# Bayesian Experimental Design for Systems Biology.

## Documentation for package ‘pauwels2014’ version 1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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.