Files in joshwlambert/DAISIEmainland
Simulates Data for Phylogenetic Data on Islands for DAISIE with the Addition of Mainland Dynamics

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.zenodo.json

DAISIEmainland.Rproj

DESCRIPTION

LICENSE.md

NAMESPACE

NEWS.md R/DAISIEmainland.R R/add_metadata_to_daisie_data.R R/all_endemic_clades.R R/all_endemic_singletons.R R/ana_event.R R/any_recols.R R/branch_code_to_y.R R/calc_ctt.R R/calc_empirical_col.R R/calc_endemic_percent.R R/calc_error.R R/calc_island_endemics.R R/calc_max_age_percent.R R/calc_num_col.R R/calc_num_spec.R R/calc_param_diffs.R R/calc_param_ratios.R R/calc_rates.R R/calc_sim_metrics.R R/check_analysis_result.R R/check_branch_code.R R/check_branching_times.R R/check_daisie_data.R R/check_daisie_mainland_data.R R/check_event_times.R R/check_island_tbl.R R/check_mainland_clade.R R/check_missing_species.R R/check_multi_daisie_data.R R/check_multi_mainland_clade.R R/check_species_type.R R/check_stac.R R/clado_event.R R/colonist_species_type_to_str.R R/common_ancestor_time.R R/create_daisie_data.R R/create_empirical_island.R R/create_false_clade_brts.R R/create_ideal_island.R R/create_non_empty_island.R R/create_test_island_tbl.R R/create_test_mainland_clade.R R/daisie_data_to_tables.R R/data.R R/default_params_doc.R R/ext_event.R R/group_multi_daisie_data.R R/immig_event.R R/is_daisie_datalist.R R/plot_ctt_boxplot.R R/plot_ctt_heatmap.R R/plot_ctt_scatter.R R/plot_daisie_data.R R/plot_daisie_mainland_data.R R/plot_endemics.R R/plot_inf_k.R R/plot_k_estimates.R R/plot_log_param_ratios.R R/plot_mainland.R R/plot_mainland_clade.R R/plot_max_age.R R/plot_param_diffs.R R/plot_sim_metrics.R R/plot_utils.R R/read_analysis_results.R R/sample_event.R R/sample_mainland.R R/sim_island.R R/sim_island_with_mainland.R R/sim_mainland.R R/sim_utils.R R/stac_to_english_str.R R/test_utils.R R/update_island_endemics.R R/update_state.R README.md

bash/install_DAISIEmainland.sh

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data-raw/param_space.R

data/param_space.rda

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inst/WORDLIST

inst/book/_bookdown.yml

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inst/book/data-standards.Rmd

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inst/book/data/error_metrics_100_rep.rds

inst/book/data/param_sets/param_set_1.rds

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inst/book/references.bib

inst/book/simulation-algorithm.Rmd inst/book/simulation-data-visualisation.Rmd inst/book/summary-error-metrics-visualisation.Rmd inst/extdata/MainlandExtinction_appendix_a.pdf man/DAISIEmainland.Rd man/add_metadata_to_daisie_data.Rd man/all_endemic_clades.Rd man/all_endemic_singletons.Rd man/ana_event.Rd man/any_recols.Rd man/branch_code_to_y.Rd man/calc_ctt.Rd man/calc_empirical_col.Rd man/calc_endemic_percent.Rd man/calc_error.Rd man/calc_island_endemics.Rd man/calc_max_age_percent.Rd man/calc_num_col.Rd man/calc_num_spec.Rd man/calc_outliers.Rd man/calc_param_diffs.Rd man/calc_param_ratios.Rd man/calc_quantiles.Rd man/calc_rates.Rd man/calc_sim_metrics.Rd man/check_analysis_result.Rd man/check_branch_code.Rd man/check_branching_times.Rd man/check_daisie_data.Rd man/check_daisie_mainland_data.Rd man/check_event_times.Rd man/check_island_tbl.Rd man/check_mainland_clade.Rd man/check_missing_species.Rd man/check_multi_daisie_data.Rd man/check_multi_mainland_clade.Rd man/check_species_type.Rd man/check_stac.Rd man/choose_scientific.Rd man/clado_event.Rd man/colonist_species_type_to_str.Rd man/common_ancestor_time.Rd man/count_extant_mainland_species.Rd man/create_daisie_data.Rd man/create_empirical_island.Rd man/create_false_clade_brts.Rd man/create_ideal_island.Rd man/create_ihs_breaks.Rd man/create_labels.Rd man/create_non_empty_island.Rd man/create_test_island_tbl.Rd man/create_test_mainland_clade.Rd man/daisie_data_colonist_info_to_braching_times_table.Rd man/daisie_data_colonist_info_to_colonisation_times_table.Rd man/daisie_data_colonist_info_to_general_table.Rd man/daisie_data_to_tables.Rd man/daisie_header_to_table.Rd man/default_params_doc.Rd man/event_to_str.Rd man/ext_event.Rd man/figures/README.md

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tests/testthat/testdata/param_set_8.rds

tests/testthat/testdata/param_set_9.rds

joshwlambert/DAISIEmainland documentation built on July 14, 2024, 5:40 p.m.

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joshwlambert/DAISIEmainland
Simulates Data for Phylogenetic Data on Islands for DAISIE with the Addition of Mainland Dynamics

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Simulates Data for Phylogenetic Data on Islands for DAISIE with the Addition of Mainland Dynamics

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joshwlambert/DAISIEmainland Simulates Data for Phylogenetic Data on Islands for DAISIE with the Addition of Mainland Dynamics

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joshwlambert/DAISIEmainland
Simulates Data for Phylogenetic Data on Islands for DAISIE with the Addition of Mainland Dynamics

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Simulates Data for Phylogenetic Data on Islands for DAISIE with the Addition of Mainland Dynamics