Other packages > Find by keyword >

pirouette  

Create a Bayesian Posterior from a Phylogeny
View on CRAN: Click here


Download and install pirouette package within the R console
Install from CRAN:
install.packages("pirouette")

Install from Github:
library("remotes")
install_github("cran/pirouette")

Install by package version:
library("remotes")
install_version("pirouette", "1.6.9")



Attach the package and use:
library("pirouette")
Maintained by
Richel Bilderbeek
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2022-10-06
Latest Update: 2023-01-20
Description:
Theoretical biologists are interested in measuring the extent at which we can measure the truth. This package allows to create a Bayesian posterior from a phylogeny that depicts the true evolutionary relationships. The given and true phylogeny can than be compared to the posterior phylogenies. Rich
How to cite:
Richel Bilderbeek (2022). pirouette: Create a Bayesian Posterior from a Phylogeny. R package version 1.6.9, https://cran.r-project.org/web/packages/pirouette. Accessed 21 Dec. 2024.
Previous versions and publish date:
1.6.4 (2022-10-06 18:30), 1.6.5 (2022-10-18 09:20), 1.6.6 (2023-01-20 17:00), 1.6.7 (2023-09-27 12:10), 1.6.8 (2023-09-29 15:42), 1.6.9 (2023-10-07 09:20)
Other packages that cited pirouette R package
View pirouette citation profile
Other R packages that pirouette depends, imports, suggests or enhances
Functions, R codes and Examples using the pirouette R package
Some associated functions: check_alignment . check_alignment_params . check_alignment_params_names . check_beast2_installed . check_candidates_save_to_same_files . check_error_fun . check_error_measure_params . check_experiment . check_experiments . check_experiments_all_inference_models_are_unique . check_experiments_candidates_have_same_mcmcs . check_gen_and_cand_exps_save_to_different_files . check_inference_conditions . check_inference_model_type_names . check_inference_model_weights . check_init_pir_params . check_is_ns_beast2_pkg_installed . check_model_type . check_mutation_rate . check_pir_out . check_pir_out_errors_above_zero . check_pir_out_names . check_pir_params . check_pir_params_data_types . check_pir_params_names . check_pir_paramses . check_reconstructed_phylogeny . check_root_sequence . check_sim_tral_fun . check_sim_twal_fun . check_sim_twin_tree_fun . check_tree_and_model . check_tree_and_model_errors . check_tree_and_models . check_tree_type . check_tree_types . check_twin_phylogeny . check_twinning_params . check_twinning_params_names . collapse_tree_and_model . collect_pir_outs . combine_brts_and_topology . combine_models . complete_treelog_filename . convert_pir_out_to_long . convert_tree2brts . copy_true_alignment . count_n_mutations . create_alignment_params . create_all_bd_experiments . create_all_coal_experiments . create_all_experiments . create_bd_tree . create_blocked_dna . create_cand_experiment . create_copy_twtr_from_true_fun . create_error_measure_params . create_exemplary_dd_tree . create_exemplary_dd_tree_giappo . create_experiment . create_gen_experiment . create_inference_conditions . create_mono_nuc_dna . create_pir_params . create_sim_yule_twin_tree_fun . create_standard_mutation_rate . create_std_pir_params . create_std_pir_paramses . create_test_alignment_params . create_test_cand_experiment . create_test_experiment . create_test_gen_experiment . create_test_marg_liks . create_test_phylogeny . create_test_pir_params . create_test_pir_params_setup . create_test_pir_run_output . create_test_pir_run_output2 . create_tral_file . create_tree_and_model_errors_from_folder . create_tree_and_model_errors_from_folders . create_true_alignment . create_twal_file . create_twin_branching_times . create_twin_tree . create_twinning_params . create_yule_tree . default_params_doc . delete_beast2_state_files . errorses_to_data_frame . est_evidences . get_alignment_n_taxa . get_alignment_sequence_length . get_alignment_sequences . get_copy_tral_fun . get_experiment_filenames . get_experiments_filenames . get_gamma_error_fun . get_model_selections . get_model_type_names . get_nltt_error_fun . get_pir_params_filenames . get_pir_plot_fill_colors . get_pir_plot_line_colors . get_pir_plot_theme . get_pir_plot_tree_and_model_descriptions . get_remove_hex_twin_fun . get_sim_bd_twin_tree_fun . get_sim_tral_with_lns_nsm_fun . get_sim_tral_with_std_nsm_fun . get_sim_tral_with_uns_nsm_fun . get_sim_twal_same_n_muts_fun . get_sim_twal_with_std_nsm_fun . get_sim_yule_twin_tree_fun . get_temp_errors_filename . get_temp_evidence_filename . get_temp_fasta_filename . get_temp_tree_filename . get_test_alignment . get_tree_and_model_descriptions . get_tree_and_model_values . get_tree_types . get_twin_methods . get_twin_models . has_candidate_experiments . has_twinning . init_experiment . init_pir_params . is_best_candidate . is_dna_seq . is_pir_params . phylo_to_errors . pipe . pir_plot . pir_plot_from_file . pir_plot_from_long . pir_plots . pir_rename . pir_rename_to_std . pir_run . pir_run_distribution . pir_run_true_tree . pir_run_twin_tree . pir_runs . pir_save . pir_to_pics . pir_to_tables . pirouette . plot_alignment_from_file . read_errors_csv . relevel_inference_model . relevel_tree_and_model . renum_rng_seeds . replicate_pir_params . rm_pir_param_files . select_candidate_evidences . select_experiments . shorten_experiments . shorten_pir_params . shorten_pir_paramses . sim_alignment_with_n_mutations . sim_alignment_with_std_nsm . sim_alignment_with_std_nsm_from_params . sim_bd_twin_tree . sim_tral_with_lns_nsm . sim_tral_with_std_nsm . sim_tral_with_uns_nsm . sim_true_alignment . sim_twal_with_lns_nsm . sim_twal_with_same_n_mutation . sim_twal_with_std_nsm . sim_twal_with_uns_nsm . sim_twin_alignment . sim_yule_twin_tree . to_evidence_filename . to_twin_filename . to_twin_filenames . will_measure_evidence . 
Some associated R codes: alignment_params_to_posterior_trees.R . check_alignment.R . check_alignment_params.R . check_beast2_installed.R . check_error_fun.R . check_error_measure_params.R . check_experiment.R . check_experiments.R . check_experiments_all_inference_models_are_unique.R . check_experiments_candidates_have_same_beast2_files.R . check_experiments_candidates_have_same_mcmcs.R . check_gen_and_cand_save_to_different_files.R . check_inference_conditions.R . check_inference_model_type_names.R . check_inference_model_weights.R . check_init_pir_params.R . check_is_ns_beast2_pkg_installed.R . check_model_type.R . check_mutation_rate.R . check_pir_out.R . check_pir_out_errors_above_zero.R . check_pir_params.R . check_pir_paramses.R . check_reconstructed_phylogeny.R . check_root_sequence.R . check_sim_tral_fun.R . check_sim_twal_fun.R . check_sim_twin_tree_fun.R . check_tree_and_model.R . check_tree_and_model_errors.R . check_tree_and_models.R . check_tree_type.R . check_tree_types.R . check_twin_phylogeny.R . check_twinning_params.R . check_twinning_params_names.R . collapse_tree_and_model.R . collect_pir_outs.R . combine_brts_and_topology.R . combine_models.R . complete_treelog_filename.R . convert_pir_out_to_long.R . copy_true_alignment.R . count_n_mutations.R . create_alignment_params.R . create_all_bd_experiments.R . create_all_coal_experiments.R . create_all_experiments.R . create_blocked_dna.R . create_cand_experiment.R . create_copy_twin_tree_from_true_fun.R . create_error_measure_params.R . create_exemplary_dd_tree.R . create_exemplary_dd_tree_giappo.R . create_experiment.R . create_gen_experiment.R . create_generative_trees.R . create_inference_conditions.R . create_mono_nuc_dna.R . create_pir_params.R . create_rate_matrix.R . create_sim_yule_twin_tree_fun.R . create_standard_mutation_rate.R . create_std_pir_params.R . create_std_pir_paramses.R . create_test_cand_experiment.R . create_test_experiment.R . create_test_gen_experiment.R . create_test_marg_liks.R . create_test_phylogeny.R . create_test_pir_params_setup.R . create_test_pir_run_output.R . create_tral_file.R . create_tree_and_model_errors_from_folder.R . create_tree_and_model_errors_from_folders.R . create_true_alignment.R . create_twal_file.R . create_twin_branching_times.R . create_twin_tree.R . create_twinning_params.R . default_params_doc.R . delete_beast2_state_files.R . errorses_to_data_frame.R . est_evidences.R . get_alignment_n_taxa.R . get_alignment_sequence_length.R . get_alignment_sequences.R . get_copy_tral_fun.R . get_experiment_filenames.R . get_experiments_filenames.R . get_gamma_error_fun.R . get_model_selections.R . get_nltt_error_fun.R . get_pir_params_filenames.R . get_pir_plot_fill_colors.R . get_pir_plot_line_colors.R . get_pir_plot_theme.R . get_pir_plot_tree_and_model_descriptions.R . get_remove_hex_twin_fun.R . get_sim_bd_twin_tree_fun.R . get_sim_tral_with_lns_site_model_fun.R . get_sim_tral_with_std_nsm_fun.R . get_sim_tral_with_uns_site_model_fun.R . get_sim_twal_with_same_n_mutation_fun.R . get_sim_twal_with_std_nsm_fun.R . get_sim_yule_twin_tree_fun.R . get_temp_errors_filename.R . get_temp_evidence_filename.R . get_temp_fasta_filename.R . get_temp_tree_filename.R . get_test_alignment.R . get_tree_and_model_descriptions.R . get_tree_and_model_values.R . has_candidate_experiments.R . has_twinning.R . init_experiment.R . init_pir_params.R . is_best_candidate.R . is_dna_seq.R . is_pir_params.R . phylo_to_errors.R . pir_plot.R . pir_plot_from_file.R . pir_plot_from_long.R . pir_plots.R . pir_rename.R . pir_rename_to_std.R . pir_run.R . pir_run_distribution.R . pir_run_true_tree.R . pir_run_twin_tree.R . pir_runs.R . pir_save.R . pir_to_pics.R . pir_to_tables.R . pirouette.R . plot_alignment_from_file.R . read_errors_csv.R . relevel_inference_model.R . relevel_tree_and_model.R . renum_rng_seeds.R . replicate_pir_params.R . rm_pir_param_files.R . select_candidate_evidences.R . select_experiments.R . shorten_experiments.R . shorten_pir_params.R . shorten_pir_paramses.R . sim_alignment_with_n_mutations.R . sim_alignment_with_std_nsm.R . sim_alignment_with_std_nsm_from_params.R . sim_bd_twin_tree.R . sim_tral_with_lns_site_model.R . sim_tral_with_nsm.R . sim_tral_with_uns_site_model.R . sim_true_alignment.R . sim_twal_with_lns_site_model.R . sim_twal_with_nsm.R . sim_twal_with_same_n_mutation.R . sim_twal_with_uns_site_model.R . sim_twin_alignment.R . to_evidence_filename.R . to_twin_filename.R . to_twin_filenames.R . twin_to_yule_tree.R . utils-pipe.R . utils.R . will_measure_evidence.R .  Full pirouette package functions and examples
Downloads during the last 30 days
Get rewarded with contribution points by helping add
Reviews / comments / questions /suggestions ↴↴↴

Today's Hot Picks in Authors and Packages

condGEE  
Parameter Estimation in Conditional GEE for Recurrent Event Gap Times
Solves for the mean parameters, the variance parameter, and their asymptotic variance in a condition ...
Download / Learn more Package Citations See dependency  
SEIRfansy  
Extended Susceptible-Exposed-Infected-Recovery Model
Extended Susceptible-Exposed-Infected-Recovery Model for handling high false negative rate and symp ...
Download / Learn more Package Citations See dependency  
batteryreduction  
An R Package for Data Reduction by Battery Reduction
Battery reduction is a method used in data reduction. It uses Gram-Schmidt orthogonal rotations to f ...
Download / Learn more Package Citations See dependency  
helda  
Preprocess Data and Get Better Insights from Machine Learning Models
The main focus is on preprocessing and data visualization of machine learning models performances.So ...
Download / Learn more Package Citations See dependency  
r2resize  
In-Text Resize for Images, Tables and Fancy Resize Containers in 'shiny', 'rmarkdown' and 'quarto' Documents
Automatic resizing toolbar for containers, images and tables. Various resizable or expandable contai ...
Download / Learn more Package Citations See dependency  
CIFsmry  
Weighted summary of cumulative incidence functions
Estimate of cumulative incidence function in two samples. Provide weighted summary statistics based ...
Download / Learn more Package Citations See dependency  

23,394

R Packages

201,798

Dependencies

63,416

Author Associations

23,395

Publication Badges

© Copyright 2022 - present. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA