Bayesian Experimental Design for Systems Biology.


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Documentation for package ‘pauwels2014’ version 1.0

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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.