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

check_alignmentCheck if the alignment is of the right type
check_alignment_paramsChecks if the argument is a valid alignment parameters...
check_alignment_params_namesChecks if the list elements' names match that of a valid...
check_beast2_installedChecks if BEAST2 is installed
check_candidates_save_to_same_filesCheck if all experiments save to the same files
check_error_funCheck that the 'error_fun' is valid.
check_error_measure_paramsChecks if the argument is a valid error_measure parameters...
check_experimentChecks if the argument is a valid pirouette experiment.
check_experimentsChecks if the argument is a list of one or more pirouette...
check_experiments_all_inference_models_are_uniqueCheck if all experiments have unique inference models.
check_experiments_candidates_have_same_mcmcsCheck that the candidate experiments have a same MCMC
check_gen_and_cand_exps_save_to_different_filesCheck that generative and candidate experiments save to...
check_inference_conditionsChecks if inference conditions are valid as created by...
check_inference_model_type_namesCheck the model type names
check_inference_model_weightsCheck the one or more inference model's weights
check_init_pir_paramsCheck if the 'pir_params' is initialized
check_is_ns_beast2_pkg_installedChecks if the 'NS' BEAST2 package is installed.
check_model_typeChecks if model type is valid Will stop if not.
check_mutation_rateCheck if the mutation rate is valid
check_pir_outChecks if the argument is a valid pirouette parameter set.
check_pir_out_errors_above_zeroChecks that 'pir_out' errors all are more than zero
check_pir_out_namesChecks if the 'pir_out' has elements with the names needed.
check_pir_paramsChecks if the argument is a valid pirouette parameter set.
check_pir_params_data_typesChecks if the 'pir_params' elements are all of the right data...
check_pir_paramsesCheck if all elements in the list of 'pir_params' are valid.
check_pir_params_namesChecks if the 'pir_params' has all the named elements needed
check_reconstructed_phylogenyCheck if the phylogeny is a reconstructed phylogeny.
check_root_sequenceCheck if the root sequence is valid
check_sim_tral_funCheck if the function to create a true alignment with (from...
check_sim_twal_funCheck if the function to create a twin alignment with (from a...
check_sim_twin_tree_funCheck if the 'sim_twin_tree_fun' is valid
check_tree_and_modelCheck if the 'tree_and_model' is valid
check_tree_and_model_errorsCheck if the 'tree_and_model_errors' is valid.
check_tree_and_modelsCheck if the 'tree_and_model' is valid
check_tree_typeChecks if tree type is valid Will stop if not.
check_tree_typesChecks if the tree types are valid Will stop if not.
check_twinning_paramsChecks if the argument is a valid twinning parameters...
check_twinning_params_namesCheck that the 'twinning_params' has all the list elements'...
check_twin_phylogenyCheck if a twin phylogeny is a valid phylogeny
collapse_tree_and_modelInternal function
collect_pir_outsCollect the results of multiple pirouette runs
combine_brts_and_topologySubstitute branching times keeping the topology
combine_modelsCombine a combination of site models, clock models and tree...
complete_treelog_filenameComplete a treelog's filename
convert_pir_out_to_longConvert a 'pir_out' to its long form
convert_tree2brtsConvert a tree into branching times
copy_true_alignmentAdapter function to create a twin alignment by simply copying...
count_n_mutationsCount mutations
create_alignment_paramsCreate the parameters for the alignment simulation.
create_all_bd_experimentsCreate all pirouette experiments that have a tree prior that...
create_all_coal_experimentsCreate all pirouette experiments that have a tree prior that...
create_all_experimentsCreate all pirouette experiments.
create_bd_treeCreate a (constant-rate) birth-death (BD) tree
create_blocked_dnaCreate a 'blocked' DNA sequence, which is a sequence with...
create_cand_experimentCreate a valid testing pirouette candidate experiment.
create_copy_twtr_from_true_funCreate a function that can simulate the twin tree from the...
create_error_measure_paramsCreate the parameters to specify how the error between the...
create_exemplary_dd_treeCreate an exemplary diversity-dependent (DD) birth-death...
create_exemplary_dd_tree_giappoCreate an exemplary diversity-dependent (DD) birth-death...
create_experimentCreate a valid pirouette experiment.
create_gen_experimentCreate a valid testing pirouette generative experiment.
create_inference_conditionsCreate the inference conditions
create_mono_nuc_dnaCreate a 'blocked' DNA sequence, which is a sequence with...
create_pir_paramsCreate the parameters for pirouette
create_sim_yule_twin_tree_funCreate a partially evaluated function to to...
create_standard_mutation_rateCreate the parameters for the mutation rate
create_std_pir_paramsCreate a standard 'pir_params'
create_std_pir_paramsesCreate a number of standard 'pir_params'
create_test_alignment_paramsCreate testing parameters for the alignment simulation.
create_test_cand_experimentCreate a valid testing pirouette candidate experiment.
create_test_experimentCreate a valid testing pirouette experiment.
create_test_gen_experimentCreate a valid testing pirouette generative experiment.
create_test_marg_liksCreate a testing marginal likelihoods data frame.
create_test_phylogenyCreate a testing phylogeny with 3 taxa and a crown age of 3
create_test_pir_paramsCreate a set of testing parameters for pirouette
create_test_pir_params_setupCreate a 'pir_params' that follows a specific setup
create_test_pir_run_outputCreate the same output of pir_run to be used for testing
create_test_pir_run_output2Create the same output of pir_run to be used for testing, but...
create_tral_fileSimulates a DNA alignment and saves it to a FASTA file.
create_tree_and_model_errors_from_folderInternal function to create a 'tree_and_model_errors' from...
create_tree_and_model_errors_from_foldersInternal function to create a 'tree_and_model_errors' from...
create_true_alignmentCreate the true alignment from the true/given phylogeny.
create_twal_fileSimulates a twin DNA alignment and saves it to a FASTA file.
create_twin_branching_timesGenerate twin branching times given estimated lambda and mu...
create_twinning_paramsCreate the parameters for the twinning simulation
create_twin_treeCreate a twin tree
create_yule_treeCreate a Yule tree.
default_params_docThis function does nothing. It is intended to inherit is...
delete_beast2_state_filesDelete the BEAST2 state files, if present.
errorses_to_data_frameConvert the collect of errors to a data frame
est_evidencesEstimate the evidences
get_alignment_n_taxaGet the number of taxa of an alignment
get_alignment_sequence_lengthGet the sequence length of an alignment
get_alignment_sequencesGet the sequences from an alignment
get_copy_tral_funGet a function to 'simulate' a twin alignment by simply...
get_experiment_filenamesExtract the filenames from an experiment
get_experiments_filenamesExtract the filesnames in the experiments
get_gamma_error_funGet an error function that uses the difference in gamma...
get_model_selectionsGet the possible ways to select an inference model
get_model_type_namesGet the names of the model types
get_nltt_error_funGet an error function that uses the nLTT statistic
get_pir_params_filenamesExtract the filenames from a 'pir_params'
get_pir_plot_fill_colorsInternal function to get the fill colors for pir_plot
get_pir_plot_line_colorsInternal function to get the line colors for pir_plot
get_pir_plot_themeGet the pir_plot theme
get_pir_plot_tree_and_model_descriptionsInternal function to obtain the pir_plot legend labels
get_remove_hex_twin_funGet a function that removes the hex string from filenames.
get_sim_bd_twin_tree_funCreate a partially evaluated function to to sim_bd_twin_tree.
get_sim_tral_with_lns_nsm_funGet a partially evaluated function to simulate a true...
get_sim_tral_with_std_nsm_funGet a function to simulate the true alignment with, that uses...
get_sim_tral_with_uns_nsm_funGet a partially evaluated function to simulate a true...
get_sim_twal_same_n_muts_funof mutations as the true alignment has.
get_sim_twal_with_std_nsm_funGet a function to simulate a twin alignment which uses a...
get_sim_yule_twin_tree_funCreate a partially evaluated function to to...
get_temp_errors_filenameGet the name for a temporary file to store inference errors.
get_temp_evidence_filenameGet the name for a temporary file to store the evidences (aka...
get_temp_fasta_filenameGet the name for a temporary file to store an alignment in...
get_temp_tree_filenameGet the name for a temporary file to store a tree in Newick...
get_test_alignmentGet an alignment for testing.
get_tree_and_model_descriptionsInternal function to create a mapping from a 'tree_and_model'...
get_tree_and_model_valuesGet the valid 'tree_and_model' values
get_tree_typesGet the names of the tree types
get_twin_methodsTwin methods
get_twin_modelsTwin models
has_candidate_experimentsDetect if there is at least one candidate model amongst the...
has_twinningDetermine if these 'pir_params' use twinning
init_experimentInitialize the 'experiment'.
init_pir_paramsInitialize the 'pir_params'.
is_best_candidateIs the experiment the one with the most evidence?
is_dna_seqDetermine if the string is a lowercase DNA sequence of at...
is_pir_paramsDetermine if the 'pir_params' is valid.
phylo_to_errorsMeasure the error BEAST2 makes from a true phylogeny.
pipePipe operator
pirouettepirouette: A package to estimate the error BEAST2 makes in...
pir_plotPlot the error 'BEAST2' makes from a known phylogeny
pir_plot_from_filePlot the error BEAST2 make from the known phylogeny
pir_plot_from_longPlot the error 'BEAST2' makes from a known phylogeny from...
pir_plotsPlot the output of pir_runs.
pir_renameRename the filenames in a 'pir_params' using a rename...
pir_rename_to_stdRename the 'pir_params' filenames to follow a standard naming...
pir_runMeasure the error BEAST2 makes from a known phylogeny.
pir_run_distributionDo multiple pirouette runs off a distribition of phylogenies
pir_runsDo multiple pirouette runs
pir_run_true_treeMeasure the error BEAST2 makes from a phylogeny
pir_run_twin_treeMeasure the error BEAST2 makes from a phylogeny
pir_saveSave all output from pir_run
pir_to_picsCreate all pictures created by the pirouette pipeline
pir_to_tablesCreate all tables to checks pirouette pipeline
plot_alignment_from_filePlot an alignment stored as a file
read_errors_csvRead the errors from a '.csv' file
relevel_inference_modelInternal function
relevel_tree_and_modelInternal function
renum_rng_seedsRenumber the RNG seeds
replicate_pir_paramsReplicate pir_params assigning new names to each file
rm_pir_param_filesDeletes all files
select_candidate_evidencesSelect the evidences for candidate experiments
select_experimentsSelect the experiments to do a Bayesian inference with.
shorten_experimentsShorten the experiments' runtime
shorten_pir_paramsShorten the 'pir_params'
shorten_pir_paramsesShorten the list of 'pir_params'
sim_alignment_with_n_mutationsConverts a phylogeny to a random DNA alignment
sim_alignment_with_std_nsmCreate an alignment with a standard site model using a raw...
sim_alignment_with_std_nsm_from_paramsCreate an alignment with a standard site model
sim_bd_twin_treeSimulate a Birth-Death (BD) twin tree from the true phylogeny
sim_tral_with_lns_nsmCreate an alignment with the 'lns' site model
sim_tral_with_std_nsmAdapter function to simulate a twin alignment using a...
sim_tral_with_uns_nsmAdapter function to simulate an alignment with the...
sim_true_alignmentSimulate the true alignment from the true phylogeny
sim_twal_with_lns_nsmAdapter function to simulte the twin alignment using the...
sim_twal_with_same_n_mutationSimulate a twin alignment using a standard site model
sim_twal_with_std_nsmSimulate a twin alignment using a standard site model
sim_twal_with_uns_nsmAdapter function to simulate an alignment with the...
sim_twin_alignmentCreates a twin alignment.
sim_yule_twin_treeCreate a twin tree from a phylogeny using a Yule process
to_evidence_filenameConverts a filename to an evidence filename
to_twin_filenameConverts true tree filenames to twin tree filenames
to_twin_filenamesConvert multiple filenames to their twin equivalent
update_pirouetteUpdate all babette dependencies
will_measure_evidenceDetermine if there is an experiment in which the evidence...
richelbilderbeek/pirouette documentation built on Aug. 5, 2020, 8:39 a.m.