| ancestral_reconstruction_by_ML |
Source code
|
| antibiotic_resistance |
Man page
|
| assign_high_confidence_to_transition_edges |
Source code
|
| assign_pheno_type |
Source code
|
| blank_plot |
Source code
|
| build_better_reconstruction |
Source code
|
| build_gene_anc_recon_and_conf_from_snp_post_ar |
Source code
|
| build_gene_genotype_from_snps_post_ar |
Source code
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| build_gene_genotype_from_snps_pre_ar |
Source code
|
| build_gene_trans_from_snp_trans_post_ar |
Source code
|
| calc_raw_diff |
Source code
|
| calc_sig |
Source code
|
| calculate_continuous_convergence |
Source code
|
| calculate_d |
Source code
|
| calculate_lambda |
Source code
|
| calculate_permutation_based_p_value |
Source code
|
| calculate_phenotype_change_on_edge |
Source code
|
| calculate_phyc_convergence |
Source code
|
| calculate_synchronous_convergence |
Source code
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| check_anc_rec_compatible |
Source code
|
| check_class |
Source code
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| check_convergence_possible |
Source code
|
| check_dimensions |
Source code
|
| check_equal |
Source code
|
| check_file_exists |
Source code
|
| check_for_NA_and_inf |
Source code
|
| check_for_root_and_bootstrap |
Source code
|
| check_if_binary_matrix |
Source code
|
| check_if_binary_vector |
Source code
|
| check_if_binary_vector_numeric |
Source code
|
| check_if_dir_exists |
Source code
|
| check_if_g_mat_can_be_plotted |
Source code
|
| check_if_permutation_num_valid |
Source code
|
| check_if_vector |
Source code
|
| check_input_format |
Source code
|
| check_is_number |
Source code
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| check_is_string |
Source code
|
| check_node_is_in_tree |
Source code
|
| check_num_between_0_and_1 |
Source code
|
| check_rownames |
Source code
|
| check_str_is_discrete_or_continuous |
Source code
|
| check_str_is_test_name |
Source code
|
| check_tree_is_valid |
Source code
|
| continuous_ancestral_reconstruction |
Source code
|
| continuous_get_recon_confidence |
Source code
|
| continuous_permutation |
Source code
|
| convert_matrix_to_vector |
Source code
|
| convert_to_edge_mat |
Source code
|
| convert_trait_vec_to_df |
Source code
|
| count_empirical_both_present |
Source code
|
| count_empirical_only_geno_present |
Source code
|
| count_hits_on_edges |
Source code
|
| create_contingency_table |
Source code
|
| discrete_ancestral_reconstruction |
Source code
|
| discrete_calculate_pvals |
Source code
|
| discrete_get_recon_confidence |
Source code
|
| discrete_permutation |
Source code
|
| discretize_conf_with_cutoff |
Source code
|
| format_tree |
Source code
|
| get_bootstrap_confidence |
Source code
|
| get_dropped_genotypes |
Source code
|
| get_sig_hit_and_mult_test_corr |
Source code
|
| group_genotypes_post_ar |
Source code
|
| growth |
Man page
|
| hist_abs_hi_conf_delta_pheno |
Source code
|
| hogwash |
Man page
Source code
|
| identify_short_edges |
Source code
|
| identify_transition_edges |
Source code
|
| internal_report_phylogenetic_signal |
Source code
|
| is_this_class |
Source code
|
| is_tip |
Source code
|
| keep_two_plus_hi_conf_tran_ed |
Source code
|
| make_manhattan_plot |
Source code
|
| match_order_to_tree_tips |
Source code
|
| plot_continuous_phenotype |
Source code
|
| plot_phyc_results |
Source code
|
| plot_tr_w_color_edges |
Source code
|
| prep_geno_trans_for_phyc |
Source code
|
| prepare_ancestral_reconstructions |
Source code
|
| prepare_genotype |
Source code
|
| prepare_grouped_genotype_post_ar |
Source code
|
| prepare_grouped_genotype_pre_ar |
Source code
|
| prepare_high_confidence_objects |
Source code
|
| prepare_phenotype |
Source code
|
| prepare_ungrouped_genotype |
Source code
|
| remove_rare_geno |
Source code
|
| remove_rare_or_common_geno |
Source code
|
| reorder_tip_and_node_to_edge |
Source code
|
| report_d |
Source code
|
| report_lambda |
Source code
|
| report_num_high_confidence_trans_edge |
Source code
|
| report_phylogenetic_signal |
Man page
Source code
|
| run_continuous |
Source code
|
| run_phyc |
Source code
|
| run_synchronous |
Source code
|
| save_continuous |
Source code
|
| save_phyc |
Source code
|
| save_results_as_r_object |
Source code
|
| save_synchronous |
Source code
|
| select_test_type |
Source code
|
| snp_gene_key |
Man page
|
| snp_genotype |
Man page
|
| tree |
Man page
|
