Package index
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add_tip_states() - Add tip states to a phylogenetic tree
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check_tree_compatibility() - Check if phylogenetic tree is compatible with
saasi -
demo_metadata - SAASI demonstration: tree metadata
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demo_pars - SAASI demonstration: birth-death-sampling process parameters
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demo_Q - SAASI demonstration: transition rate matrix
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demo_tree - SAASI demonstration: timed phylogenetic tree
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demo_tree_prepared - SAASI demonstration: pre-prepared tree
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drop_tips_by_state() - Drop tips from a phylogenetic tree by their state values
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estimate_bds_parameters() - Estimate rate parameters of a birth-death-sampling process
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estimate_transition_rates() - Estimate the transition rate matrix of the discrete trait process
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plot_saasi() - Plot a phylogenetic tree with SAASI tip annotations
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prepare_tree_for_saasi() - Reformat a phylogenetic tree to be compatible with
saasi -
saasi() - Sampling-Aware Ancestral State Inference
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sim_bds_tree() - Simulate a phylogenetic tree from a birth-death-sampling process