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#
# This file is part of the CNO software
#
# Copyright (c) 2011-2013 - EMBL-EBI
#
# File author(s): CNO developers (cno-dev@ebi.ac.uk)
#
# Distributed under the GPLv3 License.
# See accompanying file LICENSE.txt or copy at
# http://www.gnu.org/licenses/gpl-3.0.html
#
# CNO website: http://www.cellnopt.org
#
##############################################################################
#' @export
simulate <-function(cnolist,model,ode_parameters=NULL,
indices=NULL, adjMatrix=NULL, time=1, verbose=0, transfer_function=3,
reltol=1e-4, atol=1e-3, maxStepSize=Inf, maxNumSteps=100000,
maxErrTestsFails=50)
{
if (class(cnolist)=="CNOlist"){cnolist = compatCNOlist(cnolist)}
if(is.null(indices))
indices=indexFinder(cnolist,model);
if(is.null(adjMatrix))
adjMatrix=incidence2Adjacency(model);
if(is.null(ode_parameters))
ode_parameters=createLBodeContPars(model);
timeSignals=NULL;
sim_data=getLBodeDataSim(cnolist,model,
ode_parameters,indices,timeSignals,time,verbose,
transfer_function,reltol,atol,maxStepSize,maxNumSteps,
maxErrTestsFails);
return(sim_data)
}
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