Extracts Phylogenetic Island Community Data from Phylogenetic Trees
Fits a model of ancestral state reconstruction of island presence
Adds an island colonists (can be either a singleton lineage or an isla...
Adds a specified number of missing species to an existing island_tbl a...
Calculates the number of missing species to be assigned to each island...
Add an outgroup species to a given phylogeny.
Checks whether all species given in the descendants vector are the sam...
All possible endemicity statuses
Detects any cases where a non-endemic species or species not present o...
Checks whether the phylogeny has an outgroup that is not present on th...
Checks whether there are any species in the phylogeny that have multip...
Converts the Island_tbl class to a data frame in the format of a DAI...
Performance analysis of the extract_island_species() function Uses sys...
Takes an existing instance of an Island_tbl class and bind the infor...
Checks the validity of the Island_colonist class
Checks the validity of the Island_tbl class
Checks the validity of the Multi_island_tbl class
Checks whether \linkS4class{phylo4d} object conforms to the requirem...
Reads in the checklist of all species on an island, including those th...
This is a wrapper function for DAISIE::DAISIE_dataprep(). It allows th...
Creates a data frame with the endemicity status (either 'endemic', 'no...
Creates phylod objects.
DAISIEprep: Extracts Phylogenetic Island Community Data from Phylogene...
Documentation for function in the DAISIEprep package
Convert endemicity to SSE states
Extracts an island clade based on the ancestral state reconstruction o...
Extract ancestral state probabilities from BioGeoBEARS output
Creates a name for a clade depending on whether all the species of the...
Extracts the information for an endemic clade (i.e. more than one spec...
Extracts the information for an endemic species from a phylogeny (spec...
Extracts the colonisation, diversification, and endemicty data from ph...
Extracts the information for a species (endemic or non-endemic) which ...
Extract non-endemic colonist that is forced to be a singleton by user
Extracts the information for a non-endemic species from a phylogeny (s...
Extracts the colonisation, diversification, and endemicty data from ph...
Extracts the colonisation, diversification, and endemicty data from ph...
Extracts the stem age from the phylogeny when the a species is known t...
Extracts the stem age from the phylogeny when the a species is known t...
Extracts the stem age from the phylogeny when the a species is known t...
Extracts the stem age from the phylogeny when the a species is known t...
Phylogenetic trees of the Galapagos bird lineages and sister species o...
Checks whether the focal species (given by its tip lable in species_la...
Extract tip states from a phylod object
Checks whether species has undergone back-colonisation from
Determines if colonist has already been stored in Island_tbl class. ...
Checks whether two Island_tbl objects are identical. If they are dif...
Checks if a species is represented in the tree has multiple tips and t...
Accessor functions for the data (slots) in objects of the `Island_colo...
Defines the island_tbl class which is used when extracting informati...
Constructor for Island_colonist
Accessor functions for the data (slots) in objects of the Island_tbl...
Defines the island_tbl class which is used when extracting informati...
Constructor function for Island_tbl class
Extracts the colonisation, diversification, and endemicty data from mu...
Defines the Multi_island_tbl class which is multiple Island_tbls.
Constructor function for Multi_island_tbl class
Plots a dot plot (cleveland dot plot when include_crown_age = TRUE) of...
Plots performance results for a grouping variable (prob_on_island or p...
Plots the phylogenetic tree and its associated tip and/or node data
Plots
Reads in performance analysis results from inst/performance_data and f...
Reads in the results from the sensitivity analysis saved in the inst/s...
Remove any duplicated species from the island_tbl after "asr" extr...
Removes an island colonist from an Island_tbl object
Loops through the genera that have missing species and removes the one...
Rounds numbers using the round up method, rather than the round to the...
Select endemicity status from ancestral states probabilities
Runs a sensitivity analysis to test the influences of changing the dat...
Convert SSE states back to endemicity status
Takes a string of the various ways the island species status can be an...
Determines the unique endemic genera that are included in the island c...
Write input files for BioGeoBEARS
Write tree input file for BioGeoBEARS
Write biogeography input file for BioGeoBEARS
Extracts colonisation and branching times of island species to be used for analysis in the R package 'DAISIE'. It uses phylogenetic and endemicity data to extract the separate island colonists and store them.
Useful links