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library(deSolve)
# parameter des models
N = 10^0.31
parameters = 10^c("k1"=0.31, "k2"=-1, "k3"=-0.49, "k4"= 0.42, "s1"=-0.21, "s2"=-0.34)
x0 = c(N, 0, 0, 0)+0.00001
inputData <- read.table('http://jeti.uni-freiburg.de/PNAS_Swameye_Data/DATA1_hall_inp')#csv
#inputData <- read.table('../data/DATA1_hall_inp.txt')#csv
inputData[nrow(inputData),2] <- 0.009
colnames(inputData) <- c('t','u')
measure <- read.table('http://jeti.uni-freiburg.de/PNAS_Swameye_Data/DATA1_hall')#csv
#measure <- read.table('../data/DATA1_hall.txt')#csv
colnames(measure) <- c("time","STAT5p_cyt" ,"sd_STAT5p_cyt","STAT5ptot_cyt","sd_STAT5ptot_cyt")
sd <- cbind(measure['time'],measure['sd_STAT5p_cyt'],measure['sd_STAT5ptot_cyt'])
# uncertainty per timepoint and endpoint
y <- cbind(measure['time'],
((measure['STAT5ptot_cyt']/parameters['s2'])-(measure['STAT5p_cyt']/parameters['s1'])),
measure['STAT5p_cyt'],
measure['STAT5ptot_cyt'],
(x0[1]-(measure['STAT5ptot_cyt']/parameters['s2']))/2/(1400/450)
)
y[y<0] <- 0
colnames(y) <- c("time", "STAT5" ,"STAT5p_cyt","STAT5ptot_cyt","STAT5_n")
modelJakStat <- function(t, x, parameters, input) {
with (as.list(parameters),{
k1 = parameters[1]
k2 = parameters[2]
k3 = parameters[3]
u <- input$u(t)
dx1 = -k1 * x[1] * u
dx2 = k1 * x[1] * u - k2 * x[2]^2
dx3 = -k3*x[3] + 0.5*k2*x[2]*x[2]
dx4 = k3 * x[3]
list(c(dx1 ,dx2 ,dx3 ,dx4 ))
})
}
objectiveJakStat<- function(x,parameter=c(0,0)) {
y1 = x[,1]
y2 = parameter[5] * (x[,2] + 2 * x[,3])
y3 = parameter[6] * (x[,1] + x[,2] + 2 * x[,3])
y4 = x[,4]
return(cbind(y1,y2,y3,y4))
}
JakStatModel <- odeModel(func = modelJakStat, parms = parameters, input = inputData, times=c(0,60),
measFunc = objectiveJakStat, y = x0, meas = y, sd = sd,custom=TRUE)
A <- BDEN(odeModel = JakStatModel,
lambda = .0001,
beta_init = c(1,1,1,0.1),
numbertrialsstep = 15,
numbertrialseps = 1000,
numbertrialinner = 25,
printstatesignore = c(1,4))
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