Package index • insitu

All functions

age_correct_events(): Flags and filters in-situ events relative to island formation age
colonization_rate(): Estimates colonization rates events per lineage per unit time
compare_islands(): Statistical comparison of diversity decomposition metrics across multiple island systems
decompose_diversity(): Partition island species richness into in-situ, import, and export components
insitu_confidence(): Computes per-node probabilities of island presence for all internal nodes
insitu_power(): Power analysis for in-situ speciation event recovery
insitu_rate_by_island_age(): Computes island-age-corrected in-situ speciation rates
insitu_speciation_index(): In-situ speciation index per island
insitu_speciation_rate(): Estimates the rate of in-situ speciation events per lineage per unit time
map_insitu_events(): Applies decision rules to reconstructed nodes to classify each speciation event as in-situ, colonization, or ambiguous
match_island_phylo(): Imports and validates dated phylogenies with associated island occurrence data
plot_classified_phylo(): Dated phylogeny with branches and nodes colored by in-situ vs. colonization classification
plot_diversity_decomposition(): Stacked bar chart of in-situ, import, and export diversity per island
prep_phylo(): Prepares a phylogeny for use in the insitu pipeline
run_geo_asr(): Runs geographic state ASR (discrete: island; mainland?)
simmap_insitu(): Uses stochastic character mapping to propagate ASR uncertainty through speciation classifications. Posterior distribution of in-situ event counts
simulate_island(): Simulates island assemblages under known colonization, speciation, and extinction parameters