laboratory_scripts/model_analysis.R
In Thibaudpmx/QSPVP: Parameter Space Mapping algorithms to accelerate the creation of plausible Virtual Patients
# Administration ----------------------------------------------------------
model_RxODE <-RxODE({
d/dt(Admin) <- -ka * Admin
d/dt(Central) <- ka * Admin - ke * Central
})
parameters_default_values <- c(psi = 20) # paremeters value to be used by default (NA if you want to force providing value)
initial_cmt_values <- c(Central = 0) # initial compartment values. At least one, and every missing cmt name would be set to 0
times <- seq(0,100, 1) # times you want to see your observations
protocols <- list( unique = tibble(cmt = "Admin", time = 0, amt = 50))
# tribblecreator(model_RxODE)
domain <- tribble(~param, ~min, ~ref, ~max,
"ka", 0.01,0.1,1,
"ke", 0.01,0.1,1
)
find_relative(Central, protocol = "unique", model = model_RxODE, values = domain)
# homostastie ----------------------------------------------------------
model_RxODE <-RxODE({
IRM(0) <- kin/kout
d/dt(IRM) <- - kout * IRM + kin
d/dt(IRM2) <- kout * IRM - kout2 * IRM2
})
parameters_default_values <- c(psi = 20) # paremeters value to be used by default (NA if you want to force providing value)
initial_cmt_values <- c(Central = 0) # initial compartment values. At least one, and every missing cmt name would be set to 0
times <- seq(0,100, 1) # times you want to see your observations
protocols <- list( unique = tibble(cmt = "IRM", time = 0, amt = 0))
# tribblecreator(model_RxODE)
domain <- tribble(~param, ~min, ~ref, ~max,
"kout", 0.01,0.1,1,
"kout2", 0.01,0.1,1,
"kin", 0.01,0.1,1
)
find_relative(IRM, IRM2, protocol = "unique", model = model_RxODE, values = domain,time_simul = times)
find_relative(IRM, IRM2, protocol = "unique", model = model_RxODE, values = domain,time_simul = times, deepAnalysis = T)
# find_relative(Central, protocol = "unique", model = model_RxODE, values = domain,time_simul = c(0,seq(5000,10000,100)))
# inhib kin------------------------------------------------------
model_RxODE <-RxODE({
IRM(0) <- kin/kout
d/dt(Drug) <- - ke * Drug
d/dt(IRM) <- - kout * IRM + kin * ( 1 - Emax * Drug / (Drug + D50))
d/dt(IRM2) <- kout * IRM - kout2 * IRM2
})
parameters_default_values <- c(psi = 20) # paremeters value to be used by default (NA if you want to force providing value)
initial_cmt_values <- c(Central = 0) # initial compartment values. At least one, and every missing cmt name would be set to 0
times <- seq(0,200, 1) # times you want to see your observations
protocols <- list( unique = tibble(cmt = "Drug", time = 50, amt = 50))
# tribblecreator(model_RxODE)
domain <- tribble(~param, ~min, ~ref, ~max,
"kout", 0.01,0.1,1,
"kout2", 0.01,0.1,1,
"kin", 0.01,0.1,1,
"ke", 0.01,0.1,1,
"Emax", 0.1,0.5,1,
"D50", 1,10,30
)
find_relative(IRM, IRM2, protocol = "unique", model = model_RxODE, values = domain,time_simul = times)
# increase kout------------------------------------------------------
model_RxODE <-RxODE({
IRM(0) <- kin/kout
d/dt(Drug) <- - ke * Drug
d/dt(IRM) <- - kout * ( 1 + Emax * Drug / (Drug + D50)) * IRM + kin
d/dt(IRM2) <- kout * IRM - kout2 * IRM2
})
parameters_default_values <- c(psi = 20) # paremeters value to be used by default (NA if you want to force providing value)
initial_cmt_values <- c(Central = 0) # initial compartment values. At least one, and every missing cmt name would be set to 0
times <- seq(0,200, 1) # times you want to see your observations
protocols <- list( unique = tibble(cmt = "Drug", time = 50, amt = 50))
# tribblecreator(model_RxODE)
domain <- tribble(~param, ~min, ~ref, ~max,
"kout", 0.01,0.1,1,
"kout2", 0.01,0.1,1,
"kin", 0.01,0.1,1,
"ke", 0.01,0.1,1,
"Emax", 0.1,0.5,1,
"D50", 1,10,30
)
find_relative(IRM, IRM2, protocol = "unique", model = model_RxODE, values = domain,time_simul = times)
# increase kin------------------------------------------------------
model_RxODE <-RxODE({
IRM(0) <- kin/kout
d/dt(Drug) <- - ke * Drug
d/dt(IRM) <- - kout * IRM + kin * ( 1 + Emax * Drug / (Drug + D50))
d/dt(IRM2) <- kout * IRM - kout2 * IRM2
})
parameters_default_values <- c(psi = 20) # paremeters value to be used by default (NA if you want to force providing value)
initial_cmt_values <- c(Central = 0) # initial compartment values. At least one, and every missing cmt name would be set to 0
times <- seq(0,200, 1) # times you want to see your observations
protocols <- list( unique = tibble(cmt = "Drug", time = 50, amt = 50))
# tribblecreator(model_RxODE)
domain <- tribble(~param, ~min, ~ref, ~max,
"kout", 0.01,0.1,1,
"kout2", 0.01,0.1,1,
"kin", 0.01,0.1,1,
"ke", 0.01,0.1,1,
"Emax", 0.1,0.5,1,
"D50", 1,10,30
)
find_relative(IRM, IRM2, protocol = "unique", model = model_RxODE, values = domain,time_simul = times)
# distribution ------------------------------------------------------------
##Pk.2comp.ke.k12.k21.difEq
#k12 <- Q/V1
#k21 <- Q/V2
#ke <- Cl/V1
model_RxODE <-RxODE({
d/dt(Central) <- k21 * Periph - k12 * Central - ke * Central
d/dt(Periph) <- - k21 * Periph + k12 * Central
Conc <- Central / V1
})
parameters_default_values <- c(psi = 20) # paremeters value to be used by default (NA if you want to force providing value)
initial_cmt_values <- c(Central = 0) # initial compartment values. At least one, and every missing cmt name would be set to 0
times <- seq(0,100, 1) # times you want to see your observations
protocols <- list( unique = tibble(cmt = "Central", time = 0, amt = 50))
# tribblecreator(model_RxODE)
domain <- tribble(~param, ~min, ~ref, ~max,
"k21", 0.01,0.1,1,
"k12", 0.01,0.1,1,
"ke", 0.01,0.1,1,
"V1", 1,5, 10)
find_relative(Conc, protocol = "unique", model = model_RxODE, values = domain)
# Distribution 2 ----------------------------------------------------------
##Pk.2comp.ke.k12.k21.difEq
#ke <- Cl/V1
model_RxODE <-RxODE({
k12 <- Q/V1
k21 <- Q/V2
d/dt(Central) <- k21 * Periph - k12 * Central - ke * Central
d/dt(Periph) <- - k21 * Periph + k12 * Central
Conc <- Central / V1
})
parameters_default_values <- c(psi = 20) # paremeters value to be used by default (NA if you want to force providing value)
initial_cmt_values <- c(Central = 0) # initial compartment values. At least one, and every missing cmt name would be set to 0
times <- seq(0,100, 1) # times you want to see your observations
protocols <- list( unique = tibble(cmt = "Central", time = 0, amt = 50))
# tribblecreator(model_RxODE)
domain <- tribble(~param, ~min, ~ref, ~max,
"V2", 1,5, 10,
"Q", 0.01,0.1,1,
"ke", 0.01,0.1,1,
"V1", 1,5, 10)
find_relative(Conc, protocol = "unique", model = model_RxODE, values = domain)
# Distribution 3 ----------------------------------------------------------
##Pk.2comp.ke.k12.k21.difEq
#ke <- Cl/V1
model_RxODE <-RxODE({
k21 <- ratio / k12
d/dt(Central) <- k21 * Periph - k12 * Central - ke * Central
d/dt(Periph) <- - k21 * Periph + k12 * Central
Conc <- Central / V1
})
parameters_default_values <- c(psi = 20) # paremeters value to be used by default (NA if you want to force providing value)
initial_cmt_values <- c(Central = 0) # initial compartment values. At least one, and every missing cmt name would be set to 0
times <- seq(0,100, 1) # times you want to see your observations
protocols <- list( unique = tibble(cmt = "Central", time = 0, amt = 50))
# tribblecreator(model_RxODE)
domain <- tribble(~param, ~min, ~ref, ~max,
"ratio", 0.01,1,10,
"k12", 0.01,0.1,1,
"ke", 0.01,0.1,1,
"V1", 1,5, 10)
find_relative(Conc, protocol = "unique", model = model_RxODE, values = domain)
# Distribution 4 ----------------------------------------------------------
##Pk.2comp.ke.k12.k21.difEq
#ke <- Cl/V1
model_RxODE <-RxODE({
k21 <- ratio / k12
d/dt(Central) <- k21 * Periph - k12 * Central - ke * Central
d/dt(Periph) <- - k21 * Periph + k12 * Central
Conc <- Central / V1
})
parameters_default_values <- c(psi = 20) # paremeters value to be used by default (NA if you want to force providing value)
initial_cmt_values <- c(Central = 0) # initial compartment values. At least one, and every missing cmt name would be set to 0
times <- seq(0,100, 1) # times you want to see your observations
protocols <- list( unique = tibble(cmt = "Central", time = 0, amt = 50))
# tribblecreator(model_RxODE)
domain <- tribble(~param, ~min, ~ref, ~max,
"ratio", 0.01,1,10,
"k12", 0.01,0.1,1,
"ke", 0.01,0.1,1,
"V1", 1,5, 10)
find_relative(Conc, protocol = "unique", model = model_RxODE, values = domain)
# dos elim ------------------------------------------------------------
##Pk.2comp.ke.k12.k21.difEq
#k12 <- Q/V1
#k21 <- Q/V2
#ke <- Cl/V1
model_RxODE <-RxODE({
d/dt(Central) <- k21 * Periph - k12 * Central - ke * Central
d/dt(Periph) <- - k21 * Periph + k12 * Central - ke2 * Periph
Conc <- Central / V1
})
parameters_default_values <- c(psi = 20) # paremeters value to be used by default (NA if you want to force providing value)
initial_cmt_values <- c(Central = 0) # initial compartment values. At least one, and every missing cmt name would be set to 0
times <- seq(0,100, 2) # times you want to see your observations
protocols <- list( unique = tibble(cmt = "Central", time = 0, amt = 50))
# tribblecreator(model_RxODE)
domain <- tribble(~param, ~min, ~ref, ~max,
"k21", 0.01,0.1,1,
"k12", 0.01,0.1,1,
"ke", 0.01,0.11,1,
"ke2", 0.01,0.1,1,
"V1", 1,5, 10)
find_relative(Conc, protocol = "unique", model = model_RxODE, values = domain)
find_relative(Conc, protocol = "unique", model = model_RxODE, values = domain, deepAnalysis = T)
#ke > ke2 -> k12 / k21 non utilisable
domain <- tribble(~param, ~min, ~ref, ~max,
"k21", 0.01,0.1,1,
"k12", 0.01,0.1,1,
"ke", 0.01,0.1,1,
"ke2", 0,0.001,0.1,
"V1", 1,5, 10)
find_relative(Conc, protocol = "unique", model = model_RxODE, values = domain)
#ke2 > ke -> k12 / k21 utilisable
domain <- tribble(~param, ~min, ~ref, ~max,
"k21", 0.01,0.1,1,
"k12", 0.01,0.1,1,
"ke", 0.01,0.1,1,
"ke2", 0.01,1,10,
"V1", 1,5, 10)
find_relative(Conc, protocol = "unique", model = model_RxODE, values = domain)
#ke2 = ke -> k12 / k21 utilisable
domain <- tribble(~param, ~min, ~ref, ~max,
"k21", 0.01,0.1,1,
"k12", 0.01,0.1,1,
"ke", 0.01,0.1,1,
"ke2", 0.01,0.1,1,
"V1", 1,5, 10)
find_relative(Conc, protocol = "unique", model = model_RxODE, values = domain,time_simul = seq(0,500,1))
# Michaelis elimination ---------------------------------------------------
model_RxODE <-RxODE({
d/dt(Central) <- - Central * Vmax / (Central + km)
})
parameters_default_values <- c(psi = 20) # paremeters value to be used by default (NA if you want to force providing value)
initial_cmt_values <- c(Central = 0) # initial compartment values. At least one, and every missing cmt name would be set to 0
times <- seq(0,52, 1) # times you want to see your observations
protocols <- list( unique = tibble(cmt = "Central", time = 0, amt = 50))
# tribblecreator(model_RxODE)
domain <- tribble(~param, ~min, ~ref, ~max,
"Vmax", 0.1,1,10 ,
"km", 1,5,25)
find_relative(Central, protocol = "unique", model = model_RxODE, values = domain)
# TMDD --------------------------------------------------------------------
model_RxODE <- RxODE({
R(0) <- ksyn/kdeg
d/dt(L) <- -ke * L - kon * L * R + koff * P - k12 * L + k21 * A
d/dt(R) <- ksyn - kdeg * R - kon * L * R + koff * P
d/dt(P) <- kon * L * R - koff * P - kint * P
d/dt(A) <- k12 * L - k21 * A
Conc <- L/Vd
LP <- (L + P) / Vd
})
parameters_default_values <- c(psi = 20) # paremeters value to be used by default (NA if you want to force providing value)
initial_cmt_values <- c(R = 0) # initial compartment values. At least one, and every missing cmt name would be set to 0
times <- seq(0,200, 1) # times you want to see your observations
protocols <- list( unique = tibble(cmt = "L", time = 0, amt = 50))
# tribblecreator(model_RxODE)
#kint > ke
domain <- domain <- tribble(~param, ~min, ~ref, ~max,
"ke", 0.01,0.1,1,
"kon", 0.01,0.1,1,
"koff", 0.01,0.1,1 ,
"k12", 0.01,0.1,1 ,
"k21", 0.01,0.1,1 ,
"ksyn", 0.01,0.1,1,
"kdeg", 0.01,0.1,1 ,
"kint", 0,0.2,10 ,
"Vd", 1,5,10)
find_relative(LP,Conc, protocol = "unique", model = model_RxODE, values = domain)
# ke > kint
domain <- domain <- tribble(~param, ~min, ~ref, ~max,
"ke", 0.01,0.6,1,
"kon", 0.01,0.1,1,
"koff", 0.01,0.1,1 ,
"k12", 0.01,0.1,1 ,
"k21", 0.01,0.1,1 ,
"ksyn", 0.01,0.1,1,
"kdeg", 0.01,0.1,1 ,
"kint", 0,0.1,10 ,
"Vd", 1,5,10)
find_relative(LP,Conc, protocol = "unique", model = model_RxODE, values = domain)
# ke > kint
domain <- domain <- tribble(~param, ~min, ~ref, ~max,
"ke", 0.01,0.1,1,
"kon", 0.01,0.1,1,
"koff", 0.01,0.1,1 ,
"k12", 0.01,0.1,1 ,
"k21", 0.01,0.1,1 ,
"ksyn", 0.01,0.1,1,
"kdeg", 0.01,0.1,1 ,
"kint", 0,0.01,10 ,
"Vd", 1,5,10)
find_relative(LP,Conc, protocol = "unique", model = model_RxODE, values = domain)
# ke == kint
domain <- domain <- tribble(~param, ~min, ~ref, ~max,
"ke", 0.01,0.1,1,
"kon", 0.01,0.1,1,
"koff", 0.01,0.1,1 ,
"k12", 0.01,0.1,1 ,
"k21", 0.01,0.1,1 ,
"ksyn", 0.01,0.1,1,
"kdeg", 0.01,0.1,1 ,
"kint", 0.01,0.1,1 ,
"Vd", 1,5,10)
find_relative(LP,Conc, protocol = "unique", model = model_RxODE, values = domain)
# QE ----------------------------------------------------------------------
dLtot <- - kin * Ltot - (kel - kint) * L
dRtot <- ksyn - kdeg * Rtot - (kint - kdeg) * ( Ltot - L )
L <- 1 / 2 * ( ( Ltot - Rtot - Kd ) + sqrt(( Ltot - Rtot - kd ) ** 2 + 4 * kd * Ltot ))
Conc_plot <- L / Vd
# QSS ---------------------------------------------------------------------
dLtot <- - kin * Ltot - (kel - kint) * L
dRtot <- ksyn - kdeg * Rtot - ( kint - kdeg ) * ( Ltot - L )
L <- 1 / 2 * ( ( Ltot - Rtot - Kss ) + sqrt(( Ltot - Rtot - kss ) ** 2 + 4 * kss * Ltot ))
Conc_plot <- L / Vd
# Rtot --------------------------------------------------------------------
model_RxODE <- RxODE({
dL <- - ( kel + kon * R0 ) * L + ( koff + kon * L ) * P
dP <- kon * R0 * L - ( koff + kint + kon * L ) * P
Conc_plot <- L / Vd
})
# Ireversible binding -----------------------------------------------------
model_RxODE <- RxODE({
R(0) <- ksyn/kdeg
d/dt(L) <- - kel * L - kon * L * R
d/dt(R) <- ksyn - kdeg * R - kon * L * R
d/dt(P) <- kon * L * R - kint * P
Conc<- L / Vd
})
parameters_default_values <- c(psi = 20) # paremeters value to be used by default (NA if you want to force providing value)
initial_cmt_values <- c(L = 0) # initial compartment values. At least one, and every missing cmt name would be set to 0
times <- seq(0,200, 1) # times you want to see your observations
protocols <- list( unique = tibble(cmt = "L", time = 0, amt = 50))
# tribblecreator(model_RxODE)
domain <- domain <- tribble(~param, ~min, ~ref, ~max,
"kel", 0.01,0.1,1,
"kon", 0.01,0.1,1 ,
"ksyn", 0.01,0.1,1 ,
"kdeg", 0.01,0.1,1 ,
"kint", 0.01,0.1,1,
"Vd", 1,5,10)
find_relative(Conc, protocol = "unique", model = model_RxODE, values = domain, sensitivity = 0.001)
# TMDD MM--------------------------------------------------------------------
model_RxODE <- RxODE({
d/dt(L) <- - ke * L - Vm * L / ( kd + L ) - k12 * L + k21 * A
d/dt(A) <- k12 * L - k21 * A
Conc <- L / Vd
})
parameters_default_values <- c(psi = 20) # paremeters value to be used by default (NA if you want to force providing value)
initial_cmt_values <- c(L = 0) # initial compartment values. At least one, and every missing cmt name would be set to 0
times <- seq(0,200, 1) # times you want to see your observations
protocols <- list( unique = tibble(cmt = "L", time = 0, amt = 50))
# tribblecreator(model_RxODE)
domain <- domain <- tribble(~param, ~min, ~ref, ~max,
"ke", 0.01,0.1,1,
"k12", 0.01,0.1,1 ,
"k21", 0.01,0.1,1 ,
"Vm", 0.1,1,10,
"kd", 1,5,25,
"Vd", 1,5,10)
find_relative(Conc, protocol = "unique", model = model_RxODE, values = domain)
Thibaudpmx/QSPVP documentation built on Nov. 14, 2022, 7:07 p.m.
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# Administration ----------------------------------------------------------
model_RxODE <-RxODE({
d/dt(Admin) <- -ka * Admin
d/dt(Central) <- ka * Admin - ke * Central
})
parameters_default_values <- c(psi = 20) # paremeters value to be used by default (NA if you want to force providing value)
initial_cmt_values <- c(Central = 0) # initial compartment values. At least one, and every missing cmt name would be set to 0
times <- seq(0,100, 1) # times you want to see your observations
protocols <- list( unique = tibble(cmt = "Admin", time = 0, amt = 50))
# tribblecreator(model_RxODE)
domain <- tribble(~param, ~min, ~ref, ~max,
"ka", 0.01,0.1,1,
"ke", 0.01,0.1,1
)
find_relative(Central, protocol = "unique", model = model_RxODE, values = domain)
# homostastie ----------------------------------------------------------
model_RxODE <-RxODE({
IRM(0) <- kin/kout
d/dt(IRM) <- - kout * IRM + kin
d/dt(IRM2) <- kout * IRM - kout2 * IRM2
})
parameters_default_values <- c(psi = 20) # paremeters value to be used by default (NA if you want to force providing value)
initial_cmt_values <- c(Central = 0) # initial compartment values. At least one, and every missing cmt name would be set to 0
times <- seq(0,100, 1) # times you want to see your observations
protocols <- list( unique = tibble(cmt = "IRM", time = 0, amt = 0))
# tribblecreator(model_RxODE)
domain <- tribble(~param, ~min, ~ref, ~max,
"kout", 0.01,0.1,1,
"kout2", 0.01,0.1,1,
"kin", 0.01,0.1,1
)
find_relative(IRM, IRM2, protocol = "unique", model = model_RxODE, values = domain,time_simul = times)
find_relative(IRM, IRM2, protocol = "unique", model = model_RxODE, values = domain,time_simul = times, deepAnalysis = T)
# find_relative(Central, protocol = "unique", model = model_RxODE, values = domain,time_simul = c(0,seq(5000,10000,100)))
# inhib kin------------------------------------------------------
model_RxODE <-RxODE({
IRM(0) <- kin/kout
d/dt(Drug) <- - ke * Drug
d/dt(IRM) <- - kout * IRM + kin * ( 1 - Emax * Drug / (Drug + D50))
d/dt(IRM2) <- kout * IRM - kout2 * IRM2
})
parameters_default_values <- c(psi = 20) # paremeters value to be used by default (NA if you want to force providing value)
initial_cmt_values <- c(Central = 0) # initial compartment values. At least one, and every missing cmt name would be set to 0
times <- seq(0,200, 1) # times you want to see your observations
protocols <- list( unique = tibble(cmt = "Drug", time = 50, amt = 50))
# tribblecreator(model_RxODE)
domain <- tribble(~param, ~min, ~ref, ~max,
"kout", 0.01,0.1,1,
"kout2", 0.01,0.1,1,
"kin", 0.01,0.1,1,
"ke", 0.01,0.1,1,
"Emax", 0.1,0.5,1,
"D50", 1,10,30
)
find_relative(IRM, IRM2, protocol = "unique", model = model_RxODE, values = domain,time_simul = times)
# increase kout------------------------------------------------------
model_RxODE <-RxODE({
IRM(0) <- kin/kout
d/dt(Drug) <- - ke * Drug
d/dt(IRM) <- - kout * ( 1 + Emax * Drug / (Drug + D50)) * IRM + kin
d/dt(IRM2) <- kout * IRM - kout2 * IRM2
})
parameters_default_values <- c(psi = 20) # paremeters value to be used by default (NA if you want to force providing value)
initial_cmt_values <- c(Central = 0) # initial compartment values. At least one, and every missing cmt name would be set to 0
times <- seq(0,200, 1) # times you want to see your observations
protocols <- list( unique = tibble(cmt = "Drug", time = 50, amt = 50))
# tribblecreator(model_RxODE)
domain <- tribble(~param, ~min, ~ref, ~max,
"kout", 0.01,0.1,1,
"kout2", 0.01,0.1,1,
"kin", 0.01,0.1,1,
"ke", 0.01,0.1,1,
"Emax", 0.1,0.5,1,
"D50", 1,10,30
)
find_relative(IRM, IRM2, protocol = "unique", model = model_RxODE, values = domain,time_simul = times)
# increase kin------------------------------------------------------
model_RxODE <-RxODE({
IRM(0) <- kin/kout
d/dt(Drug) <- - ke * Drug
d/dt(IRM) <- - kout * IRM + kin * ( 1 + Emax * Drug / (Drug + D50))
d/dt(IRM2) <- kout * IRM - kout2 * IRM2
})
parameters_default_values <- c(psi = 20) # paremeters value to be used by default (NA if you want to force providing value)
initial_cmt_values <- c(Central = 0) # initial compartment values. At least one, and every missing cmt name would be set to 0
times <- seq(0,200, 1) # times you want to see your observations
protocols <- list( unique = tibble(cmt = "Drug", time = 50, amt = 50))
# tribblecreator(model_RxODE)
domain <- tribble(~param, ~min, ~ref, ~max,
"kout", 0.01,0.1,1,
"kout2", 0.01,0.1,1,
"kin", 0.01,0.1,1,
"ke", 0.01,0.1,1,
"Emax", 0.1,0.5,1,
"D50", 1,10,30
)
find_relative(IRM, IRM2, protocol = "unique", model = model_RxODE, values = domain,time_simul = times)
# distribution ------------------------------------------------------------
##Pk.2comp.ke.k12.k21.difEq
#k12 <- Q/V1
#k21 <- Q/V2
#ke <- Cl/V1
model_RxODE <-RxODE({
d/dt(Central) <- k21 * Periph - k12 * Central - ke * Central
d/dt(Periph) <- - k21 * Periph + k12 * Central
Conc <- Central / V1
})
parameters_default_values <- c(psi = 20) # paremeters value to be used by default (NA if you want to force providing value)
initial_cmt_values <- c(Central = 0) # initial compartment values. At least one, and every missing cmt name would be set to 0
times <- seq(0,100, 1) # times you want to see your observations
protocols <- list( unique = tibble(cmt = "Central", time = 0, amt = 50))
# tribblecreator(model_RxODE)
domain <- tribble(~param, ~min, ~ref, ~max,
"k21", 0.01,0.1,1,
"k12", 0.01,0.1,1,
"ke", 0.01,0.1,1,
"V1", 1,5, 10)
find_relative(Conc, protocol = "unique", model = model_RxODE, values = domain)
# Distribution 2 ----------------------------------------------------------
##Pk.2comp.ke.k12.k21.difEq
#ke <- Cl/V1
model_RxODE <-RxODE({
k12 <- Q/V1
k21 <- Q/V2
d/dt(Central) <- k21 * Periph - k12 * Central - ke * Central
d/dt(Periph) <- - k21 * Periph + k12 * Central
Conc <- Central / V1
})
parameters_default_values <- c(psi = 20) # paremeters value to be used by default (NA if you want to force providing value)
initial_cmt_values <- c(Central = 0) # initial compartment values. At least one, and every missing cmt name would be set to 0
times <- seq(0,100, 1) # times you want to see your observations
protocols <- list( unique = tibble(cmt = "Central", time = 0, amt = 50))
# tribblecreator(model_RxODE)
domain <- tribble(~param, ~min, ~ref, ~max,
"V2", 1,5, 10,
"Q", 0.01,0.1,1,
"ke", 0.01,0.1,1,
"V1", 1,5, 10)
find_relative(Conc, protocol = "unique", model = model_RxODE, values = domain)
# Distribution 3 ----------------------------------------------------------
##Pk.2comp.ke.k12.k21.difEq
#ke <- Cl/V1
model_RxODE <-RxODE({
k21 <- ratio / k12
d/dt(Central) <- k21 * Periph - k12 * Central - ke * Central
d/dt(Periph) <- - k21 * Periph + k12 * Central
Conc <- Central / V1
})
parameters_default_values <- c(psi = 20) # paremeters value to be used by default (NA if you want to force providing value)
initial_cmt_values <- c(Central = 0) # initial compartment values. At least one, and every missing cmt name would be set to 0
times <- seq(0,100, 1) # times you want to see your observations
protocols <- list( unique = tibble(cmt = "Central", time = 0, amt = 50))
# tribblecreator(model_RxODE)
domain <- tribble(~param, ~min, ~ref, ~max,
"ratio", 0.01,1,10,
"k12", 0.01,0.1,1,
"ke", 0.01,0.1,1,
"V1", 1,5, 10)
find_relative(Conc, protocol = "unique", model = model_RxODE, values = domain)
# Distribution 4 ----------------------------------------------------------
##Pk.2comp.ke.k12.k21.difEq
#ke <- Cl/V1
model_RxODE <-RxODE({
k21 <- ratio / k12
d/dt(Central) <- k21 * Periph - k12 * Central - ke * Central
d/dt(Periph) <- - k21 * Periph + k12 * Central
Conc <- Central / V1
})
parameters_default_values <- c(psi = 20) # paremeters value to be used by default (NA if you want to force providing value)
initial_cmt_values <- c(Central = 0) # initial compartment values. At least one, and every missing cmt name would be set to 0
times <- seq(0,100, 1) # times you want to see your observations
protocols <- list( unique = tibble(cmt = "Central", time = 0, amt = 50))
# tribblecreator(model_RxODE)
domain <- tribble(~param, ~min, ~ref, ~max,
"ratio", 0.01,1,10,
"k12", 0.01,0.1,1,
"ke", 0.01,0.1,1,
"V1", 1,5, 10)
find_relative(Conc, protocol = "unique", model = model_RxODE, values = domain)
# dos elim ------------------------------------------------------------
##Pk.2comp.ke.k12.k21.difEq
#k12 <- Q/V1
#k21 <- Q/V2
#ke <- Cl/V1
model_RxODE <-RxODE({
d/dt(Central) <- k21 * Periph - k12 * Central - ke * Central
d/dt(Periph) <- - k21 * Periph + k12 * Central - ke2 * Periph
Conc <- Central / V1
})
parameters_default_values <- c(psi = 20) # paremeters value to be used by default (NA if you want to force providing value)
initial_cmt_values <- c(Central = 0) # initial compartment values. At least one, and every missing cmt name would be set to 0
times <- seq(0,100, 2) # times you want to see your observations
protocols <- list( unique = tibble(cmt = "Central", time = 0, amt = 50))
# tribblecreator(model_RxODE)
domain <- tribble(~param, ~min, ~ref, ~max,
"k21", 0.01,0.1,1,
"k12", 0.01,0.1,1,
"ke", 0.01,0.11,1,
"ke2", 0.01,0.1,1,
"V1", 1,5, 10)
find_relative(Conc, protocol = "unique", model = model_RxODE, values = domain)
find_relative(Conc, protocol = "unique", model = model_RxODE, values = domain, deepAnalysis = T)
#ke > ke2 -> k12 / k21 non utilisable
domain <- tribble(~param, ~min, ~ref, ~max,
"k21", 0.01,0.1,1,
"k12", 0.01,0.1,1,
"ke", 0.01,0.1,1,
"ke2", 0,0.001,0.1,
"V1", 1,5, 10)
find_relative(Conc, protocol = "unique", model = model_RxODE, values = domain)
#ke2 > ke -> k12 / k21 utilisable
domain <- tribble(~param, ~min, ~ref, ~max,
"k21", 0.01,0.1,1,
"k12", 0.01,0.1,1,
"ke", 0.01,0.1,1,
"ke2", 0.01,1,10,
"V1", 1,5, 10)
find_relative(Conc, protocol = "unique", model = model_RxODE, values = domain)
#ke2 = ke -> k12 / k21 utilisable
domain <- tribble(~param, ~min, ~ref, ~max,
"k21", 0.01,0.1,1,
"k12", 0.01,0.1,1,
"ke", 0.01,0.1,1,
"ke2", 0.01,0.1,1,
"V1", 1,5, 10)
find_relative(Conc, protocol = "unique", model = model_RxODE, values = domain,time_simul = seq(0,500,1))
# Michaelis elimination ---------------------------------------------------
model_RxODE <-RxODE({
d/dt(Central) <- - Central * Vmax / (Central + km)
})
parameters_default_values <- c(psi = 20) # paremeters value to be used by default (NA if you want to force providing value)
initial_cmt_values <- c(Central = 0) # initial compartment values. At least one, and every missing cmt name would be set to 0
times <- seq(0,52, 1) # times you want to see your observations
protocols <- list( unique = tibble(cmt = "Central", time = 0, amt = 50))
# tribblecreator(model_RxODE)
domain <- tribble(~param, ~min, ~ref, ~max,
"Vmax", 0.1,1,10 ,
"km", 1,5,25)
find_relative(Central, protocol = "unique", model = model_RxODE, values = domain)
# TMDD --------------------------------------------------------------------
model_RxODE <- RxODE({
R(0) <- ksyn/kdeg
d/dt(L) <- -ke * L - kon * L * R + koff * P - k12 * L + k21 * A
d/dt(R) <- ksyn - kdeg * R - kon * L * R + koff * P
d/dt(P) <- kon * L * R - koff * P - kint * P
d/dt(A) <- k12 * L - k21 * A
Conc <- L/Vd
LP <- (L + P) / Vd
})
parameters_default_values <- c(psi = 20) # paremeters value to be used by default (NA if you want to force providing value)
initial_cmt_values <- c(R = 0) # initial compartment values. At least one, and every missing cmt name would be set to 0
times <- seq(0,200, 1) # times you want to see your observations
protocols <- list( unique = tibble(cmt = "L", time = 0, amt = 50))
# tribblecreator(model_RxODE)
#kint > ke
domain <- domain <- tribble(~param, ~min, ~ref, ~max,
"ke", 0.01,0.1,1,
"kon", 0.01,0.1,1,
"koff", 0.01,0.1,1 ,
"k12", 0.01,0.1,1 ,
"k21", 0.01,0.1,1 ,
"ksyn", 0.01,0.1,1,
"kdeg", 0.01,0.1,1 ,
"kint", 0,0.2,10 ,
"Vd", 1,5,10)
find_relative(LP,Conc, protocol = "unique", model = model_RxODE, values = domain)
# ke > kint
domain <- domain <- tribble(~param, ~min, ~ref, ~max,
"ke", 0.01,0.6,1,
"kon", 0.01,0.1,1,
"koff", 0.01,0.1,1 ,
"k12", 0.01,0.1,1 ,
"k21", 0.01,0.1,1 ,
"ksyn", 0.01,0.1,1,
"kdeg", 0.01,0.1,1 ,
"kint", 0,0.1,10 ,
"Vd", 1,5,10)
find_relative(LP,Conc, protocol = "unique", model = model_RxODE, values = domain)
# ke > kint
domain <- domain <- tribble(~param, ~min, ~ref, ~max,
"ke", 0.01,0.1,1,
"kon", 0.01,0.1,1,
"koff", 0.01,0.1,1 ,
"k12", 0.01,0.1,1 ,
"k21", 0.01,0.1,1 ,
"ksyn", 0.01,0.1,1,
"kdeg", 0.01,0.1,1 ,
"kint", 0,0.01,10 ,
"Vd", 1,5,10)
find_relative(LP,Conc, protocol = "unique", model = model_RxODE, values = domain)
# ke == kint
domain <- domain <- tribble(~param, ~min, ~ref, ~max,
"ke", 0.01,0.1,1,
"kon", 0.01,0.1,1,
"koff", 0.01,0.1,1 ,
"k12", 0.01,0.1,1 ,
"k21", 0.01,0.1,1 ,
"ksyn", 0.01,0.1,1,
"kdeg", 0.01,0.1,1 ,
"kint", 0.01,0.1,1 ,
"Vd", 1,5,10)
find_relative(LP,Conc, protocol = "unique", model = model_RxODE, values = domain)
# QE ----------------------------------------------------------------------
dLtot <- - kin * Ltot - (kel - kint) * L
dRtot <- ksyn - kdeg * Rtot - (kint - kdeg) * ( Ltot - L )
L <- 1 / 2 * ( ( Ltot - Rtot - Kd ) + sqrt(( Ltot - Rtot - kd ) ** 2 + 4 * kd * Ltot ))
Conc_plot <- L / Vd
# QSS ---------------------------------------------------------------------
dLtot <- - kin * Ltot - (kel - kint) * L
dRtot <- ksyn - kdeg * Rtot - ( kint - kdeg ) * ( Ltot - L )
L <- 1 / 2 * ( ( Ltot - Rtot - Kss ) + sqrt(( Ltot - Rtot - kss ) ** 2 + 4 * kss * Ltot ))
Conc_plot <- L / Vd
# Rtot --------------------------------------------------------------------
model_RxODE <- RxODE({
dL <- - ( kel + kon * R0 ) * L + ( koff + kon * L ) * P
dP <- kon * R0 * L - ( koff + kint + kon * L ) * P
Conc_plot <- L / Vd
})
# Ireversible binding -----------------------------------------------------
model_RxODE <- RxODE({
R(0) <- ksyn/kdeg
d/dt(L) <- - kel * L - kon * L * R
d/dt(R) <- ksyn - kdeg * R - kon * L * R
d/dt(P) <- kon * L * R - kint * P
Conc<- L / Vd
})
parameters_default_values <- c(psi = 20) # paremeters value to be used by default (NA if you want to force providing value)
initial_cmt_values <- c(L = 0) # initial compartment values. At least one, and every missing cmt name would be set to 0
times <- seq(0,200, 1) # times you want to see your observations
protocols <- list( unique = tibble(cmt = "L", time = 0, amt = 50))
# tribblecreator(model_RxODE)
domain <- domain <- tribble(~param, ~min, ~ref, ~max,
"kel", 0.01,0.1,1,
"kon", 0.01,0.1,1 ,
"ksyn", 0.01,0.1,1 ,
"kdeg", 0.01,0.1,1 ,
"kint", 0.01,0.1,1,
"Vd", 1,5,10)
find_relative(Conc, protocol = "unique", model = model_RxODE, values = domain, sensitivity = 0.001)
# TMDD MM--------------------------------------------------------------------
model_RxODE <- RxODE({
d/dt(L) <- - ke * L - Vm * L / ( kd + L ) - k12 * L + k21 * A
d/dt(A) <- k12 * L - k21 * A
Conc <- L / Vd
})
parameters_default_values <- c(psi = 20) # paremeters value to be used by default (NA if you want to force providing value)
initial_cmt_values <- c(L = 0) # initial compartment values. At least one, and every missing cmt name would be set to 0
times <- seq(0,200, 1) # times you want to see your observations
protocols <- list( unique = tibble(cmt = "L", time = 0, amt = 50))
# tribblecreator(model_RxODE)
domain <- domain <- tribble(~param, ~min, ~ref, ~max,
"ke", 0.01,0.1,1,
"k12", 0.01,0.1,1 ,
"k21", 0.01,0.1,1 ,
"Vm", 0.1,1,10,
"kd", 1,5,25,
"Vd", 1,5,10)
find_relative(Conc, protocol = "unique", model = model_RxODE, values = domain)
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