Man pages for abichat/zazou
Z-Scores As Ornstein-Uhlenbeck
| alcohol | Datasets |
| as_shiftconf | 'shiftconf' object |
| as_shiftpunct | 'shiftpunct' object |
| bic | Information criteria |
| calculate_Z | Score system |
| calculate_Z_column_with_best_lambda | Compute a column of the score system |
| calculate_Z_with_best_lambda | Compute the score system once lambda is chosen |
| check_selection | Check if a shiftpunct came from model selection |
| choose_best_lambda | Choose best lambda by cross-validation |
| compute_gradient_function | Compute gradient function |
| compute_objective_function | Compute objective function |
| confint_colwiseinverse | Desparsified lasso based on column-wise inverse matrix |
| confint_scoresystem | Desparsified lasso based on score system |
| correct_pvalues | Correct p-values |
| covariance_noise_matrix_scoresystem | Covariance noise matrix |
| covarianceOU_matrix | Covariance matrix |
| create_clusters | Create clusters |
| create_listopt_pms | Create a list from |
| df_confint_pvalue | Confidence interval and p-values for estimates |
| estimate_confint | Estimate confidence interval from scaled lasso. |
| estimate_shifts | Estimate shifts |
| estimate_tstar | Estimate threshold of rejection for t-scores |
| extract_models | Extract models computed during selection |
| extract_significant_leaves | Extract significant leafs |
| extract_significant_leaves.shiftconf | Extract significant leafs |
| extract_significant_leaves.shiftpunct | Extract significant leafs |
| fast_solve_colwiseinverse_col | Compute a column for the column-wise inverse. |
| find_feasible | Find a feasible solution for a set of linear constraints |
| fitch | Fitch parsimony score |
| force_ultrametric | Force a tree to be ultrametric |
| generate_gamma | Gamma |
| get_lambda_sequence | Vector of lambdas to test |
| incidence_matrix | Incidence matrix |
| inverse_sqrt | Inverse of the square root of a matrix |
| lambda_grid | Generate a logarithmic lambda grid |
| noise_factor_scoresystem | Noise factor |
| norm0 | Norm 0 |
| open_doc | Open documentation site of the package |
| p2z | Transform p-values to z-scores |
| plot_shifts | Plot shift amplitude and location on the tree |
| pull_pvalues | Pull p-values |
| pull_pvalues.shiftconf | Pull p-values |
| pull_pvalues.shiftpunct | Pull p-values |
| rescale_score_system | Rescale the score system |
| rmse_glmnet | Compute prediction errors |
| simu_zscores | Simulation of z-scores on branches |
| smooth_pvalues | Hierarchical correction of p-values |
| solve_colwiseinverse | Solve column-wise inverse |
| solve_scaled_lasso | Scaled lasso |
| solve_univariate | Solve unidirectional constrained problem |
| test_wilcoxon | Vectorized tests |
| tree_height | Tree height |
| update_beta_scoresystem | Update beta |
| update_confint | Update confidence interval |
| update_sigma | Update sigma in the scaled lasso algorithm |
| zazou-package | zazou: Z-Scores As Ornstein-Uhlenbeck |
