| add_asr_node_states | Fits a model of ancestral state reconstruction of island... |
| add_island_colonist | Adds an island colonists (can be either a singleton lineage... |
| add_missing_species | Adds a specified number of missing species to an existing... |
| add_multi_missing_species | Calculates the number of missing species to be assigned to... |
| add_outgroup | Add an outgroup species to a given phylogeny. |
| all_descendants_conspecific | Checks whether all species given in the descendants vector... |
| all_endemicity_status | All possible endemicity statuses |
| any_back_colonisation | Detects any cases where a non-endemic species or species not... |
| any_outgroup | Checks whether the phylogeny has an outgroup that is not... |
| any_polyphyly | Checks whether there are any species in the phylogeny that... |
| as_daisie_datatable | Converts the 'Island_tbl' class to a data frame in the format... |
| benchmark | Performance analysis of the extract_island_species() function... |
| bind_colonist_to_tbl | Takes an existing instance of an 'Island_tbl' class and bind... |
| check_island_colonist | Checks the validity of the Island_colonist class |
| check_island_tbl | Checks the validity of the Island_tbl class |
| check_multi_island_tbl | Checks the validity of the Multi_island_tbl class |
| check_phylo_data | Checks whether \linkS4class{phylo4d} object conforms to the... |
| coccyzus_phylod | A phylogenetic tree of coccyzus species with endemicity... |
| columbiformes_phylod | A phylogenetic tree of columbiformes species with endemicity... |
| count_missing_species | Reads in the checklist of all species on an island, including... |
| create_daisie_data | This is a wrapper function for DAISIE::DAISIE_dataprep(). It... |
| create_endemicity_status | Creates a data frame with the endemicity status (either... |
| create_test_phylod | Creates phylod objects. |
| DAISIEprep-package | DAISIEprep: Extracts Phylogenetic Island Community Data from... |
| default_params_doc | Documentation for function in the DAISIEprep package |
| endemicity_to_sse_states | Convert endemicity to SSE states |
| extract_asr_clade | Extracts an island clade based on the ancestral state... |
| extract_biogeobears_ancestral_states_probs | Extract ancestral state probabilities from BioGeoBEARS output |
| extract_clade_name | Creates a name for a clade depending on whether all the... |
| extract_endemic_clade | Extracts the information for an endemic clade (i.e. more than... |
| extract_endemic_singleton | Extracts the information for an endemic species from a... |
| extract_island_species | Extracts the colonisation, diversification, and endemicty... |
| extract_multi_tip_species | Extracts the information for a species (endemic or... |
| extract_nonendemic | Extracts the information for a non-endemic species from a... |
| extract_nonendemic_forced | Extract non-endemic colonist that is forced to be a singleton... |
| extract_species_asr | Extracts the colonisation, diversification, and endemicty... |
| extract_species_min | Extracts the colonisation, diversification, and endemicty... |
| extract_stem_age | Extracts the stem age from the phylogeny when the a species... |
| extract_stem_age_asr | Extracts the stem age from the phylogeny when the a species... |
| extract_stem_age_genus | Extracts the stem age from the phylogeny when the a species... |
| extract_stem_age_min | Extracts the stem age from the phylogeny when the a species... |
| finches_phylod | A phylogenetic tree of finches species with endemicity status... |
| GalapagosTrees | Phylogenetic trees of the Galapagos bird lineages and sister... |
| get_endemic_species | Checks whether the focal species (given by its tip lable in... |
| get_sse_tip_states | Extract tip states from a phylod object |
| is_back_colonisation | Checks whether species has undergone back-colonisation from |
| is_duplicate_colonist | Determines if colonist has already been stored in... |
| is_identical_island_tbl | Checks whether two 'Island_tbl' objects are identical. If... |
| island_colonist | Constructor for Island_colonist |
| Island_colonist-accessors | Accessor functions for the data (slots) in objects of the... |
| Island_colonist-class | Defines the 'island_tbl' class which is used when extracting... |
| island_tbl | Constructor function for 'Island_tbl' class |
| Island_tbl-accessors | Accessor functions for the data (slots) in objects of the... |
| Island_tbl-class | Defines the 'island_tbl' class which is used when extracting... |
| is_multi_tip_species | Checks if a species is represented in the tree has multiple... |
| mimus_phylod | A phylogenetic tree of mimus species with endemicity status... |
| multi_extract_island_species | Extracts the colonisation, diversification, and endemicty... |
| multi_island_tbl | Constructor function for 'Multi_island_tbl' class |
| Multi_island_tbl-class | Defines the 'Multi_island_tbl' class which is multiple... |
| myiarchus_phylod | A phylogenetic tree of myiarchus species with endemicity... |
| plant_phylo | A phylogenetic tree of plant species. |
| plot_colonisation | Plots a dot plot (cleveland dot plot when include_crown_age =... |
| plot_performance | Plots performance results for a grouping variable... |
| plot_phylod | Plots the phylogenetic tree and its associated tip and/or... |
| plot_sensitivity | Plots |
| progne_phylod | A phylogenetic tree of progne species with endemicity status... |
| pyrocephalus_phylod | A phylogenetic tree of pyrocephalus species with endemicity... |
| read_performance | Reads in performance analysis results from... |
| read_sensitivity | Reads in the results from the sensitivity analysis saved in... |
| rm_duplicate_island_species | Remove any duplicated species from the 'island_tbl' after... |
| rm_island_colonist | Removes an island colonist from an 'Island_tbl' object |
| rm_multi_missing_species | Loops through the genera that have missing species and... |
| round_up | Rounds numbers using the round up method, rather than the... |
| select_endemicity_status | Select endemicity status from ancestral states probabilities |
| sensitivity | Runs a sensitivity analysis to test the influences of... |
| setophaga_phylod | A phylogenetic tree of setophaga species with endemicity... |
| sse_states_to_endemicity | Convert SSE states back to endemicity status |
| translate_status | Takes a string of the various ways the island species status... |
| unique_island_genera | Determines the unique endemic genera that are included in the... |
| write_biogeobears_input | Write input files for BioGeoBEARS |
| write_newick_file | Write tree input file for BioGeoBEARS |
| write_phylip_biogeo_file | Write biogeography input file for BioGeoBEARS |
