build your PK model
shinyUI(fluidPage(
titlePanel(
list(HTML('<p style="color:#4C0B5F; font-size:24px" fontsize=14>build your PK model</p>' )),
windowTitle="build PK model"),
tabsetPanel(
tabPanel("Plot",
fluidRow(
column(3,
tabsetPanel(
tabPanel("administration",
radioButtons("administration", "",
c("iv bolus" = "bolus","iv infusion" = "infusion","oral" = "oral")),
# selectInput("administration","",c("iv bolus" = "bolus","iv infusion" = "infusion","oral" = "oral")),
sliderInput("tfd", "time of first dose:", value=0, min=0, max = 20, step=1),
sliderInput("nd", "Number of doses:", value=3, min=0, max = 10, step=1),
sliderInput("ii", "Interdose interval:", value = 9, min = 0.5, max = 15, step=0.5),
sliderInput("amt", "Amount:", value = 5, min = 0, max = 20, step=1),
conditionalPanel(condition = "input.administration == 'infusion'",
sliderInput("tinf", "Infusion time:", value = 1, min = 0, max = 5, step=0.2)
),
br(),
br()
),
tabPanel("model",
tabsetPanel(
tabPanel("absorption",
conditionalPanel(condition = "input.administration == 'oral'",
radioButtons("absorption","",c("first order" = "1","zero order" = "0")),
conditionalPanel(condition = "input.absorption == '1'",
sliderInput("ka", "absorption rate constant ka:", value = 0.8, min = 0, max = 4, step=0.1)
),
conditionalPanel(condition = "input.absorption == '0'",
sliderInput("tk0", "absorption duration Tk0:", value = 3, min = 0, max = 10, step=0.5)
),
conditionalPanel(condition = "input.absorption == '0'",
selectInput("delay0","delay",c("none" = "0","lag time" = "1")),
conditionalPanel(condition = "input.delay0 == '1'",
sliderInput("tlag0", "lag time Tlag:", value = 1, min = 0, max = 10, step=0.5)
)
),
conditionalPanel(condition = "input.absorption == '1'",
selectInput("delay1","delay",c("none" = "0","lag time" = "1","transit compartment" = "2")),
conditionalPanel(condition = "input.delay1 == '1'",
sliderInput("tlag1", "lag time Tlag:", value = 1, min = 0, max = 10, step=0.5)
),
conditionalPanel(condition = "input.delay1 == '2'",
sliderInput("mtt", "mean transit time Mtt:", value = 1, min = 0, max = 10, step=0.5),
sliderInput("ntr", "number of compartments Ntr:", value = 2, min = 0.5, max = 10, step=0.5)
)
),
br(),
br(),
br(),
br()
)
),
tabPanel("distribution",
radioButtons("distribution","",c("1 compartment" = "1","2 compartments" = "2","3 compartments" = "3")),
sliderInput("v", "volume V:", value = 10, min = 1, max = 20, step=1),
conditionalPanel(condition = "input.distribution != '1'",
sliderInput("k12", "transition rate constant k12:", value = 0.4, min = 0, max = 2, step=0.05),
sliderInput("k21", "transition rate constant k21:", value = 0.2, min = 0, max = 2, step=0.05)
),
conditionalPanel(condition = "input.distribution == '3'",
sliderInput("k13", "transition rate constant k13:", value = 0.4, min = 0, max = 2, step=0.05),
sliderInput("k31", "transition rate constant k31:", value = 0.2, min = 0, max = 2, step=0.05)
),
br()
),
tabPanel("elimination",
radioButtons("elimination","",c("linear" = "1","Michaelis Menten" = "2")),
conditionalPanel(condition = "input.elimination == '1'",
sliderInput("k", "elimination rate constant k:", value = 0.2, min = 0, max = 2, step=0.05)
),
conditionalPanel(condition = "input.elimination == '2'",
sliderInput("vm", "Vm:", value = 1, min = 0, max = 5, step=0.05),
sliderInput("km", "Km:", value = 1, min = 0, max = 5, step=0.05)
),
br()
))
),
tabPanel("output",
br(),
# selectInput("output","",c("concentration (Cc)" = "Cc","amount (Ac)" = "Ac")),
# br(),
sliderInput("range", "time range", min = -10, max = 200, value = c(-5,100), step=5),
br(),
sliderInput("ngp", "grid size", min = 10, max = 1000, value = 200, step=10),
br()
),
tabPanel("settings",
sliderInput("lsize", "line width", min = 0, max = 2, value = 0.75, step=0.25),
br(),
checkboxInput("log", "Plot y axis on log scale", value = FALSE),
br()
)
)),
column(9,
plotOutput("plot", height="500px"))
)),
tabPanel("Table", tableOutput("table")),
tabPanel("Simulx", verbatimTextOutput("RFile")),
tabPanel("ui.R", pre(includeText("ui.R"))),
tabPanel("server.R", pre(includeText("server.R"))),
tabPanel("ReadMe", withMathJax(), includeMarkdown("ReadMe.Rmd"))
)
))
# source("../../initMlxR.R") #initialization for simulx.R
library(mlxR)
pkmodel.text <- ("
res <- pkmodel(t,adm,p)
print(ggplot(data=res, aes(x=time, y=cc)) + geom_line(size=1) +
xlab('time (h)') + ylab('concentration (mg/L)'))
")
shinyServer(function(input, output){
r <- reactive({
param.name=NULL
param.value=NULL
if (input$administration=="oral"){
if (input$absorption=="1"){
if (input$delay1=="1"){
param.name=c(param.name,'Tlag')
param.value=c(param.value,input$tlag1)
}
if (input$delay1=="2"){
param.name=c(param.name,'Mtt','Ktr')
param.value=c(param.value,input$mtt,(input$ntr+1)/input$mtt)
}
param.name=c(param.name,'ka')
param.value=c(param.value,input$ka)
}else{
param.name=c(param.name,'Tk0')
param.value=c(param.value,input$tk0)
if (input$delay0=="1"){
param.name=c(param.name,'Tlag')
param.value=c(param.value,input$tlag0)
}
}
}
param.name=c(param.name,'V')
param.value=c(param.value,input$v)
if (input$distribution!="1"){
param.name=c(param.name,'k12','k21')
param.value=c(param.value,input$k12,input$k21)
}
if (input$distribution=="3"){
param.name=c(param.name,'k13','k31')
param.value=c(param.value,input$k13,input$k31)
}
if (input$elimination=="1"){
param.name=c(param.name,'k')
param.value=c(param.value,input$k)
}else{
param.name=c(param.name,'Vm','Km')
param.value=c(param.value,input$vm,input$km)
}
p=list(name=param.name,value=param.value)
t.value=seq(input$range[1],input$range[2],length.out=input$ngp)
t1=input$tfd
t2=input$ii*(input$nd-1)+t1
if (t2>=t1){
t.dose=seq(t1,t2,by=input$ii)
adm <- list(time=t.dose, amount=input$amt)
}else{
adm <- list(time=t1, amount=0)
}
if (input$administration == 'infusion'){
adm$rate <- input$amt/input$tinf
}
res <- pkmodel(t.value,adm,p)
model.text <- includeText("temp_model.txt")
a.text <- 'adm <- list('
if (input$nd==0){
a.text <- 'adm <- list(amount=0, time=0'
} else if(input$nd==1){
a.text <- paste0('adm <- list(amount=',input$amt,', time=',input$tfd)
} else{
t1=input$tfd
t2=input$ii*(input$nd-1)+t1
a.text <- paste0('adm <- list(amount=',input$amt,
', time=seq(',t1,', ',t2,', by=',input$ii,')')
}
if (input$administration == 'infusion'){
a.text <- paste0(a.text,', tinf=',input$tinf,')')
}else{
a.text <- paste0(a.text,')')
}
K <- length(param.value)
p.text <- 'p <- c('
for (k in (1:(K-1))){
p.text <- paste0(p.text,param.name[k],'=',param.value[k],', ')
}
p.text <- paste0(p.text,param.name[K],'=',param.value[K],')')
t.text <- paste0('t <- seq(',input$range[1],', ',input$range[2],
', length=',length.out=input$ngp,')')
pkmodel.text <- paste0(a.text,'\n',p.text,'\n',t.text,'\n',pkmodel.text)
out <- list(res,model.text,pkmodel.text)
return(out)
})
output$plot <- renderPlot({
pl=ggplotmlx(data=r()[[1]], aes(x=time, y=cc)) + geom_line(size=input$lsize)
if (input$log==TRUE)
pl=pl + scale_y_log10()
print(pl)
})
output$table <- renderTable({ r()[[1]] })
output$mlxtranFile <- renderText(r()[[2]])
output$RFile <- renderText(r()[[3]])
})
Select the administration route and the dosage regimen in the tab administration:
Define the PK model in the tab model:
Define the absorption process for oral administration in the tab absorption:
Define the distribution process in the tab distribution: 1, 2 or 3 compartments
Define the eliination process in the tab elimination: linear or Michaelis Menten elimination process
Define the output in the tab outputs:
Set some settings in the tab settings: line width, linear or semi-log scale.