Personal Details
Age Group
Gender
Cyclosporine Medication
Dose Recommendation
Cyclosporine Medication
Concurrent Disorders
route of administration
absorption
delay
distribution
elimination
output
pkmodelCode.R
ui.R
Download
library(shinydashboard)
sidebar <- dashboardSidebar(width = 300,
hr(),
sidebarMenu(id="tabs",
menuItem("Plot", tabName = "plot", icon = icon("line-chart"), selected=TRUE)
),
hr(),
conditionalPanel("input.tabs=='plot'",
sidebarMenu(
menuItem("Personal Details", tabName = "details", icon = icon("chevron-circle-right"),selected=TRUE ),
menuItem("Disease State", tabName = "DisState", icon = icon("chevron-circle-right")),
menuItem("Cyclosporine PK Details", tabName = "PkDetails", icon = icon("chevron-circle-right")),
menuItem("Administration", tabName = "admin", icon = icon("chevron-circle-right") ,selected=TRUE),
menuItem("Parameterization", icon = icon("chevron-circle-right"),
fluidRow(
column(1),
column(10,
radioButtons("parameterization","",c("rate constant" = "1","clearance" = "2"),selected = "2")
)) ),
menuItem("Model", icon = icon("chevron-circle-right"),
menuSubItem("Absorption", tabName = "absorption", icon = icon("angle-right")),
menuSubItem("Distribution", tabName = "distribution", icon = icon("angle-right")),
menuSubItem("Elimination", tabName = "elimination", icon = icon("angle-right"))
),
menuItem("Output", tabName = "output", icon = icon("chevron-circle-right"))
)
)
)
body <- dashboardBody(
tabItems(
tabItem(tabName = "plot",
fluidRow(
box(width = 12, status = "primary",
downloadButton('downloadPlot','Download'), br(),
plotOutput("plot", height="300px")
),
tabItems(
tabItem(tabName = "details",
box(width = 4, status = "primary",solidHeader = TRUE, title="Personal Details",
sliderInput("age", "Age(yrs):", value=30, min=1, max = 100, step=1),
sliderInput("weight", "Weight(Kgs):", value=75, min=1, max = 125, step=1),
sliderInput("height", "height(inches,12 inches = 1 feet):", value=66, min=36, max = 80, step=1)
),
box(width = 4, status = "primary", solidHeader = TRUE, title = "Age Group",
radioButtons("ageG", "Select the Age Group",
c("Pediatric (2 yrs - 16 yrs)" = "pediatric","Adult (16 yrs -60 yrs)"="adult","Geriatric (60 yrs-80 yrs)"="geriatric"),selected="adult")
),
box(width = 4, status = "primary", solidHeader = TRUE, title="Gender",
radioButtons("gender", "Select the Gender Type",
c("Male" = "male","Female"="female"),selected="male")
)
),
tabItem(tabName = "PkDetails",
box(width = 4, status = "primary", solidHeader = TRUE,title="Cyclosporine Medication",
sliderInput("css", "Average Concentration(ng/mL)", value=250, min=100, max = 2000, step=1),
sliderInput("F", "Bioavailability:", value=0.3, min=0.3, max = 0.3, step=0.1)
),
#conditionalPanel(condition = "input.administration == 'infusion'",
#box(width = 4, status = "warning", solidHeader = TRUE,title="Therapeutic Range",
# htmlOutput("printCssAvgI")
# )
# ),
#conditionalPanel(condition = "input.administration == 'oral'",
# box(width = 4, status = "warning", solidHeader = TRUE,title="Therapeutic Range",
# htmlOutput("printCssAvgO")
# )
# ),
box(width = 4, status = "primary", solidHeader = TRUE,title="Dose Recommendation",
htmlOutput("printDosage"),
htmlOutput("DoseRange")
)
),
tabItem(tabName = "DisState",
box(width = 4, status = "primary", solidHeader = TRUE,title="Cyclosporine Medication",
radioButtons("disease", "",
c("Renal Transplant" = "RenalTransplant","Liver Transplant"="LiverTransplant","Heart Transplant"="HeartTransplant","BoneMarrow Transplant"="BoneMarrowTransplant","Stem Cell Transplant"="StemCellTransplant","Rheumatoid Arthritis" = "RhematoidArthritis","Psoriasis" = "Psoriasis","Atopic Dermatitis"="AtopicDermatitis","Endogenous Uveitis"="EndogenousUveitis"),selected="RenalTransplant")
),
box(width = 4, status = "primary", solidHeader = TRUE,title="Concurrent Disorders",
radioButtons("condisease", "",
c("Normal Liver" = "NormalLiver","Liver Disorder" = "LiverDisorder"),selected="NormalLiver")
)
),
tabItem(tabName = "admin",
box(width = 4, status = "primary", solidHeader = TRUE, title="route of administration",
radioButtons("administration", "",
c("iv infusion" = "infusion","oral" = "oral"),selected="oral")
),
box(width = 4, status = "primary",
sliderInput("tfd", "Time of first dose:", value=0, min=0, max = 20, step=1),
sliderInput("nd", "Number of doses:", value=6, min=0, max = 10, step=1)
),
box(width = 4, status = "primary",
sliderInput("ii", "Interdose interval:", value = 12, min = 10, max = 15, step=1),
conditionalPanel(condition = "input.administration == 'infusion'",
sliderInput("tinf", "Infusion time:", value = 1, min = 0, max = 5, step=0.2)
)
)
),
tabItem(tabName = "absorption",
conditionalPanel(condition = "input.administration == 'oral'",
box(width = 4, status = "primary", solidHeader = TRUE, title="absorption",
radioButtons("absorption","",c("first order" = "1"))
),
box(width = 4, status = "primary", solidHeader = TRUE, title="delay",
conditionalPanel(condition = "input.absorption == '1'",
radioButtons("delay1","",c("none" = "0","lag time" = "1"))
)
),
box(width = 4, status = "primary",
conditionalPanel(condition = "input.absorption == '1'",
sliderInput("ka", "rate constant ka:", value = 0.5, min = 0, max = 3, step=0.1)
),
conditionalPanel(condition = "(input.absorption == '1' & input.delay1 == '1') ",
sliderInput("tlag", "lag time Tlag:", value = 1, min = 0, max = 10, step=0.5)
)
)
)
),
tabItem(tabName = "distribution",
# fluidRow(
box(width = 4, status = "primary", solidHeader = TRUE, title="distribution",
# h5("Number of compartments:"),
radioButtons("distribution","Number of compartments:",c("1" = "1","2" = "2"), inline=TRUE),
sliderInput("v", "volume V:(L/kg)", value = 4, min = 4, max = 5, step=0.1)
),
conditionalPanel(condition = "input.distribution != '1' & input.parameterization=='1'",
box(width = 4, status = "primary",
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 != '1' & input.parameterization=='2'",
box(width = 4, status = "primary",
sliderInput("v2", "periph. comp. volume V2:", value = 20, min = 2, max = 40, step=2),
sliderInput("q2", "inter comp. clearance Q2:", value = 4, min = 1, max = 10, step=0.5)
)
)
),
tabItem(tabName = "elimination",
box(width = 4, status = "primary", solidHeader = TRUE, title="elimination",
radioButtons("elimination","",c("linear" = "1"))
),
box(width = 4, status = "primary",
conditionalPanel(condition = "input.elimination=='1' & input.parameterization=='1'",
sliderInput("k", "elimination rate constant k:", value = 0.1, min = 0, max = 2, step=0.05)
),
conditionalPanel(condition = "input.elimination == '1' & input.parameterization=='2'",
sliderInput("Cl", "Clearance Cl:", value = 4, min = 4, max = 5, step=1)
)
)
),
tabItem(tabName = "output",
box(width = 4, status = "primary", solidHeader = TRUE, title="output",
radioButtons("log", "", c("linear scale" = FALSE,"log scale" = TRUE))
),
box(width = 4, status = "primary",
sliderInput("range", "time range", min = -10, max = 200, value = c(-5,100), step=5),
sliderInput("ngp", "grid size", min = 50, max = 1000, value = 500, step=50)
),
box(width = 4, status = "primary",
sliderInput("lsize", "line width", min = 0, max = 5, value = 0.75, step=0.25)
)
)#ad
)#before plot
)
),
tabItem(tabName = "pkmodel",
box( width = NULL, status = "primary", solidHeader = TRUE, title="pkmodelCode.R",
downloadButton('downloadData1', 'Download'),
br(),br(),
verbatimTextOutput("RFile")
)
),
tabItem(tabName = "ui",
box( width = NULL, status = "primary", solidHeader = TRUE, title="ui.R",
downloadButton('downloadData2', 'Download'),
br(),br(),
pre(includeText("ui.R"))
)
),
tabItem(tabName = "server",
box( width = NULL, status = "primary", solidHeader = TRUE, title="server.R",
downloadButton('downloadData3', 'Download'),
br(),br(),
pre(includeText("server.R"))
)
)
)
)
dashboardPage(
dashboardHeader(title = "Cyclosprorine Drug"),
sidebar,
body
)
server.R
Download
# This is the server logic for a Shiny web application.
# You can find out more about building applications with Shiny here:
#
# http://shiny.rstudio.com
#
library(shinydashboard)
library(mlxR)
library(ggplot2)
shinyServer(function(input, output) {
l.text <- ("library(mlxR)\n")
iModel <- "
[LONGITUDINAL]
input = {V, Cl}
EQUATION:
Cc = pkmodel(V, Cl)
"
oModel <-
"
[LONGITUDINAL]
input = {ka, V, Cl}
EQUATION:
Cc = pkmodel(ka, V, Cl)
"
myModel <- inlineModel(oModel,"pk_model.txt")
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 (ng/L)'))
")
CalABW<-reactive({
IBWm=50+(2.3)*((input$height)-60)
cIBWm=(0.3)*(IBWm)
IBWw=45.5+(2.3)*((input$height)-60)
cIBWw=(0.3)*(IBWw)
ABWm=0
ABWw=0
if(input$height>60 & input$gender=="male")
{
print("value of ibw and cib")
print(input$weight)
print(IBWm)
print(cIBWm)
print(cIBWm+IBWm)
if(input$weight<(cIBWm+IBWm))
{
print("inside if")
ABWm=input$weight
}else
{
print("inside else")
ABWm=54.7+0.4*((input$weight)-(54.7))
}
print(ABWm)
print("above adjusted body weight")
return(ABWm)
}
if(input$height>60 & input$gender=="female")
{
if(input$weight<(cIBWw+IBWw))
{
ABWw=input$weight
}else
{
ABWw=54.7+0.4*((input$weight)-(54.7))
}
return(ABWw)
}
})
CalTRDose <- reactive({
param.name=NULL
param.value=NULL
print("Value of ideal body weight")
print(CalABW())
RT1D=(CalABW())*6*(0.5)
RT2D=(CalABW())*12*(0.5)
RT=list(RT1D,RT2D)
LT1D=(CalABW())*4*(0.5)
LT2D=(CalABW())*12*(0.5)
LT=list(LT1D,LT2D)
HT1D=(CalABW())*4*(0.5)
HT2D=(CalABW())*10*(0.5)
HT=list(HT1D,HT2D)
BMT1D=(CalABW())*2*(0.5)
BMT2D=(CalABW())*15*(0.5)
BMT=list(BMT1D,BMT2D)
SCT1D=(CalABW())*2*(0.5)
SCT2D=(CalABW())*15*(0.5)
SCT=list(SCT1D,SCT2D)
R1D=(CalABW())*3*(0.5)
R2D=(CalABW())*5*(0.5)
R=list(R1D,R2D)
P1D=(CalABW())*2.5*(0.5)
P2D=(CalABW())*5*(0.5)
P=list(P1D,P2D)
AD1D=(CalABW())*2.5*(0.5)
AD2D=(CalABW())*5*(0.5)
AD=list(AD1D,AD2D)
E1D=(CalABW())*5*(0.5)
E2D=(CalABW())*7*(0.5)
E=list(E1D,E2D)
edf<-expand.grid(weight=input$weight,disease=c("RenalTransplant","LiverTransplant","HeartTransplant","BoneMarrowTransplant","StemCellTransplant","RhematoidArthritis","Psoriasis","AtopicDermatitis","EndogenousUveitis"))
edf$rt<-ifelse((input$disease=="RenalTransplant"),(list(RT)),0)
edf$lt<-ifelse((input$disease=="LiverTransplant"),(list(LT)),0)
edf$ht<-ifelse((input$disease=="HeartTransplant"),(list(HT)),0)
edf$bmt<-ifelse((input$disease=="BoneMarrowTransplant"),(list(BMT)),0)
edf$sct<-ifelse((input$disease=="StemCellTransplant"),(list(SCT)),0)
edf$r<-ifelse((input$disease=="RhematoidArthritis"),(list(R)),0)
edf$p<-ifelse((input$disease=="Psoriasis"),(list(P)),0)
edf$ad<-ifelse((input$disease=="AtopicDermatitis"),(list(AD)),0)
edf$e<-ifelse((input$disease=="EndogenousUveitis"),(list(E)),0)
adf<-subset(edf,disease==input$disease )
ad<-adf[, sapply(adf, function(x) is.list(x))]
TRdoses<-unlist(ad)
param.name=c(param.name,'DoseMin')
param.value=c(param.value,TRdoses[1])
param.name=c(param.name,'DoseMax')
param.value=c(param.value,TRdoses[2])
dosedf<-data.frame(name=param.name,value=param.value)
return(dosedf)
})
caldose<-reactive({
param.name=NULL
param.value=NULL
Clm=0
Clf=0
#Formula for Clearance Calculation
if(input$gender=='male')
{
Clm=(CalABW())*(60/1000)
}
else
{
Clf=(CalABW())*(60/1000)
}
#concurrent disease
#for Normal Liver in dAdult and Geriatric
NClm=6*(Clm) #60/1000
print("d: value of clearance after L/Hour")
print(NClm)
NClw=6*(Clf)
#Liver disorder Clearance for Adults and Gediatric
DLClm=3*(Clm)
DLClw=3*(Clf)
#check when pediatric add some more if required
#get the values for dosage regimen calculation
d<-input$css
t=input$ii
# Part II calculation , multiply dosing interval with Css and divide by 1000
c=(((input$ii)*(d))/((1000)))
print("d: value of the c ")
print(c)
#----------------------Calculate thalf,cl,vd,Cmax,Cmin,ke,dose Adult Male
NACl<-NClm
DNclAm<-((NACl)*(c))
print("d: value of NaCl")
print(DNclAm)
#----------------------Calculation for Adult female Normal Liver----
NAFCl<-NClw
DNclFm<-((NAFCl)*(c))
#----------------------Calculation for Adult male Disorder Liver----
DLAClm<-DLClm
DLclAm<-((DLAClm)*(c))
#----------------------Calculation for Adult female Disorder Liver----
DLAClw<-DLClw
DNclAw<-((DLAClw)*(c))
#----------------------Calculate thalf,cl,vd,Cmax,Cmin,ke,dose Geriatric Male
NGCl<-NClm
DNclGm<-((NACl)*(c))
#----------------------Calculation for Geriatric female Normal Liver----
NAGFCl<- NClw
DNclG<- ((NAFCl)*(c))
#----------------------Calculation for Geriatric male Disorder Liver----
DLGClm<-DLAClm
DLGlAm<-DLclAm
#----------------------Calculation for Geriatric female Disorder Liver----
DLGClw<-DLAClw
DNclAw<-DNclAw
#Pediatric Clearance
NClPw=10*(Clf)
NClPm=10*(Clm)
DLClm=3*(Clm)
DLClw=3*(Clf)
#----------------------Calculation for Pediatric female Disorder Liver----
DLPClw<-DLClw
DNclPw<-DNclAw
#----------------------Calculation for Pediatric male Disorder Liver----
DLClPm<-DLClm
DLDclPm<-DLClPm
#----------------------Calculation for Pediatric female Normal Liver----
NPwCl<-NClPw
DNclPw<-((NPwCl)*(c))
#----------------------Calculate thalf,cl,vd,Cmax,Cmin,ke,dose Pediatric Normal liver
NPmCl<-NClPm
DNPmclAm<-((NPmCl)*(c))
#debug is giving correct answer till this
MNA=c(NACl,DNclAm)
FNA=c(NAFCl,DNclFm)
MLDA=c(DLAClm,DLclAm)
FLDA=c(DLAClw,DNclAw)
MNG=c(NGCl,DNclGm)
FNG=c(NAGFCl,DNclG)
MDLG=c(DLGClm,DLGlAm)
FDLG=c(DLGClw,DNclAw)
MNP=c(NPmCl,DNPmclAm)
FNP=c(NPwCl,DNclPw)
MDLP=c(DLClPm,DLDclPm)
NDLP=c(DLPClw,DNclPw)
edf<-expand.grid(age=input$age,height=input$height,weight=input$weight,ageG=c("pediatric","adult","geriatric"),gender=c("male","female"),administration=c("infusion","oral"),condisease=c("NormalLiver","LiverDisorder"),disease=c("RenalTransplant","LiverTransplant","HeartTransplant","BoneMarrowTransplant","StemCellTransplant","RhematoidArthritis","Psoriasis","AtopicDermatitis","EndogenousUveitis"),css=input$css)
edf$DNClAm<-ifelse(((input$gender=="male") & (input$condisease=="NormalLiver")& (input$ageG =="adult")&(NACl>0)), ( list(MNA)),0)
edf$DNClAw<-ifelse(((input$gender=="female") & (input$condisease=="NormalLiver")& (input$ageG =="adult")& (NAFCl>0)),(list(FNA)),0)
edf$DDLClAm<-ifelse(((input$gender=="male") & (input$condisease=="LiverDisorder")& (input$ageG =="adult")&(DLAClm>0)),(list(MLDA)),0)
edf$DDLClAw<-ifelse(((input$gender=="female") & (input$condisease=="LiverDisorder")& (input$ageG =="adult")&(DLAClw>0)),(list(FLDA)),0)
edf$DNClGm<-ifelse(((input$gender=="male") & (input$condisease=="NormalLiver")& (input$ageG =="geriatric")&(NGCl>0)),(list(MNG)),0)
edf$DNClGw<-ifelse(((input$gender=="female") & (input$condisease=="NormalLiver")& (input$ageG =="geriatric")&(NAGFCl>0)),(list(FNG)),0)
edf$DDLClGm<-ifelse(((input$gender=="male") & (input$condisease=="LiverDisorder")& (input$ageG =="geriatric")&(DLGClm>0)),(list(MDLG)),0)
edf$DDLClGw<-ifelse(((input$gender=="female") & (input$condisease=="LiverDisorder")& (input$ageG =="geriatric")&(DLGClw>0)),(list(FDLG)),0)
edf$DNClPm<-ifelse(((input$gender=="male") & (input$condisease=="NormalLiver") &(input$ageG =="pediatric")&(NPmCl>0)),(list(MNP)),0)
edf$DNClPw<-ifelse(((input$gender=="female") & (input$condisease=="NormalLiver") &(input$ageG =="pediatric")&(NPwCl>0)),(list(FNP)),0)
edf$DDLClPm<-ifelse(((input$gender=="male") & (input$condisease=="LiverDisorder") &(input$ageG =="pediatric")&(DLClPm>0)),(list(MDLP)),0)
edf$DDLClPw<-ifelse(((input$gender=="female") & (input$condisease=="LiverDisorder") &(input$ageG =="pediatric")&(DLPClw>0)),(list(NDLP)),0)
adf<-subset(edf,ageG==input$ageG & gender==input$gender & administration==input$administration & condisease==input$condisease & disease==input$disease )
ad<-adf[, sapply(adf, function(x) is.list(x))]
ClDose<-unlist(ad)
print("d: cldose result")
print(ClDose)
CD<-ClDose[2]
#Formula for Clearance Calculation
if(input$administration=='oral')
{
CD=(ClDose[2])/(0.3)
print("value of CD")
print(CD)
}
else
{
CD=ClDose[2]
}
print("d: value of calculated dose")
print(CD)
#calculate Avg Css for Disease Therapeutic range Dose1 and Dose2
CssAvg1o=((0.3*1000)*(CalTRDose()[[2]][1]))/((ClDose[1])*(input$ii))
CssAvg1i=((CalTRDose()[[2]][1])*(1000))/((ClDose[1])*(input$ii))
CssAvg2o=((0.3*1000)*(CalTRDose()[[2]][2]))/((ClDose[1])*(input$ii))
CssAvg2i=((CalTRDose()[[2]][2])*(1000))/((ClDose[1])*(input$ii))
param.name=c(param.name,'Cl')
param.value=c(param.value,ClDose[1])
param.name=c(param.name,'mdose')
param.value=c(param.value,CD)
param.name=c(param.name,'CssAvgMino')
param.value=c(param.value,CssAvg1o)
param.name=c(param.name,'CssAvgMini')
param.value=c(param.value,CssAvg1i)
param.name=c(param.name,'CssAvgMaxo')
param.value=c(param.value,CssAvg2o)
param.name=c(param.name,'CssAvgMaxi')
param.value=c(param.value,CssAvg2i)
param.name=c(param.name,'DoseMin')
param.value=c(param.value,CalTRDose()[[2]][1])
param.name=c(param.name,'DoseMax')
param.value=c(param.value,CalTRDose()[[2]][2])
pkvalues<-data.frame(name=param.name,value=param.value)
return(pkvalues)
})
output$printCssAvgO<-reactive({
print("value of Average concentration")
a<-caldose()[[2]][5]
b<-caldose()[[2]][3]
paste0("<b>","Maximum Css ",as.integer(a)," micrograms" ,"<br>", "Minimum Css " ,as.integer(b)," micrograms","</b>")
})
output$printCssAvgI<-reactive({
print("value of Average concentration")
a<-caldose()[[2]][5]
b<-caldose()[[2]][3]
paste0("<b>","Maximum Css " ,as.integer(a)," micrograms" ,"</b>","<br>", "Minimum Css " ,"<b>",as.integer(b)," micrograms","</b>")
})
output$printDosage<-reactive({
a<-caldose()[[2]][2]
paste0("<b>","Dosage Recommended For every ",input$ii," Hrs is ", as.integer(a)," milligrams","</b>")
})
#output$DoseRange<-reactive({
# a<-CalTRDose()[[2]][1]
# b<-CalTRDose()[[2]][2]
# paste0("<b>","Maximum Recommended Dosage " ,as.integer(a)," mg" ,"</b>","<br>", "Minimum Recommended Dosage " ,"<b>",as.integer(b)," mg","for",input$disease,"</b>")
# })
output$DoseRange<-reactive({
a<-CalTRDose()[[2]][1]
b<-CalTRDose()[[2]][2]
paste0("<b>",input$disease,"(",as.integer(a)," mg","-",as.integer(b),"mg", ")","</b>")
})
recaldose <- reactive({
Doselst=list(caldose()[[2]][2],caldose()[[2]][7],caldose()[[2]][8])
vod=(input$v) *(input$weight)
pkMaxlist=list()
pkMinlist=list()
i=1
for(Dose in Doselst)
{
if(input$administration=='oral')
{
Dose<-Dose*0.3
myModel <- inlineModel(oModel,"pk_model.txt")
p <- c(ka=input$ka, V=vod, Cl=caldose()[[2]][1])
adm <- list(tfd=input$tfd, ii=input$ii, amount=Dose*input$F)
}
else
{
myModel <- inlineModel(iModel,"pk_model.txt")
p <- c( V=vod, Cl=caldose()[[2]][1])
adm <- list(tfd=input$tfd, ii=input$ii, amount=Dose )
}
out<-list(name="Cc",time='steady.state')
#----------------------------------------------------
res <- exposure(model=myModel, parameter=p, output=out, treatment=adm)
#---------------------------------------------------
pkMaxlist[[i]]<-res$Cc[["cmax"]]
pkMinlist[[i]]<-res$Cc[["cmin"]]
rm(p,adm,res)
i=i+1
}
mylst=c(pkMaxlist,pkMinlist)
return(mylst)
})
output$plot <- renderPlot({
pl <- myplot(r()[[1]]$f, input$lsize, input$log)
print(pl)
})
myplot <- function(r,lsize,ilog){
yi=recaldose()
# ylst=c(yi[[2]],yi[[3]],yi[[5]],yi[[6]])
# clst=c("green","Red","green","Red")
ylst=c(yi[[3]],yi[[5]])
clst=c("Red","green")
pl=ggplotmlx(data=r, aes(x=time, y=cc)) + geom_line(size=lsize)+(geom_hline(yintercept=ylst, linetype="dashed", color = clst))+ xlab("time(h)")+ylab("Concentration(ng)")
if (ilog==TRUE)
pl=pl + scale_y_log10()
return(pl)
}
r <- reactive({
param.name=NULL
param.value=NULL
if(input$administration=="oral")
{
dose=caldose()[[2]][2]*0.3
}
else{
dose=caldose()[[2]][2]
}
if (input$administration=="oral"){
if (input$absorption=="1"){
if (input$delay1=="1"){
param.name=c(param.name,'Tlag')
param.value=c(param.value,input$tlag)
}
param.name=c(param.name,'ka')
param.value=c(param.value,input$ka)
}
}
param.name=c(param.name,'V')
param.value=c(param.value,((input$v)*(input$weight)))
if (input$distribution!="1"){
if (input$parameterization=="1"){
param.name=c(param.name,'k12','k21')
param.value=c(param.value,input$k12,input$k21)
}else{
param.name=c(param.name,'Q2','V2')
param.value=c(param.value,input$q2,input$v2)
}
}
if (input$elimination=="1"){
if (input$parameterization=="1"){
param.name=c(param.name,'k')
param.value=c(param.value,input$k)
}else{
param.name=c(param.name,'Cl')
param.value=c(param.value,caldose()[[2]][1])
}
}
p=param.value
names(p)=param.name
t.value=seq(input$range[1],input$range[2],length.out=(input$ngp+1))
t1=input$tfd
t2=input$ii*(input$nd-1)+t1
a.names <- c("amount","tfd","nd","ii")
a.values <- c(dose,input$tfd,input$nd,input$ii)
if (t2>=t1){
t.dose=seq(t1,t2,by=input$ii)
adm <- list(time=t.dose, amount=dose)
}else{
adm <- list(time=t1, amount=0)
}
if (input$administration == 'infusion'){
adm$rate <- dose/input$tinf
a.names <- c(a.names, "tinf")
a.values <- c(a.values, input$tinf)
}
#----------------------------------------------------
res <- pkmodel(time=t.value,treatment=adm,parameter=p)
#----------------------------------------------------
a.text <- 'adm <- list('
if (input$nd==0){
a.text <- 'adm <- list(amount=0, time=0'
} else if(input$nd==1){
a.text <- paste0('adm <- list(amount=',dose,', time=',input$tfd)
} else{
t1=input$tfd
t2=input$ii*(input$nd-1)+t1
a.text <- paste0('adm <- list(amount=',dose,
', time=seq(',t1,', ',t2,', by=',input$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$ngp,')')
pkmodel.text <- paste0(l.text,a.text,'\n',p.text,'\n',t.text,'\n',pkmodel.text)
parameter <- data.frame(row.names= names(p), value=p)
treatment <- data.frame(row.names= a.names, value=a.values)
res <- list(parameter=p, f=res, treatment=treatment)
out <- list(res,pkmodel.text)
return(out)
})
output$tablef <- renderTable({ r()[[1]]$f })
output$tablep <- renderTable({ r()[[1]]$parameter },include.colnames=FALSE)
output$tablea <- renderTable({ r()[[1]]$treatment },include.colnames=FALSE)
output$RFile <- renderText(r()[[2]])
output$downloadTablef <- downloadHandler(
filename = paste("concentration", Sys.Date(), ".csv", sep=""),
content = function(file) {
write.csv(r()[[1]]$f, file, row.names=FALSE)
}
)
output$downloadTablep <- downloadHandler(
filename = paste("parameter", Sys.Date(), ".csv", sep=""),
content = function(file) {
write.table(r()[[1]]$parameter, file, col.names=FALSE, sep=",")
}
)
output$downloadTablea <- downloadHandler(
filename = paste("dosage", Sys.Date(), ".csv", sep=""),
content = function(file) {
write.table(r()[[1]]$treatment, file, col.names=FALSE, sep=",")
}
)
output$downloadData1 <- downloadHandler(
filename = "pkmodelCode.R",
content = function(file) {
write(r()[[2]], file)
}
)
output$downloadData2 <- downloadHandler(
filename = "ui.R",
content = function(file) {
con = file("ui.R", open = "r")
lines = readLines(con)
close(con)
write(lines, file)
}
)
output$downloadData3 <- downloadHandler(
filename = "server.R",
content = function(file) {
con = file("server.R", open = "r")
lines = readLines(con)
close(con)
write(lines, file)
}
)
output$downloadPlot <- downloadHandler(
filename <- function() {
paste("concentration", Sys.Date(), ".png", sep="") },
content <- function(file) {
png(file, width = 980, height = 600, units = "px", pointsize = 12, bg = "white", res = NA)
# png(file, bg = "white", res = NA)
pl <- myplot(r()[[1]]$f, input$lsize, input$log)
print(pl)
dev.off()},
contentType = 'image/png'
)
})