DAISIEprep Tutorial2 years ago
The tutorial is divided into 3 sections: | 1. Single Phylogeny Example | In this section we demonstrate a simple example of extracting and formatting data from a single phylogeny. We use an example phylogeny of an imaginary clade of plant species, which includes 2 species occurring on an example focal island. | Load the phylogeny | Convert the phylogeny to phylo4 | Add endemicity statuses | Create island_tbl object | Extract data with the DAISIEprep "min" algorithm | Extract data with the DAISIEprep "asr" algorithm | Format data to prepare if for DAISIE | 2. Multiple phylogenies example | In this section we demonstrate an empirical use case of the package on the avifauna of the Galápagos archipelago, which uses several phylogenies for different island colonists. | 3. Adding missing species | 3.1 Adding missing species to an island clade that has been sampled in the phylogeny | 3.2 Adding a lineage with just one species on the island (singleton) when a phylogeny is not available for the lineage, but a colonisation time estimate exists | 3.3 Adding a lineage with 2 or more species on the island when a phylogeny is not available for the lineage, but a colonisation time estimate exists | 3.4 Adding a lineage when a phylogeny is not available for the lineage, and no colonisation estimate is available. | 3.5 Adding a lineage when a phylogeny is not available for the entire island lineage, but a crown age or minimum colonisation time estimate exists
DAISIEprep 1.0.1.9000Joshua W. Lambert Tutorial.Rmd
