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... |
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-package | 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. |
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