Nothing
## ---- eval = FALSE------------------------------------------------------------
# library(seeds)
#
# # usb network example
# uvbParameter = c( ks1=0.23,
# ks2=4.0526,
# kdr1=0.1,
# kdr2=0.2118,
# k1=0.0043,
# k2=161.62,
# ka1=0.0372,
# ka2=0.0611,
# ka3=4.7207,
# kd1=94.3524,
# kd2=50.6973,
# kd3=0.5508,
# ks3=0.4397,
# kdr3=1.246,
# uv=1,
# ka4=10.1285,
# kd4=1.1999,
# n1=3,
# n2=2,
# n3=3.5,
# kdr3a=0.9735,
# kdr3b=0.406,
# ksr=0.7537,
# fhy3_s=5)
# # initial state
# x0 = c(0.2,10,2,0,0,20,0,0,0,4.2,0.25,20,0)
#
# # model ode
# uvbModel <- function(t,x,parameters) {
# with (as.list(parameters),{
#
# dx1 = ((-2) * ((ka1 * (x[1]^2) * (x[4]^2)) - (kd1 * x[5])) +
# (-2) * ((ka2 * (x[1]^2) * x[2]) - (kd2 * x[3])) +
# ((ks1 *((1) + (uv * n3 * (x[11] + fhy3_s)))) -
# (kdr1 * ((1) + (n1 * uv)) * x[1])))
# dx2 = ((-1) * ((ka2*(x[1]^2) * x[2]) - (kd2 * x[3])) +
# (-1) * ((ka4 * x[2] * x[12]) - (kd4 * x[13])))
# dx3 = (((ka2 * (x[1]^2) * x[2]) - (kd2* x[3])))
# dx4 = ((-2) * (k1*(x[4]^2)) + (2) * (k2 * x[6]) +
# (-2) * ((ka1 * (x[1]^2)* (x[4]^2)) - (kd1 * x[5])) +
# (-1)* (ka3 * x[4] *x[7]))
# dx5 = (((ka1 * (x[1]^2) * (x[4]^2)) -(kd1 * x[5])))
# dx6 = ((-1) * (k2 * x[6]) + (k1 * (x[4]^2)) +(kd3 * (x[8]^2)))
# dx7 = ((-1) * (ka3 * x[4] * x[7]) + ((ks2 * ((1) + (uv * x[5]))) -
# (kdr2 * x[7])) + (2) * (kd3 * (x[8]^2)))
# dx8 = ((-2) * (kd3 * x[8]^2) + (ka3 * x[4] * x[7]))
# dx9 = 0
# dx10 = 0
# dx11 = (((ks3 * ((1) + (n2 * uv))) -(kdr3 * (((x[3] / (kdr3a + x[3])) +
# (x[13] / (kdr3b + x[13]))) -(x[5] / (ksr + x[5]))) * x[11])))
# dx12 = ((-1) * (ka4 * x[2] * x[12]) + (kd4 * x[13]))
# dx13 =((ka4 * x[2] * x[12]) - (kd4 * x[13]))
#
# list(c(dx1,dx2,dx3,dx4,dx5,dx6,dx7,dx8,dx9,dx10,dx11,dx12,dx13))
# })
# }
#
# # measurement function
# uvbMeasure <- function(x) {
#
# y1 = 2*x[,5] + x[,4] + x[,8]
# y2 = 2*x[,5] + 2* x[,3] + x[,1]
# y3 = x[,6]
# y4 = x[,11]
# y5 = x[,4]
#
# return(cbind(y1,y2,y3,y4,y5))
# }
#
# # measurement data
# y <- uvbData[,1:6]
# # timesteps
# t <- uvbData$t
# # standard deviation of the measurements
# sd <- uvbData[,7:11]
#
# uvbModel <- odeModel(func = uvbModel, parms = uvbParameter, times = t,
# measFunc = uvbMeasure, y = x0, meas = y, sd = sd)
#
#
# res <- DEN(odeModel = uvbModel, alphaStep = 500, alpha2 = 0.0001, epsilon = 0.2, plotEstimates = FALSE)
#
#
## ---- eval = FALSE------------------------------------------------------------
#
# # plot the solution of the second iteration
# plot(res[[2]])
#
## ---- eval = FALSE------------------------------------------------------------
#
# library(seeds)
#
#
# uvbParameter = c( ks1=0.23,
# ks2=4.0526,
# kdr1=0.1,
# kdr2=0.2118,
# k1=0.0043,
# k2=161.62,
# ka1=0.0372,
# ka2=0.0611,
# ka3=4.7207,
# kd1=94.3524,
# kd2=50.6973,
# kd3=0.5508,
# ks3=0.4397,
# kdr3=1.246,
# uv=1,
# ka4=10.1285,
# kd4=1.1999,
# n1=3,
# n2=2,
# n3=3.5,
# kdr3a=0.9735,
# kdr3b=0.406,
# ksr=0.7537,
# fhy3_s=5)
#
# x0 = c(0.2,10,2,0,0,20,0,0,0,4.2,0.25,20,0)+0.00001
#
# uvbModel <- function(t,x,parameters) {
# with (as.list(parameters),{
#
# dx1 = ((-2) * ((ka1 * (x[1]^2) * (x[4]^2)) - (kd1 * x[5])) +
# (-2) * ((ka2 * (x[1]^2) * x[2]) - (kd2 * x[3])) +
# ((ks1 *((1) + (uv * n3 * (x[11] + fhy3_s)))) -
# (kdr1 * ((1) + (n1 * uv)) * x[1])))
# dx2 = ((-1) * ((ka2*(x[1]^2) * x[2]) - (kd2 * x[3])) +
# (-1) * ((ka4 * x[2] * x[12]) - (kd4 * x[13])))
# dx3 = (((ka2 * (x[1]^2) * x[2]) - (kd2* x[3])))
# dx4 = ((-2) * (k1*(x[4]^2)) + (2) * (k2 * x[6]) +
# (-2) * ((ka1 * (x[1]^2)* (x[4]^2)) - (kd1 * x[5])) +
# (-1)* (ka3 * x[4] *x[7]))
# dx5 = (((ka1 * (x[1]^2) * (x[4]^2)) -(kd1 * x[5])))
# dx6 = ((-1) * (k2 * x[6]) + (k1 * (x[4]^2)) +(kd3 * (x[8]^2)))
# dx7 = ((-1) * (ka3 * x[4] * x[7]) + ((ks2 * ((1) + (uv * x[5]))) -
# (kdr2 * x[7])) + (2) * (kd3 * (x[8]^2)))
# dx8 = ((-2) * (kd3 * x[8]^2) + (ka3 * x[4] * x[7]))
# dx9 = 0
# dx10 = 0
# dx11 = (((ks3 * ((1) + (n2 * uv))) -(kdr3 * (((x[3] / (kdr3a + x[3])) +
# (x[13] / (kdr3b + x[13]))) -(x[5] / (ksr + x[5]))) * x[11])))
# dx12 = ((-1) * (ka4 * x[2] * x[12]) + (kd4 * x[13]))
# dx13 =((ka4 * x[2] * x[12]) - (kd4 * x[13]))
#
# list(c(dx1,dx2,dx3,dx4,dx5,dx6,dx7,dx8,dx9,dx10,dx11,dx12,dx13))
# })
# }
#
#
# uvbMeasure <- function(y,parameter){
#
# y1 = 2*y[,5] + y[,4] + y[,8]
# y2 = 2*y[,5] + 2* y[,3] + y[,1]
# y3 = y[,6]
# y4 = y[,11]
# y5 = y[,4]
#
# return(cbind(y1,y2,y3,y4,y5))
# }
#
#
# testNN = rep(0,length(x0))
# testNN[1] = 1
#
#
# y <- uvbData[,1:6]
# t <- uvbData$t
# sd <- uvbData[,7:11]
#
#
# Model <- odeModel(func = uvbModel, parms = uvbParameter,times=c(0.025),
# measFunc = uvbMeasure, y = x0, meas = y, sd = sd,custom=TRUE)
#
#
#
# A <- BDEN(odeModel = Model,
# lambda = .001,
# beta_init = c(1,1,1,1,1),
# numbertrialsstep = 15,
# numbertrialseps = 2000,
# numbertrialinner = 10)
#
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