Nothing
## ----setup, include = FALSE---------------------------------------------------
library(pksensi)
#mcsim_install(version = "6.1.0")
knitr::opts_chunk$set(
eval = F,
dev = "png",
dpi = 200,
fig.align = "center",
fig.width = 7,
out.width = "90%",
fig.height = 4,
comment = "#>"
)
## -----------------------------------------------------------------------------
# mcsim_install(version = "6.1.0")
## ---- echo=F------------------------------------------------------------------
# #Nominal value
# Tg <- log(0.23)
# Tp <- log(0.033)
# CYP_Km <- log(130)
# SULT_Km_apap <- log(300)
# SULT_Ki <- log(526)
# SULT_Km_paps <- log(0.5)
# UGT_Km <- log(6.0e3)
# UGT_Ki <- log(5.8e4)
# UGT_Km_GA <-log(0.5)
# Km_AG <- log(1.99e4)
# Km_AS <- log(2.29e4)
#
# r <- 1.96 # exp(1.96)/exp(-1.96) ~ 50
#
# x <- c("Tg", "Tp", "CYP_Km", "CYP_VmaxC",
# "SULT_Km_apap","SULT_Ki","SULT_Km_paps","SULT_VmaxC",
# "UGT_Km","UGT_Ki","UGT_Km_GA","UGT_VmaxC",
# "Km_AG","Vmax_AG","Km_AS","Vmax_AS",
# "kGA_syn","PAPS_syn", "CLC_APAP","CLC_AG","CLC_AS")
# y <- c("Gatric emptying time constant",
# "GI perfusion time constant",
# "Cytochrome P450 metabolism, Km",
# "Cytochrome P450 metabolism, VMax",
# "Sulfation pathway acetaminophen, Km",
# "Sulfation pathway substrate inhibition, Ki",
# "Sulfation pathway PAPS, Km",
# "Sulfation pathway acetaminophen, Vmax",
# "Glucronidation pathway acetaminophen, Km",
# "Glucronidation pathway substrate inhibition, Ki",
# "Glucronidation pathway GA, Km",
# "Glucronidation pathway acetaminophen, Vmax",
# "APAP-G hepatic transporter, Km",
# "APAP-G hepatic transporter, Vmax",
# "APAP-S hepatic transporter, Km",
# "APAP-S hepatic transporter, Vmax",
# "UDPGA synthesis",
# "PAPS synthesis",
# "APAP clearance",
# "APAP-G clearance",
# "APAP-S clearance")
# z <- c("$h$", "$h$", "$\\mu{M}$", "$\\mu{mole}/h\\cdot{BW}^{0.75}$",
# "$\\mu{M}$", "$\\mu{M}$", "$-$", "$\\mu{mole}/h\\cdot{BW}^{0.75}$",
# "$\\mu{M}$", "$\\mu{M}$", "$-$", "$\\mu{mole}/h\\cdot{BW}^{0.75}$",
# "$\\mu{M}$", "$\\mu{mole}/h$", "$\\mu{M}$", "$\\mu{mole}/h$",
# "$1/h$", "$1/h$",
# "$L/h\\cdot{BW}^{0.75}$", "$L/h\\cdot{BW}^{0.75}$", "$L/h\\cdot{BW}^{0.75}$")
# min <- c(round(Tg-r, 3), round(Tp-r, 3), round(CYP_Km-r), round(log(0.14), 3),
# round(SULT_Km_apap-r, 3), round(SULT_Ki-r, 3), round(SULT_Km_paps-r), log(1),
# round(UGT_Km-r, 3), round(UGT_Ki-r, 3), round(UGT_Km_GA-r), log(1),
# round(Km_AG-r, 3), round(log(1.09e3), 3), round(Km_AS-r), round(log(1.09e3), 3),
# log(1), log(1), round(log(2.48e-3), 3), round(log(2.48e-3), 3), round(log(2.48e-3), 3))
# max <- c(round(Tg+r, 3), round(Tp+r, 3), round(CYP_Km+r), round(log(2900), 3),
# round(SULT_Km_apap+r, 3), round(SULT_Ki+r, 3), round(SULT_Km_paps+r), round(log(22026), 3),
# round(UGT_Km+r, 3), round(UGT_Ki+r, 3), round(UGT_Km_GA+r), round(log(22026), 3),
# round(Km_AG+r, 3), round(log(3.26e6), 3), round(Km_AS+r), round(log(3.26e6), 3),
# round(log(4.43e5), 3), round(log(4.43e5),3),
# round(log(2.718), 3), round(log(2.718), 3), round(log(2.718), 3))
#
# df <- data.frame(x, y, z, min, max)
# names(df) <- c("Parameter","Description", "Unit", "Min", "Max")
#
# #if (require(kableExtra)) {
# knitr::kable(df, format = 'html', align=c("l","l","l", "c", "c"),
# caption = "Table 1 Description of sampling range of model parameter")
# #%>% kableExtra::add_footnote(c("The parameter valur are showed in log-transformed scale."), notation = "number")
# #}
#
## -----------------------------------------------------------------------------
# # Nominal value
# Tg <- log(0.23)
# Tp <- log(0.033)
# CYP_Km <- log(130)
# SULT_Km_apap <- log(300)
# SULT_Ki <- log(526)
# SULT_Km_paps <- log(0.5)
# UGT_Km <- log(6.0e3)
# UGT_Ki <- log(5.8e4)
# UGT_Km_GA <-log(0.5)
# Km_AG <- log(1.99e4)
# Km_AS <- log(2.29e4)
#
# rng <- 1.96
## -----------------------------------------------------------------------------
# mName <- "pbpk_apap"
# pbpk_apap_model()
# compile_model(mName, application = "mcsim")
## -----------------------------------------------------------------------------
# params <- c("lnTg", "lnTp", "lnCYP_Km","lnCYP_VmaxC",
# "lnSULT_Km_apap","lnSULT_Ki","lnSULT_Km_paps","lnSULT_VmaxC",
# "lnUGT_Km","lnUGT_Ki","lnUGT_Km_GA","lnUGT_VmaxC",
# "lnKm_AG","lnVmax_AG","lnKm_AS","lnVmax_AS",
# "lnkGA_syn","lnkPAPS_syn", "lnCLC_APAP","lnCLC_AG","lnCLC_AS")
# dist <- rep("Uniform", 21)
# q <- rep("qunif", 21)
# q.arg <-list(list(Tg-rng, Tg+rng), list(Tp-rng, Tp+rng),
# list(CYP_Km-rng, CYP_Km+rng), list(-2., 5.),
# list(SULT_Km_apap-rng, SULT_Km_apap+rng),
# list(SULT_Ki-rng, SULT_Ki+rng),
# list(SULT_Km_paps-rng, SULT_Km_paps+rng),
# list(0, 10), list(UGT_Km-rng, UGT_Km+rng),
# list(UGT_Ki-rng, UGT_Ki+rng),
# list(UGT_Km_GA-rng, UGT_Km_GA+rng),
# list(0, 10), list(Km_AG-rng, Km_AG+rng),
# list(7., 15), list(Km_AS-rng, Km_AS+rng),
# list(7., 15), list(0., 13), list(0., 13),
# list(-6., 1), list(-6., 1), list(-6., 1))
## -----------------------------------------------------------------------------
# conditions <- c("mgkg_flag = 1",
# "OralExp_APAP = NDoses(2, 1, 0, 0, 0.001)",
# "OralDose_APAP_mgkg = 20.0")
# vars <- c("lnCPL_APAP_mcgL", "lnCPL_AG_mcgL", "lnCPL_AS_mcgL")
# times <- seq(0.1, 0.5, 1, 2, 3, 4, 6, 8, 12)
## -----------------------------------------------------------------------------
# head(APAP)
## -----------------------------------------------------------------------------
# set.seed(1111)
# out <- solve_mcsim(mName = mName, params = params, vars = vars,
# monte_carlo = 1000, dist = dist, q.arg = q.arg,
# time = times, condition = conditions,
# rtol = 1e-7, atol = 1e-9)
## ---- fig.height=3.5, fig.width=9---------------------------------------------
# par(mfrow = c(1,3), mar = c(4,4,1,1))
# pksim(out, xlab = "Time (h)", ylab = "Conc. (ug/L)", main = "APAP")
# points(APAP$Time, log(APAP$APAP * 1000))
# pksim(out, vars = "lnCPL_AG_mcgL", xlab = "Time (h)", main = "APAP-G",
# ylab = " ", legend = FALSE)
# points(APAP$Time, log(APAP$AG * 1000))
# pksim(out, vars = "lnCPL_AS_mcgL", xlab = "Time (h)", main = "APAP-S",
# ylab = " ", legend = FALSE)
# points(APAP$Time, log(APAP$AS * 1000))
## -----------------------------------------------------------------------------
# set.seed(1234)
# x <- rfast99(params = params, n = 512, q = q, q.arg = q.arg, replicate = 10)
## -----------------------------------------------------------------------------
# out <- solve_mcsim(x, mName = mName,
# params = params,
# time = times,
# vars = vars,
# condition = conditions,
# rtol = 1e-7, atol = 1e-9)
## ---- fig.height=8, fig.width=8-----------------------------------------------
# plot(out, vars = "lnCPL_APAP_mcgL")
## ---- fig.height=5------------------------------------------------------------
# heat_check(out, order = "total order", show.all = T)
## ---- fig.height=5------------------------------------------------------------
# heat_check(out, index = "CI", order = "total order")
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