DAISIEprep: an R package for the extraction and formatting of data for the island biogeography model DAISIE

Abstract

AbstractPhylogenetic trees are commonly used to answer questions on biogeographical and diversification histories of different groups.Recently, new approaches have been developed that use community phylogenetic trees requiring a data structure distinct from the single phylogenetic trees that are commonly used, which may be a barrier to the utilisation of these approaches.DAISIE (Dynamic Assembly of Islands through Speciation, Immigration and Extinction) is an island biogeography model that can estimate rates of colonisation, speciation and extinction from phylogenetic data across insular communities, as well as simulate islands under those rates.Here we describe theDAISIEprepR package, a set of pre-processing tools to aid the extraction of data from one or many phylogenetic trees to generate data in a format interpretable by DAISIE for the application of island biogeography inference models. We present examples to illustrate the various data types that can be used.The package includes simple algorithms to extract data on island colonists and account for bio-geographical, topological and taxonomic uncertainty. It also allows flexible incorporation of either missing species or entire insular lineages when phylogenetic data are not available.DAISIEprepenables reproducible and user-friendly data extraction and formatting, and will facili-tate addressing questions about island biogeography, diversification and anthropogenic impacts in insular systems.