urban disease, rural communities are also at high risk. To clarify dynamics of dengue virus (DENV) transmission in settings with characteristics generally considered rural (e.g., lower population density, remoteness), we conducted a phylogenetic analysis in 6 communities in northwestern … WebJul 1, 2024 · Details. Rao's quadratic entropy (Rao 1982) is a measure of diversity in ecological communities that can optionally take species differences (e.g. phylogenetic dissimilarity) into account. This method is conceptually similar to analyses of genetic diversity among populations (Nei 1973), but instead of diversity of alleles among … WebJul 11, 2024 · A New Phylogenetic Diversity Measure Generalizing the Shannon Index and Its Application to Phyllostomid Bats. American Naturalist 174(2): 236-243. Leinster, T. and Cobbold, C. (2011). Measuring diversity: the importance … freckle school program