geese 0.0-9000
  • Reference

    Reference

    All functions

    new_flock() add_geese()

    Flock of GEESE

    new_geese()

    GEne Evolutionary model using SufficiEncy (GEESE)

    init_model() nterms() nnodes() ntrees() nleafs() likelihood() get_probabilities() get_sequence() set_seed() sim_geese() observed_counts() print_observed_counts() support_size() parse_polytomies() nfuns() names(<geese>) predict_geese() predict_flock() predict_geese_simulate() names(<flock>) print(<geese>) print_nodes() print(<flock>)

    Common functions for geese and flock.

    rule_limit_changes() term_gains() term_loss() term_cogain() term_neofun() term_subfun() term_maxfuns() term_overall_changes() term_overall_gains() term_overall_loss() term_kgains() term_neofun_a2b() term_genes_changing() term_prop_genes_changing() term_coopt() term_k_genes_changing() term_less_than_p_prop_genes_changing() term_pairwise_preserving() term_gains_from_0() term_overall_gains_from_0() term_pairwise_first_gain() term_preserve_pseudogene() term_pairwise_overall_change() term_pairwise_neofun_singlefun()

    Evolutionary terms

    geese_mcmc()

    MCMC for geese

    geese_mle()

    MLE for geese

    get_support()

    Returns the support of the model

    transition_prob() conditional_prob()

    Compute the transition probability

    Contents

    Developed by George Vega Yon, National Cancer Institute (NCI).

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