Package index • treepplr

All functions

tp_compile(): Compile a TreePPL model and create inference machinery
tp_compile_options(): Options that can be passed to TreePPL compiler
tp_data(): Import data for TreePPL program
tp_expected_input(): List expected input variables for a model
tp_json_to_phylo(): Convert TreePPL multi-line JSON to R phylo/multiPhylo object with associated weights
tp_list(): Create a flat list
tp_map_tree(): Find the Maximum A Posteriori (MAP) Tree from weighted samples
tp_mcmc_convergence(): Check for convergence across multiple MCMC runs.
tp_model(): Import a TreePPL model
tp_model_library(): Model names supported by treepplr
tp_parse_host_rep(): Parse TreePPL json output for host repertoire model
tp_parse_mcmc(): Parse simple TreePPL json MCMC output
tp_parse_smc(): Parse simple TreePPL json SMC output
tp_phylo_to_tpjson(): Convert phylo obj to TreePPL tree
tp_phylo_to_tppl_tree(): Convert phylo to a tppl_tree
tp_run(): Run a TreePPL program
tp_run_options(): Options that can be passed to a TreePPL program
tp_smc_convergence(): Check for convergence across multiple SMC sweeps.
tp_tempdir(): Temporary directory for running treeppl
tp_treeppl_json(): Convert a tppl_tree to TreePPL json str
tp_write_data(): Write data to file
tp_write_model(): Write out a custom model to tp_tempdir()
tree_age_cumul(): Calculate age in a tppl_tree