| add_asr_node_states |
Fits a model of ancestral state reconstruction of island presence |
| add_island_colonist |
Adds an island colonists (can be either a singleton lineage or an island clade) to the island community (island_tbl). |
| add_missing_species |
Adds a specified number of missing species to an existing island_tbl at the colonist specified by the species_to_add_to argument given. The species given is located within the island_tbl data and missing species are assigned. This is to be used after 'extract_island_species()' to input missing species. |
| add_multi_missing_species |
Calculates the number of missing species to be assigned to each island clade in the island_tbl object and assigns the missing species to them. In the case that multiple genera are in an island clade and each have missing species the number of missing species is summed. Currently the missing species are assigned to the genus that first matches with the missing species table, however a more biologically or stochastic assignment is in development. |
| add_outgroup |
Add an outgroup species to a given phylogeny. |
| all_descendants_conspecific |
Checks whether all species given in the descendants vector are the same species. |
| all_endemicity_status |
All possible endemicity statuses |
| any_back_colonisation |
Detects any cases where a non-endemic species or species not present on the island has likely been on the island given its ancestral state reconstruction indicating ancestral presence on the island and so is likely a back colonisation from the island to the mainland (or potentially different island). This function is useful if using extraction_method = "min" in 'DAISIEprep::extract_island_species()' as it may brake up a single colonist into multiple colonists because of back-colonisation. |
| any_outgroup |
Checks whether the phylogeny has an outgroup that is not present on the island. This is critical when extracting data from the phylogeny so the stem age (colonisation time) is correct. |
| any_polyphyly |
Checks whether there are any species in the phylogeny that have multiple tips (i.e. multiple subspecies per species) and whether any of those tips are paraphyletic (i.e. are their subspecies more distantly related to each other than to other subspecies or species). |
| as_daisie_datatable |
Converts the 'Island_tbl' class to a data frame in the format of a DAISIE data table (see DAISIE R package for details). This can then be input into 'DAISIEprep::create_daisie_data()' function which creates the list input into the DAISIE ML models. |
| 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 requirements of the DAISIEprep package. If the function does not return anything the data is ready to be used, if an error is returned the data requires some pre-processing before DAISIEprep can be used |
| coccyzus_phylod |
A phylogenetic tree of coccyzus species with endemicity status as tip states. |
| coccyzus_tree |
Phylogenetic trees of the Galapagos bird lineages and sister species on the mainland. |
| columbiformes_phylod |
A phylogenetic tree of columbiformes species with endemicity status as tip states. |
| columbiformes_tree |
Phylogenetic trees of the Galapagos bird lineages and sister species on the mainland. |
| count_missing_species |
Reads in the checklist of all species on an island, including those that are not in the phylogeny (represented by NA) and counts the number of species missing from the phylogeny each genus |
| create_daisie_data |
This is a wrapper function for DAISIE::DAISIE_dataprep(). It allows the final DAISIE data structure to be produced from within DAISIEprep. For detailed documentation see the help documentation in the DAISIE package (?DAISIE::DAISIE_dataprep). |
| create_endemicity_status |
Creates a data frame with the endemicity status (either 'endemic', 'nonendemic', 'not_present') of every species in the phylogeny using a phylogeny and a data frame of the island species and their endemicity (either 'endemic' or 'nonendemic') provided. |
| create_test_phylod |
Creates phylod objects. |
| endemicity_to_sse_states |
Convert endemicity to SSE states |
| extract_asr_clade |
Extracts an island clade based on the ancestral state reconstruction of the species presence on the island, therefore this clade can contain non-endemic species as well as endemic species. |
| 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 species of the clade have the same genus name or whether the clade is composed of multiple genera, in which case it will create a unique clade name by concatinating the genus names |
| extract_endemic_clade |
Extracts the information for an endemic clade (i.e. more than one species on the island more closely related to each other than other mainland species) from a phylogeny (specifically 'phylo4d' object from 'phylobase' package) and stores it in an 'Island_colonist' class |
| extract_endemic_singleton |
Extracts the information for an endemic species from a phylogeny (specifically 'phylo4d' object from 'phylobase' package) and stores it in in an 'Island_colonist' class |
| extract_island_species |
Extracts the colonisation, diversification, and endemicty data from phylogenetic and endemicity data and stores it in an 'Island_tbl' object |
| extract_multi_tip_species |
Extracts the information for a species (endemic or non-endemic) which has multiple tips in the phylogeny (i.e. more than one sample per species) from a phylogeny (specifically 'phylo4d' object from 'phylobase' package) and stores it in an 'Island_colonist' class |
| extract_nonendemic |
Extracts the information for a non-endemic species from a phylogeny (specifically 'phylo4d' object from 'phylobase' package) and stores it in in an 'island_colonist' class |
| extract_species_asr |
Extracts the colonisation, diversification, and endemicty data from phylogenetic and endemicity data and stores it in an 'Island_tbl' object using the "asr" algorithm that extract island species given their ancestral states of either island presence or absence. |
| extract_species_min |
Extracts the colonisation, diversification, and endemicty data from phylogenetic and endemicity data and stores it in an 'Island_tbl' object using the "min" algorithm that extract island species as the shortest time to the present. |
| extract_stem_age |
Extracts the stem age from the phylogeny when the a species is known to belong to a genus but is not itself in the phylogeny and there are members of the same genus are in the phylogeny. The stem age can either be for the genus (or several genera) in the tree ('stem = "genus"') or use an extraction algorithm to find the stem of when the species colonised the island (stem = "island_presence), either 'min' or 'asr' as in extract_island_species(). When 'stem = "island_presence"' the reconstructed node states are used to determine the stem age. |
| extract_stem_age_asr |
Extracts the stem age from the phylogeny when the a species is known to belong to a genus but is not itself in the phylogeny and there are members of the same genus are in the phylogeny using the 'asr' extraction method |
| extract_stem_age_genus |
Extracts the stem age from the phylogeny when the a species is known to belong to a genus but is not itself in the phylogeny and there are members of the same genus are in the phylogeny |
| extract_stem_age_min |
Extracts the stem age from the phylogeny when the a species is known to belong to a genus but is not itself in the phylogeny and there are members of the same genus are in the phylogeny using the 'min' extraction method |
| GalapagosTrees |
Phylogenetic trees of the Galapagos bird lineages and sister species on the mainland. |
| get_branching_times |
Accessor functions for the data (slots) in objects of the 'Island_colonist' class |
| get_branching_times-method |
Accessor functions for the data (slots) in objects of the 'Island_colonist' class |
| get_clade_name |
Accessor functions for the data (slots) in objects of the 'Island_colonist' class |
| get_clade_name-method |
Accessor functions for the data (slots) in objects of the 'Island_colonist' class |
| get_clade_type |
Accessor functions for the data (slots) in objects of the 'Island_colonist' class |
| get_clade_type-method |
Accessor functions for the data (slots) in objects of the 'Island_colonist' class |
| get_col_max_age |
Accessor functions for the data (slots) in objects of the 'Island_colonist' class |
| get_col_max_age-method |
Accessor functions for the data (slots) in objects of the 'Island_colonist' class |
| get_col_time |
Accessor functions for the data (slots) in objects of the 'Island_colonist' class |
| get_col_time-method |
Accessor functions for the data (slots) in objects of the 'Island_colonist' class |
| get_extracted_species |
Accessor functions for the data (slots) in objects of the 'Island_tbl' class |
| get_extracted_species-method |
Accessor functions for the data (slots) in objects of the 'Island_tbl' class |
| get_island_tbl |
Accessor functions for the data (slots) in objects of the 'Island_tbl' class |
| get_island_tbl-method |
Accessor functions for the data (slots) in objects of the 'Island_tbl' class |
| get_min_age |
Accessor functions for the data (slots) in objects of the 'Island_colonist' class |
| get_min_age-method |
Accessor functions for the data (slots) in objects of the 'Island_colonist' class |
| get_missing_species |
Accessor functions for the data (slots) in objects of the 'Island_colonist' class |
| get_missing_species-method |
Accessor functions for the data (slots) in objects of the 'Island_colonist' class |
| get_num_phylo_used |
Accessor functions for the data (slots) in objects of the 'Island_tbl' class |
| get_num_phylo_used-method |
Accessor functions for the data (slots) in objects of the 'Island_tbl' class |
| get_species |
Accessor functions for the data (slots) in objects of the 'Island_colonist' class |
| get_species-method |
Accessor functions for the data (slots) in objects of the 'Island_colonist' class |
| get_sse_tip_states |
Extract tip states from a phylod object |
| get_status |
Accessor functions for the data (slots) in objects of the 'Island_colonist' class |
| get_status-method |
Accessor functions for the data (slots) in objects of the 'Island_colonist' class |
| mimus_phylod |
A phylogenetic tree of mimus species with endemicity status as tip states. |
| mimus_tree |
Phylogenetic trees of the Galapagos bird lineages and sister species on the mainland. |
| multi_extract_island_species |
Extracts the colonisation, diversification, and endemicty data from multiple 'phylod' ('phylo4d' class from 'phylobase') objects (composed of phylogenetic and endemicity data) and stores each in an 'Island_tbl' object which are stored in a 'Multi_island_tbl' object. |
| multi_island_tbl |
Constructor function for 'Multi_island_tbl' class |
| Multi_island_tbl-class |
Defines the 'Multi_island_tbl' class which is multiple 'Island_tbl's. |
| myiarchus_phylod |
A phylogenetic tree of myiarchus species with endemicity status as tip states. |
| myiarchus_tree |
Phylogenetic trees of the Galapagos bird lineages and sister species on the mainland. |
| select_endemicity_status |
Select endemicity status from ancestral states probabilities |
| sensitivity |
Runs a sensitivity analysis to test the influences of changing the data on the parameter estimates for the DAISIE maximum likelihood inference model |
| setophaga_phylod |
A phylogenetic tree of setophaga species with endemicity status as tip states. |
| setophaga_tree |
Phylogenetic trees of the Galapagos bird lineages and sister species on the mainland. |
| set_branching_times<- |
Accessor functions for the data (slots) in objects of the 'Island_colonist' class |
| set_branching_times<--method |
Accessor functions for the data (slots) in objects of the 'Island_colonist' class |
| set_clade_name<- |
Accessor functions for the data (slots) in objects of the 'Island_colonist' class |
| set_clade_name<--method |
Accessor functions for the data (slots) in objects of the 'Island_colonist' class |
| set_clade_type<- |
Accessor functions for the data (slots) in objects of the 'Island_colonist' class |
| set_clade_type<--method |
Accessor functions for the data (slots) in objects of the 'Island_colonist' class |
| set_col_max_age<- |
Accessor functions for the data (slots) in objects of the 'Island_colonist' class |
| set_col_max_age<--method |
Accessor functions for the data (slots) in objects of the 'Island_colonist' class |
| set_col_time<- |
Accessor functions for the data (slots) in objects of the 'Island_colonist' class |
| set_col_time<--method |
Accessor functions for the data (slots) in objects of the 'Island_colonist' class |
| set_extracted_species<- |
Accessor functions for the data (slots) in objects of the 'Island_tbl' class |
| set_extracted_species<--method |
Accessor functions for the data (slots) in objects of the 'Island_tbl' class |
| set_island_tbl<- |
Accessor functions for the data (slots) in objects of the 'Island_tbl' class |
| set_island_tbl<--method |
Accessor functions for the data (slots) in objects of the 'Island_tbl' class |
| set_min_age<- |
Accessor functions for the data (slots) in objects of the 'Island_colonist' class |
| set_min_age<--method |
Accessor functions for the data (slots) in objects of the 'Island_colonist' class |
| set_missing_species<- |
Accessor functions for the data (slots) in objects of the 'Island_colonist' class |
| set_missing_species<--method |
Accessor functions for the data (slots) in objects of the 'Island_colonist' class |
| set_num_phylo_used<- |
Accessor functions for the data (slots) in objects of the 'Island_tbl' class |
| set_num_phylo_used<--method |
Accessor functions for the data (slots) in objects of the 'Island_tbl' class |
| set_species<- |
Accessor functions for the data (slots) in objects of the 'Island_colonist' class |
| set_species<--method |
Accessor functions for the data (slots) in objects of the 'Island_colonist' class |
| set_status<- |
Accessor functions for the data (slots) in objects of the 'Island_colonist' class |
| set_status<--method |
Accessor functions for the data (slots) in objects of the 'Island_colonist' class |
| sse_states_to_endemicity |
Convert SSE states back to endemicity status |
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