pauwels2014 (version 1.0)

observables: Observable quantities of the model

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]