Man pages for joshwlambert/DAISIEmainland
Simulates Data for Phylogenetic Data on Islands for DAISIE with the Addition of Mainland Dynamics
| add_metadata_to_daisie_data | Formats simulation output into standard DAISIE list output. |
| all_endemic_clades | Checks if all island species are endemic clades. Clade are... |
| all_endemic_singletons | Checks if all island species are endemic singletons.... |
| ana_event | Updates the island_tbl and max_spec_id when an anagenesis... |
| any_recols | Determines if the island contains any recolonisations that... |
| branch_code_to_y | Convert a 'branch_code' to a y coordinat in range [0, 1] |
| calc_ctt | Calculates the delta colonisation through time (CTT)... |
| calc_empirical_col | Calculates whether colonisations from different mainland... |
| calc_endemic_percent | Calculates what percentage of island species are endemic. |
| calc_error | Calculates the colonisation through time (CTT) statistic,... |
| calc_island_endemics | Calculates the number of endemic and non-endemics species on... |
| calc_max_age_percent | Calculates the percent of max age species on the island for... |
| calc_num_col | Calculates summary metrics from a simulation |
| calc_num_spec | Calculates summary metrics from a simulation |
| calc_outliers | Subsets the data to those less than the 5th percentile and... |
| calc_param_diffs | Calculates the differences in parameter estimates... |
| calc_param_ratios | Calculates the ratio in parameter estimates (cladogenesis,... |
| calc_quantiles | Calculates the 5th, 25th, 50th, 75th and 95th percentile of... |
| calc_rates | Calculate rates for island processes |
| calc_sim_metrics | Calculates the summary metrics for the entire parameter space |
| check_analysis_result | Checks whether the analysis results read by... |
| check_branch_code | Check if a 'branch_code' is valid. |
| check_branching_times | Check if a 'branching_times' is valid. |
| check_daisie_data | Check if a 'daisie_data' (i.e. a 'DAISIE' 'datalist') is... |
| check_daisie_mainland_data | Check if a 'daisie_mainland_data' is valid. Will stop if not. |
| check_event_times | Check if a 'event_times' is valid. |
| check_island_tbl | Check if an 'island_tbl' is valid. |
| check_mainland_clade | Check if an 'mainland_clade' is valid. |
| check_missing_species | Check if a 'missing_species' is valid. |
| check_multi_daisie_data | Check if an 'multi_daisie_data' is valid for both... |
| check_multi_mainland_clade | Check if an 'multi_mainland_clade' is valid. Will stop if... |
| check_species_type | Check if a 'species_type' is valid. |
| check_stac | Check if a 'stac' is valid. |
| choose_scientific | Decides whether number should be in normal or scientific form... |
| clado_event | Updates the island_tbl and max_spec_id when a cladogenesis... |
| colonist_species_type_to_str | Convert a 'colonist_species_type' to a string |
| common_ancestor_time | Calculates the branching time of the common ancestor of two... |
| count_extant_mainland_species | Count the number of extant mainland species |
| create_daisie_data | Converts simulation output into island output |
| create_empirical_island | Convert intermediate output to final simulation output for... |
| create_false_clade_brts | Creates a vector of branching times when empirical data is a... |
| create_ideal_island | Convert intermediate output to final simulation output for... |
| create_ihs_breaks | Creates the axis numbers (breaks) for plotting with an... |
| create_labels | Creates labels for plots by calling 'scientific'. |
| create_non_empty_island | Creates an ideal and empirical data set for a single non... |
| create_test_island_tbl | Creates an island community for testing purposes |
| create_test_mainland_clade | Creates a clade on the mainland for testing purposes |
| daisie_data_colonist_info_to_braching_times_table | Internal function |
| daisie_data_colonist_info_to_colonisation_times_table | Internal function |
| daisie_data_colonist_info_to_general_table | Internal function |
| daisie_data_to_tables | Convert 'daisie_data' into a tabular format |
| daisie_header_to_table | Convert a 'daisie_data_header' into a tabular format |
| DAISIEmainland | 'DAISIEmainland': A package to simulate phylogenetic data on... |
| default_params_doc | Documentation for function arguments in the DAISIEmainland... |
| event_to_str | Convert an event to a string |
| ext_event | Updates the island_tbl when an extinction event occurs |
| group_multi_daisie_data | Takes mixed multi_daisie_data produced by the looping over... |
| immig_event | Updates the island_tbl when an immigration event occurs |
| is_daisie_data | Determine if a 'daisie_data' is valid. |
| param_space | Parameter space for the analysis of the DAISIE mainland... |
| plot_ctt_boxplot | Plots a boxplot of the delta colonisation through time... |
| plot_ctt_heatmap | Plots a heatmap of the colonisation through time statistic... |
| plot_ctt_scatter | Plots points of the mean delta colonisation through time... |
| plot_daisie_data | Plot the 'daisie_data'. |
| plot_daisie_mainland_data | Plot the 'daisie_mainland_data' for a certain replicate |
| plot_endemics | Plots two faceted boxplots of the percent of endemics on the... |
| plot_inf_k | Plots the percentage of carrying capacity (K') estimates that... |
| plot_k_estimates | Boxplots of the estimated carrying capacity faceted for ideal... |
| plot_log_param_ratios | Plots a grid of density plots of parameter estimates on the... |
| plot_mainland | Plot the simulated mainland. |
| plot_mainland_clade | Plot the simulated mainland. |
| plot_max_age | Plots two faceted boxplots of the percent of max age... |
| plot_param_diffs | Plots a grid of density plots of parameter estimates on the... |
| plot_sim_metrics | Plots metrics from simulations |
| read_analysis_results | Reads all the the results from a directory, with path is... |
| sample_event | Samples what event to happen next on the island. |
| sample_mainland | Samples the mainland clade with the mainland sampling... |
| scientific | Creates the axis numbers (labels) for plotting with... |
| sim_island | Simulates the island given rates and a mainland clade |
| sim_island_with_mainland | Simulate oceanic islands with mainland extinction given... |
| sim_mainland | Simulates mainland extinction as a species-level moran... |
| species_type_to_str | Convert an 'species_type' to a string, where the... |
| stac_to_english_str | Convert a 'stac' (status of colonist) to an... |
| stac_to_str | Convert a 'stac' (status of colonist) to a string |
| str_to_event | Convert a string to an event |
| str_to_stac | Convert a string to a 'stac' |
| update_island_endemics | Checks and updates if any changes on the mainland change the... |
| update_state | Updates state of island given sampled event for a constant... |
