| pauwels2014-package | Reproduce numerical experiments |
| active_design | Simulates the active design process. |
| add_infinitesimal | Finite difference function |
| add_noise | Noise generative process for the simulations |
| armijo | Performs armijo line searcc |
| BFGS_special | An implementation of BFGS method for posterior maximization. |
| compute_gradient | Finite difference function |
| compute_gradient_coordinate | Finite difference function |
| compute_mean_risks | Compute an average risk as a function of credit spent |
| dmvnorm | Gaussian multivariate density |
| dream6_design | Simulates the active design process using the comparison criterion (see article for details). |
| estimate_risk_dream6 | Expected risk estimation (comparison with litterature). |
| estimate_risk_out_all | Expected risk estimation. |
| eval_kn_log_like | Evaluates the likelihood of a parameter value |
| eval_log_like_knobj | Posterior function. |
| experiment_list1 | Molecular perturbations. |
| exps | List of possible experiments |
| generate_our_knowledge | Initialize a knowledge list. |
| generate_sample | An implementation of the Metropolis Hasting algorithm |
| knobjs | Knowledge lists |
| log_likelihood | User defined likelihood function. |
| log_normalize | Normalize in log space |
| log_prior | User defined log prior |
| observables | Observable quantities of the model |
| pauwels2014 | Reproduce numerical experiments |
| proj_grad | Least square on the positive orthant |
| random_design | Simulates a randim design process. |
| read_knobjs | Summarizes pre-computed results. |
| reverse_params | Transform log space parameters back to the original space |
| risk_theta_fun | Risk function |
| risk_theta_vect | Expected risk based on a posterior sample |
| sample_function | Generates posterior samples |
| sample_function_multi_mod_weight | Sample function visiting multiple modes of the posterior |
| sample_function_single_mod | Sample function visiting a single mode of the posterior. |
| simulate_experiment | Simulates the dynamics of a molecular perturbation |
| simulate_experiment_no_transform | Link to the ode solver. |
| transform_params | User defined parameter transformation function. |