knobjs: Knowledge lists

In pauwels2014: Bayesian Experimental Design for Systems Biology.

Description

A list of knwoledge list

Usage

data(knobjs)

Format

A list of lists that were generated using generate_our_knowledge function and updated using different strategy functions and sampling functions. The name of the object defines which strategy and which sampling function was used:

• Rand: random_design strategy

• Act: active_design strategy

• Dream6: dream6_design strategy

• Sing: sample_function_single_mod sampling function

• Mult: sample_function_multi_mod_weight sampling function

The integer at the end of the name is the random number generator seed used to perform the corresponding simulation.

Details

The update performed by the strategies consists in filling the experiments slot of knobj with the sequence experiments performed. See exps. The corresponding data is available in the datas slot. This slot is a list. Each element of this list is a list with the following entries

• manip: the molecular perturbation performed, an element of experiment_list1

• data: the associated noisy observations, based on the chosen observable, an element of observables

• thetas: a posterior sample generated by the corresponding sample_function.

• risks: the risk associated to all potential new experiments computed by estimate_risk_out_all

The knowledge lists updated using random_design strategy do not provide any risk information.

Examples

data(knobjs)
names(knobjs)

sapply(	
	1:length(knobjs),
	function(k){
		assign(names(knobjs)[k], knobjs[[k]], envir = .GlobalEnv)
	}
)
ls()

pauwels2014 documentation built on May 1, 2019, 6:29 p.m.