time.series: Create a Time Series Simulation Experiment

In a-kramer/SBtabVFGEN: Converts from SBtab to vf,mod,[sbml]

Create a Time Series Simulation Experiment

Description

Given the constituents of a time series simulation experiment, return a list that rgsl will understand as a simulation.

Usage

## S3 method for class 'series'
time(
  outputValues,
  outputTimes = as.double(1:dim(outputValues)[2]),
  errorValues = 0.05 * outputValues + 0.05 * max(outputValues),
  inputParameters = NULL,
  initialTime = as.double(min(outputTimes)),
  initialState,
  events = NA
)

Arguments

outputValues	(data.frame) measured data, to be replicated by the simulation
outputTimes	(vector) time values at which the outputValues were measured
errorValues	(data.frame) an estimate of the measurement noise, if available
inputParameters	(vector) a parameter vector that the model needs to operate (can be some default value to be changed later)
initialTime	t0 for the time series experiment: y(t0) = y0
initialState	(vector) initial values of the state variables, at t0

Details

The output of a real experiment can be a function of the state variables, not necessarily the state variable trajectories themselves. We assume that parameter estimation of some sort will happen.

If an estimate of the measurement error is not available, then –strictly speaking– the data is useless: the noise must be understood as unbounded. But, instead, we assume that the case is very complex and the user knows what to do about it. We automatically set the noise to 5 another 5 represents the absolute error:

tl;dr default_error = 5

The user should replace these values with something, or simply not use them, if the application goes beyond testing.

Value

list with these quantities as list items

a-kramer/SBtabVFGEN documentation built on Dec. 15, 2024, 1:52 a.m.