Files in DAISIEprep
Extracts Phylogenetic Island Community Data from Phylogenetic Trees
MD5
NEWS.md
README.md
NAMESPACE
DESCRIPTION
R/count_missing_species.R
R/sensitivity.R
R/rm_multi_missing_species.R
R/any_polyphyly.R
R/read_sensitivity.R
R/extract_stem_age_asr.R
R/endemicity_to_sse_states.R
R/extract_multi_tip_species.R
R/read_performance.R
R/extract_species_min.R
R/add_asr_node_states.R
R/is_back_colonisation.R
R/is_multi_tip_species.R
R/get_endemic_species.R
R/all_descendants_conspecific.R
R/translate_status.R
R/extract_endemic_clade.R
R/extract_island_species.R
R/add_multi_missing_species.R
R/bind_colonist_to_tbl.R
R/data.R
R/create_daisie_data.R
R/is_identical_island_tbl.R
R/check_phylo_data.R
R/default_params_doc.R
R/create_endemicity_status.R
R/island_tbl-methods.R
R/extract_nonendemic.R
R/benchmark.R
R/extract_stem_age_min.R
R/DAISIEprep-package.R
R/plot_phylod.R
R/island_colonist-accessors.R
R/any_back_colonisation.R
R/extract_stem_age.R
R/island_tbl-accessors.R
R/as_daisie_datatable.R
R/island_tbl-class.R
R/plot_sensitivity.R
R/extract_endemic_singleton.R
R/create_test_phylod.R
R/unique_island_genera.R
R/rm_nonendemic_in_clade.R
R/extract_clade_name.R
R/is_duplicate_colonist.R
R/multi_island_tbl-class.R
R/add_outgroup.R
R/island_colonist-class.R
R/print-methods.R
R/extract_asr_clade.R
R/rm_duplicate_island_species.R
R/any_outgroup.R
R/plot_colonisation.R
R/add_island_colonist.R
R/write_biogeobears_input.R
R/extract_species_asr.R
R/multi_extract_island_species.R
R/rm_island_colonist.R
R/plot_performance.R
R/multi_island_tbl-methods.R
R/extract_stem_age_genus.R
R/add_missing_species.R
R/utils.R
inst/doc/Forcing_nonendemic_singleton.html
inst/doc/Forcing_nonendemic_singleton.Rmd
inst/doc/Multi_tip_extraction.html
inst/doc/Tutorial.Rmd
inst/doc/Tutorial.html
inst/doc/Performance.Rmd
inst/doc/Forcing_nonendemic_singleton.R
inst/doc/Tutorial.R
inst/doc/Performance.html
inst/doc/Sensitivity.R
inst/doc/Sensitivity.Rmd
inst/doc/Performance.R
inst/doc/Multi_tip_extraction.Rmd
inst/doc/Sensitivity.html
inst/doc/Multi_tip_extraction.R
inst/extdata/Columbiformes.tre
inst/extdata/Myiarchus.tre
inst/extdata/Mimus.tre
inst/extdata/Finches.tre
inst/extdata/Setophaga.tre
inst/extdata/plant_phylo.rds
inst/extdata/Progne.tre
inst/extdata/Coccyzus.tre
inst/extdata/Pyrocephalus.tre
inst/sensitivity_data/sensitivity_tree_index_64.rds
inst/sensitivity_data/sensitivity_tree_index_22.rds
inst/sensitivity_data/sensitivity_tree_index_59.rds
inst/sensitivity_data/sensitivity_tree_index_70.rds
inst/sensitivity_data/sensitivity_tree_index_71.rds
inst/sensitivity_data/sensitivity_tree_index_57.rds
inst/sensitivity_data/sensitivity_tree_index_62.rds
inst/sensitivity_data/sensitivity_tree_index_25.rds
inst/sensitivity_data/sensitivity_tree_index_11.rds
inst/sensitivity_data/sensitivity_tree_index_94.rds
inst/sensitivity_data/sensitivity_tree_index_41.rds
inst/sensitivity_data/sensitivity_tree_index_89.rds
inst/sensitivity_data/sensitivity_tree_index_69.rds
inst/sensitivity_data/sensitivity_tree_index_73.rds
inst/sensitivity_data/sensitivity_tree_index_92.rds
inst/sensitivity_data/sensitivity_tree_index_54.rds
inst/sensitivity_data/sensitivity_tree_index_43.rds
inst/sensitivity_data/sensitivity_tree_index_48.rds
inst/sensitivity_data/sensitivity_tree_index_44.rds
inst/sensitivity_data/sensitivity_tree_index_16.rds
inst/sensitivity_data/sensitivity_tree_index_85.rds
inst/sensitivity_data/sensitivity_tree_index_65.rds
inst/sensitivity_data/sensitivity_tree_index_7.rds
inst/sensitivity_data/sensitivity_tree_index_15.rds
inst/sensitivity_data/sensitivity_tree_index_49.rds
inst/sensitivity_data/sensitivity_tree_index_75.rds
inst/sensitivity_data/sensitivity_tree_index_8.rds
inst/sensitivity_data/sensitivity_tree_index_81.rds
inst/sensitivity_data/sensitivity_tree_index_38.rds
inst/sensitivity_data/sensitivity_tree_index_18.rds
inst/sensitivity_data/sensitivity_tree_index_77.rds
inst/sensitivity_data/sensitivity_tree_index_87.rds
inst/sensitivity_data/sensitivity_tree_index_58.rds
inst/sensitivity_data/sensitivity_tree_index_50.rds
inst/sensitivity_data/sensitivity_tree_index_31.rds
inst/sensitivity_data/sensitivity_tree_index_67.rds
inst/sensitivity_data/sensitivity_tree_index_99.rds
inst/sensitivity_data/sensitivity_tree_index_37.rds
inst/sensitivity_data/sensitivity_tree_index_2.rds
inst/sensitivity_data/sensitivity_tree_index_14.rds
inst/sensitivity_data/sensitivity_tree_index_84.rds
inst/sensitivity_data/sensitivity_tree_index_19.rds
inst/sensitivity_data/sensitivity_tree_index_79.rds
inst/sensitivity_data/sensitivity_tree_index_97.rds
inst/sensitivity_data/sensitivity_tree_index_93.rds
inst/sensitivity_data/sensitivity_tree_index_63.rds
inst/sensitivity_data/sensitivity_tree_index_35.rds
inst/sensitivity_data/sensitivity_tree_index_80.rds
inst/sensitivity_data/sensitivity_tree_index_82.rds
inst/sensitivity_data/sensitivity_tree_index_90.rds
inst/sensitivity_data/sensitivity_tree_index_13.rds
inst/sensitivity_data/sensitivity_tree_index_27.rds
inst/sensitivity_data/sensitivity_tree_index_28.rds
inst/sensitivity_data/sensitivity_tree_index_3.rds
inst/sensitivity_data/sensitivity_tree_index_21.rds
inst/sensitivity_data/sensitivity_tree_index_10.rds
inst/sensitivity_data/sensitivity_tree_index_36.rds
inst/sensitivity_data/sensitivity_tree_index_40.rds
inst/sensitivity_data/sensitivity_tree_index_32.rds
inst/sensitivity_data/sensitivity_tree_index_47.rds
inst/sensitivity_data/sensitivity_tree_index_42.rds
inst/sensitivity_data/sensitivity_tree_index_74.rds
inst/sensitivity_data/sensitivity_tree_index_83.rds
inst/sensitivity_data/sensitivity_tree_index_29.rds
inst/sensitivity_data/sensitivity_tree_index_46.rds
inst/sensitivity_data/sensitivity_tree_index_96.rds
inst/sensitivity_data/sensitivity_tree_index_26.rds
inst/sensitivity_data/sensitivity_tree_index_1.rds
inst/sensitivity_data/sensitivity_tree_index_100.rds
inst/sensitivity_data/sensitivity_tree_index_78.rds
inst/sensitivity_data/sensitivity_tree_index_5.rds
inst/sensitivity_data/sensitivity_tree_index_6.rds
inst/sensitivity_data/sensitivity_tree_index_61.rds
inst/sensitivity_data/sensitivity_tree_index_24.rds
inst/sensitivity_data/sensitivity_tree_index_53.rds
inst/sensitivity_data/sensitivity_tree_index_20.rds
inst/sensitivity_data/sensitivity_tree_index_30.rds
inst/sensitivity_data/sensitivity_tree_index_9.rds
inst/sensitivity_data/sensitivity_tree_index_72.rds
inst/sensitivity_data/sensitivity_tree_index_68.rds
inst/sensitivity_data/sensitivity_tree_index_95.rds
inst/sensitivity_data/sensitivity_tree_index_98.rds
inst/sensitivity_data/sensitivity_tree_index_88.rds
inst/sensitivity_data/sensitivity_tree_index_45.rds
inst/sensitivity_data/sensitivity_tree_index_91.rds
inst/sensitivity_data/sensitivity_tree_index_23.rds
inst/sensitivity_data/sensitivity_tree_index_33.rds
inst/sensitivity_data/sensitivity_tree_index_39.rds
inst/sensitivity_data/sensitivity_tree_index_52.rds
inst/sensitivity_data/sensitivity_tree_index_66.rds
inst/sensitivity_data/sensitivity_tree_index_60.rds
inst/sensitivity_data/sensitivity_tree_index_76.rds
inst/sensitivity_data/sensitivity_tree_index_55.rds
inst/sensitivity_data/sensitivity_tree_index_56.rds
inst/sensitivity_data/sensitivity_tree_index_51.rds
inst/sensitivity_data/sensitivity_tree_index_4.rds
inst/sensitivity_data/sensitivity_tree_index_86.rds
inst/sensitivity_data/sensitivity_tree_index_34.rds
inst/sensitivity_data/sensitivity_tree_index_12.rds
inst/sensitivity_data/sensitivity_tree_index_17.rds
inst/performance_data/performance_param_set_7.rds
inst/performance_data/performance_param_set_56.rds
inst/performance_data/performance_param_set_47.rds
inst/performance_data/performance_param_set_17.rds
inst/performance_data/performance_param_set_23.rds
inst/performance_data/performance_param_set_8.rds
inst/performance_data/performance_param_set_12.rds
inst/performance_data/performance_param_set_6.rds
inst/performance_data/performance_param_set_55.rds
inst/performance_data/performance_param_set_60.rds
inst/performance_data/performance_param_set_34.rds
inst/performance_data/performance_param_set_48.rds
inst/performance_data/performance_param_set_39.rds
inst/performance_data/performance_param_set_43.rds
inst/performance_data/performance_param_set_41.rds
inst/performance_data/performance_param_set_53.rds
inst/performance_data/performance_param_set_9.rds
inst/performance_data/performance_param_set_45.rds
inst/performance_data/performance_param_set_19.rds
inst/performance_data/performance_param_set_5.rds
inst/performance_data/performance_param_set_31.rds
inst/performance_data/performance_param_set_16.rds
inst/performance_data/performance_param_set_38.rds
inst/performance_data/performance_param_set_58.rds
inst/performance_data/performance_param_set_27.rds
inst/performance_data/performance_param_set_37.rds
inst/performance_data/performance_param_set_14.rds
inst/performance_data/performance_param_set_32.rds
inst/performance_data/performance_param_set_1.rds
inst/performance_data/performance_param_set_36.rds
inst/performance_data/performance_param_set_15.rds
inst/performance_data/performance_param_set_28.rds
inst/performance_data/performance_param_set_49.rds
inst/performance_data/performance_param_set_51.rds
inst/performance_data/performance_param_set_3.rds
inst/performance_data/performance_param_set_24.rds
inst/performance_data/performance_param_set_50.rds
inst/performance_data/performance_param_set_54.rds
inst/performance_data/performance_param_set_33.rds
inst/performance_data/performance_param_set_35.rds
inst/performance_data/performance_param_set_21.rds
inst/performance_data/performance_param_set_52.rds
inst/performance_data/performance_param_set_44.rds
inst/performance_data/performance_param_set_29.rds
inst/performance_data/performance_param_set_40.rds
inst/performance_data/performance_param_set_42.rds
inst/performance_data/performance_param_set_18.rds
inst/performance_data/performance_param_set_13.rds
inst/performance_data/performance_param_set_11.rds
inst/performance_data/performance_param_set_46.rds
inst/performance_data/performance_param_set_4.rds
inst/performance_data/performance_param_set_26.rds
inst/performance_data/performance_param_set_10.rds
inst/performance_data/performance_param_set_2.rds
inst/performance_data/performance_empirical.rds
inst/performance_data/performance_param_set_22.rds
inst/performance_data/performance_param_set_25.rds
inst/performance_data/performance_param_set_30.rds
inst/performance_data/performance_param_set_57.rds
inst/performance_data/performance_param_set_20.rds
inst/performance_data/performance_param_set_59.rds
inst/extending_asr/biogeobears_ex_biogeo.txt
inst/extending_asr/biogeobears_ex_phylo.txt
build/vignette.rds
tests/testthat.R
tests/testthat/test-island_colonist-class.R
tests/testthat/test-read_sensitivity.R
tests/testthat/test-add_asr_node_states.R
tests/testthat/test-as_daisie_datatable.R
tests/testthat/test-multi_island_tbl-methods.R
tests/testthat/test-rm_island_colonist.R
tests/testthat/test-plot_phylod.R
tests/testthat/test-is_multi_tip_species.R
tests/testthat/test-add_outgroup.R
tests/testthat/test-all_descendants_conspecific.R
tests/testthat/test-utils.R
tests/testthat/test-extract_asr_clade.R
tests/testthat/test-island_tbl-accessors.R
tests/testthat/test-translate_status.R
tests/testthat/test-extract_endemic_singleton.R
tests/testthat/test-extract_stem_age_asr.R
tests/testthat/test-extract_stem_age_min.R
tests/testthat/test-extract_species_min.R
tests/testthat/test-unique_island_genera.R
tests/testthat/test-island_tbl-class.R
tests/testthat/test-create_endemicity_status.R
tests/testthat/test-plot_performance.R
tests/testthat/test-endemicity_to_sse_states.R
tests/testthat/test-read_performance.R
tests/testthat/test-is_identical_island_tbl.R
tests/testthat/test-is_back_colonisation.R
tests/testthat/test-extract_multi_tip_species.R
tests/testthat/test-any_outgroup.R
tests/testthat/test-extract_species_asr.R
tests/testthat/test-extract_island_species.R
tests/testthat/test-any_polyphyly.R
tests/testthat/test-plot_colonisation.R
tests/testthat/test-count_missing_species.R
tests/testthat/test-add_missing_species.R
tests/testthat/test-any_back_colonisation.R
tests/testthat/test-create_daisie_data.R
tests/testthat/test-extract_stem_age.R
tests/testthat/test-extract_endemic_clade.R
tests/testthat/test-print-methods.R
tests/testthat/test-get_endemic_species.R
tests/testthat/test-extract_nonendemic.R
tests/testthat/test-rm_multi_missing_species.R
tests/testthat/test-bind_colonist_to_tbl.R
tests/testthat/test-rm_duplicate_island_species.R
tests/testthat/test-sensitivity.R
tests/testthat/test-multi_island_tbl-class.R
tests/testthat/test-add_island_colonist.R
tests/testthat/test-benchmark.R
tests/testthat/test-is_duplicate_colonist.R
tests/testthat/test-extract_stem_age_genus.R
tests/testthat/test-add_multi_missing_species.R
tests/testthat/test-create_test_phylod.R
tests/testthat/test-plot_sensitivity.R
vignettes/Forcing_nonendemic_singleton.Rmd
vignettes/Tutorial.Rmd
vignettes/references.bib
vignettes/Performance.Rmd
vignettes/evolution.csl
vignettes/Sensitivity.Rmd
vignettes/Multi_tip_extraction.Rmd
data/coccyzus_tree.rda
data/plant_phylo.rda
data/progne_tree.rda
data/finches_tree.rda
data/setophaga_tree.rda
data/progne_phylod.rda
data/pyrocephalus_phylod.rda
data/finches_phylod.rda
data/columbiformes_phylod.rda
data/mimus_tree.rda
data/setophaga_phylod.rda
data/myiarchus_phylod.rda
data/myiarchus_tree.rda
data/coccyzus_phylod.rda
data/mimus_phylod.rda
data/columbiformes_tree.rda
data/pyrocephalus_tree.rda
man/finches_phylod.Rd
man/island_colonist.Rd
man/is_identical_island_tbl.Rd
man/extract_species_min.Rd
man/Island_colonist-accessors.Rd
man/multi_island_tbl.Rd
man/round_up.Rd
man/coccyzus_phylod.Rd
man/any_outgroup.Rd
man/sse_states_to_endemicity.Rd
man/plant_phylo.Rd
man/add_asr_node_states.Rd
man/extract_stem_age.Rd
man/any_back_colonisation.Rd
man/Multi_island_tbl-class.Rd
man/extract_nonendemic_forced.Rd
man/bind_colonist_to_tbl.Rd
man/add_island_colonist.Rd
man/is_duplicate_colonist.Rd
man/benchmark.Rd
man/extract_nonendemic.Rd
man/multi_extract_island_species.Rd
man/island_tbl.Rd
man/any_polyphyly.Rd
man/DAISIEprep-package.Rd
man/read_performance.Rd
man/columbiformes_phylod.Rd
man/write_biogeobears_input.Rd
man/get_sse_tip_states.Rd
man/setophaga_phylod.Rd
man/translate_status.Rd
man/extract_island_species.Rd
man/write_phylip_biogeo_file.Rd
man/check_island_colonist.Rd
man/write_newick_file.Rd
man/create_test_phylod.Rd
man/create_endemicity_status.Rd
man/extract_species_asr.Rd
man/add_outgroup.Rd
man/check_multi_island_tbl.Rd
man/get_endemic_species.Rd
man/progne_phylod.Rd
man/check_phylo_data.Rd
man/create_daisie_data.Rd
man/is_multi_tip_species.Rd
man/rm_island_colonist.Rd
man/plot_performance.Rd
man/endemicity_to_sse_states.Rd
man/read_sensitivity.Rd
man/all_descendants_conspecific.Rd
man/extract_stem_age_genus.Rd
man/as_daisie_datatable.Rd
man/GalapagosTrees.Rd
man/Island_tbl-class.Rd
man/add_multi_missing_species.Rd
man/default_params_doc.Rd
man/extract_clade_name.Rd
man/Island_tbl-accessors.Rd
man/unique_island_genera.Rd
man/myiarchus_phylod.Rd
man/count_missing_species.Rd
man/rm_duplicate_island_species.Rd
man/plot_colonisation.Rd
man/Island_colonist-class.Rd
man/check_island_tbl.Rd
man/rm_multi_missing_species.Rd
man/mimus_phylod.Rd
man/extract_biogeobears_ancestral_states_probs.Rd
man/extract_stem_age_min.Rd
man/extract_asr_clade.Rd
man/plot_sensitivity.Rd
man/extract_endemic_singleton.Rd
man/extract_endemic_clade.Rd
man/extract_multi_tip_species.Rd
man/pyrocephalus_phylod.Rd
man/all_endemicity_status.Rd
man/extract_stem_age_asr.Rd
man/select_endemicity_status.Rd
man/plot_phylod.Rd
man/is_back_colonisation.Rd
man/add_missing_species.Rd
man/sensitivity.Rd
man/figures/logo.png
