Protracted Birth-Death Model of Diversification

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Documentation for package ‘PBD’ version 1.6

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pbd_bootstrap Bootstrap analysis under protracted birth-death model of diversification
pbd_brts_density Node depth probbaility density for protracted birth-death model of diversification
pbd_durspec_cumdensity Cumulative density of duration of speciation under protracted birth-death model of diversification
pbd_durspec_density Probability density for duration of speciation under protracted birth-death model of diversification
pbd_durspec_mean Mean duration of speciation under protracted birth-death model of diversification
pbd_durspec_mean_impl Actual calculation of the mean duration of speciation (equations 19 and 20 of reference article) assuming all inputs are correct
pbd_durspec_mode mode of the duration of speciation under protracted birth-death model of diversification
pbd_durspec_moment Moments of duration of speciation under protracted birth-death model of diversification
pbd_durspec_quantile Quantiles of duration of speciation under protracted birth-death model of diversification
pbd_durspec_var Variance in duration of speciation under protracted birth-death model of diversification
pbd_loglik Loglikelihood for protracted birth-death model of diversification
pbd_LR Bootstrap likelihood ratio test of protracted birth-death model of diversification
pbd_mean_durspec Calculate the mean duration of speciation (equations 19 and 20 of reference article), non-vectorized
pbd_mean_durspecs Calculate the mean durations of speciation (equations 19 and 20 of reference article)
pbd_ML Maximization of loglikelihood under protracted birth-death model of diversification
pbd_numspec_mean Mean number of species under protracted birth-death model of diversification
pbd_numspec_median Median number of species under protracted birth-death model of diversification
pbd_numspec_quantile Number of species for a given quantile under protracted birth-death model of diversification
pbd_numspec_vec Mean number of good and incipient species under protracted birth-death model of diversification
pbd_numspec_vec2 Mean number of good species with n incipient species and of n orphaned incipient species under protracted birth-death model of diversification
pbd_sim Function to simulate the protracted speciation process
pbd_sim_checked Checked and safer version of PBD::pbd_sim
pbd_sim_cpp Function to simulate the approximate protracted speciation process