| DAISIEprep |
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| DAISIEprep-package |
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| GalapagosTrees |
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| Island_colonist-class |
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| Island_tbl-class |
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| Multi_island_tbl-class |
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| add_asr_node_states |
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| add_island_colonist |
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| add_missing_species |
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| add_multi_missing_species |
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| add_outgroup |
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| all_descendants_conspecific |
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| all_endemicity_status |
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| any_back_colonisation |
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| any_outgroup |
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| any_polyphyly |
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| as_daisie_datatable |
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| benchmark |
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| bind_colonist_to_tbl |
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| check_island_colonist |
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| check_island_tbl |
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| check_multi_island_tbl |
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| check_phylo_data |
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| coccyzus_phylod |
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| coccyzus_tree |
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| columbiformes_phylod |
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| columbiformes_tree |
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| count_missing_species |
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| create_daisie_data |
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| create_endemicity_status |
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| create_test_phylod |
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| default_params_doc |
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| endemicity_to_sse_states |
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| extract_asr_clade |
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| extract_biogeobears_ancestral_states_probs |
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| extract_clade_name |
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| extract_endemic_clade |
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| extract_endemic_singleton |
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| extract_island_species |
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| extract_multi_tip_species |
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| extract_nonendemic |
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| extract_nonendemic_forced |
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| extract_species_asr |
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| extract_species_min |
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| extract_stem_age |
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| extract_stem_age_asr |
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| extract_stem_age_genus |
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| extract_stem_age_min |
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| finches_phylod |
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| finches_tree |
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| get_branching_times |
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| get_branching_times,Island_colonist-method |
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| get_clade_name |
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| get_clade_name,Island_colonist-method |
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| get_clade_type |
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| get_clade_type,Island_colonist-method |
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| get_col_max_age |
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| get_col_max_age,Island_colonist-method |
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| get_col_time |
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| get_col_time,Island_colonist-method |
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| get_endemic_species |
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| get_extracted_species |
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| get_extracted_species,Island_tbl-method |
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| get_island_tbl |
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| get_island_tbl,Island_tbl-method |
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| get_min_age |
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| get_min_age,Island_colonist-method |
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| get_missing_species |
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| get_missing_species,Island_colonist-method |
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| get_num_phylo_used |
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| get_num_phylo_used,Island_tbl-method |
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| get_species |
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| get_species,Island_colonist-method |
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| get_sse_tip_states |
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| get_status |
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| get_status,Island_colonist-method |
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| is_back_colonisation |
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| is_duplicate_colonist |
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| is_identical_island_tbl |
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| is_multi_tip_species |
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| island_colonist |
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| island_tbl |
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| mimus_phylod |
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| mimus_tree |
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| multi_extract_island_species |
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| multi_island_tbl |
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| myiarchus_phylod |
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| myiarchus_tree |
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| plant_phylo |
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| plot_colonisation |
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| plot_performance |
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| plot_phylod |
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| plot_sensitivity |
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| progne_phylod |
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| progne_tree |
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| pyrocephalus_phylod |
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| pyrocephalus_tree |
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| read_performance |
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| read_sensitivity |
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| rm_duplicate_island_species |
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| rm_island_colonist |
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| rm_multi_missing_species |
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| rm_nonendemic_in_clade |
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| round_up |
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| select_endemicity_status |
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| sensitivity |
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| set_branching_times<- |
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| set_branching_times<-,Island_colonist-method |
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| set_clade_name<- |
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| set_clade_name<-,Island_colonist-method |
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| set_clade_type<- |
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| set_clade_type<-,Island_colonist-method |
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| set_col_max_age<- |
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| set_col_max_age<-,Island_colonist-method |
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| set_col_time<- |
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| set_col_time<-,Island_colonist-method |
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| set_extracted_species<- |
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| set_extracted_species<-,Island_tbl-method |
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| set_island_tbl<- |
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| set_island_tbl<-,Island_tbl-method |
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| set_min_age<- |
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| set_min_age<-,Island_colonist-method |
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| set_missing_species<- |
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| set_missing_species<-,Island_colonist-method |
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| set_num_phylo_used<- |
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| set_num_phylo_used<-,Island_tbl-method |
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| set_species<- |
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| set_species<-,Island_colonist-method |
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| set_status<- |
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| set_status<-,Island_colonist-method |
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| setophaga_phylod |
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| setophaga_tree |
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| sse_states_to_endemicity |
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| translate_status |
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| unique_island_genera |
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| write_biogeobears_input |
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| write_newick_file |
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| write_phylip_biogeo_file |
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