observables: Observable quantities of the model

In pauwels2014: Bayesian Experimental Design for Systems Biology.

Description

A list of quantities that can be observed. Each entry describes the quantity to observe and its time resolution as well as the cost of the corresponding observation.

Usage

data(observables)

Format

A list with the follwing entries: "p6", "p7", "p8", "mrnaHigh", "mrnaLow". Each of those entries is a list with the following slots:

• name: (chr) name of the observable

• obs: (chr) the subset of kinetic variables to observe

• reso: (num) time points to observe

• cost: (nul) the cost of observing this quantity

Details

The complete description of the list is as follows

• "p6":

  • name: "p6"

  • obs: c("time", "p6")

  • reso: from 0 to 100 by steps of 0.5

  • cost: 400

• "p7":

  • name: "p7"

  • obs: c("time", "p7")

  • reso: from 0 to 100 by steps of 0.5

  • cost: 400

• "p8":

  • name: "p8"

  • obs: c("time", "p8")

  • reso: from 0 to 100 by steps of 0.5

  • cost: 400

• "mrnaHigh":

  • name: "mrnaHigh"

  • obs: c("time", "v6_mrna", "v7_mrna", "v8_mrna")

  • reso: from 0 to 100 by steps of 2

  • cost: 1000

• "mrnaLow":

  • name: "mrnaLow"

  • obs: c("time", "v6_mrna", "v7_mrna", "v8_mrna")

  • reso: from 0 to 100 by steps of 4

  • cost: 500

Examples

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

theta <- knobjActMult1$datas[[1]]$thetas[1,]
thetaT <- knobjActMult1$transform_params(theta)

temp <- simulate_experiment_no_transform(thetaT, 
	knobjActMult1$global_parameters$initial_conditions, knobjActMult1)

observable <- observables$mrnaLow
temp[temp[,1] %in% observable$reso, colnames(temp) %in% observable$obs]

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