Man pages for DAISIE
Dynamical Assembly of Islands by Speciation, Immigration and Extinction

archipelago_dataPhysical data on 41 archipelagos
archipelagos41DAISIE datalist object including bird phylogenetic data and...
are_area_parsTest if list has area parameters
are_hyper_parsTest if a list has hyperparameters
are_max_ratesDetermines if object max_rates are max_rates
are_max_rates_gt_ratesCheck if maximum rates are greater or equal to rates
are_ratesDetermines if object rates are rates
are_trait_parsTest if list has trait state parameters
Bats_GreaterAntillesColonization and branching times of Noctilionoid bats from...
Biwa_datalistColonization and branching times of 68 fish clades.
calc_AbetaCalculates the area at a point in time from a beta function
calc_next_timevalCalculates when the next timestep will be.
calc_next_timeval_shiftCalculates when the next timestep will be, and if a shift has...
calc_peakCalculates the peak of ontogeny curve (beta function)
countspeciesCount the number of species
create_area_parsCreate named list of area parameters
create_CS_versionCreates the list object for CS_version argument in...
create_full_CS_sttUnsampled CS full STT
create_hyper_parsCreate list of hyperparameters
create_trait_parsCreate named list of trait state parameters
DAISIE_calc_clade_ana_rateCalculate the clade-wide effective anagenesis rate. With...
DAISIE_calc_clade_clado_rateCalculate the clade-wide cladogenesis rate.
DAISIE_calc_clade_ext_rateCalculate the clade-wide extinction rate
DAISIE_calc_clade_imm_rateCalculate the clade-wide immigration rate.
DAISIE_calc_sumstats_pcratesCalculate summary statistics of per capita rates
DAISIE_convertprobdistConverts the joint distribution of endemics and non-endemics...
DAISIE_convert_to_classic_plotPrepare input for DAISIE_stt
DAISIE_create_islandConverts simulation output into island output
DAISIE_dataprepPrepare colonisation and branching time data to run in...
DAISIE_ExpEINThe expected number of endemics and non-endemics under the...
DAISIE_extract_stt_medianExtract the STT median from the output of DAISIE_sim...
DAISIE_format_CSWrapper function around for the DAISIE_format_CS_full_stt and...
DAISIE_format_CS_full_sttFormats clade-specific simulation output into standard DAISIE...
DAISIE_format_CS_sampled_sttFormats clade-specific simulation output into standard DAISIE...
DAISIE_format_GWFormats guild-wide simulation output into standard DAISIE...
DAISIE_format_IWFormats island-wide simulation output into standard DAISIE...
DAISIE_get_brts_myaExtract the sorted branching times, in million years ago....
DAISIE_ICCalculates information criterion from DAISIE ML estimates?
DAISIE_loglik_CSComputes the loglikelihood of the DAISIE model with...
DAISIE_loglik_integrandIntegrand to be integrated to calculate the log likelihood...
DAISIE_loglik_integrateIntegrates the loglikelihood of a single clade across a...
DAISIE_loglik_IWComputes the loglikelihood of the DAISIE model with...
DAISIE_make_archipelagoDoes some things
DAISIE_make_globalDoes something
DAISIE_margprobdistThe marginal distribution of endemics and non-endemics under...
DAISIE_MLMaximization of the loglikelihood under the DAISIE model with...
DAISIE_ML1Computes MLE for single type species under a clade specific...
DAISIE_ML2Computes MLE for multiple islands under a clade specific...
DAISIE_ML3Computes MLE for single type species under a clade specific...
DAISIE_ML4Computes MLE for single type species under a clade specific...
DAISIE_ML_IWMaximization of the loglikelihood under the DAISIE model with...
DAISIE_MW_MLMaximization of the loglikelihood under the DAISIE model with...
DAISIE_nonoceanic_specCalculates the species on the island initially when...
DAISIE_numcolThe expectation and marginal distribution of the number of...
DAISIE_ONEcolonistTitle
DAISIE-packageDAISIE: Dynamical Assembly of Islands by Speciation,...
DAISIE_plot_age_diversityPlot clade age against clade diversity.
DAISIE_plot_areaPlots island area function through time
DAISIE_plot_cladogenesisPlot cladogenesis rate through time
DAISIE_plot_comparison_sttsPlot STT and overlay additional STT curves.
DAISIE_plot_extinctionPlots extinction rate function through time
DAISIE_plot_immigrationPlot immigration rate through time
DAISIE_plot_inputDAISIE tree plot
DAISIE_plot_islandPlot colonisation and branching time of species found on an...
DAISIE_plot_pc_ratesPlot per capita STT and per-capita rate change thourgh...
DAISIE_plot_simsPlot island species-through-time (STT) plots
DAISIE_plot_sttCreate the Species-Through-Time plot. This is used to...
DAISIE_probdistThe joint distribution of endemics and non-endemics under the...
DAISIE_sample_event_constant_rateSamples what event to happen next
DAISIE_sample_event_time_dependentSamples what event to happen next
DAISIE_sample_event_trait_dependentSamples what event to happen next
DAISIE_simSimulate (non-)oceanic islands with given parameters under...
DAISIE_sim_constant_rate_shiftSimulate (non-)oceanic islands with given parameters under a...
DAISIE_sim_core_1_4Internal function of the DAISIE simulation Taken from CRAN,...
DAISIE_sim_core_1_4aInternal function of the DAISIE simulation Taken from CRAN,...
DAISIE_sim_core_constant_rateInternal function of the DAISIE simulation
DAISIE_sim_core_constant_rate_shiftInternal function of the DAISIE simulation
DAISIE_sim_core_time_dependentInternal function of the DAISIE simulation
DAISIE_sim_core_trait_dependentInternal function of the DAISIE simulation
DAISIE_sim_min_type2Internal function of the DAISIE simulation
DAISIE_sim_MWSimulate multiple islands based on hyperparameters that...
DAISIE_sim_relaxed_rateSimulate (non-)oceanic islands with given parameters under a...
DAISIE_sim_time_dependentSimulate (non-)oceanic islands with given parameters under a...
DAISIE_sim_trait_dependentSimulate islands with given parameters.
DAISIE_sim_update_state_constant_rateUpdates state of island given sampled event for a constant...
DAISIE_sim_update_state_time_dependentUpdates state of island given sampled event
DAISIE_sim_update_state_trait_dependentUpdates state of island given sampled event with two trait...
DAISIE_single_branchSingle-branch phylogenetic tree
DAISIE_SR_loglik_CSComputes the loglikelihood of the DAISIE model with...
DAISIE_SR_MLMaximization of the loglikelihood under the DAISIE model with...
DAISIE_SR_simDEPRECATED - Simulate islands with given parameters.
DAISIE_SR_sim_coreDEPRECATED - Algorithm component of DAISIE_SR_sim.
default_params_docDefault parameter documentation
frogs_datalistColonization and branching times of 5 Eleutherodactylus...
frogs_datatableColonization and branching times of 5 Eleutherodactylus...
Galapagos_datalistColonization and branching times of 8 terrestrial avifaunal...
Galapagos_datalist_2typesColonization and branching times of 8 terrestrial avifaunal...
Galapagos_datatableColonization and branching times of 8 terrestrial avifaunal...
get_ana_rateCalculate anagenesis rate
get_clado_rateCalculate cladogenesis rate
get_ext_rateFunction to describe changes in extinction rate through time.
get_global_max_areaGet the maximum area
get_global_min_areaGet the minimum area
get_immig_rateCalculate immigration rate
get_trans_rateCalculate transition rate
integral_peakComputes integral of a very peaked function, modified from...
is_island_ontogeny_inputCheck if island_ontogeny is correct after user input
island_areaFunction to describe changes in area through time.
island_area_vectorComputes island_area, but takes vector as argument (needed by...
islands_10reps_RAW1000 islands in RAW format simulated with the ML parameters...
islands_1type_1000reps1000 islands in DAISIE format simulated with the ML...
islands_2types_1000reps1000 islands in DAISIE format simulated with the ML...
is_sea_level_inputCheck if sea_level is correct after user input
is_simulation_outputsMeasures if the input is a valid collection of simulation...
Macaronesia_datalistColonization and branching times of terrestrial avifaunal...
NewZealand_birds_datalistColonization and branching times of New Zealand birds.
pipePipe operator
remove_empty_elementsRemove superfluous lines in empty simulations
rhoGamma distribution density parameterised with mean and...
sample_relaxed_rateSamples from distribution when parameter is relaxed
translate_island_ontogenyTranslate user-friendly ontogeny codes to numerics
translate_sea_levelTranslate user-friendly sea-level codes to numerics
update_max_ratesCalculates the maximum rates for a Gillespie simulation
update_ratesCalculates algorithm rates
DAISIE documentation built on Aug. 26, 2020, 5:12 p.m.