Update an oncology xenograft model based on Simeoni 2004
Source:R/updateOncologyXenograftSimeoni2004.R
updateOncologyXenograftSimeoni2004.RdUpdate an oncology xenograft model based on Simeoni 2004
Usage
updateOncologyXenograftSimeoni2004(
object,
ncmt,
damagedCmtName = "damagedCells",
drugEffectName = "drugEffectCyclingCells",
undamagedCmtName = "cyclingCells",
tumorVolName = "tumorVol",
transitRateName = "damageTransit"
)Arguments
- object
Fitted object or function specifying the model.
- ncmt
The desired number of damaged cell compartments
- damagedCmtName, undamagedCmtName, tumorVolName
character string names for the compartments for damaged cells, undamaged cells, and the calculated tumor volume (the sum of undamaged and damaged cells)
- drugEffectName, transitRateName
character string names of the drug effect and transit rate (as used in the model block)
Examples
library(rxode2)
readModelDb("oncology_xenograft_simeoni_2004") %>%
updateOncologyXenograftSimeoni2004(ncmt = 5)
#> ℹ You can modify the number of damaged cell compartments in the model using the function updateOncologyXenograftSimeoni2004(model, ncmt)
#>
#>
#> ℹ add covariate `damagedCells1`
#> ℹ add covariate `damagedCells2`
#> ℹ add covariate `damagedCells3`
#> ℹ add covariate `damagedCells4`
#> ℹ add covariate `damagedCells5`
#> ── rxode2-based free-form 6-cmt ODE model ──────────────────────────────────────
#> ── Initalization: ──
#> Fixed Effects ($theta):
#> ldamageTransit ldrugSlope ltumorExpGrowth ltumorLinGrowth tumorVolpropSd
#> -0.03252319 -7.37137930 -1.29828348 -0.20579491 0.20000000
#> tumorVoladdSd
#> 30.00000000
#>
#> States ($state or $stateDf):
#> Compartment Number Compartment Name
#> 1 1 cyclingCells
#> 2 2 damagedCells1
#> 3 3 damagedCells2
#> 4 4 damagedCells3
#> 5 5 damagedCells4
#> 6 6 damagedCells5
#> ── Model (Normalized Syntax): ──
#> function() {
#> description <- "Oncology tumor growth model in xenograft models"
#> reference <- "Monica Simeoni, Paolo Magni, Cristiano Cammia, Giuseppe De Nicolao, Valter Croci, Enrico Pesenti, Massimiliano Germani, Italo Poggesi, Maurizio Rocchetti; Predictive Pharmacokinetic-Pharmacodynamic Modeling of Tumor Growth Kinetics in Xenograft Models after Administration of Anticancer Agents. Cancer Res 1 February 2004; 64 (3): 1094–1101. https://doi.org/10.1158/0008-5472.CAN-03-2524"
#> ini({
#> ldamageTransit <- c(-2.30258509299405, -0.0325231917055601,
#> 2.30258509299405)
#> label("Transit rate through damage (1/day)")
#> ldrugSlope <- c(-11.5129254649702, -7.37137930126383,
#> -2.30258509299405)
#> label("Linear drug effect on cycling cells (1/(day*ng/mL))")
#> ltumorExpGrowth <- c(-6.90775527898214, -1.29828348379718,
#> 0.693147180559945)
#> label("Tumor exponential growth rate (1/day)")
#> ltumorLinGrowth <- c(-4.60517018598809, -0.205794912979597,
#> 1.6094379124341)
#> label("Tumor linear growth rate (tumor volume/day)")
#> tumorVolpropSd <- c(0, 0.2)
#> label("Proportional residual error (fraction)")
#> tumorVoladdSd <- c(0, 30)
#> label("Additive residual error (tumor volume)")
#> })
#> model({
#> damageTransit <- exp(ldamageTransit)
#> drugSlope <- exp(ldrugSlope)
#> tumorExpGrowth <- exp(ltumorExpGrowth)
#> tumorLinGrowth <- exp(ltumorLinGrowth)
#> cyclingCells(0) <- tumorVol0
#> psi <- 20
#> tumorVol <- cyclingCells + damagedCells1 + damagedCells2 +
#> damagedCells3 + damagedCells4 + damagedCells5
#> drugEffectCyclingCells <- drugSlope * cp
#> d/dt(cyclingCells) <- tumorExpGrowth * cyclingCells/(1 +
#> (tumorExpGrowth/tumorLinGrowth * tumorVol)^psi)^(1/psi) -
#> drugEffectCyclingCells * cyclingCells
#> tumorVol ~ prop(tumorVolpropSd) + add(tumorVoladdSd)
#> d/dt(damagedCells1) <- drugEffectCyclingCells * cyclingCells -
#> damageTransit * damagedCells1
#> d/dt(damagedCells2) <- damageTransit * (damagedCells1 -
#> damagedCells2)
#> d/dt(damagedCells3) <- damageTransit * (damagedCells2 -
#> damagedCells3)
#> d/dt(damagedCells4) <- damageTransit * (damagedCells3 -
#> damagedCells4)
#> d/dt(damagedCells5) <- damageTransit * (damagedCells4 -
#> damagedCells5)
#> })
#> }