R/defaultParametersSSm.R

In CNORode: ODE add-on to CellNOptR

#
#  This file is part of the CNO software
#
#  Copyright (c) 2011-2013 - 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
defaultParametersSSm <-
function(){

    params = list()
    params$maxeval=Inf
    params$maxtime=100
    params$ndiverse=NULL
    params$dim_refset=NULL
    params$local_solver=NULL
	  params$verbose = 0
    params$transfer_function = 3
    params$reltol = 1e-04
    params$atol = 0.001
	  params$maxStepSize = Inf
    params$maxNumSteps = 1e+05
    params$maxErrTestsFails = 50
    params$nan_fac = 1
    params$time = 1 
    
    # added for Eduati et al. 2017 paper (with default parameters should be same as original CNORode)
    params$lambda_tau=0
    params$lambda_k=0
    params$bootstrap=F
    params$SSpenalty_fac=0
    params$SScontrolPenalty_fac=0
    params$boot_seed=sample(1:10000,1)

    return(params)
}