Man pages for richelbilderbeek/pirouette
Create a Bayesian Posterior From a Phylogeny

alignment_params_to_posterior_treesCreates a posterior of phylogenies from a known alignment.
bd_phylo_2_l_tableConvert bd phylo to L table
check_alignment_paramsChecks if the argument is a valid alignment parameters...
check_inference_paramCheck if the inference parameters are valid. Throws if these...
check_model_select_paramChecks if the argument is a valid model selection parameters...
check_model_select_paramsChecks if the argument is a valid list of one or more model...
combine_brts_and_topologySubstitute branching times keeping the topology
convert_tree2brtsConvert a tree into branching times
create_alignment_paramsCreate the parameters for the alignment simulation. The site...
create_bd_treeCreate an BD twin tree from an MBD tree and save it as a file
create_best_model_select_paramCreate model selection parameters for the model with the...
create_blocked_dnaCreate a 'blocked' DNA sequence, which is a sequence with...
create_gen_model_select_paramSelect the generative model to be used in inference
create_inference_paramCreates the parameters all BEAST2 runs share.
create_model_select_paramCreate model selection parameters.
create_mono_nuc_dnaCreate a 'blocked' DNA sequence, which is a sequence with...
create_pir_run_test_outputCreate the same output of pir_run to be used for testing
create_test_marg_liksCreate a testing marginal likelihoods data frame.
create_twin_treeCreate a twin tree
default_params_docThis function does nothing. It is intended to inherit is...
get_clock_modelsClock models
get_model_selectionsGet the possible ways to select an inference model
get_site_modelsSite models
is_dna_seqDetermine if the string is a lowercase DNA sequence of at...
phylo_to_errorsMeasure the error BEAST2 makes from a true phylogeny.
pir_plotPlot the error BEAST2 make from the known phylogeny
pir_runMeasure the error BEAST2 makes from a known phylogeny.
pir_run_check_inputsChecks the pir_run inputs.
select_inference_modelsSelect inference models.
sim_alignmentConverts a phylogeny to a random DNA alignment
sim_alignment_fileSimulates a DNA alignment and saves it to a FASTA file.
richelbilderbeek/pirouette documentation built on Jan. 15, 2019, 9:05 a.m.