Nothing
## ----setup, include = FALSE---------------------------------------------------
library(pksensi)
#mcsim_install(version = "6.1.0")
knitr::opts_chunk$set(
eval = F,
dev = "png",
dpi = 200,
fig.align = "center",
fig.width = 7,
out.width = "90%",
fig.height = 4,
comment = "#>"
)
## -----------------------------------------------------------------------------
# pbtk1cpt <- function(t, state, parameters) {
# with(as.list(c(state, parameters)), {
# dAgutlument = - kgutabs * Agutlument
# dAcompartment = kgutabs * Agutlument - ke * Acompartment
# dAmetabolized = ke * Acompartment
# Ccompartment = Acompartment / vdist * BW;
# list(c(dAgutlument, dAcompartment, dAmetabolized),
# "Ccompartment" = Ccompartment)
# })
# }
## ---- warning=F---------------------------------------------------------------
# library(httk)
# pars1comp <- (parameterize_1comp(chem.name = "acetaminophen"))
# unlist(pars1comp)
## -----------------------------------------------------------------------------
# parms <- c(vdist = pars1comp$Vdist,
# ke = pars1comp$kelim,
# kgutabs = pars1comp$kgutabs,
# BW = pars1comp$BW)
# initState <- c(Agutlument = 10, Acompartment = 0, Ametabolized = 0)
# parms
## -----------------------------------------------------------------------------
# library(deSolve)
# t <- seq(from = 0.01, to = 24.01, by = 1)
# y <- ode(y = initState, times = t, func = pbtk1cpt, parms = parms)
## ---- fig.height=6, fig.width=5-----------------------------------------------
# plot(y)
## -----------------------------------------------------------------------------
# params <- c("vdist", "ke", "kgutabs", "BW")
# q <- c("qunif", "qunif", "qunif", "qnorm")
# q.arg <- list(list(min = pars1comp$Vdist / 2, max = pars1comp$Vdist * 2),
# list(min = pars1comp$kelim / 2, max = pars1comp$kelim * 2),
# list(min = pars1comp$kgutabs / 2, max = pars1comp$kgutabs * 2),
# list(mean = pars1comp$BW, sd = 5))
# q.arg
## -----------------------------------------------------------------------------
# set.seed(1234)
# x <- rfast99(params, n = 200, q = q, q.arg = q.arg, replicate = 10)
## -----------------------------------------------------------------------------
# dim(x$a)
## ---- fig.height=5------------------------------------------------------------
# par(mfrow=c(4,4),mar=c(0.8,0.8,0.8,0),oma=c(4,4,2,1), pch =".")
# for (j in c("vdist", "ke", "kgutabs", "BW")) {
# if ( j == "BW") {
# plot(x$a[,1,j], ylab = "BW")
# } else plot(x$a[,1,j], xaxt="n", ylab = "")
# for (i in 2:3) {
# if ( j == "BW") {
# plot(x$a[,i,j], ylab = "", yaxt="n")
# } else plot(x$a[,i,j], xaxt="n", yaxt="n", ylab = "")
# }
# hist <- hist(x$a[,,j], plot=FALSE,
# breaks=seq(from=min(x$a[,,j]), to=max(x$a[,,j]), length.out=20))
# barplot(hist$density, axes=FALSE, space=0, horiz = T, main = j)
# }
# mtext("Model evaluation", SOUTH<-1, line=2, outer=TRUE)
## -----------------------------------------------------------------------------
# outputs <- c("Ccompartment", "Ametabolized")
# out <- solve_fun(x, time = t, func = pbtk1cpt, initState = initState, outnames = outputs)
## -----------------------------------------------------------------------------
# plot(out)
## -----------------------------------------------------------------------------
# plot(out, vars = "Ametabolized")
## ---- fig.height=5------------------------------------------------------------
# par(mfcol=c(4,4),mar=c(0.8,0.8,0,0),oma=c(4,4,2,1), pch = ".")
# plot(x$a[,1,"vdist"], out$y[,1,"0.01",1], xaxt="n", main = "\nvdist")
# plot(x$a[,1,"vdist"], out$y[,1,"2.01",1], xaxt="n")
# plot(x$a[,1,"vdist"], out$y[,1,"6.01",1], xaxt="n")
# plot(x$a[,1,"vdist"], out$y[,1,"24.01",1])
# for (j in c("ke", "kgutabs", "BW")){
# for (k in c("0.01", "2.01", "6.01", "24.01")){
# if (k == "0.01") {
# plot(x$a[,1,j], out$y[,1,k,1], yaxt = "n", xaxt="n", main = paste0("\n", j))
# } else if (k == "24.01") {
# plot(x$a[,1,j], out$y[,1,k,1], yaxt = "n")
# } else plot(x$a[,1,j], out$y[,1,k,1], xaxt = "n", yaxt = "n")
# }
# }
# mtext("Parameter", SOUTH<-1, line=2, outer=TRUE)
# mtext("Ccompartment", WEST<-2, line=2, outer=TRUE)
## -----------------------------------------------------------------------------
# dim(out$y)
## -----------------------------------------------------------------------------
# check(out, cutoff = 0.05)
## -----------------------------------------------------------------------------
# pbtk1cpt_model()
# cat(readLines("pbtk1cpt.model"), sep = "\n")
## ---- message=FALSE, warning=FALSE--------------------------------------------
# mName <- "pbtk1cpt"
# compile_model(mName, application = "R")
## -----------------------------------------------------------------------------
# source(paste0(mName, "_inits.R"))
## -----------------------------------------------------------------------------
# parms <- initParms()
# parms["vdist"] <- pars1comp$Vdist
# parms["ke"] <- pars1comp$kelim
# parms["kgutabs"] <- pars1comp$kgutabs
# parms["BW"] <- pars1comp$BW
# initState <- initStates(parms=parms)
# initState["Agutlument"] <- 10
## -----------------------------------------------------------------------------
# parms
## -----------------------------------------------------------------------------
# initState
## -----------------------------------------------------------------------------
# Outputs
## -----------------------------------------------------------------------------
# t <- seq(from = 0.01, to = 24.01, by = 1)
# y <- ode(y = initState, times = t, func = "derivs", parms = parms,
# dllname = mName, initfunc = "initmod",
# nout = 1, outnames = Outputs)
## -----------------------------------------------------------------------------
# head(y)
## -----------------------------------------------------------------------------
# # Define parameter distribution
# q <- c("qunif", "qunif", "qunif", "qnorm")
# q.arg <- list(list(min = parms["vdist"] / 2, max = parms["vdist"] * 2),
# list(min = parms["ke"] / 2, max = parms["ke"] * 2),
# list(min = parms["kgutabs"] / 2, max = parms["kgutabs"] * 2),
# list(mean = parms["BW"], sd = 5))
# params <- c("vdist", "ke", "kgutabs", "BW")
#
# # Generate parameter matrix
# set.seed(1234)
# x <- rfast99(params, n = 200, q = q, q.arg = q.arg, replicate = 10)
## -----------------------------------------------------------------------------
# outputs <- c("Ccompartment", "Ametabolized")
# out <- solve_fun(x, time = t, initState = initState, outnames = outputs, dllname = mName)
# check(out)
## -----------------------------------------------------------------------------
# system.time(out<-solve_fun(x, t, initState = initState, outnames = Outputs, dllname = mName))
## ---- message=F, warning=F----------------------------------------------------
# compile_model(mName, application = "mcsim")
## -----------------------------------------------------------------------------
# conditions <- c("Agutlument = 10")
# system.time(out <- solve_mcsim(x, mName = mName, params = params,
# vars = Outputs, time = t,
# condition = conditions))
## -----------------------------------------------------------------------------
# sessionInfo()
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.