Nothing
R/PKconverterApp.R
In PKconverter: The Parameter Converter of the Pharmacokinetic Models
Defines functions
PKconverterApp
Documented in
PKconverterApp
#' Shiny App for converting the pharmacokinetic parameters
#'
#' Pharmacokinetics is the study of drug absorption, distribution, metabolism,
#' and excretion. The pharmacokinetics model explains that how the drug
#' concentration change as the drug moves through the different compartments
#' of the body. For pharmacokinetic modeling and analysis, it is essential
#' to understand the basic pharmacokinetic parameters. All parameters are
#' considered, but only some of parameters are used in the model.
#' Therefore,we need to convert the estimated parameters to the other
#' parameters after fitting the specific pharmacokinetic model.
#' @usage PKconverterApp()
#' @examples
#' #PKconverterApp()
#' @export
#'
PKconverterApp<-function(){
PKconverter.env<-new.env()
PK_app=shiny::shinyApp(
ui=shiny::fluidPage(
theme=shinythemes::shinytheme("cerulean"),
shiny::shinyUI(
shiny::navbarPage("PK Parameter Converter",
############################sheet1############################
shiny::tabPanel(title="Model 1",
shiny::sidebarLayout(
shiny::column(width=5,
shinydashboard::box(title="Select your model",width=NULL,
solidHeader=TRUE,status="warning",
background="light-blue",
shiny::radioButtons("model1", "MODEL TYPE :",
list("One compartment model" ="one",
"Two compartment model" ="two",
"Three compartment model" ="three"))),
shiny::tags$hr(),
shiny::tags$hr(),
shinydashboard::box(title="Enter your estimate and std.err",
width=NULL,solidHeader=TRUE,status="warning",
background="light-blue",
shiny::tabsetPanel(id="input1",type="pills",
shiny::tabPanel("Estimate / Std.err", value="meanandsd",
shiny::tags$hr(),
shiny::conditionalPanel(condition="input.model1=='one'",
shiny::uiOutput("comp1_1_1"),
shiny::uiOutput("comp1_1_2")),
shiny::conditionalPanel(condition="input.model1=='two'",
shiny::uiOutput("comp2_1_1"),
shiny::uiOutput("comp2_1_2"),
shiny::uiOutput("comp2_1_3"),
shiny::uiOutput("comp2_1_4")),
shiny::conditionalPanel(condition="input.model1=='three' ",
shiny::uiOutput("comp3_1_1"),
shiny::uiOutput("comp3_1_2"),
shiny::uiOutput("comp3_1_3"),
shiny::uiOutput("comp3_1_4"),
shiny::uiOutput("comp3_1_5"),
shiny::uiOutput("comp3_1_6"))),
shiny::tabPanel("Covariance", value="varcov",
shiny::conditionalPanel(condition="input.model1=='one'||
input.model1=='two'||input.model1=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("v1cl1_1")))),
shiny::conditionalPanel(condition="input.model1=='two'||
input.model1=='three'",
shiny::fluidRow(shiny::column(4,shiny::uiOutput("v2cl1_1")),
shiny::column(4,shiny::uiOutput("v1v2_1")))),
shiny::conditionalPanel(condition="input.model1=='three'",
shiny::fluidRow(shiny::column(4,shiny::uiOutput("v3cl1_1")),
shiny::column(4,shiny::uiOutput("v1v3_1")),
shiny::column(4,shiny::uiOutput("v2v3_1")))),
shiny::conditionalPanel(condition="input.model1=='two'||
input.model1=='three'",
shiny::fluidRow(shiny::column(4,shiny::uiOutput("v1cl2_1")),
shiny::column(4,shiny::uiOutput("v2cl2_1")),
shiny::column(4,shiny::uiOutput("cl1cl2_1")))),
shiny::conditionalPanel(condition="input.model1=='three'",
shiny::fluidRow(shiny::column(4,shiny::uiOutput("v1cl3_1")),
shiny::column(4,shiny::uiOutput("v3cl2_1")),
shiny::column(4,shiny::uiOutput("cl1cl3_1")))),
shiny::conditionalPanel(condition="input.model1=='three'",
shiny::fluidRow(shiny::column(4,shiny::uiOutput("v2cl3_1")),
shiny::column(4,shiny::uiOutput("v3cl3_1")),
shiny::column(4,shiny::uiOutput("cl2cl3_1"))))))),
shiny::tags$hr(),
shiny::tags$hr(),
shinydashboard::box(title="Save results as a file",width=NULL,
solidHeader=TRUE,status="warning",
background="light-blue",
shiny::radioButtons("type1", "File type:",
choices = c("Excel (CSV)" ,
"Text (tab separated)" ,
"Text (Space Separated)")),
shiny::conditionalPanel(condition = "input.model1=='one'",
shiny::downloadButton("downloadData1_1",
"Save results to file")),
shiny::conditionalPanel(condition = "input.model1=='two'",
shiny::downloadButton("downloadData1_2",
"Save results to file")),
shiny::conditionalPanel(condition = "input.model1=='three'",
shiny::downloadButton("downloadData1_3",
"Save results to file")))),
shiny::column(width=7,
shiny::wellPanel(
shiny::h2("Model 1: Volumes and Clearances"),
shiny::tags$br(),
shiny::conditionalPanel(condition = "input.model1=='one'",
shiny::h3("One compartment model"),
shiny::tableOutput("T1_1")),
shiny::conditionalPanel(condition = "input.model1=='two'",
shiny::h3("Two compartment model"),
shiny::tableOutput("T1_2")),
shiny::conditionalPanel(condition = "input.model1=='three'",
shiny::h3("Three compartment model"),
shiny::tableOutput("T1_3")))))),
############################sheet2############################
shiny::tabPanel(title="Model 2",
shiny::sidebarLayout(
shiny::column(width=5,
shinydashboard::box(title="Select your model",width=NULL,
solidHeader=TRUE,status="warning",
background="light-blue",
shiny::radioButtons("model2", "MODEL TYPE :",
list("One compartment model" ="one",
"Two compartment model" ="two",
"Three compartment model" ="three"))),
shiny::tags$hr(),
shiny::tags$hr(),
shinydashboard::box(title="Enter your estimate and std.err",
width=NULL,solidHeader=TRUE,status="warning",
background="light-blue",
shiny::tabsetPanel(id="input2",
shiny::tabPanel("Estimate / Std.err", value="meanandsd2",
shiny::tags$hr(),
shiny::conditionalPanel(condition="input.model2=='one'",
shiny::uiOutput("comp1_2_1"),
shiny::uiOutput("comp1_2_2")),
shiny::conditionalPanel(condition="input.model2=='two'",
shiny::uiOutput("comp2_2_1"),
shiny::uiOutput("comp2_2_2"),
shiny::uiOutput("comp2_2_3"),
shiny::uiOutput("comp2_2_4")),
shiny::conditionalPanel(condition="input.model2=='three'",
shiny::uiOutput("comp3_2_1"),
shiny::uiOutput("comp3_2_2"),
shiny::uiOutput("comp3_2_3"),
shiny::uiOutput("comp3_2_4"),
shiny::uiOutput("comp3_2_5"),
shiny::uiOutput("comp3_2_6"))),
shiny::tabPanel("Covariance", value="varcov2",
shiny::conditionalPanel(
condition="input.model2=='one'||input.model2=='two'
||input.model2=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("v1k10_2")))),
shiny::conditionalPanel(
condition="input.model2=='two'||input.model2=='three'",
shiny::fluidRow(shiny::column(4,shiny::uiOutput("v1k12_2")),
shiny::column(4,shiny::uiOutput("v1k21_2")))),
shiny::conditionalPanel(condition="input.model2=='three'",
shiny::fluidRow(shiny::column(4,shiny::uiOutput("v1k13_2")),
shiny::column(4,shiny::uiOutput("v1k31_2")),
shiny::column(4,shiny::uiOutput("k13k31_2")))),
shiny::conditionalPanel(
condition="input.model2=='two'||input.model2=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("k10k12_2")),
shiny::column(4,shiny::uiOutput("k10k21_2")),
shiny::column(4,shiny::uiOutput("k12k21_2")))),
shiny::conditionalPanel(condition="input.model2=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("k10k13_2")),
shiny::column(4,shiny::uiOutput("k10k31_2")),
shiny::column(4,shiny::uiOutput("k12k31_2"))),
shiny::conditionalPanel(condition="input.model2=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("k21k13_2")),
shiny::column(4,shiny::uiOutput("k21k31_2")),
shiny::column(4,shiny::uiOutput("k12k13_2")))))))),
shiny::tags$hr(),
shiny::tags$hr(),
shinydashboard::box(title="Save the result as a file",width=NULL,
solidHeader=TRUE,status="warning",
background="light-blue",
shiny::radioButtons("type2", "File type:",
choices = c("Excel (CSV)" ,
"Text (tab separated)" ,
"Text (Space Separated)")),
shiny::conditionalPanel(condition = "input.model2=='one'",
shiny::downloadButton("downloadData2_1",
"Save results to file")),
shiny::conditionalPanel(condition = "input.model2=='two'",
shiny::downloadButton("downloadData2_2",
"Save results to file")),
shiny::conditionalPanel(condition = "input.model2=='three'",
shiny::downloadButton("downloadData2_3",
"Save results to file")))),
shiny::column(width=7,
shiny::wellPanel(
shiny::h2("Model 2: V1, Rate Constants"),
shiny::tags$br(),
shiny::conditionalPanel(condition = "input.model2=='one'",
shiny::h3("One compartment model"),
shiny::tableOutput("T2_1")),
shiny::conditionalPanel(condition = "input.model2=='two'",
shiny::h3("Two compartment model"),
shiny::tableOutput("T2_2")),
shiny::conditionalPanel(condition = "input.model2=='three'",
shiny::h3("Three compartment model"),
shiny::tableOutput("T2_3")))))),
############################sheet3############################
shiny::tabPanel(title="Model 3",
shiny::sidebarLayout(
shiny::column(width=5,
shinydashboard::box(title="Select your model",width=NULL,
solidHeader=TRUE,status="warning",
background="light-blue",
shiny::radioButtons("model3", "MODEL TYPE :",
list("One compartment model" ="one",
"Two compartment model" ="two",
"Three compartment model" ="three"))),
shiny::tags$hr(),
shiny::tags$hr(),
shinydashboard::box(title="Enter your estimate and std.err",
width=NULL,solidHeader=TRUE,status="warning",
background="light-blue",
shiny::tabsetPanel(id="input3",
shiny::tabPanel("Estimate / Std.err", value="meanandsd3",
shiny::conditionalPanel(condition="input.model3=='one' ",
shiny::uiOutput("comp1_3_1"),
shiny::uiOutput("comp1_3_2")),
shiny::conditionalPanel(condition="input.model3=='two'",
shiny::uiOutput("comp2_3_1"),
shiny::uiOutput("comp2_3_2"),
shiny::uiOutput("comp2_3_3"),
shiny::uiOutput("comp2_3_4")),
shiny::conditionalPanel(condition="input.model3=='three' ",
shiny::uiOutput("comp3_3_1"),
shiny::uiOutput("comp3_3_2"),
shiny::uiOutput("comp3_3_3"),
shiny::uiOutput("comp3_3_4"),
shiny::uiOutput("comp3_3_5"),
shiny::uiOutput("comp3_3_6"))),
shiny::tabPanel("Covariance", value="varcov3",
shiny::conditionalPanel(condition="input.model3=='one'||
input.model3=='two'||input.model3=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("cl1talpha_3")))),
shiny::conditionalPanel(condition="input.model3=='two'||
input.model3=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("v1talpha_3")),
shiny::column(4,shiny::uiOutput("v1tbeta_3")))),
shiny::conditionalPanel(condition="input.model3=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("vdtalpha_3")),
shiny::column(4,shiny::uiOutput("vdtbeta_3")),
shiny::column(4,shiny::uiOutput("vdtgamma_3")))),
shiny::conditionalPanel(condition="input.model3=='two'||
input.model3=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("v1cl1_3")),
shiny::column(4,shiny::uiOutput("cl1tbeta_3")),
shiny::column(4,shiny::uiOutput("talphatbeta_3")))),
shiny::conditionalPanel(condition="input.model3=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("v1vd_3")),
shiny::column(4,shiny::uiOutput("v1tgamma_3")),
shiny::column(4,shiny::uiOutput("vdcl1_3")))),
shiny::conditionalPanel(condition="input.model3=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("cl1tgamma_3")),
shiny::column(4,shiny::uiOutput("talphatgamma_3")),
shiny::column(4,shiny::uiOutput("tbetatgamma_3"))))))),
shiny::tags$hr(),
shiny::tags$hr(),
shinydashboard::box(title="Save the result as a file",width=NULL,
solidHeader=TRUE,status="warning",
background="light-blue",
shiny::radioButtons("type3", "File type:",
choices = c("Excel (CSV)" ,
"Text (tab separated)" ,
"Text (Space Separated)")),
shiny::conditionalPanel(condition = "input.model3=='one'",
shiny::downloadButton("downloadData3_1",
"Save results to file")),
shiny::conditionalPanel(condition = "input.model3=='two'",
shiny::downloadButton("downloadData3_2",
"Save results to file")),
shiny::conditionalPanel(condition = "input.model3=='three'",
shiny::downloadButton("downloadData3_3",
"Save results to file")))),
shiny::column(width=7,
shiny::wellPanel(
shiny::h2("Model 3: V1, Vdss, Cl, half-lives"),
shiny::tags$br(),
shiny::conditionalPanel(condition = "input.model3=='one'",
shiny::h3("One compartment model"),
shiny::tableOutput("T3_1")),
shiny::conditionalPanel(condition = "input.model3=='two'",
shiny::h3("Two compartment model"),
shiny::tableOutput("T3_2")),
shiny::conditionalPanel(condition = "input.model3=='three'",
shiny::h3("Three compartment model"),
shiny::tableOutput("T3_3")))))),
############################sheet4############################
shiny::tabPanel(title="Model 4",
shiny::sidebarLayout(
shiny::column(width=5,
shinydashboard::box(title="Select your model",width=NULL,
solidHeader=TRUE,status="warning",
background="light-blue",
shiny::radioButtons("model4", "MODEL TYPE :",
list("One compartment model" ="one",
"Two compartment model" ="two",
"Three compartment model" ="three"))),
shiny::tags$hr(),
shiny::tags$hr(),
shinydashboard::box(title="Enter your estimate and std.err",
width=NULL,solidHeader=TRUE,status="warning",
background="light-blue",
shiny::tabsetPanel(id="input4",
shiny::tabPanel("Estimate / Std.err", value="meanandsd4",
shiny::conditionalPanel(condition="input.model4=='one' ",
shiny::uiOutput("comp1_4_1"),
shiny::uiOutput("comp1_4_2")),
shiny::conditionalPanel(condition="input.model4=='two' ",
shiny::uiOutput("comp2_4_1"),
shiny::uiOutput("comp2_4_2"),
shiny::uiOutput("comp2_4_3"),
shiny::uiOutput("comp2_4_4")),
shiny::conditionalPanel(condition="input.model4=='three' ",
shiny::uiOutput("comp3_4_1"),
shiny::uiOutput("comp3_4_2"),
shiny::uiOutput("comp3_4_3"),
shiny::uiOutput("comp3_4_4"),
shiny::uiOutput("comp3_4_5"),
shiny::uiOutput("comp3_4_6"))),
shiny::tabPanel("Covariance", value="varcov4",
shiny::conditionalPanel(condition="input.model4=='one'||
input.model4=='two'||input.model4=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("aalpha_4")))),
shiny::conditionalPanel(condition="input.model4=='two'||
input.model4=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("abeta_4")),
shiny::column(4,shiny::uiOutput("ab_4")))),
shiny::conditionalPanel(condition="input.model4=='two'||
input.model4=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("balpha_4")),
shiny::column(4,shiny::uiOutput("bbeta_4")),
shiny::column(4,shiny::uiOutput("alphabeta_4")))),
shiny::conditionalPanel(condition="input.model4=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("agamma_4")),
shiny::column(4,shiny::uiOutput("bgamma_4")),
shiny::column(4,shiny::uiOutput("cgamma_4")))),
shiny::conditionalPanel(condition="input.model4=='three'",
shiny::fluidRow(shiny::column(4,shiny::uiOutput("ac_4")),
shiny::column(4,shiny::uiOutput("bc_4")),
shiny::column(4,shiny::uiOutput("betagamma_4")))),
shiny::conditionalPanel(condition="input.model4=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("alphagamma_4")),
shiny::column(4,shiny::uiOutput("calpha_4")),
shiny::column(4,shiny::uiOutput("cbeta_4"))))))),
shiny::tags$hr(),
shiny::tags$hr(),
shinydashboard::box(title="Save the result as a file",
width=NULL,solidHeader=TRUE,status="warning",
background="light-blue",
shiny::radioButtons("type4", "File type:",
choices = c("Excel (CSV)" ,
"Text (tab separated)" ,
"Text (Space Separated)")),
shiny::conditionalPanel(condition = "input.model4=='one'",
shiny::downloadButton("downloadData4_1",
"Save results to file")),
shiny::conditionalPanel(condition = "input.model4=='two'",
shiny::downloadButton("downloadData4_2",
"Save results to file")),
shiny::conditionalPanel(condition = "input.model4=='three'",
shiny::downloadButton("downloadData4_3"
,"Save results to file")))),
shiny::column(width=7,
shiny::wellPanel(
shiny::h2("Model 4: Coefficients and Exponents"),
shiny::tags$br(),
shiny::conditionalPanel(condition = "input.model4=='one'",
shiny::h3("One compartment model"),
shiny::tableOutput("T4_1")),
shiny::conditionalPanel(condition = "input.model4=='two'",
shiny::h3("Two compartment model"),
shiny::tableOutput("T4_2")),
shiny::conditionalPanel(condition = "input.model4=='three'",
shiny::h3("Three compartment model"),
shiny::tableOutput("T4_3")))))),
############################sheet5############################
shiny::tabPanel(title="Model 5",
shiny::sidebarLayout(
shiny::column(width=5,
shinydashboard::box(title="Select your model",width=NULL,
solidHeader=TRUE,status="warning",
background="light-blue",
shiny::radioButtons("model5", "MODEL TYPE :",
list("One compartment model" ="one",
"Two compartment model" ="two",
"Three compartment model" ="three"))),
shiny::tags$hr(),
shiny::tags$hr(),
shinydashboard::box(title="Enter your estimate and std.err",
width=NULL,solidHeader=TRUE,status="warning",
background="light-blue",
shiny::tabsetPanel(id="input5",
shiny::tabPanel("Estimate / Std.err", value="meanandsd5",
shiny::conditionalPanel(condition="input.model5=='one' ",
shiny::uiOutput("comp1_5_1"),
shiny::uiOutput("comp1_5_2")),
shiny::conditionalPanel(condition="input.model5=='two' ",
shiny::uiOutput("comp2_5_1"),
shiny::uiOutput("comp2_5_2"),
shiny::uiOutput("comp2_5_3"),
shiny::uiOutput("comp2_5_4")),
shiny::conditionalPanel(condition="input.model5=='three' ",
shiny::uiOutput("comp3_5_1"),
shiny::uiOutput("comp3_5_2"),
shiny::uiOutput("comp3_5_3"),
shiny::uiOutput("comp3_5_4"),
shiny::uiOutput("comp3_5_5"),
shiny::uiOutput("comp3_5_6"))),
shiny::tabPanel("Covariance", value="varcov5",
shiny::conditionalPanel(condition="input.model5=='one'||
input.model5=='two'||input.model5=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("v1alpha_5")))),
shiny::conditionalPanel(condition="input.model5=='two'||
input.model5=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("v1beta_5")),
shiny::column(4,shiny::uiOutput("v1k21_5")))),
shiny::conditionalPanel(condition="input.model5=='two'||
input.model5=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("alphabeta_5")),
shiny::column(4,shiny::uiOutput("alphak21_5")),
shiny::column(4,shiny::uiOutput("betak21_5")))),
shiny::conditionalPanel(condition="input.model5=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("alphak31_5")),
shiny::column(4,shiny::uiOutput("betak31_5")),
shiny::column(4,shiny::uiOutput("gammak31_5")))),
shiny::conditionalPanel(condition="input.model5=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("v1gamma_5")),
shiny::column(4,shiny::uiOutput("v1k31_5")),
shiny::column(4,shiny::uiOutput("alphagamma_5")))),
shiny::conditionalPanel(condition="input.model5=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("betagamma_5")),
shiny::column(4,shiny::uiOutput("gammak21_5")),
shiny::column(4,shiny::uiOutput("k21k31_5"))))))),
shiny::tags$hr(),
shiny::tags$hr(),
shinydashboard::box(title="Save the result as a file",
width=NULL,solidHeader=TRUE,status="warning",
background="light-blue",
shiny::radioButtons("type5", "File type:",
choices = c("Excel (CSV)" ,
"Text (tab separated)" ,
"Text (Space Separated)")),
shiny::conditionalPanel(condition = "input.model5=='one'",
shiny::downloadButton("downloadData5_1",
"Save results to file")),
shiny::conditionalPanel(condition = "input.model5=='two'",
shiny::downloadButton("downloadData5_2",
"Save results to file")),
shiny::conditionalPanel(condition = "input.model5=='three'",
shiny::downloadButton("downloadData5_3",
"Save results to file")))),
shiny::column(width=7,
shiny::wellPanel(
shiny::h2("Model 5: V1, Exponents, K21, K31"),
shiny::tags$br(),
shiny::conditionalPanel(condition = "input.model5=='one'",
shiny::h3("One compartment model"),
shiny::tableOutput("T5_1")),
shiny::conditionalPanel(condition = "input.model5=='two'",
shiny::h3("Two compartment model"),
shiny::tableOutput("T5_2")),
shiny::conditionalPanel(condition = "input.model5=='three'",
shiny::h3("Three compartment model"),
shiny::tableOutput("T5_3")))))),
######################### Indiv parameter converter ##################
shiny::tabPanel("Indiv. Parameter Converter",
shiny::fluidRow(
shiny::column(6,
shinydashboard::box(title="Select your compartment model",
width=NULL,solidHeader=TRUE,status="warning",
background="light-blue",
shiny::radioButtons("modelF1", "MODEL TYPE :",
list("One compartment model" ="one",
"Two compartment model" ="two",
"Three compartment model" ="three"))),
shiny::tags$hr(),
shiny::tags$hr(),
shinydashboard::box(title="Select your input data type",
width=NULL,solidHeader=TRUE,status="warning",
background="light-blue",
shiny::radioButtons("modelF2", "DATA TYPE :",
list("Model 1: Volumes and Clearances" ="M1",
"Model 2: V1, Rate Constants" ="M2",
"Model 3: V1, Vdss, Cl, half-lives" ="M3",
"Model 4: Coefficients and Exponents" ="M4",
"Model 5: V1,Exponents,K21,K31" ="M5"))),
shiny::tags$hr(),
shiny::tags$hr(),
shinydashboard::box(title="Open your individual PK parameters",
width=NULL,solidHeader=TRUE,status="warning",
background="light-blue",
shiny::fileInput("inputfile",
label="File should be saved as CSV")),
shiny::tags$hr(),
shiny::tags$hr(),
shinydashboard::box(title="Match PK parameters",
width=NULL,solidHeader=TRUE,status="warning",
background="light-blue",
shiny::uiOutput("choose_PK"))),
shiny::column(6,
shiny::downloadButton("SaveIndivResult",
"Save individual parameters to file"),
shiny::tags$hr(),
shiny::tags$hr(),
shiny::tableOutput("ShowResult"))))))), #end ui
############################ SERVER ####################################
server<-function(input,output,session){
## sheet1 ########
###### INPUT #####
output$comp1_1_1<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "volume_mean1_1",
label = "V1 Estimate")),
shiny::column(6,shiny::textInput(inputId = "volume_sd1_1",
label = "V1 Std.err")))})
output$comp1_1_2<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "Clearance_mean1_1",
label = "Cl1 Estimate")),
shiny::column(6,shiny::textInput(inputId = "Clearance_sd1_1",
label = "Cl1 Std.err")))})
output$comp2_1_1<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "volume_mean1_2",
label = "V1 Estimate")),
shiny::column(6,shiny::textInput(inputId = "volume_sd1_2",
label = "V1 Std.err")))})
output$comp2_1_2<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "volume_mean2_2",
label = "V2 Estimate")),
shiny::column(6,shiny::textInput(inputId = "volume_sd2_2",
label = "V2 Std.err")))})
output$comp2_1_3<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "Clearance_mean1_2",
label = "Cl1 Estimate")),
shiny::column(6,shiny::textInput(inputId = "Clearance_sd1_2",
label = "Cl1 Std.err")))})
output$comp2_1_4<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "Clearance_mean2_2",
label = "Cl2 Estimate")),
shiny::column(6,shiny::textInput(inputId = "Clearance_sd2_2",
label = "Cl2 Std.err")))})
output$comp3_1_1<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "volume_mean1_3",
label = "V1 Estimate")),
shiny::column(6,shiny::textInput(inputId = "volume_sd1_3",
label = "V1 Std.err")))})
output$comp3_1_2<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "volume_mean2_3",
label = "V2 Estimate")),
shiny::column(6,shiny::textInput(inputId = "volume_sd2_3",
label = "V2 Std.err")))})
output$comp3_1_3<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "volume_mean3_3",
label = "V3 Estimate")),
shiny::column(6,shiny::textInput(inputId = "volume_sd3_3",
label = "V3 Std.err")))})
output$comp3_1_4<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "Clearance_mean1_3",
label = "Cl1 Estimate")),
shiny::column(6,shiny::textInput(inputId = "Clearance_sd1_3",
label = "Cl1 Std.err")))})
output$comp3_1_5<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "Clearance_mean2_3",
label = "Cl2 Estimate")),
shiny::column(6,shiny::textInput(inputId = "Clearance_sd2_3",
label = "Cl2 Std.err")))})
output$comp3_1_6<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "Clearance_mean3_3",
label = "Cl3 Estimate")),
shiny::column(6,shiny::textInput(inputId = "Clearance_sd3_3",
label = "Cl3 Std.err")))})
##### covariance #####
##### One compartment #####
output$v1cl1_1<-shiny::renderUI({
shiny::textInput(inputId = "v1cl1_1",
label = "Cov(V1,Cl1)", value = 0)})
##### Two compartment #####
output$v1cl2_1<-shiny::renderUI({
shiny::textInput(inputId = "v1cl2_1",
label = "Cov(V1,Cl2)", value = 0)})
output$v2cl1_1<-shiny::renderUI({
shiny::textInput(inputId = "v2cl1_1",
label = "Cov(V2,Cl1)", value = 0)})
output$v2cl2_1<-shiny::renderUI({
shiny::textInput(inputId = "v2cl2_1",
label = "Cov(V2,Cl2)", value = 0)})
output$v1v2_1<-shiny::renderUI({
shiny::textInput(inputId = "v1v2_1",
label = "Cov(V1,V2)", value = 0)})
output$cl1cl2_1<-shiny::renderUI({
shiny::textInput(inputId = "cl1cl2_1",
label = "Cov(Cl1,Cl2)", value = 0)})
##### Three compartment #####
output$v1cl3_1<-shiny::renderUI({
shiny::textInput(inputId = "v1cl3_1",
label = "Cov(V1,Cl3)", value = 0)})
output$v2cl3_1<-shiny::renderUI({
shiny::textInput(inputId = "v2cl3_1",
label = "Cov(V2,Cl3)", value = 0)})
output$v3cl1_1<-shiny::renderUI({
shiny::textInput(inputId = "v3cl1_1",
label = "Cov(V3,Cl1)", value = 0)})
output$v3cl2_1<-shiny::renderUI({
shiny::textInput(inputId = "v3cl2_1",
label = "Cov(V3,Cl2)", value = 0)})
output$v3cl3_1<-shiny::renderUI({
shiny::textInput(inputId = "v3cl3_1",
label = "Cov(V3,Cl3)", value = 0)})
output$v1v3_1<-shiny::renderUI({
shiny::textInput(inputId = "v1v3_1",
label = "Cov(V1,V3)", value = 0)})
output$v2v3_1<-shiny::renderUI({
shiny::textInput(inputId = "v2v3_1",
label = "Cov(V2,V3)", value = 0)})
output$cl1cl3_1<-shiny::renderUI({
shiny::textInput(inputId = "cl1cl3_1",
label = "Cov(Cl1,Cl3)", value = 0)})
output$cl2cl3_1<-shiny::renderUI({
shiny::textInput(inputId = "cl2cl3_1",
label = "Cov(Cl2,Cl3)", value = 0)})
##### Results ######
###### One compartment #####
result1_1<-shiny::reactive({
V1<-as.numeric(input$volume_mean1_1)
Cl1<-as.numeric(input$Clearance_mean1_1)
V1.sd<-as.numeric(input$volume_sd1_1)
Cl1.sd<-as.numeric(input$Clearance_sd1_1)
V1Cl1<-as.numeric(input$v1cl1_1)
if(length(V1Cl1)==0) V1Cl1<-NA
OneComp_Volume_Clearance(V1,Cl1,V1.sd,Cl1.sd,V1Cl1)})
output$T1_1<-shiny::renderTable({
Label<-c("Volume","","Clearnace","Micro Rate Constant","Exponent",
"Half-lives","True Coeffficient","Fractional Coefficient")
T1.1<-data.frame(Label,result1_1())
colnames(T1.1)[1]<-""
T1.1},align="?",digits=4,rownames=FALSE)
total1_1<-shiny::reactive({
result1_1()})
fileext <- shiny::reactive({switch(input$type1,
"Excel (CSV)" = "csv",
"Text (tab separated)" = "tab",
"Text (Space Separated)" = "txt")})
output$downloadData1_1<-shiny::downloadHandler(
filename <- function() {
paste("one_compartment_sheet1", fileext(), sep = ".")},
content <- function(file){
sep.t=switch(fileext(),
csv=",",
tab="\t",
txt=" ")
utils::write.table(total1_1(), file, sep = sep.t,
row.names = FALSE,col.names = TRUE,append=FALSE)})
##### Two compartment #####
result1_2<-shiny::reactive({
V1<-as.numeric(input$volume_mean1_2)
V2<-as.numeric(input$volume_mean2_2)
Cl1<-as.numeric(input$Clearance_mean1_2)
Cl2<-as.numeric(input$Clearance_mean2_2)
V1.sd<-as.numeric(input$volume_sd1_2)
V2.sd<-as.numeric(input$volume_sd2_2)
Cl1.sd<-as.numeric(input$Clearance_sd1_2)
Cl2.sd<-as.numeric(input$Clearance_sd2_2)
V1V2<-as.numeric(input$v1v2_1)
V1Cl1<-as.numeric(input$v1cl1_1)
V1Cl2<-as.numeric(input$v1cl2_1)
V2Cl1<-as.numeric(input$v2cl1_1)
V2Cl2<-as.numeric(input$v2cl2_1)
Cl1Cl2<-as.numeric(input$cl1cl2_1)
TwoComp_Volume_Clearance(V1,V2,Cl1,Cl2,V1.sd,V2.sd,Cl1.sd,Cl2.sd,
covar=c(V1V2,V1Cl1,V1Cl2,V2Cl1,V2Cl2,Cl1Cl2))})
output$T1_2<-shiny::renderTable({
Label<-c("Volume","","","Clearnace","","Micro Rate Constant","","",
"Exponent","","Half-lives","","True Coeffficient","",
"Fractional Coefficient","")
T1.2<-data.frame(Label,result1_2())
colnames(T1.2)[1]<-""
T1.2},align="?",digits=4,rownames=FALSE)
total1_2<-shiny::reactive({
result1_2()})
output$downloadData1_2<-shiny::downloadHandler(
filename = function() {
paste("two_compartment_sheet1", fileext(), sep = ".")},
content = function(file){
sep.t=switch(fileext(),
csv=",",
tab="\t",
txt=" ")
utils::write.table(total1_2(), file, sep = sep.t,
row.names = FALSE,col.names = TRUE)})
######################Three compartment######################
result1_3<-shiny::reactive({
V1<-as.numeric(input$volume_mean1_3)
V2<-as.numeric(input$volume_mean2_3)
V3<-as.numeric(input$volume_mean3_3)
Cl1<-as.numeric(input$Clearance_mean1_3)
Cl2<-as.numeric(input$Clearance_mean2_3)
Cl3<-as.numeric(input$Clearance_mean3_3)
V1.sd<-as.numeric(input$volume_sd1_3)
V2.sd<-as.numeric(input$volume_sd2_3)
V3.sd<-as.numeric(input$volume_sd3_3)
Cl1.sd<-as.numeric(input$Clearance_sd1_3)
Cl2.sd<-as.numeric(input$Clearance_sd2_3)
Cl3.sd<-as.numeric(input$Clearance_sd3_3)
V1V2<-as.numeric(input$v1v2_1); V1V3<-as.numeric(input$v1v3_1)
V1Cl1<-as.numeric(input$v1cl1_1); V1Cl2<-as.numeric(input$v1cl2_1)
V1Cl3<-as.numeric(input$v1cl3_1); V2V3<-as.numeric(input$v2v3_1)
V2Cl1<-as.numeric(input$v2cl1_1); V2Cl2<-as.numeric(input$v2cl2_1)
V2Cl3<-as.numeric(input$v2cl3_1); V3Cl1<-as.numeric(input$v3cl1_1)
V3Cl2<-as.numeric(input$v3cl2_1); V3Cl3<-as.numeric(input$v3cl3_1)
Cl1Cl2<-as.numeric(input$cl1cl2_1);Cl1Cl3<-as.numeric(input$cl1cl3_1)
Cl2Cl3<-as.numeric(input$cl2cl3_1)
ThreeComp_Volume_Clearance(V1,V2,V3,Cl1,Cl2,Cl3,
V1.sd,V2.sd,V3.sd,Cl1.sd,Cl2.sd,Cl3.sd,
covar=c(V1V2,V1V3,V1Cl1,V1Cl2,V1Cl3,V2V3,V2Cl1,V2Cl2,V2Cl3,
V3Cl1,V3Cl2,V3Cl3,Cl1Cl2,Cl1Cl3,Cl2Cl3))})
output$T1_3<-shiny::renderTable({
Label<-c("Volume","","","","Clearnace","","",
"Micro Rate Constant","","","","",
"Exponent","","","Half-lives","","",
"True Coeffficient","","","Fractional Coefficient","","")
T1.3<-data.frame(Label,result1_3())
colnames(T1.3)[1]<-""
T1.3},align="?",digits=4,rownames=FALSE)
total1_3<-shiny::reactive({
result1_3()})
output$downloadData1_3<-shiny::downloadHandler(
filename = function() {
paste("three_compartment_sheet1", fileext(), sep = ".")},
content = function(file){
sep.t=switch(fileext(),
csv=",",
tab="\t",
txt=" ")
utils::write.table(total1_3(), file, sep = sep.t,
row.names = FALSE,col.names = TRUE)})
#########################sheet2#########################################
output$comp1_2_1<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "volume_mean21_1",
label = "V1 Estimate")),
shiny::column(6,shiny::textInput(inputId = "volume_sd21_1",
label = "V1 Std.err")))})
output$comp1_2_2<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "k10_mean_1",
label = "k10 Estimate")),
shiny::column(6,shiny::textInput(inputId = "k10_sd_1",
label = "k10 Std.err")))})
output$comp2_2_1<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "volume_mean21_2",
label = "V1 Estimate")),
shiny::column(6,shiny::textInput(inputId = "volume_sd21_2",
label = "V1 Std.err")))})
output$comp2_2_2<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "k10_mean_2",
label = "k10 Estimate")),
shiny::column(6,shiny::textInput(inputId = "k10_sd_2",
label = "k10 Std.err")))})
output$comp2_2_3<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "k12_mean_2",
label = "k12 Estimate")),
shiny::column(6,shiny::textInput(inputId = "k12_sd_2",
label = "k12 Std.err")))})
output$comp2_2_4<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "k21_mean_2",
label = "k21 Estimate")),
shiny::column(6,shiny::textInput(inputId = "k21_sd_2",
label = "k21 Std.err")))})
output$comp3_2_1<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "volume_mean21_3",
label = "V1 Estimate")),
shiny::column(6,shiny::textInput(inputId = "volume_sd21_3",
label = "V1 Std.err")))})
output$comp3_2_2<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "k10_mean_3",
label = "k10 Estimate")),
shiny::column(6,shiny::textInput(inputId = "k10_sd_3",
label = "k10 Std.err")))})
output$comp3_2_3<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "k12_mean_3",
label = "k12 Estimate")),
shiny::column(6,shiny::textInput(inputId = "k12_sd_3",
label = "k12 Std.err")))})
output$comp3_2_4<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "k13_mean_3",
label = "k13 Estimate")),
shiny::column(6,shiny::textInput(inputId = "k13_sd_3",
label = "k13 Std.err")))})
output$comp3_2_5<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "k21_mean_3",
label = "k21 Estimate")),
shiny::column(6,shiny::textInput(inputId = "k21_sd_3",
label = "k21 Std.err")))})
output$comp3_2_6<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "k31_mean_3",
label = "k31 Estimate")),
shiny::column(6,shiny::textInput(inputId = "k31_sd_3",
label = "k31 Std.err")))})
###################### covariance ######################
######################One compartment###################
output$v1k10_2<-shiny::renderUI({
shiny::textInput(inputId = "v1k10_2",
label = "Cov(V1,k10)", value = 0)})
######################Two compartment######################
output$v1k12_2<-shiny::renderUI({
shiny::textInput(inputId = "v1k12_2",
label = "Cov(V1,k12)", value = 0)})
output$v1k21_2<-shiny::renderUI({
shiny::textInput(inputId = "v1k21_2",
label = "Cov(V1,k21)", value = 0)})
output$k10k12_2<-shiny::renderUI({
shiny::textInput(inputId = "k10k12_2",
label = "Cov(k10,k12)", value = 0)})
output$k10k21_2<-shiny::renderUI({
shiny::textInput(inputId = "k10k21_2",
label = "Cov(k10,k21)", value = 0)})
output$k12k21_2<-shiny::renderUI({
shiny::textInput(inputId = "k12k21_2",
label = "Cov(k12,k21)", value = 0)})
######################Three compartment######################
output$v1k13_2<-shiny::renderUI({
shiny::textInput(inputId = "v1k13_2",
label = "Cov(V1,k13)", value = 0)})
output$v1k31_2<-shiny::renderUI({
shiny::textInput(inputId = "v1k31_2",
label = "Cov(V1,k31)", value = 0)})
output$k13k31_2<-shiny::renderUI({
shiny::textInput(inputId = "k13k31_2",
label = "Cov(k13,k31)", value = 0)})
output$k10k13_2<-shiny::renderUI({
shiny::textInput(inputId = "k10k13_2",
label = "Cov(k10,k13)", value = 0)})
output$k10k31_2<-shiny::renderUI({
shiny::textInput(inputId = "k10k31_2",
label = "Cov(k10,k31)", value = 0)})
output$k12k31_2<-shiny::renderUI({
shiny::textInput(inputId = "k12k31_2",
label = "Cov(k12,k31)", value = 0)})
output$k21k13_2<-shiny::renderUI({
shiny::textInput(inputId = "k21k13_2",
label = "Cov(k21,k13)", value = 0)})
output$k21k31_2<-shiny::renderUI({
shiny::textInput(inputId = "k21k31_2",
label = "Cov(k21,k31)", value = 0)})
output$k12k13_2<-shiny::renderUI({
shiny::textInput(inputId = "k12k13_2",
label = "Cov(k12,k13)", value = 0)})
###########################################################
#########################Results###########################
###########################################################
######################One compartment######################
result2_1<-shiny::reactive({
V1<-as.numeric(input$volume_mean21_1)
k10<-as.numeric(input$k10_mean_1)
V1.sd<-as.numeric(input$volume_sd21_1)
k10.sd<-as.numeric(input$k10_sd_1)
V1k10<-as.numeric(input$v1k10_2)
OneComp_Volume_RateConstant(V1,k10,V1.sd,k10.sd,covar=c(V1k10))})
output$T2_1<-shiny::renderTable({
Label<-c("Volume","","Clearnace","Micro Rate Constant",
"Exponent","Half-lives",
"True Coeffficient","Fractional Coefficient")
T2.1<-data.frame(Label,result2_1())
colnames(T2.1)[1]<-""
T2.1},align="?",digits=4,rownames=FALSE)
total2_1<-shiny::reactive({result2_1()})
fileext2 <- shiny::reactive({switch(input$type2,
"Excel (CSV)" = "csv",
"Text (tab separated)" = "tab",
"Text (Space Separated)" = "txt")})
output$downloadData2_1<-shiny::downloadHandler(
filename = function() {
paste("one_compartment_sheet2", fileext2(), sep = ".")},
content = function(file){sep.t=switch(fileext2(),
csv=",",
tab="\t",
txt=" ")
utils::write.table(total2_1(), file, sep = sep.t,
row.names = FALSE,col.names = TRUE)})
######################Two compartment######################
result2_2<-shiny::reactive({
V1<-as.numeric(input$volume_mean21_2)
k10<-as.numeric(input$k10_mean_2)
k12<-as.numeric(input$k12_mean_2)
k21<-as.numeric(input$k21_mean_2)
V1.sd<-as.numeric(input$volume_sd21_2)
k10.sd<-as.numeric(input$k12_sd_2)
k12.sd<-as.numeric(input$k12_sd_2)
k21.sd<-as.numeric(input$k21_sd_2)
V1k10<-as.numeric(input$v1k10_2)
V1k12<-as.numeric(input$v1k12_2)
V1k21<-as.numeric(input$v1k21_2)
k10k12<-as.numeric(input$k10k12_2)
k10k21<-as.numeric(input$k10k21_2)
k12k21<-as.numeric(input$k12k21_2)
TwoComp_Volume_RateConstant(V1,k10,k12,k21,V1.sd,k10.sd,k12.sd,k21.sd,
covar=c(V1k10,V1k12,V1k21,k10k12,k10k21,k12k21))})
output$T2_2<-shiny::renderTable({
Label<-c("Volume","","","Clearnace","","Micro Rate Constant","","",
"Exponent","","Half-lives","",
"True Coeffficient","","Fractional Coefficient","")
T2.2<-data.frame(Label,result2_2())
colnames(T2.2)[1]<-""
T2.2},align="?",digits=4,rownames=FALSE)
total2_2<-shiny::reactive({result2_2()})
output$downloadData2_2<-shiny::downloadHandler(
filename = function() {
paste("two_compartment_sheet2", fileext2(), sep = ".")},
content = function(file){
sep.t=switch(fileext2(),
csv=",",
tab="\t",
txt=" ")
utils::write.table(total2_2(), file, sep = sep.t,
row.names = FALSE,col.names = TRUE)})
######################Three compartment######################
result2_3<-shiny::reactive({
V1<-as.numeric(input$volume_mean21_3)
k10<-as.numeric(input$k10_mean_3)
k12<-as.numeric(input$k12_mean_3)
k13<-as.numeric(input$k13_mean_3)
k21<-as.numeric(input$k21_mean_3)
k31<-as.numeric(input$k31_mean_3)
V1.sd<-as.numeric(input$volume_sd21_3)
k10.sd<-as.numeric(input$k10_sd_3);
k12.sd<-as.numeric(input$k12_sd_3)
k13.sd<-as.numeric(input$k13_sd_3);
k21.sd<-as.numeric(input$k21_sd_3)
k31.sd<-as.numeric(input$k31_sd_3)
V1k10<-as.numeric(input$v1k10_2);
V1k12<-as.numeric(input$v1k12_2)
V1k13<-as.numeric(input$v1k13_2);
V1k21<-as.numeric(input$v1k21_2)
V1k31<-as.numeric(input$v1k31_2);
k10k12<-as.numeric(input$k10k12_2)
k10k13<-as.numeric(input$k10k13_2);
k10k21<-as.numeric(input$k10k21_2)
k10k31<-as.numeric(input$k10k31_2);
k12k13<-as.numeric(input$k12k13_2)
k12k21<-as.numeric(input$k12k21_2);
k12k31<-as.numeric(input$k12k31_2)
k21k31<-as.numeric(input$k21k31_2);
k13k21<-as.numeric(input$k13k21_2)
k13k31<-as.numeric(input$k13k31_2)
ThreeComp_Volume_RateConstant(V1,k10,k12,k13,k21,k31,V1.sd,
k10.sd,k12.sd,k13.sd,k21.sd,k31.sd,
covar=c(V1k10,V1k12,V1k13,V1k21,V1k31,k10k12,k10k13,k10k21,k10k31,
k12k13,k12k21,k12k31,k13k21,k13k31,k21k31))})
output$T2_3<-shiny::renderTable({
Label<-c("Volume","","","","Clearnace","","",
"Micro Rate Constant","","","","",
"Exponent","","","Half-lives","","",
"True Coeffficient","","","Fractional Coefficient","","")
T2.3<-data.frame(Label,result2_3())
colnames(T2.3)[1]<-""
T2.3},align="?",digits=4,rownames=FALSE)
total2_3<-shiny::reactive({result2_3()})
output$downloadData2_3<-shiny::downloadHandler(
filename = function() {
paste("three_compartment_sheet2", fileext2(), sep = ".")},
content = function(file){
sep.t=switch(fileext2(),
csv=",",
tab="\t",
txt=" ")
utils::write.table(total2_3(), file, sep = sep.t,
row.names = FALSE,col.names = TRUE)})
######################sheet3############################################
output$comp1_3_1<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "Cl1_mean_1",
label = "Cl1 Estimate")),
shiny::column(6,shiny::textInput(inputId = "Cl1_sd_1",
label = "Cl1 Std.err")))})
output$comp1_3_2<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "t_alpha_mean_1",
label = "t_alpha Estimate")),
shiny::column(6,shiny::textInput(inputId = "t_alpha_sd_1",
label = "t_alpha Std.err")))})
output$comp2_3_1<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "volume_mean31_2",
label = "V1 Estimate")),
shiny::column(6,shiny::textInput(inputId = "volume_sd31_2",
label = "V1 Std.err")))})
output$comp2_3_2<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "Cl1_mean_2",
label = "Cl1 Estimate")),
shiny::column(6,shiny::textInput(inputId = "Cl1_sd_2",
label = "Cl1 Std.err")))})
output$comp2_3_3<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "t_alpha_mean_2",
label = "t_alpha Estimate")),
shiny::column(6,shiny::textInput(inputId = "t_alpha_sd_2",
label = "t_alpha Std.err")))})
output$comp2_3_4<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "t_beta_mean_2",
label = "t_beta Estimate")),
shiny::column(6,shiny::textInput(inputId = "t_beta_sd_2",
label = "t_beta Std.err")))})
output$comp3_3_1<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "volume_mean31_3",
label = "V1 Estimate")),
shiny::column(6,shiny::textInput(inputId = "volume_sd31_3",
label = "V1 Std.err")))})
output$comp3_3_2<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "Vd_mean_3",
label = "Vd Estimate")),
shiny::column(6,shiny::textInput(inputId = "Vd_sd_3",
label = "Vd Std.err")))})
output$comp3_3_3<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "Cl1_mean_3",
label = "Cl1 Estimate")),
shiny::column(6,shiny::textInput(inputId = "Cl1_sd_3",
label = "Cl1 Std.err")))})
output$comp3_3_4<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "t_alpha_mean_3",
label = "t_alpha Estimate")),
shiny::column(6,shiny::textInput(inputId = "t_alpha_sd_3",
label = "t_alpha Std.err")))})
output$comp3_3_5<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "t_beta_mean_3",
label = "t_beta Estimate")),
shiny::column(6,shiny::textInput(inputId = "t_beta_sd_3",
label = "t_beta Std.err")))})
output$comp3_3_6<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "t_gamma_mean_3",
label = "t_gamma Estimate")),
shiny::column(6,shiny::textInput(inputId = "t_gamma_sd_3",
label = "t_gamma Std.err")))})
###################### covariance ######################
######################One compartment######################
output$cl1talpha_3<-shiny::renderUI({
shiny::textInput(inputId = "cl1talpha_3",
label = "Cov(Cl1,t_alpha)", value = 0) })
######################Two compartment######################
output$v1cl1_3<-shiny::renderUI({
shiny::textInput(inputId = "v1cl1_3",
label = "Cov(V1,Cl1)", value = 0)})
output$cl1tbeta_3<-shiny::renderUI({
shiny::textInput(inputId = "cl1tbeta_3",
label = "Cov(Cl1,t_beta)", value = 0)})
output$v1talpha_3<-shiny::renderUI({
shiny::textInput(inputId = "v1talpha_3",
label = "Cov(V1,t_alpha)", value = 0)})
output$v1tbeta_3<-shiny::renderUI({
shiny::textInput(inputId = "v1tbeta_3",
label = "Cov(V1,t_beta)", value = 0)})
output$talphatbeta_3<-shiny::renderUI({
shiny::textInput(inputId = "talphatbeta_3",
label = "Cov(t_alpha,t_beta)",value = 0)})
######################Three compartment######################
output$v1vd_3<-shiny::renderUI({
shiny::textInput(inputId = "v1vd_3",
label = "Cov(V1,Vd)", value = 0)})
output$v1tgamma_3<-shiny::renderUI({
shiny::textInput(inputId = "v1tgamma_3",
label = "Cov(V1,t_gamma)", value = 0)})
output$vdtgamma_3<-shiny::renderUI({
shiny::textInput(inputId = "vdtgamma_3",
label = "Cov(Vd,t_gamma)", value = 0)})
output$cl1tgamma_3<-shiny::renderUI({
shiny::textInput(inputId = "cl1tgamma_3",
label = "Cov(Cl1,t_gamma)",value = 0)})
output$talphatgamma_3<-shiny::renderUI({
shiny::textInput(inputId = "talphatgamma_3",
label = "Cov(t_alpha,t_gamma)", value = 0)})
output$tbetatgamma_3<-shiny::renderUI({
shiny::textInput(inputId = "tbetatgamma_3",
label = "Cov(t_beta,t_gamma)",value = 0)})
output$vdtalpha_3<-shiny::renderUI({
shiny::textInput(inputId = "vdtalpha_3",
label = "Cov(Vd,t_alpha)", value = 0)})
output$vdtbeta_3<-shiny::renderUI({
shiny::textInput(inputId = "vdtbeta_3",
label = "Cov(Vd,t_beta)", value = 0)})
output$vdcl1_3<-shiny::renderUI({
shiny::textInput(inputId = "vdcl1_3",
label = "Cov(Vd,Cl1)", value = 0)})
###########################################################
#########################Results###########################
###########################################################
######################One compartment######################
result3_1<-shiny::reactive({
Cl1<-as.numeric(input$Cl1_mean_1)
t_alpha<-as.numeric(input$t_alpha_mean_1)
Cl1.sd<-as.numeric(input$Cl1_sd_1)
t_alpha.sd<-as.numeric(input$t_alpha_sd_1)
Cl1talpha<-as.numeric(input$cl1talpha_3)
OneComp_Volume_Clearance_HalfLife(Cl1,t_alpha,Cl1.sd,t_alpha.sd,
covar=c(Cl1talpha))})
output$T3_1<-shiny::renderTable({
Label<-c("Volume","","Clearnace","Micro Rate Constant",
"Exponent","Half-lives",
"True Coeffficient","Fractional Coefficient")
T3.1<-data.frame(Label,result3_1())
colnames(T3.1)[1]<-""
T3.1},align="?",digits=4,rownames=FALSE)
total3_1<-shiny::reactive({result3_1() })
fileext3 <- shiny::reactive({switch(input$type3,
"Excel (CSV)" = "csv",
"Text (tab separated)" = "tab",
"Text (Space Separated)" = "txt")})
output$downloadData3_1<-shiny::downloadHandler(
filename = function() {
paste("one_compartment_sheet3", fileext3(), sep = ".")},
content = function(file){
sep.t=switch(fileext3(),
csv=",",
tab="\t",
txt=" ")
utils::write.table(total3_1(), file, sep = sep.t,
row.names = FALSE,col.names = TRUE)})
####################Two compartment######################
result3_2<-shiny::reactive({
V1<-as.numeric(input$volume_mean31_2)
Cl1<-as.numeric(input$Cl1_mean_2)
t_alpha<-as.numeric(input$t_alpha_mean_2)
t_beta<-as.numeric(input$t_beta_mean_2)
V1.sd<-as.numeric(input$volume_sd31_2)
Cl1.sd<-as.numeric(input$Cl1_sd_2)
t_alpha.sd<-as.numeric(input$t_alpha_sd_2)
t_beta.sd<-as.numeric(input$t_beta_sd_2)
V1Cl1<-as.numeric(input$v1cl1_2)
V1talpha<-as.numeric(input$v1talpha_2)
V1tbeta<-as.numeric(input$v1tbeta_2)
Cl1talpha<-as.numeric(input$cl1talpha_2)
Cl1tbeta<-as.numeric(input$cl1tbeta_2)
talphatbeta<-as.numeric(input$talphatbeta_2)
TwoComp_Volume_Clearance_HalfLife(V1,Cl1,t_alpha,t_beta,
V1.sd,Cl1.sd,t_alpha.sd,t_beta.sd,
covar=c(V1Cl1,V1talpha,V1tbeta,Cl1talpha,Cl1tbeta,talphatbeta))})
output$T3_2<-shiny::renderTable({
Label<-c("Volume","","","Clearnace","",
"Micro Rate Constant","","",
"Exponent","","Half-lives","",
"True Coeffficient","","Fractional Coefficient","")
T3.2<-data.frame(Label,result3_2())
colnames(T3.2)[1]<-""
T3.2},align="?",digits=4,rownames=FALSE)
total3_2<-shiny::reactive({ result3_2()})
output$downloadData3_2<-shiny::downloadHandler(
filename = function() {
paste("two_compartment_sheet3", fileext3(), sep = ".")},
content = function(file){
sep.t=switch(fileext3(),
csv=",",
tab="\t",
txt=" ")
utils::write.table(total3_2(), file, sep = sep.t,
row.names = FALSE,col.names = TRUE)})
######################Three compartment######################
result3_3<-shiny::reactive({
V1<-as.numeric(input$volume_mean31_3)
Vd<-as.numeric(input$Vd_mean_3)
Cl1<-as.numeric(input$Cl1_mean_3)
t_alpha<-as.numeric(input$t_alpha_mean_3)
t_beta<-as.numeric(input$t_beta_mean_3)
t_gamma<-as.numeric(input$t_gamma_mean_3)
V1.sd<-as.numeric(input$volume_sd31_3)
Vd.sd<-as.numeric(input$Vd_sd_3)
Cl1.sd<-as.numeric(input$Cl1_sd_3)
t_alpha.sd<-as.numeric(input$t_alpha_sd_3)
t_beta.sd<-as.numeric(input$t_beta_sd_3)
t_gamma.sd<-as.numeric(input$t_gamma_sd_3)
V1Vd<-as.numeric(input$v1vd_3)
V1Cl1<-as.numeric(input$v1cl1_3)
V1talpha<-as.numeric(input$v1talpha_3)
V1tbeta<-as.numeric(input$v1tbeta_3)
V1tgamma<-as.numeric(input$v1tgamma_3)
VdCl1<-as.numeric(input$vdcl1_3)
Vdtalpha<-as.numeric(input$vdtalpha_3)
Vdtbeta<-as.numeric(input$vdtbeta_3)
Vdtgamma<-as.numeric(input$vdtgamma_3)
Cl1talpha<-as.numeric(input$cl1talpha_3)
Cl1tbeta<-as.numeric(input$cl1tbeta_3)
Cl1tgamma<-as.numeric(input$cl1tgamma_3)
talphatbeta<-as.numeric(input$talphatbeta_3)
talphatgamma<-as.numeric(input$talphatgamma_3)
tbetatgamma<-as.numeric(input$tbetatgamma_3)
ThreeComp_Volume_Clearance_HalfLife(V1,Vd,Cl1,t_alpha,t_beta,t_gamma,
V1.sd,Vd.sd,Cl1.sd,t_alpha.sd,t_beta.sd,t_gamma.sd,
covar=c(V1Vd,V1Cl1,V1talpha,V1tbeta,V1tgamma,
VdCl1,Vdtalpha,Vdtbeta,Vdtgamma,Cl1talpha,Cl1tbeta,Cl1tgamma,
talphatbeta,talphatgamma,tbetatgamma))})
output$T3_3<-shiny::renderTable({
Label<-c("Volume","","","","Clearnace","","",
"Micro Rate Constant","","","","",
"Exponent","","","Half-lives","","",
"True Coeffficient","","","Fractional Coefficient","","")
T3.3<-data.frame(Label,result3_3())
colnames(T3.3)[1]<-""
T3.3},align="?",digits=4,rownames=FALSE)
total3_3<-shiny::reactive({result3_3()})
output$downloadData3_3<-shiny::downloadHandler(
filename = function() {
paste("three_compartment_sheet3", fileext3(), sep = ".")},
content = function(file){
sep.t=switch(fileext3(),
csv=",",
tab="\t",
txt=" ")
utils::write.table(total3_3(), file, sep = sep.t,
row.names = FALSE,col.names = TRUE)})
##############sheet4############################################
output$comp1_4_1<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "A_mean_1",
label = "A Estimate")),
shiny::column(6,shiny::textInput(inputId = "A_sd_1",
label = "A Std.err")))})
output$comp1_4_2<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "alpha_mean_1",
label = "alpha Estimate")),
shiny::column(6,shiny::textInput(inputId = "alpha_sd_1",
label = "alpha Std.err")))})
output$comp1_4_1<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "A_mean_1",
label = "A Estimate")),
shiny::column(6,shiny::textInput(inputId = "A_sd_1",
label = "A Std.err")))})
output$comp2_4_1<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "A_mean_2",
label = "A Estimate")),
shiny::column(6,shiny::textInput(inputId = "A_sd_2",
label = "A Std.err")))})
output$comp2_4_2<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "B_mean_2",
label = "B Estimate")),
shiny::column(6,shiny::textInput(inputId = "B_sd_2",
label = "B Std.err")))})
output$comp2_4_1<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "A_mean_2",
label = "A Estimate")),
shiny::column(6,shiny::textInput(inputId = "A_sd_2",
label = "A Std.err")))})
output$comp2_4_2<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "B_mean_2",
label = "B Estimate")),
shiny::column(6,shiny::textInput(inputId = "B_sd_2",
label = "B Std.err")))})
output$comp2_4_3<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "alpha_mean_2",
label = "alpha Estimate")),
shiny::column(6,shiny::textInput(inputId = "alpha_sd_2",
label = "alpha Std.err")))})
output$comp2_4_4<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "beta_mean_2",
label = "beta Estimate")),
shiny::column(6,shiny::textInput(inputId = "beta_sd_2",
label = "beta Std.err")))})
output$comp3_4_1<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "A_mean_3",
label = "A Estimate")),
shiny::column(6,shiny::textInput(inputId = "A_sd_3",
label = "A Std.err")))})
output$comp3_4_2<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "B_mean_3",
label = "B Estimate")),
shiny::column(6,shiny::textInput(inputId = "B_sd_3",
label = "B Std.err")))})
output$comp3_4_3<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "C_mean_3",
label = "C Estimate")),
shiny::column(6,shiny::textInput(inputId = "C_sd_3",
label = "C Std.err")))})
output$comp3_4_4<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "alpha_mean_3",
label = "alpha Estimate")),
shiny::column(6,shiny::textInput(inputId = "alpha_sd_3",
label = "alpha Std.err")))})
output$comp3_4_5<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "beta_mean_3",
label = "beta Estimate")),
shiny::column(6,shiny::textInput(inputId = "beta_sd_3",
label = "beta Std.err")))})
output$comp3_4_6<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "gamma_mean_3",
label = "gamma Estimate")),
shiny::column(6,shiny::textInput(inputId = "gamma_sd_3",
label = "gamma Std.err")))})
###################### covariance ######################
######################One compartment######################
output$aalpha_4<-shiny::renderUI({
shiny::textInput(inputId = "aalpha_4",
label = "Cov(A,alpha)", value = 0)})
######################Two compartment######################
output$ab_4<-shiny::renderUI({
shiny::textInput(inputId = "ab_4",
label = "Cov(A,B)", value = 0)})
output$abeta_4<-shiny::renderUI({
shiny::textInput(inputId = "abeta_4",
label = "Cov(A,beta)", value = 0)})
output$balpha_4<-shiny::renderUI({
shiny::textInput(inputId = "balpha_4",
label = "Cov(B,alpha)", value = 0)})
output$bbeta_4<-shiny::renderUI({
shiny::textInput(inputId = "bbeta_4",
label = "Cov(B,beta)", value = 0)})
output$alphabeta_4<-shiny::renderUI({
shiny::textInput(inputId = "alphabeta_4",
label = "Cov(alpha,beta)", value = 0)})
######################Three compartment######################
output$ac_4<-shiny::renderUI({
shiny::textInput(inputId = "ac_4",
label = "Cov(A,C)", value = 0)})
output$agamma_4<-shiny::renderUI({
shiny::textInput(inputId = "agamma_4",
label = "Cov(A,gamma)", value = 0)})
output$bgamma_4<-shiny::renderUI({
shiny::textInput(inputId = "bgamma_4",
label = "Cov(B,gamma)", value = 0)})
output$cbeta_4<-shiny::renderUI({
shiny::textInput(inputId = "cbeta_4",
label = "Cov(C,beta)", value = 0)})
output$cgamma_4<-shiny::renderUI({
shiny::textInput(inputId = "cgamma_4",
label = "Cov(C,gamma)", value = 0)})
output$alphagamma_4<-shiny::renderUI({
shiny::textInput(inputId = "alphagamma_4",
label = "Cov(alpha,gamma)", value = 0)})
output$betagamma_4<-shiny::renderUI({
shiny::textInput(inputId = "betagamma_4",
label = "Cov(beta,gamma)", value = 0)})
output$bc_4<-shiny::renderUI({
shiny::textInput(inputId = "bc_4",
label = "Cov(B,C)", value = 0)})
output$calpha_4<-shiny::renderUI({
shiny::textInput(inputId = "calpha_4",
label = "Cov(C,alpha)", value = 0)})
###########################################################
#########################Results###########################
###########################################################
######################One compartment######################
result4_1<-shiny::reactive({
A<-as.numeric(input$A_mean_1)
alpha<-as.numeric(input$alpha_mean_1)
A.sd<-as.numeric(input$A_sd_1)
alpha.sd<-as.numeric(input$alpha_sd_1)
Aalpha<-as.numeric(input$aalpha_4)
OneComp_Coefficient_Exponent(A,alpha,A.sd,alpha.sd,covar=Aalpha)})
output$T4_1<-shiny::renderTable({
Label<-c("Volume","","Clearnace","Micro Rate Constant",
"Exponent","Half-lives",
"True Coeffficient","Fractional Coefficient")
T4.1<-data.frame(Label,result4_1())
colnames(T4.1)[1]<-""
T4.1},align="?",digits=4,rownames=FALSE)
total4_1<-shiny::reactive({result4_1()})
fileext4 <- shiny::reactive({switch(input$type4,
"Excel (CSV)" = "csv",
"Text (tab separated)" = "tab",
"Text (Space Separated)" = "txt")})
output$downloadData4_1<-shiny::downloadHandler(
filename = function() {
paste("one_compartment_sheet4", fileext4(), sep = ".")},
content = function(file){
sep.t=switch(fileext4(),
csv=",",
tab="\t",
txt=" ")
utils::write.table(total4_1(), file, sep = sep.t,
row.names = FALSE,col.names = TRUE)})
######################Two compartment######################
result4_2<-shiny::reactive({
A<-as.numeric(input$A_mean_2)
B<-as.numeric(input$B_mean_2)
alpha<-as.numeric(input$alpha_mean_2)
beta<-as.numeric(input$beta_mean_2)
A.sd<-as.numeric(input$A_sd_2)
B.sd<-as.numeric(input$B_sd_2)
alpha.sd<-as.numeric(input$alpha_sd_2)
beta.sd<-as.numeric(input$beta_sd_2)
AB<-as.numeric(input$ab_4)
Aalpha<-as.numeric(input$aalpha_4)
Abeta<-as.numeric(input$abeta_4)
Balpha<-as.numeric(input$balpha_4)
Bbeta<-as.numeric(input$bbeta_4)
alphabeta<-as.numeric(input$alphabeta_4)
TwoComp_Coefficient_Exponent(A,B,alpha,beta,A.sd,B.sd,alpha.sd,beta.sd,
covar=c(AB,Aalpha,Abeta,Balpha,Bbeta,alphabeta))})
output$T4_2<-shiny::renderTable({
Label<-c("Volume","","","Clearnace","",
"Micro Rate Constant","","",
"Exponent","","Half-lives","",
"True Coeffficient","","Fractional Coefficient","")
T4.2<-data.frame(Label,result4_2())
colnames(T4.2)[1]<-""
T4.2},align="?",digits=4,rownames=FALSE)
total4_2<-shiny::reactive({result4_2()})
output$downloadData4_2<-shiny::downloadHandler(
filename = function() {
paste("two_compartment_sheet4", fileext4(), sep = ".")},
content = function(file){
sep.t=switch(fileext4(),
csv=",",
tab="\t",
txt=" ")
utils::write.table(total4_2(), file, sep = sep.t,
row.names = FALSE,col.names = TRUE)})
######################Three compartment######################
result4_3<-shiny::reactive({
A<-as.numeric(input$A_mean_3)
B<-as.numeric(input$B_mean_3)
C<-as.numeric(input$C_mean_3)
alpha<-as.numeric(input$alpha_mean_3)
beta<-as.numeric(input$beta_mean_3)
gamma<-as.numeric(input$gamma_mean_3)
A.sd<-as.numeric(input$A_sd_3)
B.sd<-as.numeric(input$B_sd_3)
C.sd<-as.numeric(input$C_sd_3)
alpha.sd<-as.numeric(input$alpha_sd_3)
beta.sd<-as.numeric(input$beta_sd_3)
gamma.sd<-as.numeric(input$gamma_sd_3)
AB<-as.numeric(input$ab_4);
AC<-as.numeric(input$ac_4)
Aalpha<-as.numeric(input$aalpha_4);
Abeta<-as.numeric(input$abeta_4)
Agamma<-as.numeric(input$agamma_4);
BC<-as.numeric(input$bc_4)
Balpha<-as.numeric(input$balpha_4);
Bbeta<-as.numeric(input$bbeta_4)
Bgamma<-as.numeric(input$bgamma_4);
Calpha<-as.numeric(input$calpha_4)
Cbeta<-as.numeric(input$cbeta_4);
Cgamma<-as.numeric(input$cgamma_4)
alphabeta<-as.numeric(input$alphabeta_4);
alphagamma<-as.numeric(input$alphagamma_4)
betagamma<-as.numeric(input$betagamma_4);
ThreeComp_Coefficient_Exponent(A,B,C,alpha,beta,gamma,A.sd,B.sd,C.sd,
alpha.sd,beta.sd,gamma.sd,
covar=c(AB,AC,Aalpha,Abeta,Agamma,BC,Balpha,Bbeta,Bgamma,Calpha,
Cbeta, Cgamma,alphabeta,alphagamma,betagamma))})
output$T4_3<-shiny::renderTable({
Label<-c("Volume","","","","Clearnace","","",
"Micro Rate Constant","","","","",
"Exponent","","","Half-lives","","",
"True Coeffficient","","","Fractional Coefficient","","")
T4.3<-data.frame(Label,result4_3())
colnames(T4.3)[1]<-""
T4.3},align="?",digits=4,rownames=FALSE)
total4_3<-shiny::reactive({result4_3()})
output$downloadData4_3<-shiny::downloadHandler(
filename = function() {
paste("three_compartment_sheet4", fileext4(), sep = ".")},
content = function(file){
sep.t=switch(fileext4(),
csv=",",
tab="\t",
txt=" ")
utils::write.table(total4_3(), file, sep = sep.t,
row.names = FALSE,col.names = TRUE)})
#####################sheet5############################################
output$comp1_5_1<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "volume_mean51_1",
label = "V1 Estimate")),
shiny::column(6,shiny::textInput(inputId = "volume_sd51_1",
label = "V1 Std.err")))})
output$comp1_5_2<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "alpha_mean51_1",
label = "alpha Estimate")),
shiny::column(6,shiny::textInput(inputId = "alpha_sd51_1",
label = "alpha Std.err")))})
output$comp2_5_1<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "volume_mean51_2",
label = "V1 Estimate")),
shiny::column(6,shiny::textInput(inputId = "volume_sd51_2",
label = "V1 Std.err")))})
output$comp2_5_2<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "alpha_mean51_2",
label = "alpha Estimate")),
shiny::column(6,shiny::textInput(inputId = "alpha_sd51_2",
label = "alpha Std.err")))})
output$comp2_5_3<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "beta_mean51_2",
label = "beta Estimate")),
shiny::column(6,shiny::textInput(inputId = "beta_sd51_2",
label = "beta Std.err")))})
output$comp2_5_4<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "k21_mean51_2",
label = "k21 Estimate")),
shiny::column(6,shiny::textInput(inputId = "k21_sd51_2",
label = "k21 Std.err")))})
output$comp3_5_1<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "volume_mean51_3",
label = "V1 Estimate")),
shiny::column(6,shiny::textInput(inputId = "volume_sd51_3",
label = "V1 Std.err")))})
output$comp3_5_2<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "alpha_mean51_3",
label = "alpha Estimate")),
shiny::column(6,shiny::textInput(inputId = "alpha_sd51_3",
label = "alpha Std.err")))})
output$comp3_5_3<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "beta_mean51_3",
label = "beta Estimate")),
shiny::column(6,shiny::textInput(inputId = "beta_sd51_3",
label = "beta Std.err")))})
output$comp3_5_4<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "gamma_mean51_3",
label = "gamma Estimate")),
shiny::column(6,shiny::textInput(inputId = "gamma_sd51_3",
label = "gamma Std.err")))})
output$comp3_5_5<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "k21_mean51_3",
label = "k21 Estimate")),
shiny::column(6,shiny::textInput(inputId = "k21_sd51_3",
label = "k21 Std.err")))})
output$comp3_5_6<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "k31_mean51_3",
label = "k31 Estimate")),
shiny::column(6,shiny::textInput(inputId = "k31_sd51_3",
label = "k31 Std.err")))})
###################### covariance ######################
######################One compartment######################
output$v1alpha_5<-shiny::renderUI({
shiny::textInput(inputId = "v1alpha_5",
label = "Cov(V1,alpha)", value = 0)})
######################Two compartment######################
output$v1beta_5<-shiny::renderUI({
shiny::textInput(inputId = "v1beta_5",
label = "Cov(V1,beta)", value = 0)})
output$v1k21_5<-shiny::renderUI({
shiny::textInput(inputId = "v1k21_5",
label = "Cov(V1,k21)", value = 0)})
output$alphabeta_5<-shiny::renderUI({
shiny::textInput(inputId = "alphabeta_5",
label = "Cov(alpha,beta)", value = 0)})
output$alphak21_5<-shiny::renderUI({
shiny::textInput(inputId = "alphak21_5",
label = "Cov(alpha,k21)", value = 0)})
output$betak21_5<-shiny::renderUI({
shiny::textInput(inputId = "betak21_5",
label = "Cov(beta,k21)", value = 0)})
######################Three compartment######################
output$v1gamma_5<-shiny::renderUI({
shiny::textInput(inputId = "v1gamma_5",
label = "Cov(V1,gamma)", value = 0)})
output$v1k31_5<-shiny::renderUI({
shiny::textInput(inputId = "v1k31_5",
label = "Cov(V1,k31)", value = 0)})
output$alphagamma_5<-shiny::renderUI({
shiny::textInput(inputId = "alphagamma_5",
label = "Cov(alpha,gamma)", value = 0)})
output$alphak31_5<-shiny::renderUI({
shiny::textInput(inputId = "alphak31_5",
label = "Cov(alpha,k31)", value = 0)})
output$betagamma_5<-shiny::renderUI({
shiny::textInput(inputId = "betagamma_5",
label = "Cov(beta,gamma)", value = 0)})
output$betak31_5<-shiny::renderUI({
shiny::textInput(inputId = "betak31_5",
label = "Cov(beta,k31)", value = 0)})
output$gammak21_5<-shiny::renderUI({
shiny::textInput(inputId = "gammak21_5",
label = "Cov(gamma,k21)", value = 0)})
output$gammak31_5<-shiny::renderUI({
shiny::textInput(inputId = "gammak31_5",
label="Cov(gamma,k31)", value=0)})
output$k21k31_5<-shiny::renderUI({
shiny::textInput(inputId = "k21k31_5",
label="Cov(k21,k31)", value = 0)})
###########################################################
#########################Results###########################
###########################################################
######################One compartment######################
result5_1<-shiny::reactive({
V1<-as.numeric(input$volume_mean51_1)
V1.sd<-as.numeric(input$volume_sd51_1)
alpha<-as.numeric(input$alpha_mean51_1)
alpha.sd<-as.numeric(input$alpha_sd51_1)
V1alpha<-as.numeric(input$v1alpha_5)
OneComp_Volume_Exponent(V1,alpha,V1.sd,alpha.sd,covar=c(V1alpha))})
output$T5_1<-shiny::renderTable({
Label<-c("Volume","","Clearnace","Micro Rate Constant",
"Exponent","Half-lives",
"True Coeffficient","Fractional Coefficient")
T5.1<-data.frame(Label,result5_1())
colnames(T5.1)[1]<-""
T5.1},align="?",digits=4,rownames=FALSE)
total5_1<-shiny::reactive({result5_1()})
fileext5 <- shiny::reactive({switch(input$type5,
"Excel (CSV)" = "csv",
"Text (tab separated)" = "tab",
"Text (Space Separated)" = "txt")})
output$downloadData5_1<-shiny::downloadHandler(
filename = function() {
paste("one_compartment_sheet5", fileext5(), sep = ".")},
content = function(file){
sep.t=switch(fileext5(),
csv=",",
tab="\t",
txt=" ")
utils::write.table(total5_1(), file, sep = sep.t,
row.names = FALSE,col.names = TRUE)})
######################Two compartment######################
result5_2<-shiny::reactive({
V1<-as.numeric(input$volume_mean51_2)
alpha<-as.numeric(input$alpha_mean51_2)
beta<-as.numeric(input$beta_mean51_2)
k21<-as.numeric(input$k21_mean51_2)
V1.sd<-as.numeric(input$volume_sd51_2)
alpha.sd<-as.numeric(input$alpha_sd51_2)
beta.sd<-as.numeric(input$beta_sd51_2)
k21.sd<-as.numeric(input$k21_sd51_2)
V1alpha<-as.numeric(input$v1alpha_5)
V1beta<-as.numeric(input$v1beta_5)
V1k21<-as.numeric(input$v1k21_5)
alphabeta<-as.numeric(input$alphabeta_5)
alphak21<-as.numeric(input$alphak21_5)
betak21<-as.numeric(input$betak21_5)
TwoComp_Volume_Exponent(V1,alpha,beta,k21,V1.sd,alpha.sd,beta.sd,k21.sd,
covar=c(V1alpha,V1beta,V1k21,alphabeta,alphak21,betak21)) })
output$T5_2<-shiny::renderTable({
Label<-c("Volume","","","Clearnace","",
"Micro Rate Constant","","",
"Exponent","","Half-lives","",
"True Coeffficient","","Fractional Coefficient","")
T5.2<-data.frame(Label,result5_2())
colnames(T5.2)[1]<-""
T5.2},align="?",digits=4,rownames=FALSE)
total5_2<-shiny::reactive({ result5_2()})
output$downloadData5_2<-shiny::downloadHandler(
filename = function() {
paste("two_compartment_sheet5", fileext5(), sep = ".")},
content = function(file){
sep.t=switch(fileext5(),
csv=",",
tab="\t",
txt=" ")
utils::write.table(total5_2(), file, sep = sep.t,
row.names = FALSE,col.names = TRUE)})
######################Three compartment######################
result5_3<-shiny::reactive({
V1<-as.numeric(input$volume_mean51_3)
alpha<-as.numeric(input$alpha_mean51_3)
beta<-as.numeric(input$beta_mean51_3)
gamma<-as.numeric(input$gamma_mean51_3)
k21<-as.numeric(input$k21_mean51_3)
k31<-as.numeric(input$k31_mean51_3)
V1.sd<-as.numeric(input$volume_sd51_3)
alpha.sd<-as.numeric(input$alpha_sd51_3)
beta.sd<-as.numeric(input$beta_sd51_3)
gamma.sd<-as.numeric(input$gamma_sd51_3)
k21.sd<-as.numeric(input$k21_sd51_3)
k31.sd<-as.numeric(input$k31_sd51_3)
V1alpha<-as.numeric(input$v1alpha_5);
V1beta<-as.numeric(input$v1beta_5)
V1gamma<-as.numeric(input$v1gamma_5);
V1k21<-as.numeric(input$v1k21_5)
V1k31<-as.numeric(input$v1k31_5);
alphabeta<-as.numeric(input$alphabeta_5)
alphagamma<-as.numeric(input$alphagamma_5)
alphak21<-as.numeric(input$alphak21_5)
alphak31<-as.numeric(input$alphak31_5)
betagamma<-as.numeric(input$betagamma_5)
betak21<-as.numeric(input$betak21_5)
betak31<-as.numeric(input$betak31_5)
gammak21<-as.numeric(input$gammak21_5)
gammak31<-as.numeric(input$gammak31_5)
k21k31<-as.numeric(input$k21k31_5)
ThreeComp_Volume_Exponent(V1,alpha,beta,gamma,k21,k31,
V1.sd,alpha.sd,beta.sd,gamma.sd,
k21.sd,k31.sd,covar=c(V1alpha,V1beta,V1gamma,V1k21,V1k31,alphabeta,
alphagamma,alphak21,alphak31,betagamma,betak21,betak31,gammak21,
gammak31,k21k31))})
output$T5_3<-shiny::renderTable({
Label<-c("Volume","","","","Clearnace","","",
"Micro Rate Constant","","","","",
"Exponent","","","Half-lives","","",
"True Coeffficient","","","Fractional Coefficient","","")
T5.3<-data.frame(Label,result3_3())
colnames(T5.3)[1]<-""
T5.3},align="?",digits=4,rownames=FALSE)
total5_3<-shiny::reactive({ result5_3()})
output$downloadData5_3<-shiny::downloadHandler(
filename = function() {
paste("three_compartment_sheet5", fileext5(), sep = ".")},
content = function(file){
sep.t=switch(fileext5(),
csv=",",
tab="\t",
txt=" ")
utils::write.table(total5_3(), file, sep = sep.t,
row.names = FALSE,col.names = TRUE)})
Dataset<-shiny::reactive({
if(is.null(input$inputfile)){return(data.frame())}
outputData<-data.frame(do.call("read.csv",
list(input$inputfile$datapath)))
return(outputData)})
output$choose_PK<-shiny::renderUI({
if(is.null(input$inputfile))
return()
if(identical(Dataset(),'')||identical(Dataset(),data.frame()))
return(NULL)
PKconverter.env$outputData<-Dataset()
PKconverter.env$labelList<-switch(
paste(input$modelF1,input$modelF2,sep="-"),
"one-M1"=c("V1","Cl1"),
"one-M2"=c("V1","k10"),
"one-M3"=c("Cl1","t_alpha"),
"one-M4"=c("True_A","alpha"),
"one-M5"=c("V1","alpha"),
"two-M1"=c("V1","V2","Cl1","Cl2"),
"two-M2"=c("V1","k10","k12","k21"),
"two-M3"=c("V1","Cl1","t_alpha","t_beta"),
"two-M4"=c("True_A","True_B","alpha","beta"),
"two-M5"=c("V1","k21","alpha","beta"),
"three-M1"=c("V1","V2","V3","Cl1","Cl2","Cl3"),
"three-M2"=c("V1","k10","k12","k21","k13","k31"),
"three-M3"=c("V1","Cl1","t_alpha","t_beta","t_gamma"),
"three-M4"=c("True_A","True_B","True_C","alpha","beta","gamma"),
"three-M5"=c("V1","k21","k31","alpha","beta","gamma"))
PKconverter.env$labelList<-c("ID",PKconverter.env$labelList)
MakeSelectList<-function(X=1){
shiny::selectInput(paste0("PK",as.character(X)),
label=PKconverter.env$labelList[X],
choices=c("",colnames(PKconverter.env$outputData)),
selected="")
}
WidgetVector<-shiny::reactive({
n<-length(PKconverter.env$labelList)
lapply(X=1:n,FUN=MakeSelectList)
})
output$choose_PK<-shiny::renderUI({
if(is.null(input$inputfile)|is.null(PKconverter.env$outputData)){
return()
} else{
shiny::tagList(WidgetVector())}})})
output$ShowResult<-shiny::renderTable({
if(is.null(input$inputfile)) return()
if(identical(Dataset(),'')||identical(Dataset(),data.frame()))
return(NULL)
if(length(PKconverter.env$labelList)==0) return()
if(length(input[["PK1"]])==0) return()
n<-length(PKconverter.env$labelList)
if(input[[paste0("PK",n)]]=="") return()
param.list<-rep("",n)
for(i in 1:n){
param.list[i]<-input[[paste0("PK",i)]]
}
PKconverter.env$param.list<-param.list
sel.data<-PKconverter.env$outputData[,param.list]
colnames(sel.data)<-PKconverter.env$labelList
modelF<-paste(input$modelF1,input$modelF2,sep="-")
tot.result<-NULL
if(input$modelF1=="one"){
for(i in 1:nrow(sel.data)){
if(input$modelF2=="M1"){
temp.result<-OneComp_Volume_Clearance(sel.data[i,2],
sel.data[i,3])
} else if(input$modelF2=="M2"){
temp.result<-OneComp_Volume_RateConstant(sel.data[i,2],
sel.data[i,3])
} else if(input$modelF2=="M3"){
temp.result<-OneComp_Volume_Clearance_HalfLife(sel.data[i,2],
sel.data[i,3])
} else if(input$modelF2=="M4"){
temp.result<-OneComp_Coefficient_Exponent(sel.data[i,2],
sel.data[i,3])
} else if(input$modelF2=="M5"){
temp.result<-OneComp_Volume_Exponent(sel.data[i,2],
sel.data[i,3])
}
tot.result<-rbind(tot.result,c(i,temp.result[,2]))
if(i==1) colnames(tot.result)<-c("ID",rownames(temp.result))
}
} else if(input$modelF1=="two"){
for(i in 1:nrow(sel.data)){
if(input$modelF2=="M1"){
temp.result<-TwoComp_Volume_Clearance(sel.data[i,2],
sel.data[i,3],sel.data[i,4],sel.data[i,5])
} else if(input$modelF2=="M2"){
print(c(input$modelF1,input$modelF2))
temp.result<-TwoComp_Volume_RateConstant(sel.data[i,2],
sel.data[i,3],sel.data[i,4],sel.data[i,5])
print(temp.result)
} else if(input$modelF2=="M3"){
temp.result<-TwoComp_Volume_Clearance_HalfLife(sel.data[i,2],
sel.data[i,3],sel.data[i,4],sel.data[i,5])
} else if(input$modelF2=="M4"){
temp.result<-TwoComp_Coefficient_Exponent(sel.data[i,2],
sel.data[i,3],sel.data[i,4],sel.data[i,5])
} else if(input$modelF2=="M5"){
temp.result<-TwoComp_Volume_Exponent(sel.data[i,2],sel.data[i,3],
sel.data[i,4],sel.data[i,5])
}
tot.result<-rbind(tot.result,c(i,temp.result[,2]))
if(i==1) colnames(tot.result)<-c("ID",rownames(temp.result))
}
} else if(input$modelF1=="three"){
for(i in 1:nrow(sel.data)){
if(input$modelF2=="M1"){
temp.result<-ThreeComp_Volume_Clearance(sel.data[i,2],
sel.data[i,3],sel.data[i,4],
sel.data[i,5],sel.data[i,6],sel.data[i,7])
} else if(input$modelF2=="M2"){
temp.result<-ThreeComp_Volume_RateConstant(sel.data[i,2],
sel.data[i,3],sel.data[i,4],
sel.data[i,5],sel.data[i,6],sel.data[i,7])
} else if(input$modelF2=="M3"){
temp.result<-ThreeComp_Volume_Clearance_HalfLife(sel.data[i,2],
sel.data[i,3],sel.data[i,4],
sel.data[i,5],sel.data[i,6],sel.data[i,7])
} else if(input$modelF2=="M4"){
temp.result<-ThreeComp_Coefficient_Exponent(sel.data[i,2],
sel.data[i,3],sel.data[i,4],
sel.data[i,5],sel.data[i,6],sel.data[i,7])
} else if(input$modelF2=="M5"){
temp.result<-ThreeComp_Volume_Exponent(sel.data[i,2],
sel.data[i,3],sel.data[i,4],
sel.data[i,5],sel.data[i,6],sel.data[i,7])
}
tot.result<-rbind(tot.result,c(i,temp.result[,2]))
if(i==1) colnames(tot.result)<-c("ID",rownames(temp.result))}}
out<-tot.result
PKconverter.env$tot.result<-tot.result})
output$SaveIndivResult<-shiny::downloadHandler(
filename = function() {
paste("IndivParam.csv")},
content = function(file){
utils::write.table(PKconverter.env$tot.result, file, sep = ",",
row.names = FALSE,col.names = TRUE)})
}#end server
)#end App
shiny::runApp(PK_app,launch.browser=TRUE)
}
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PKconverter documentation built on Feb. 6, 2020, 5:08 p.m.
R Package Documentation
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Defines functions PKconverterApp
Documented in PKconverterApp
#' Shiny App for converting the pharmacokinetic parameters
#'
#' Pharmacokinetics is the study of drug absorption, distribution, metabolism,
#' and excretion. The pharmacokinetics model explains that how the drug
#' concentration change as the drug moves through the different compartments
#' of the body. For pharmacokinetic modeling and analysis, it is essential
#' to understand the basic pharmacokinetic parameters. All parameters are
#' considered, but only some of parameters are used in the model.
#' Therefore,we need to convert the estimated parameters to the other
#' parameters after fitting the specific pharmacokinetic model.
#' @usage PKconverterApp()
#' @examples
#' #PKconverterApp()
#' @export
#'
PKconverterApp<-function(){
PKconverter.env<-new.env()
PK_app=shiny::shinyApp(
ui=shiny::fluidPage(
theme=shinythemes::shinytheme("cerulean"),
shiny::shinyUI(
shiny::navbarPage("PK Parameter Converter",
############################sheet1############################
shiny::tabPanel(title="Model 1",
shiny::sidebarLayout(
shiny::column(width=5,
shinydashboard::box(title="Select your model",width=NULL,
solidHeader=TRUE,status="warning",
background="light-blue",
shiny::radioButtons("model1", "MODEL TYPE :",
list("One compartment model" ="one",
"Two compartment model" ="two",
"Three compartment model" ="three"))),
shiny::tags$hr(),
shiny::tags$hr(),
shinydashboard::box(title="Enter your estimate and std.err",
width=NULL,solidHeader=TRUE,status="warning",
background="light-blue",
shiny::tabsetPanel(id="input1",type="pills",
shiny::tabPanel("Estimate / Std.err", value="meanandsd",
shiny::tags$hr(),
shiny::conditionalPanel(condition="input.model1=='one'",
shiny::uiOutput("comp1_1_1"),
shiny::uiOutput("comp1_1_2")),
shiny::conditionalPanel(condition="input.model1=='two'",
shiny::uiOutput("comp2_1_1"),
shiny::uiOutput("comp2_1_2"),
shiny::uiOutput("comp2_1_3"),
shiny::uiOutput("comp2_1_4")),
shiny::conditionalPanel(condition="input.model1=='three' ",
shiny::uiOutput("comp3_1_1"),
shiny::uiOutput("comp3_1_2"),
shiny::uiOutput("comp3_1_3"),
shiny::uiOutput("comp3_1_4"),
shiny::uiOutput("comp3_1_5"),
shiny::uiOutput("comp3_1_6"))),
shiny::tabPanel("Covariance", value="varcov",
shiny::conditionalPanel(condition="input.model1=='one'||
input.model1=='two'||input.model1=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("v1cl1_1")))),
shiny::conditionalPanel(condition="input.model1=='two'||
input.model1=='three'",
shiny::fluidRow(shiny::column(4,shiny::uiOutput("v2cl1_1")),
shiny::column(4,shiny::uiOutput("v1v2_1")))),
shiny::conditionalPanel(condition="input.model1=='three'",
shiny::fluidRow(shiny::column(4,shiny::uiOutput("v3cl1_1")),
shiny::column(4,shiny::uiOutput("v1v3_1")),
shiny::column(4,shiny::uiOutput("v2v3_1")))),
shiny::conditionalPanel(condition="input.model1=='two'||
input.model1=='three'",
shiny::fluidRow(shiny::column(4,shiny::uiOutput("v1cl2_1")),
shiny::column(4,shiny::uiOutput("v2cl2_1")),
shiny::column(4,shiny::uiOutput("cl1cl2_1")))),
shiny::conditionalPanel(condition="input.model1=='three'",
shiny::fluidRow(shiny::column(4,shiny::uiOutput("v1cl3_1")),
shiny::column(4,shiny::uiOutput("v3cl2_1")),
shiny::column(4,shiny::uiOutput("cl1cl3_1")))),
shiny::conditionalPanel(condition="input.model1=='three'",
shiny::fluidRow(shiny::column(4,shiny::uiOutput("v2cl3_1")),
shiny::column(4,shiny::uiOutput("v3cl3_1")),
shiny::column(4,shiny::uiOutput("cl2cl3_1"))))))),
shiny::tags$hr(),
shiny::tags$hr(),
shinydashboard::box(title="Save results as a file",width=NULL,
solidHeader=TRUE,status="warning",
background="light-blue",
shiny::radioButtons("type1", "File type:",
choices = c("Excel (CSV)" ,
"Text (tab separated)" ,
"Text (Space Separated)")),
shiny::conditionalPanel(condition = "input.model1=='one'",
shiny::downloadButton("downloadData1_1",
"Save results to file")),
shiny::conditionalPanel(condition = "input.model1=='two'",
shiny::downloadButton("downloadData1_2",
"Save results to file")),
shiny::conditionalPanel(condition = "input.model1=='three'",
shiny::downloadButton("downloadData1_3",
"Save results to file")))),
shiny::column(width=7,
shiny::wellPanel(
shiny::h2("Model 1: Volumes and Clearances"),
shiny::tags$br(),
shiny::conditionalPanel(condition = "input.model1=='one'",
shiny::h3("One compartment model"),
shiny::tableOutput("T1_1")),
shiny::conditionalPanel(condition = "input.model1=='two'",
shiny::h3("Two compartment model"),
shiny::tableOutput("T1_2")),
shiny::conditionalPanel(condition = "input.model1=='three'",
shiny::h3("Three compartment model"),
shiny::tableOutput("T1_3")))))),
############################sheet2############################
shiny::tabPanel(title="Model 2",
shiny::sidebarLayout(
shiny::column(width=5,
shinydashboard::box(title="Select your model",width=NULL,
solidHeader=TRUE,status="warning",
background="light-blue",
shiny::radioButtons("model2", "MODEL TYPE :",
list("One compartment model" ="one",
"Two compartment model" ="two",
"Three compartment model" ="three"))),
shiny::tags$hr(),
shiny::tags$hr(),
shinydashboard::box(title="Enter your estimate and std.err",
width=NULL,solidHeader=TRUE,status="warning",
background="light-blue",
shiny::tabsetPanel(id="input2",
shiny::tabPanel("Estimate / Std.err", value="meanandsd2",
shiny::tags$hr(),
shiny::conditionalPanel(condition="input.model2=='one'",
shiny::uiOutput("comp1_2_1"),
shiny::uiOutput("comp1_2_2")),
shiny::conditionalPanel(condition="input.model2=='two'",
shiny::uiOutput("comp2_2_1"),
shiny::uiOutput("comp2_2_2"),
shiny::uiOutput("comp2_2_3"),
shiny::uiOutput("comp2_2_4")),
shiny::conditionalPanel(condition="input.model2=='three'",
shiny::uiOutput("comp3_2_1"),
shiny::uiOutput("comp3_2_2"),
shiny::uiOutput("comp3_2_3"),
shiny::uiOutput("comp3_2_4"),
shiny::uiOutput("comp3_2_5"),
shiny::uiOutput("comp3_2_6"))),
shiny::tabPanel("Covariance", value="varcov2",
shiny::conditionalPanel(
condition="input.model2=='one'||input.model2=='two'
||input.model2=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("v1k10_2")))),
shiny::conditionalPanel(
condition="input.model2=='two'||input.model2=='three'",
shiny::fluidRow(shiny::column(4,shiny::uiOutput("v1k12_2")),
shiny::column(4,shiny::uiOutput("v1k21_2")))),
shiny::conditionalPanel(condition="input.model2=='three'",
shiny::fluidRow(shiny::column(4,shiny::uiOutput("v1k13_2")),
shiny::column(4,shiny::uiOutput("v1k31_2")),
shiny::column(4,shiny::uiOutput("k13k31_2")))),
shiny::conditionalPanel(
condition="input.model2=='two'||input.model2=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("k10k12_2")),
shiny::column(4,shiny::uiOutput("k10k21_2")),
shiny::column(4,shiny::uiOutput("k12k21_2")))),
shiny::conditionalPanel(condition="input.model2=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("k10k13_2")),
shiny::column(4,shiny::uiOutput("k10k31_2")),
shiny::column(4,shiny::uiOutput("k12k31_2"))),
shiny::conditionalPanel(condition="input.model2=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("k21k13_2")),
shiny::column(4,shiny::uiOutput("k21k31_2")),
shiny::column(4,shiny::uiOutput("k12k13_2")))))))),
shiny::tags$hr(),
shiny::tags$hr(),
shinydashboard::box(title="Save the result as a file",width=NULL,
solidHeader=TRUE,status="warning",
background="light-blue",
shiny::radioButtons("type2", "File type:",
choices = c("Excel (CSV)" ,
"Text (tab separated)" ,
"Text (Space Separated)")),
shiny::conditionalPanel(condition = "input.model2=='one'",
shiny::downloadButton("downloadData2_1",
"Save results to file")),
shiny::conditionalPanel(condition = "input.model2=='two'",
shiny::downloadButton("downloadData2_2",
"Save results to file")),
shiny::conditionalPanel(condition = "input.model2=='three'",
shiny::downloadButton("downloadData2_3",
"Save results to file")))),
shiny::column(width=7,
shiny::wellPanel(
shiny::h2("Model 2: V1, Rate Constants"),
shiny::tags$br(),
shiny::conditionalPanel(condition = "input.model2=='one'",
shiny::h3("One compartment model"),
shiny::tableOutput("T2_1")),
shiny::conditionalPanel(condition = "input.model2=='two'",
shiny::h3("Two compartment model"),
shiny::tableOutput("T2_2")),
shiny::conditionalPanel(condition = "input.model2=='three'",
shiny::h3("Three compartment model"),
shiny::tableOutput("T2_3")))))),
############################sheet3############################
shiny::tabPanel(title="Model 3",
shiny::sidebarLayout(
shiny::column(width=5,
shinydashboard::box(title="Select your model",width=NULL,
solidHeader=TRUE,status="warning",
background="light-blue",
shiny::radioButtons("model3", "MODEL TYPE :",
list("One compartment model" ="one",
"Two compartment model" ="two",
"Three compartment model" ="three"))),
shiny::tags$hr(),
shiny::tags$hr(),
shinydashboard::box(title="Enter your estimate and std.err",
width=NULL,solidHeader=TRUE,status="warning",
background="light-blue",
shiny::tabsetPanel(id="input3",
shiny::tabPanel("Estimate / Std.err", value="meanandsd3",
shiny::conditionalPanel(condition="input.model3=='one' ",
shiny::uiOutput("comp1_3_1"),
shiny::uiOutput("comp1_3_2")),
shiny::conditionalPanel(condition="input.model3=='two'",
shiny::uiOutput("comp2_3_1"),
shiny::uiOutput("comp2_3_2"),
shiny::uiOutput("comp2_3_3"),
shiny::uiOutput("comp2_3_4")),
shiny::conditionalPanel(condition="input.model3=='three' ",
shiny::uiOutput("comp3_3_1"),
shiny::uiOutput("comp3_3_2"),
shiny::uiOutput("comp3_3_3"),
shiny::uiOutput("comp3_3_4"),
shiny::uiOutput("comp3_3_5"),
shiny::uiOutput("comp3_3_6"))),
shiny::tabPanel("Covariance", value="varcov3",
shiny::conditionalPanel(condition="input.model3=='one'||
input.model3=='two'||input.model3=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("cl1talpha_3")))),
shiny::conditionalPanel(condition="input.model3=='two'||
input.model3=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("v1talpha_3")),
shiny::column(4,shiny::uiOutput("v1tbeta_3")))),
shiny::conditionalPanel(condition="input.model3=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("vdtalpha_3")),
shiny::column(4,shiny::uiOutput("vdtbeta_3")),
shiny::column(4,shiny::uiOutput("vdtgamma_3")))),
shiny::conditionalPanel(condition="input.model3=='two'||
input.model3=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("v1cl1_3")),
shiny::column(4,shiny::uiOutput("cl1tbeta_3")),
shiny::column(4,shiny::uiOutput("talphatbeta_3")))),
shiny::conditionalPanel(condition="input.model3=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("v1vd_3")),
shiny::column(4,shiny::uiOutput("v1tgamma_3")),
shiny::column(4,shiny::uiOutput("vdcl1_3")))),
shiny::conditionalPanel(condition="input.model3=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("cl1tgamma_3")),
shiny::column(4,shiny::uiOutput("talphatgamma_3")),
shiny::column(4,shiny::uiOutput("tbetatgamma_3"))))))),
shiny::tags$hr(),
shiny::tags$hr(),
shinydashboard::box(title="Save the result as a file",width=NULL,
solidHeader=TRUE,status="warning",
background="light-blue",
shiny::radioButtons("type3", "File type:",
choices = c("Excel (CSV)" ,
"Text (tab separated)" ,
"Text (Space Separated)")),
shiny::conditionalPanel(condition = "input.model3=='one'",
shiny::downloadButton("downloadData3_1",
"Save results to file")),
shiny::conditionalPanel(condition = "input.model3=='two'",
shiny::downloadButton("downloadData3_2",
"Save results to file")),
shiny::conditionalPanel(condition = "input.model3=='three'",
shiny::downloadButton("downloadData3_3",
"Save results to file")))),
shiny::column(width=7,
shiny::wellPanel(
shiny::h2("Model 3: V1, Vdss, Cl, half-lives"),
shiny::tags$br(),
shiny::conditionalPanel(condition = "input.model3=='one'",
shiny::h3("One compartment model"),
shiny::tableOutput("T3_1")),
shiny::conditionalPanel(condition = "input.model3=='two'",
shiny::h3("Two compartment model"),
shiny::tableOutput("T3_2")),
shiny::conditionalPanel(condition = "input.model3=='three'",
shiny::h3("Three compartment model"),
shiny::tableOutput("T3_3")))))),
############################sheet4############################
shiny::tabPanel(title="Model 4",
shiny::sidebarLayout(
shiny::column(width=5,
shinydashboard::box(title="Select your model",width=NULL,
solidHeader=TRUE,status="warning",
background="light-blue",
shiny::radioButtons("model4", "MODEL TYPE :",
list("One compartment model" ="one",
"Two compartment model" ="two",
"Three compartment model" ="three"))),
shiny::tags$hr(),
shiny::tags$hr(),
shinydashboard::box(title="Enter your estimate and std.err",
width=NULL,solidHeader=TRUE,status="warning",
background="light-blue",
shiny::tabsetPanel(id="input4",
shiny::tabPanel("Estimate / Std.err", value="meanandsd4",
shiny::conditionalPanel(condition="input.model4=='one' ",
shiny::uiOutput("comp1_4_1"),
shiny::uiOutput("comp1_4_2")),
shiny::conditionalPanel(condition="input.model4=='two' ",
shiny::uiOutput("comp2_4_1"),
shiny::uiOutput("comp2_4_2"),
shiny::uiOutput("comp2_4_3"),
shiny::uiOutput("comp2_4_4")),
shiny::conditionalPanel(condition="input.model4=='three' ",
shiny::uiOutput("comp3_4_1"),
shiny::uiOutput("comp3_4_2"),
shiny::uiOutput("comp3_4_3"),
shiny::uiOutput("comp3_4_4"),
shiny::uiOutput("comp3_4_5"),
shiny::uiOutput("comp3_4_6"))),
shiny::tabPanel("Covariance", value="varcov4",
shiny::conditionalPanel(condition="input.model4=='one'||
input.model4=='two'||input.model4=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("aalpha_4")))),
shiny::conditionalPanel(condition="input.model4=='two'||
input.model4=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("abeta_4")),
shiny::column(4,shiny::uiOutput("ab_4")))),
shiny::conditionalPanel(condition="input.model4=='two'||
input.model4=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("balpha_4")),
shiny::column(4,shiny::uiOutput("bbeta_4")),
shiny::column(4,shiny::uiOutput("alphabeta_4")))),
shiny::conditionalPanel(condition="input.model4=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("agamma_4")),
shiny::column(4,shiny::uiOutput("bgamma_4")),
shiny::column(4,shiny::uiOutput("cgamma_4")))),
shiny::conditionalPanel(condition="input.model4=='three'",
shiny::fluidRow(shiny::column(4,shiny::uiOutput("ac_4")),
shiny::column(4,shiny::uiOutput("bc_4")),
shiny::column(4,shiny::uiOutput("betagamma_4")))),
shiny::conditionalPanel(condition="input.model4=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("alphagamma_4")),
shiny::column(4,shiny::uiOutput("calpha_4")),
shiny::column(4,shiny::uiOutput("cbeta_4"))))))),
shiny::tags$hr(),
shiny::tags$hr(),
shinydashboard::box(title="Save the result as a file",
width=NULL,solidHeader=TRUE,status="warning",
background="light-blue",
shiny::radioButtons("type4", "File type:",
choices = c("Excel (CSV)" ,
"Text (tab separated)" ,
"Text (Space Separated)")),
shiny::conditionalPanel(condition = "input.model4=='one'",
shiny::downloadButton("downloadData4_1",
"Save results to file")),
shiny::conditionalPanel(condition = "input.model4=='two'",
shiny::downloadButton("downloadData4_2",
"Save results to file")),
shiny::conditionalPanel(condition = "input.model4=='three'",
shiny::downloadButton("downloadData4_3"
,"Save results to file")))),
shiny::column(width=7,
shiny::wellPanel(
shiny::h2("Model 4: Coefficients and Exponents"),
shiny::tags$br(),
shiny::conditionalPanel(condition = "input.model4=='one'",
shiny::h3("One compartment model"),
shiny::tableOutput("T4_1")),
shiny::conditionalPanel(condition = "input.model4=='two'",
shiny::h3("Two compartment model"),
shiny::tableOutput("T4_2")),
shiny::conditionalPanel(condition = "input.model4=='three'",
shiny::h3("Three compartment model"),
shiny::tableOutput("T4_3")))))),
############################sheet5############################
shiny::tabPanel(title="Model 5",
shiny::sidebarLayout(
shiny::column(width=5,
shinydashboard::box(title="Select your model",width=NULL,
solidHeader=TRUE,status="warning",
background="light-blue",
shiny::radioButtons("model5", "MODEL TYPE :",
list("One compartment model" ="one",
"Two compartment model" ="two",
"Three compartment model" ="three"))),
shiny::tags$hr(),
shiny::tags$hr(),
shinydashboard::box(title="Enter your estimate and std.err",
width=NULL,solidHeader=TRUE,status="warning",
background="light-blue",
shiny::tabsetPanel(id="input5",
shiny::tabPanel("Estimate / Std.err", value="meanandsd5",
shiny::conditionalPanel(condition="input.model5=='one' ",
shiny::uiOutput("comp1_5_1"),
shiny::uiOutput("comp1_5_2")),
shiny::conditionalPanel(condition="input.model5=='two' ",
shiny::uiOutput("comp2_5_1"),
shiny::uiOutput("comp2_5_2"),
shiny::uiOutput("comp2_5_3"),
shiny::uiOutput("comp2_5_4")),
shiny::conditionalPanel(condition="input.model5=='three' ",
shiny::uiOutput("comp3_5_1"),
shiny::uiOutput("comp3_5_2"),
shiny::uiOutput("comp3_5_3"),
shiny::uiOutput("comp3_5_4"),
shiny::uiOutput("comp3_5_5"),
shiny::uiOutput("comp3_5_6"))),
shiny::tabPanel("Covariance", value="varcov5",
shiny::conditionalPanel(condition="input.model5=='one'||
input.model5=='two'||input.model5=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("v1alpha_5")))),
shiny::conditionalPanel(condition="input.model5=='two'||
input.model5=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("v1beta_5")),
shiny::column(4,shiny::uiOutput("v1k21_5")))),
shiny::conditionalPanel(condition="input.model5=='two'||
input.model5=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("alphabeta_5")),
shiny::column(4,shiny::uiOutput("alphak21_5")),
shiny::column(4,shiny::uiOutput("betak21_5")))),
shiny::conditionalPanel(condition="input.model5=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("alphak31_5")),
shiny::column(4,shiny::uiOutput("betak31_5")),
shiny::column(4,shiny::uiOutput("gammak31_5")))),
shiny::conditionalPanel(condition="input.model5=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("v1gamma_5")),
shiny::column(4,shiny::uiOutput("v1k31_5")),
shiny::column(4,shiny::uiOutput("alphagamma_5")))),
shiny::conditionalPanel(condition="input.model5=='three'",
shiny::fluidRow(shiny::column(4,
shiny::uiOutput("betagamma_5")),
shiny::column(4,shiny::uiOutput("gammak21_5")),
shiny::column(4,shiny::uiOutput("k21k31_5"))))))),
shiny::tags$hr(),
shiny::tags$hr(),
shinydashboard::box(title="Save the result as a file",
width=NULL,solidHeader=TRUE,status="warning",
background="light-blue",
shiny::radioButtons("type5", "File type:",
choices = c("Excel (CSV)" ,
"Text (tab separated)" ,
"Text (Space Separated)")),
shiny::conditionalPanel(condition = "input.model5=='one'",
shiny::downloadButton("downloadData5_1",
"Save results to file")),
shiny::conditionalPanel(condition = "input.model5=='two'",
shiny::downloadButton("downloadData5_2",
"Save results to file")),
shiny::conditionalPanel(condition = "input.model5=='three'",
shiny::downloadButton("downloadData5_3",
"Save results to file")))),
shiny::column(width=7,
shiny::wellPanel(
shiny::h2("Model 5: V1, Exponents, K21, K31"),
shiny::tags$br(),
shiny::conditionalPanel(condition = "input.model5=='one'",
shiny::h3("One compartment model"),
shiny::tableOutput("T5_1")),
shiny::conditionalPanel(condition = "input.model5=='two'",
shiny::h3("Two compartment model"),
shiny::tableOutput("T5_2")),
shiny::conditionalPanel(condition = "input.model5=='three'",
shiny::h3("Three compartment model"),
shiny::tableOutput("T5_3")))))),
######################### Indiv parameter converter ##################
shiny::tabPanel("Indiv. Parameter Converter",
shiny::fluidRow(
shiny::column(6,
shinydashboard::box(title="Select your compartment model",
width=NULL,solidHeader=TRUE,status="warning",
background="light-blue",
shiny::radioButtons("modelF1", "MODEL TYPE :",
list("One compartment model" ="one",
"Two compartment model" ="two",
"Three compartment model" ="three"))),
shiny::tags$hr(),
shiny::tags$hr(),
shinydashboard::box(title="Select your input data type",
width=NULL,solidHeader=TRUE,status="warning",
background="light-blue",
shiny::radioButtons("modelF2", "DATA TYPE :",
list("Model 1: Volumes and Clearances" ="M1",
"Model 2: V1, Rate Constants" ="M2",
"Model 3: V1, Vdss, Cl, half-lives" ="M3",
"Model 4: Coefficients and Exponents" ="M4",
"Model 5: V1,Exponents,K21,K31" ="M5"))),
shiny::tags$hr(),
shiny::tags$hr(),
shinydashboard::box(title="Open your individual PK parameters",
width=NULL,solidHeader=TRUE,status="warning",
background="light-blue",
shiny::fileInput("inputfile",
label="File should be saved as CSV")),
shiny::tags$hr(),
shiny::tags$hr(),
shinydashboard::box(title="Match PK parameters",
width=NULL,solidHeader=TRUE,status="warning",
background="light-blue",
shiny::uiOutput("choose_PK"))),
shiny::column(6,
shiny::downloadButton("SaveIndivResult",
"Save individual parameters to file"),
shiny::tags$hr(),
shiny::tags$hr(),
shiny::tableOutput("ShowResult"))))))), #end ui
############################ SERVER ####################################
server<-function(input,output,session){
## sheet1 ########
###### INPUT #####
output$comp1_1_1<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "volume_mean1_1",
label = "V1 Estimate")),
shiny::column(6,shiny::textInput(inputId = "volume_sd1_1",
label = "V1 Std.err")))})
output$comp1_1_2<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "Clearance_mean1_1",
label = "Cl1 Estimate")),
shiny::column(6,shiny::textInput(inputId = "Clearance_sd1_1",
label = "Cl1 Std.err")))})
output$comp2_1_1<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "volume_mean1_2",
label = "V1 Estimate")),
shiny::column(6,shiny::textInput(inputId = "volume_sd1_2",
label = "V1 Std.err")))})
output$comp2_1_2<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "volume_mean2_2",
label = "V2 Estimate")),
shiny::column(6,shiny::textInput(inputId = "volume_sd2_2",
label = "V2 Std.err")))})
output$comp2_1_3<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "Clearance_mean1_2",
label = "Cl1 Estimate")),
shiny::column(6,shiny::textInput(inputId = "Clearance_sd1_2",
label = "Cl1 Std.err")))})
output$comp2_1_4<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "Clearance_mean2_2",
label = "Cl2 Estimate")),
shiny::column(6,shiny::textInput(inputId = "Clearance_sd2_2",
label = "Cl2 Std.err")))})
output$comp3_1_1<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "volume_mean1_3",
label = "V1 Estimate")),
shiny::column(6,shiny::textInput(inputId = "volume_sd1_3",
label = "V1 Std.err")))})
output$comp3_1_2<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "volume_mean2_3",
label = "V2 Estimate")),
shiny::column(6,shiny::textInput(inputId = "volume_sd2_3",
label = "V2 Std.err")))})
output$comp3_1_3<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "volume_mean3_3",
label = "V3 Estimate")),
shiny::column(6,shiny::textInput(inputId = "volume_sd3_3",
label = "V3 Std.err")))})
output$comp3_1_4<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "Clearance_mean1_3",
label = "Cl1 Estimate")),
shiny::column(6,shiny::textInput(inputId = "Clearance_sd1_3",
label = "Cl1 Std.err")))})
output$comp3_1_5<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "Clearance_mean2_3",
label = "Cl2 Estimate")),
shiny::column(6,shiny::textInput(inputId = "Clearance_sd2_3",
label = "Cl2 Std.err")))})
output$comp3_1_6<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "Clearance_mean3_3",
label = "Cl3 Estimate")),
shiny::column(6,shiny::textInput(inputId = "Clearance_sd3_3",
label = "Cl3 Std.err")))})
##### covariance #####
##### One compartment #####
output$v1cl1_1<-shiny::renderUI({
shiny::textInput(inputId = "v1cl1_1",
label = "Cov(V1,Cl1)", value = 0)})
##### Two compartment #####
output$v1cl2_1<-shiny::renderUI({
shiny::textInput(inputId = "v1cl2_1",
label = "Cov(V1,Cl2)", value = 0)})
output$v2cl1_1<-shiny::renderUI({
shiny::textInput(inputId = "v2cl1_1",
label = "Cov(V2,Cl1)", value = 0)})
output$v2cl2_1<-shiny::renderUI({
shiny::textInput(inputId = "v2cl2_1",
label = "Cov(V2,Cl2)", value = 0)})
output$v1v2_1<-shiny::renderUI({
shiny::textInput(inputId = "v1v2_1",
label = "Cov(V1,V2)", value = 0)})
output$cl1cl2_1<-shiny::renderUI({
shiny::textInput(inputId = "cl1cl2_1",
label = "Cov(Cl1,Cl2)", value = 0)})
##### Three compartment #####
output$v1cl3_1<-shiny::renderUI({
shiny::textInput(inputId = "v1cl3_1",
label = "Cov(V1,Cl3)", value = 0)})
output$v2cl3_1<-shiny::renderUI({
shiny::textInput(inputId = "v2cl3_1",
label = "Cov(V2,Cl3)", value = 0)})
output$v3cl1_1<-shiny::renderUI({
shiny::textInput(inputId = "v3cl1_1",
label = "Cov(V3,Cl1)", value = 0)})
output$v3cl2_1<-shiny::renderUI({
shiny::textInput(inputId = "v3cl2_1",
label = "Cov(V3,Cl2)", value = 0)})
output$v3cl3_1<-shiny::renderUI({
shiny::textInput(inputId = "v3cl3_1",
label = "Cov(V3,Cl3)", value = 0)})
output$v1v3_1<-shiny::renderUI({
shiny::textInput(inputId = "v1v3_1",
label = "Cov(V1,V3)", value = 0)})
output$v2v3_1<-shiny::renderUI({
shiny::textInput(inputId = "v2v3_1",
label = "Cov(V2,V3)", value = 0)})
output$cl1cl3_1<-shiny::renderUI({
shiny::textInput(inputId = "cl1cl3_1",
label = "Cov(Cl1,Cl3)", value = 0)})
output$cl2cl3_1<-shiny::renderUI({
shiny::textInput(inputId = "cl2cl3_1",
label = "Cov(Cl2,Cl3)", value = 0)})
##### Results ######
###### One compartment #####
result1_1<-shiny::reactive({
V1<-as.numeric(input$volume_mean1_1)
Cl1<-as.numeric(input$Clearance_mean1_1)
V1.sd<-as.numeric(input$volume_sd1_1)
Cl1.sd<-as.numeric(input$Clearance_sd1_1)
V1Cl1<-as.numeric(input$v1cl1_1)
if(length(V1Cl1)==0) V1Cl1<-NA
OneComp_Volume_Clearance(V1,Cl1,V1.sd,Cl1.sd,V1Cl1)})
output$T1_1<-shiny::renderTable({
Label<-c("Volume","","Clearnace","Micro Rate Constant","Exponent",
"Half-lives","True Coeffficient","Fractional Coefficient")
T1.1<-data.frame(Label,result1_1())
colnames(T1.1)[1]<-""
T1.1},align="?",digits=4,rownames=FALSE)
total1_1<-shiny::reactive({
result1_1()})
fileext <- shiny::reactive({switch(input$type1,
"Excel (CSV)" = "csv",
"Text (tab separated)" = "tab",
"Text (Space Separated)" = "txt")})
output$downloadData1_1<-shiny::downloadHandler(
filename <- function() {
paste("one_compartment_sheet1", fileext(), sep = ".")},
content <- function(file){
sep.t=switch(fileext(),
csv=",",
tab="\t",
txt=" ")
utils::write.table(total1_1(), file, sep = sep.t,
row.names = FALSE,col.names = TRUE,append=FALSE)})
##### Two compartment #####
result1_2<-shiny::reactive({
V1<-as.numeric(input$volume_mean1_2)
V2<-as.numeric(input$volume_mean2_2)
Cl1<-as.numeric(input$Clearance_mean1_2)
Cl2<-as.numeric(input$Clearance_mean2_2)
V1.sd<-as.numeric(input$volume_sd1_2)
V2.sd<-as.numeric(input$volume_sd2_2)
Cl1.sd<-as.numeric(input$Clearance_sd1_2)
Cl2.sd<-as.numeric(input$Clearance_sd2_2)
V1V2<-as.numeric(input$v1v2_1)
V1Cl1<-as.numeric(input$v1cl1_1)
V1Cl2<-as.numeric(input$v1cl2_1)
V2Cl1<-as.numeric(input$v2cl1_1)
V2Cl2<-as.numeric(input$v2cl2_1)
Cl1Cl2<-as.numeric(input$cl1cl2_1)
TwoComp_Volume_Clearance(V1,V2,Cl1,Cl2,V1.sd,V2.sd,Cl1.sd,Cl2.sd,
covar=c(V1V2,V1Cl1,V1Cl2,V2Cl1,V2Cl2,Cl1Cl2))})
output$T1_2<-shiny::renderTable({
Label<-c("Volume","","","Clearnace","","Micro Rate Constant","","",
"Exponent","","Half-lives","","True Coeffficient","",
"Fractional Coefficient","")
T1.2<-data.frame(Label,result1_2())
colnames(T1.2)[1]<-""
T1.2},align="?",digits=4,rownames=FALSE)
total1_2<-shiny::reactive({
result1_2()})
output$downloadData1_2<-shiny::downloadHandler(
filename = function() {
paste("two_compartment_sheet1", fileext(), sep = ".")},
content = function(file){
sep.t=switch(fileext(),
csv=",",
tab="\t",
txt=" ")
utils::write.table(total1_2(), file, sep = sep.t,
row.names = FALSE,col.names = TRUE)})
######################Three compartment######################
result1_3<-shiny::reactive({
V1<-as.numeric(input$volume_mean1_3)
V2<-as.numeric(input$volume_mean2_3)
V3<-as.numeric(input$volume_mean3_3)
Cl1<-as.numeric(input$Clearance_mean1_3)
Cl2<-as.numeric(input$Clearance_mean2_3)
Cl3<-as.numeric(input$Clearance_mean3_3)
V1.sd<-as.numeric(input$volume_sd1_3)
V2.sd<-as.numeric(input$volume_sd2_3)
V3.sd<-as.numeric(input$volume_sd3_3)
Cl1.sd<-as.numeric(input$Clearance_sd1_3)
Cl2.sd<-as.numeric(input$Clearance_sd2_3)
Cl3.sd<-as.numeric(input$Clearance_sd3_3)
V1V2<-as.numeric(input$v1v2_1); V1V3<-as.numeric(input$v1v3_1)
V1Cl1<-as.numeric(input$v1cl1_1); V1Cl2<-as.numeric(input$v1cl2_1)
V1Cl3<-as.numeric(input$v1cl3_1); V2V3<-as.numeric(input$v2v3_1)
V2Cl1<-as.numeric(input$v2cl1_1); V2Cl2<-as.numeric(input$v2cl2_1)
V2Cl3<-as.numeric(input$v2cl3_1); V3Cl1<-as.numeric(input$v3cl1_1)
V3Cl2<-as.numeric(input$v3cl2_1); V3Cl3<-as.numeric(input$v3cl3_1)
Cl1Cl2<-as.numeric(input$cl1cl2_1);Cl1Cl3<-as.numeric(input$cl1cl3_1)
Cl2Cl3<-as.numeric(input$cl2cl3_1)
ThreeComp_Volume_Clearance(V1,V2,V3,Cl1,Cl2,Cl3,
V1.sd,V2.sd,V3.sd,Cl1.sd,Cl2.sd,Cl3.sd,
covar=c(V1V2,V1V3,V1Cl1,V1Cl2,V1Cl3,V2V3,V2Cl1,V2Cl2,V2Cl3,
V3Cl1,V3Cl2,V3Cl3,Cl1Cl2,Cl1Cl3,Cl2Cl3))})
output$T1_3<-shiny::renderTable({
Label<-c("Volume","","","","Clearnace","","",
"Micro Rate Constant","","","","",
"Exponent","","","Half-lives","","",
"True Coeffficient","","","Fractional Coefficient","","")
T1.3<-data.frame(Label,result1_3())
colnames(T1.3)[1]<-""
T1.3},align="?",digits=4,rownames=FALSE)
total1_3<-shiny::reactive({
result1_3()})
output$downloadData1_3<-shiny::downloadHandler(
filename = function() {
paste("three_compartment_sheet1", fileext(), sep = ".")},
content = function(file){
sep.t=switch(fileext(),
csv=",",
tab="\t",
txt=" ")
utils::write.table(total1_3(), file, sep = sep.t,
row.names = FALSE,col.names = TRUE)})
#########################sheet2#########################################
output$comp1_2_1<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "volume_mean21_1",
label = "V1 Estimate")),
shiny::column(6,shiny::textInput(inputId = "volume_sd21_1",
label = "V1 Std.err")))})
output$comp1_2_2<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "k10_mean_1",
label = "k10 Estimate")),
shiny::column(6,shiny::textInput(inputId = "k10_sd_1",
label = "k10 Std.err")))})
output$comp2_2_1<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "volume_mean21_2",
label = "V1 Estimate")),
shiny::column(6,shiny::textInput(inputId = "volume_sd21_2",
label = "V1 Std.err")))})
output$comp2_2_2<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "k10_mean_2",
label = "k10 Estimate")),
shiny::column(6,shiny::textInput(inputId = "k10_sd_2",
label = "k10 Std.err")))})
output$comp2_2_3<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "k12_mean_2",
label = "k12 Estimate")),
shiny::column(6,shiny::textInput(inputId = "k12_sd_2",
label = "k12 Std.err")))})
output$comp2_2_4<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "k21_mean_2",
label = "k21 Estimate")),
shiny::column(6,shiny::textInput(inputId = "k21_sd_2",
label = "k21 Std.err")))})
output$comp3_2_1<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "volume_mean21_3",
label = "V1 Estimate")),
shiny::column(6,shiny::textInput(inputId = "volume_sd21_3",
label = "V1 Std.err")))})
output$comp3_2_2<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "k10_mean_3",
label = "k10 Estimate")),
shiny::column(6,shiny::textInput(inputId = "k10_sd_3",
label = "k10 Std.err")))})
output$comp3_2_3<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "k12_mean_3",
label = "k12 Estimate")),
shiny::column(6,shiny::textInput(inputId = "k12_sd_3",
label = "k12 Std.err")))})
output$comp3_2_4<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "k13_mean_3",
label = "k13 Estimate")),
shiny::column(6,shiny::textInput(inputId = "k13_sd_3",
label = "k13 Std.err")))})
output$comp3_2_5<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "k21_mean_3",
label = "k21 Estimate")),
shiny::column(6,shiny::textInput(inputId = "k21_sd_3",
label = "k21 Std.err")))})
output$comp3_2_6<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "k31_mean_3",
label = "k31 Estimate")),
shiny::column(6,shiny::textInput(inputId = "k31_sd_3",
label = "k31 Std.err")))})
###################### covariance ######################
######################One compartment###################
output$v1k10_2<-shiny::renderUI({
shiny::textInput(inputId = "v1k10_2",
label = "Cov(V1,k10)", value = 0)})
######################Two compartment######################
output$v1k12_2<-shiny::renderUI({
shiny::textInput(inputId = "v1k12_2",
label = "Cov(V1,k12)", value = 0)})
output$v1k21_2<-shiny::renderUI({
shiny::textInput(inputId = "v1k21_2",
label = "Cov(V1,k21)", value = 0)})
output$k10k12_2<-shiny::renderUI({
shiny::textInput(inputId = "k10k12_2",
label = "Cov(k10,k12)", value = 0)})
output$k10k21_2<-shiny::renderUI({
shiny::textInput(inputId = "k10k21_2",
label = "Cov(k10,k21)", value = 0)})
output$k12k21_2<-shiny::renderUI({
shiny::textInput(inputId = "k12k21_2",
label = "Cov(k12,k21)", value = 0)})
######################Three compartment######################
output$v1k13_2<-shiny::renderUI({
shiny::textInput(inputId = "v1k13_2",
label = "Cov(V1,k13)", value = 0)})
output$v1k31_2<-shiny::renderUI({
shiny::textInput(inputId = "v1k31_2",
label = "Cov(V1,k31)", value = 0)})
output$k13k31_2<-shiny::renderUI({
shiny::textInput(inputId = "k13k31_2",
label = "Cov(k13,k31)", value = 0)})
output$k10k13_2<-shiny::renderUI({
shiny::textInput(inputId = "k10k13_2",
label = "Cov(k10,k13)", value = 0)})
output$k10k31_2<-shiny::renderUI({
shiny::textInput(inputId = "k10k31_2",
label = "Cov(k10,k31)", value = 0)})
output$k12k31_2<-shiny::renderUI({
shiny::textInput(inputId = "k12k31_2",
label = "Cov(k12,k31)", value = 0)})
output$k21k13_2<-shiny::renderUI({
shiny::textInput(inputId = "k21k13_2",
label = "Cov(k21,k13)", value = 0)})
output$k21k31_2<-shiny::renderUI({
shiny::textInput(inputId = "k21k31_2",
label = "Cov(k21,k31)", value = 0)})
output$k12k13_2<-shiny::renderUI({
shiny::textInput(inputId = "k12k13_2",
label = "Cov(k12,k13)", value = 0)})
###########################################################
#########################Results###########################
###########################################################
######################One compartment######################
result2_1<-shiny::reactive({
V1<-as.numeric(input$volume_mean21_1)
k10<-as.numeric(input$k10_mean_1)
V1.sd<-as.numeric(input$volume_sd21_1)
k10.sd<-as.numeric(input$k10_sd_1)
V1k10<-as.numeric(input$v1k10_2)
OneComp_Volume_RateConstant(V1,k10,V1.sd,k10.sd,covar=c(V1k10))})
output$T2_1<-shiny::renderTable({
Label<-c("Volume","","Clearnace","Micro Rate Constant",
"Exponent","Half-lives",
"True Coeffficient","Fractional Coefficient")
T2.1<-data.frame(Label,result2_1())
colnames(T2.1)[1]<-""
T2.1},align="?",digits=4,rownames=FALSE)
total2_1<-shiny::reactive({result2_1()})
fileext2 <- shiny::reactive({switch(input$type2,
"Excel (CSV)" = "csv",
"Text (tab separated)" = "tab",
"Text (Space Separated)" = "txt")})
output$downloadData2_1<-shiny::downloadHandler(
filename = function() {
paste("one_compartment_sheet2", fileext2(), sep = ".")},
content = function(file){sep.t=switch(fileext2(),
csv=",",
tab="\t",
txt=" ")
utils::write.table(total2_1(), file, sep = sep.t,
row.names = FALSE,col.names = TRUE)})
######################Two compartment######################
result2_2<-shiny::reactive({
V1<-as.numeric(input$volume_mean21_2)
k10<-as.numeric(input$k10_mean_2)
k12<-as.numeric(input$k12_mean_2)
k21<-as.numeric(input$k21_mean_2)
V1.sd<-as.numeric(input$volume_sd21_2)
k10.sd<-as.numeric(input$k12_sd_2)
k12.sd<-as.numeric(input$k12_sd_2)
k21.sd<-as.numeric(input$k21_sd_2)
V1k10<-as.numeric(input$v1k10_2)
V1k12<-as.numeric(input$v1k12_2)
V1k21<-as.numeric(input$v1k21_2)
k10k12<-as.numeric(input$k10k12_2)
k10k21<-as.numeric(input$k10k21_2)
k12k21<-as.numeric(input$k12k21_2)
TwoComp_Volume_RateConstant(V1,k10,k12,k21,V1.sd,k10.sd,k12.sd,k21.sd,
covar=c(V1k10,V1k12,V1k21,k10k12,k10k21,k12k21))})
output$T2_2<-shiny::renderTable({
Label<-c("Volume","","","Clearnace","","Micro Rate Constant","","",
"Exponent","","Half-lives","",
"True Coeffficient","","Fractional Coefficient","")
T2.2<-data.frame(Label,result2_2())
colnames(T2.2)[1]<-""
T2.2},align="?",digits=4,rownames=FALSE)
total2_2<-shiny::reactive({result2_2()})
output$downloadData2_2<-shiny::downloadHandler(
filename = function() {
paste("two_compartment_sheet2", fileext2(), sep = ".")},
content = function(file){
sep.t=switch(fileext2(),
csv=",",
tab="\t",
txt=" ")
utils::write.table(total2_2(), file, sep = sep.t,
row.names = FALSE,col.names = TRUE)})
######################Three compartment######################
result2_3<-shiny::reactive({
V1<-as.numeric(input$volume_mean21_3)
k10<-as.numeric(input$k10_mean_3)
k12<-as.numeric(input$k12_mean_3)
k13<-as.numeric(input$k13_mean_3)
k21<-as.numeric(input$k21_mean_3)
k31<-as.numeric(input$k31_mean_3)
V1.sd<-as.numeric(input$volume_sd21_3)
k10.sd<-as.numeric(input$k10_sd_3);
k12.sd<-as.numeric(input$k12_sd_3)
k13.sd<-as.numeric(input$k13_sd_3);
k21.sd<-as.numeric(input$k21_sd_3)
k31.sd<-as.numeric(input$k31_sd_3)
V1k10<-as.numeric(input$v1k10_2);
V1k12<-as.numeric(input$v1k12_2)
V1k13<-as.numeric(input$v1k13_2);
V1k21<-as.numeric(input$v1k21_2)
V1k31<-as.numeric(input$v1k31_2);
k10k12<-as.numeric(input$k10k12_2)
k10k13<-as.numeric(input$k10k13_2);
k10k21<-as.numeric(input$k10k21_2)
k10k31<-as.numeric(input$k10k31_2);
k12k13<-as.numeric(input$k12k13_2)
k12k21<-as.numeric(input$k12k21_2);
k12k31<-as.numeric(input$k12k31_2)
k21k31<-as.numeric(input$k21k31_2);
k13k21<-as.numeric(input$k13k21_2)
k13k31<-as.numeric(input$k13k31_2)
ThreeComp_Volume_RateConstant(V1,k10,k12,k13,k21,k31,V1.sd,
k10.sd,k12.sd,k13.sd,k21.sd,k31.sd,
covar=c(V1k10,V1k12,V1k13,V1k21,V1k31,k10k12,k10k13,k10k21,k10k31,
k12k13,k12k21,k12k31,k13k21,k13k31,k21k31))})
output$T2_3<-shiny::renderTable({
Label<-c("Volume","","","","Clearnace","","",
"Micro Rate Constant","","","","",
"Exponent","","","Half-lives","","",
"True Coeffficient","","","Fractional Coefficient","","")
T2.3<-data.frame(Label,result2_3())
colnames(T2.3)[1]<-""
T2.3},align="?",digits=4,rownames=FALSE)
total2_3<-shiny::reactive({result2_3()})
output$downloadData2_3<-shiny::downloadHandler(
filename = function() {
paste("three_compartment_sheet2", fileext2(), sep = ".")},
content = function(file){
sep.t=switch(fileext2(),
csv=",",
tab="\t",
txt=" ")
utils::write.table(total2_3(), file, sep = sep.t,
row.names = FALSE,col.names = TRUE)})
######################sheet3############################################
output$comp1_3_1<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "Cl1_mean_1",
label = "Cl1 Estimate")),
shiny::column(6,shiny::textInput(inputId = "Cl1_sd_1",
label = "Cl1 Std.err")))})
output$comp1_3_2<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "t_alpha_mean_1",
label = "t_alpha Estimate")),
shiny::column(6,shiny::textInput(inputId = "t_alpha_sd_1",
label = "t_alpha Std.err")))})
output$comp2_3_1<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "volume_mean31_2",
label = "V1 Estimate")),
shiny::column(6,shiny::textInput(inputId = "volume_sd31_2",
label = "V1 Std.err")))})
output$comp2_3_2<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "Cl1_mean_2",
label = "Cl1 Estimate")),
shiny::column(6,shiny::textInput(inputId = "Cl1_sd_2",
label = "Cl1 Std.err")))})
output$comp2_3_3<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "t_alpha_mean_2",
label = "t_alpha Estimate")),
shiny::column(6,shiny::textInput(inputId = "t_alpha_sd_2",
label = "t_alpha Std.err")))})
output$comp2_3_4<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "t_beta_mean_2",
label = "t_beta Estimate")),
shiny::column(6,shiny::textInput(inputId = "t_beta_sd_2",
label = "t_beta Std.err")))})
output$comp3_3_1<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "volume_mean31_3",
label = "V1 Estimate")),
shiny::column(6,shiny::textInput(inputId = "volume_sd31_3",
label = "V1 Std.err")))})
output$comp3_3_2<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "Vd_mean_3",
label = "Vd Estimate")),
shiny::column(6,shiny::textInput(inputId = "Vd_sd_3",
label = "Vd Std.err")))})
output$comp3_3_3<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "Cl1_mean_3",
label = "Cl1 Estimate")),
shiny::column(6,shiny::textInput(inputId = "Cl1_sd_3",
label = "Cl1 Std.err")))})
output$comp3_3_4<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "t_alpha_mean_3",
label = "t_alpha Estimate")),
shiny::column(6,shiny::textInput(inputId = "t_alpha_sd_3",
label = "t_alpha Std.err")))})
output$comp3_3_5<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "t_beta_mean_3",
label = "t_beta Estimate")),
shiny::column(6,shiny::textInput(inputId = "t_beta_sd_3",
label = "t_beta Std.err")))})
output$comp3_3_6<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "t_gamma_mean_3",
label = "t_gamma Estimate")),
shiny::column(6,shiny::textInput(inputId = "t_gamma_sd_3",
label = "t_gamma Std.err")))})
###################### covariance ######################
######################One compartment######################
output$cl1talpha_3<-shiny::renderUI({
shiny::textInput(inputId = "cl1talpha_3",
label = "Cov(Cl1,t_alpha)", value = 0) })
######################Two compartment######################
output$v1cl1_3<-shiny::renderUI({
shiny::textInput(inputId = "v1cl1_3",
label = "Cov(V1,Cl1)", value = 0)})
output$cl1tbeta_3<-shiny::renderUI({
shiny::textInput(inputId = "cl1tbeta_3",
label = "Cov(Cl1,t_beta)", value = 0)})
output$v1talpha_3<-shiny::renderUI({
shiny::textInput(inputId = "v1talpha_3",
label = "Cov(V1,t_alpha)", value = 0)})
output$v1tbeta_3<-shiny::renderUI({
shiny::textInput(inputId = "v1tbeta_3",
label = "Cov(V1,t_beta)", value = 0)})
output$talphatbeta_3<-shiny::renderUI({
shiny::textInput(inputId = "talphatbeta_3",
label = "Cov(t_alpha,t_beta)",value = 0)})
######################Three compartment######################
output$v1vd_3<-shiny::renderUI({
shiny::textInput(inputId = "v1vd_3",
label = "Cov(V1,Vd)", value = 0)})
output$v1tgamma_3<-shiny::renderUI({
shiny::textInput(inputId = "v1tgamma_3",
label = "Cov(V1,t_gamma)", value = 0)})
output$vdtgamma_3<-shiny::renderUI({
shiny::textInput(inputId = "vdtgamma_3",
label = "Cov(Vd,t_gamma)", value = 0)})
output$cl1tgamma_3<-shiny::renderUI({
shiny::textInput(inputId = "cl1tgamma_3",
label = "Cov(Cl1,t_gamma)",value = 0)})
output$talphatgamma_3<-shiny::renderUI({
shiny::textInput(inputId = "talphatgamma_3",
label = "Cov(t_alpha,t_gamma)", value = 0)})
output$tbetatgamma_3<-shiny::renderUI({
shiny::textInput(inputId = "tbetatgamma_3",
label = "Cov(t_beta,t_gamma)",value = 0)})
output$vdtalpha_3<-shiny::renderUI({
shiny::textInput(inputId = "vdtalpha_3",
label = "Cov(Vd,t_alpha)", value = 0)})
output$vdtbeta_3<-shiny::renderUI({
shiny::textInput(inputId = "vdtbeta_3",
label = "Cov(Vd,t_beta)", value = 0)})
output$vdcl1_3<-shiny::renderUI({
shiny::textInput(inputId = "vdcl1_3",
label = "Cov(Vd,Cl1)", value = 0)})
###########################################################
#########################Results###########################
###########################################################
######################One compartment######################
result3_1<-shiny::reactive({
Cl1<-as.numeric(input$Cl1_mean_1)
t_alpha<-as.numeric(input$t_alpha_mean_1)
Cl1.sd<-as.numeric(input$Cl1_sd_1)
t_alpha.sd<-as.numeric(input$t_alpha_sd_1)
Cl1talpha<-as.numeric(input$cl1talpha_3)
OneComp_Volume_Clearance_HalfLife(Cl1,t_alpha,Cl1.sd,t_alpha.sd,
covar=c(Cl1talpha))})
output$T3_1<-shiny::renderTable({
Label<-c("Volume","","Clearnace","Micro Rate Constant",
"Exponent","Half-lives",
"True Coeffficient","Fractional Coefficient")
T3.1<-data.frame(Label,result3_1())
colnames(T3.1)[1]<-""
T3.1},align="?",digits=4,rownames=FALSE)
total3_1<-shiny::reactive({result3_1() })
fileext3 <- shiny::reactive({switch(input$type3,
"Excel (CSV)" = "csv",
"Text (tab separated)" = "tab",
"Text (Space Separated)" = "txt")})
output$downloadData3_1<-shiny::downloadHandler(
filename = function() {
paste("one_compartment_sheet3", fileext3(), sep = ".")},
content = function(file){
sep.t=switch(fileext3(),
csv=",",
tab="\t",
txt=" ")
utils::write.table(total3_1(), file, sep = sep.t,
row.names = FALSE,col.names = TRUE)})
####################Two compartment######################
result3_2<-shiny::reactive({
V1<-as.numeric(input$volume_mean31_2)
Cl1<-as.numeric(input$Cl1_mean_2)
t_alpha<-as.numeric(input$t_alpha_mean_2)
t_beta<-as.numeric(input$t_beta_mean_2)
V1.sd<-as.numeric(input$volume_sd31_2)
Cl1.sd<-as.numeric(input$Cl1_sd_2)
t_alpha.sd<-as.numeric(input$t_alpha_sd_2)
t_beta.sd<-as.numeric(input$t_beta_sd_2)
V1Cl1<-as.numeric(input$v1cl1_2)
V1talpha<-as.numeric(input$v1talpha_2)
V1tbeta<-as.numeric(input$v1tbeta_2)
Cl1talpha<-as.numeric(input$cl1talpha_2)
Cl1tbeta<-as.numeric(input$cl1tbeta_2)
talphatbeta<-as.numeric(input$talphatbeta_2)
TwoComp_Volume_Clearance_HalfLife(V1,Cl1,t_alpha,t_beta,
V1.sd,Cl1.sd,t_alpha.sd,t_beta.sd,
covar=c(V1Cl1,V1talpha,V1tbeta,Cl1talpha,Cl1tbeta,talphatbeta))})
output$T3_2<-shiny::renderTable({
Label<-c("Volume","","","Clearnace","",
"Micro Rate Constant","","",
"Exponent","","Half-lives","",
"True Coeffficient","","Fractional Coefficient","")
T3.2<-data.frame(Label,result3_2())
colnames(T3.2)[1]<-""
T3.2},align="?",digits=4,rownames=FALSE)
total3_2<-shiny::reactive({ result3_2()})
output$downloadData3_2<-shiny::downloadHandler(
filename = function() {
paste("two_compartment_sheet3", fileext3(), sep = ".")},
content = function(file){
sep.t=switch(fileext3(),
csv=",",
tab="\t",
txt=" ")
utils::write.table(total3_2(), file, sep = sep.t,
row.names = FALSE,col.names = TRUE)})
######################Three compartment######################
result3_3<-shiny::reactive({
V1<-as.numeric(input$volume_mean31_3)
Vd<-as.numeric(input$Vd_mean_3)
Cl1<-as.numeric(input$Cl1_mean_3)
t_alpha<-as.numeric(input$t_alpha_mean_3)
t_beta<-as.numeric(input$t_beta_mean_3)
t_gamma<-as.numeric(input$t_gamma_mean_3)
V1.sd<-as.numeric(input$volume_sd31_3)
Vd.sd<-as.numeric(input$Vd_sd_3)
Cl1.sd<-as.numeric(input$Cl1_sd_3)
t_alpha.sd<-as.numeric(input$t_alpha_sd_3)
t_beta.sd<-as.numeric(input$t_beta_sd_3)
t_gamma.sd<-as.numeric(input$t_gamma_sd_3)
V1Vd<-as.numeric(input$v1vd_3)
V1Cl1<-as.numeric(input$v1cl1_3)
V1talpha<-as.numeric(input$v1talpha_3)
V1tbeta<-as.numeric(input$v1tbeta_3)
V1tgamma<-as.numeric(input$v1tgamma_3)
VdCl1<-as.numeric(input$vdcl1_3)
Vdtalpha<-as.numeric(input$vdtalpha_3)
Vdtbeta<-as.numeric(input$vdtbeta_3)
Vdtgamma<-as.numeric(input$vdtgamma_3)
Cl1talpha<-as.numeric(input$cl1talpha_3)
Cl1tbeta<-as.numeric(input$cl1tbeta_3)
Cl1tgamma<-as.numeric(input$cl1tgamma_3)
talphatbeta<-as.numeric(input$talphatbeta_3)
talphatgamma<-as.numeric(input$talphatgamma_3)
tbetatgamma<-as.numeric(input$tbetatgamma_3)
ThreeComp_Volume_Clearance_HalfLife(V1,Vd,Cl1,t_alpha,t_beta,t_gamma,
V1.sd,Vd.sd,Cl1.sd,t_alpha.sd,t_beta.sd,t_gamma.sd,
covar=c(V1Vd,V1Cl1,V1talpha,V1tbeta,V1tgamma,
VdCl1,Vdtalpha,Vdtbeta,Vdtgamma,Cl1talpha,Cl1tbeta,Cl1tgamma,
talphatbeta,talphatgamma,tbetatgamma))})
output$T3_3<-shiny::renderTable({
Label<-c("Volume","","","","Clearnace","","",
"Micro Rate Constant","","","","",
"Exponent","","","Half-lives","","",
"True Coeffficient","","","Fractional Coefficient","","")
T3.3<-data.frame(Label,result3_3())
colnames(T3.3)[1]<-""
T3.3},align="?",digits=4,rownames=FALSE)
total3_3<-shiny::reactive({result3_3()})
output$downloadData3_3<-shiny::downloadHandler(
filename = function() {
paste("three_compartment_sheet3", fileext3(), sep = ".")},
content = function(file){
sep.t=switch(fileext3(),
csv=",",
tab="\t",
txt=" ")
utils::write.table(total3_3(), file, sep = sep.t,
row.names = FALSE,col.names = TRUE)})
##############sheet4############################################
output$comp1_4_1<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "A_mean_1",
label = "A Estimate")),
shiny::column(6,shiny::textInput(inputId = "A_sd_1",
label = "A Std.err")))})
output$comp1_4_2<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "alpha_mean_1",
label = "alpha Estimate")),
shiny::column(6,shiny::textInput(inputId = "alpha_sd_1",
label = "alpha Std.err")))})
output$comp1_4_1<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "A_mean_1",
label = "A Estimate")),
shiny::column(6,shiny::textInput(inputId = "A_sd_1",
label = "A Std.err")))})
output$comp2_4_1<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "A_mean_2",
label = "A Estimate")),
shiny::column(6,shiny::textInput(inputId = "A_sd_2",
label = "A Std.err")))})
output$comp2_4_2<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "B_mean_2",
label = "B Estimate")),
shiny::column(6,shiny::textInput(inputId = "B_sd_2",
label = "B Std.err")))})
output$comp2_4_1<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "A_mean_2",
label = "A Estimate")),
shiny::column(6,shiny::textInput(inputId = "A_sd_2",
label = "A Std.err")))})
output$comp2_4_2<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "B_mean_2",
label = "B Estimate")),
shiny::column(6,shiny::textInput(inputId = "B_sd_2",
label = "B Std.err")))})
output$comp2_4_3<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "alpha_mean_2",
label = "alpha Estimate")),
shiny::column(6,shiny::textInput(inputId = "alpha_sd_2",
label = "alpha Std.err")))})
output$comp2_4_4<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "beta_mean_2",
label = "beta Estimate")),
shiny::column(6,shiny::textInput(inputId = "beta_sd_2",
label = "beta Std.err")))})
output$comp3_4_1<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "A_mean_3",
label = "A Estimate")),
shiny::column(6,shiny::textInput(inputId = "A_sd_3",
label = "A Std.err")))})
output$comp3_4_2<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "B_mean_3",
label = "B Estimate")),
shiny::column(6,shiny::textInput(inputId = "B_sd_3",
label = "B Std.err")))})
output$comp3_4_3<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "C_mean_3",
label = "C Estimate")),
shiny::column(6,shiny::textInput(inputId = "C_sd_3",
label = "C Std.err")))})
output$comp3_4_4<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "alpha_mean_3",
label = "alpha Estimate")),
shiny::column(6,shiny::textInput(inputId = "alpha_sd_3",
label = "alpha Std.err")))})
output$comp3_4_5<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "beta_mean_3",
label = "beta Estimate")),
shiny::column(6,shiny::textInput(inputId = "beta_sd_3",
label = "beta Std.err")))})
output$comp3_4_6<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "gamma_mean_3",
label = "gamma Estimate")),
shiny::column(6,shiny::textInput(inputId = "gamma_sd_3",
label = "gamma Std.err")))})
###################### covariance ######################
######################One compartment######################
output$aalpha_4<-shiny::renderUI({
shiny::textInput(inputId = "aalpha_4",
label = "Cov(A,alpha)", value = 0)})
######################Two compartment######################
output$ab_4<-shiny::renderUI({
shiny::textInput(inputId = "ab_4",
label = "Cov(A,B)", value = 0)})
output$abeta_4<-shiny::renderUI({
shiny::textInput(inputId = "abeta_4",
label = "Cov(A,beta)", value = 0)})
output$balpha_4<-shiny::renderUI({
shiny::textInput(inputId = "balpha_4",
label = "Cov(B,alpha)", value = 0)})
output$bbeta_4<-shiny::renderUI({
shiny::textInput(inputId = "bbeta_4",
label = "Cov(B,beta)", value = 0)})
output$alphabeta_4<-shiny::renderUI({
shiny::textInput(inputId = "alphabeta_4",
label = "Cov(alpha,beta)", value = 0)})
######################Three compartment######################
output$ac_4<-shiny::renderUI({
shiny::textInput(inputId = "ac_4",
label = "Cov(A,C)", value = 0)})
output$agamma_4<-shiny::renderUI({
shiny::textInput(inputId = "agamma_4",
label = "Cov(A,gamma)", value = 0)})
output$bgamma_4<-shiny::renderUI({
shiny::textInput(inputId = "bgamma_4",
label = "Cov(B,gamma)", value = 0)})
output$cbeta_4<-shiny::renderUI({
shiny::textInput(inputId = "cbeta_4",
label = "Cov(C,beta)", value = 0)})
output$cgamma_4<-shiny::renderUI({
shiny::textInput(inputId = "cgamma_4",
label = "Cov(C,gamma)", value = 0)})
output$alphagamma_4<-shiny::renderUI({
shiny::textInput(inputId = "alphagamma_4",
label = "Cov(alpha,gamma)", value = 0)})
output$betagamma_4<-shiny::renderUI({
shiny::textInput(inputId = "betagamma_4",
label = "Cov(beta,gamma)", value = 0)})
output$bc_4<-shiny::renderUI({
shiny::textInput(inputId = "bc_4",
label = "Cov(B,C)", value = 0)})
output$calpha_4<-shiny::renderUI({
shiny::textInput(inputId = "calpha_4",
label = "Cov(C,alpha)", value = 0)})
###########################################################
#########################Results###########################
###########################################################
######################One compartment######################
result4_1<-shiny::reactive({
A<-as.numeric(input$A_mean_1)
alpha<-as.numeric(input$alpha_mean_1)
A.sd<-as.numeric(input$A_sd_1)
alpha.sd<-as.numeric(input$alpha_sd_1)
Aalpha<-as.numeric(input$aalpha_4)
OneComp_Coefficient_Exponent(A,alpha,A.sd,alpha.sd,covar=Aalpha)})
output$T4_1<-shiny::renderTable({
Label<-c("Volume","","Clearnace","Micro Rate Constant",
"Exponent","Half-lives",
"True Coeffficient","Fractional Coefficient")
T4.1<-data.frame(Label,result4_1())
colnames(T4.1)[1]<-""
T4.1},align="?",digits=4,rownames=FALSE)
total4_1<-shiny::reactive({result4_1()})
fileext4 <- shiny::reactive({switch(input$type4,
"Excel (CSV)" = "csv",
"Text (tab separated)" = "tab",
"Text (Space Separated)" = "txt")})
output$downloadData4_1<-shiny::downloadHandler(
filename = function() {
paste("one_compartment_sheet4", fileext4(), sep = ".")},
content = function(file){
sep.t=switch(fileext4(),
csv=",",
tab="\t",
txt=" ")
utils::write.table(total4_1(), file, sep = sep.t,
row.names = FALSE,col.names = TRUE)})
######################Two compartment######################
result4_2<-shiny::reactive({
A<-as.numeric(input$A_mean_2)
B<-as.numeric(input$B_mean_2)
alpha<-as.numeric(input$alpha_mean_2)
beta<-as.numeric(input$beta_mean_2)
A.sd<-as.numeric(input$A_sd_2)
B.sd<-as.numeric(input$B_sd_2)
alpha.sd<-as.numeric(input$alpha_sd_2)
beta.sd<-as.numeric(input$beta_sd_2)
AB<-as.numeric(input$ab_4)
Aalpha<-as.numeric(input$aalpha_4)
Abeta<-as.numeric(input$abeta_4)
Balpha<-as.numeric(input$balpha_4)
Bbeta<-as.numeric(input$bbeta_4)
alphabeta<-as.numeric(input$alphabeta_4)
TwoComp_Coefficient_Exponent(A,B,alpha,beta,A.sd,B.sd,alpha.sd,beta.sd,
covar=c(AB,Aalpha,Abeta,Balpha,Bbeta,alphabeta))})
output$T4_2<-shiny::renderTable({
Label<-c("Volume","","","Clearnace","",
"Micro Rate Constant","","",
"Exponent","","Half-lives","",
"True Coeffficient","","Fractional Coefficient","")
T4.2<-data.frame(Label,result4_2())
colnames(T4.2)[1]<-""
T4.2},align="?",digits=4,rownames=FALSE)
total4_2<-shiny::reactive({result4_2()})
output$downloadData4_2<-shiny::downloadHandler(
filename = function() {
paste("two_compartment_sheet4", fileext4(), sep = ".")},
content = function(file){
sep.t=switch(fileext4(),
csv=",",
tab="\t",
txt=" ")
utils::write.table(total4_2(), file, sep = sep.t,
row.names = FALSE,col.names = TRUE)})
######################Three compartment######################
result4_3<-shiny::reactive({
A<-as.numeric(input$A_mean_3)
B<-as.numeric(input$B_mean_3)
C<-as.numeric(input$C_mean_3)
alpha<-as.numeric(input$alpha_mean_3)
beta<-as.numeric(input$beta_mean_3)
gamma<-as.numeric(input$gamma_mean_3)
A.sd<-as.numeric(input$A_sd_3)
B.sd<-as.numeric(input$B_sd_3)
C.sd<-as.numeric(input$C_sd_3)
alpha.sd<-as.numeric(input$alpha_sd_3)
beta.sd<-as.numeric(input$beta_sd_3)
gamma.sd<-as.numeric(input$gamma_sd_3)
AB<-as.numeric(input$ab_4);
AC<-as.numeric(input$ac_4)
Aalpha<-as.numeric(input$aalpha_4);
Abeta<-as.numeric(input$abeta_4)
Agamma<-as.numeric(input$agamma_4);
BC<-as.numeric(input$bc_4)
Balpha<-as.numeric(input$balpha_4);
Bbeta<-as.numeric(input$bbeta_4)
Bgamma<-as.numeric(input$bgamma_4);
Calpha<-as.numeric(input$calpha_4)
Cbeta<-as.numeric(input$cbeta_4);
Cgamma<-as.numeric(input$cgamma_4)
alphabeta<-as.numeric(input$alphabeta_4);
alphagamma<-as.numeric(input$alphagamma_4)
betagamma<-as.numeric(input$betagamma_4);
ThreeComp_Coefficient_Exponent(A,B,C,alpha,beta,gamma,A.sd,B.sd,C.sd,
alpha.sd,beta.sd,gamma.sd,
covar=c(AB,AC,Aalpha,Abeta,Agamma,BC,Balpha,Bbeta,Bgamma,Calpha,
Cbeta, Cgamma,alphabeta,alphagamma,betagamma))})
output$T4_3<-shiny::renderTable({
Label<-c("Volume","","","","Clearnace","","",
"Micro Rate Constant","","","","",
"Exponent","","","Half-lives","","",
"True Coeffficient","","","Fractional Coefficient","","")
T4.3<-data.frame(Label,result4_3())
colnames(T4.3)[1]<-""
T4.3},align="?",digits=4,rownames=FALSE)
total4_3<-shiny::reactive({result4_3()})
output$downloadData4_3<-shiny::downloadHandler(
filename = function() {
paste("three_compartment_sheet4", fileext4(), sep = ".")},
content = function(file){
sep.t=switch(fileext4(),
csv=",",
tab="\t",
txt=" ")
utils::write.table(total4_3(), file, sep = sep.t,
row.names = FALSE,col.names = TRUE)})
#####################sheet5############################################
output$comp1_5_1<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "volume_mean51_1",
label = "V1 Estimate")),
shiny::column(6,shiny::textInput(inputId = "volume_sd51_1",
label = "V1 Std.err")))})
output$comp1_5_2<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "alpha_mean51_1",
label = "alpha Estimate")),
shiny::column(6,shiny::textInput(inputId = "alpha_sd51_1",
label = "alpha Std.err")))})
output$comp2_5_1<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "volume_mean51_2",
label = "V1 Estimate")),
shiny::column(6,shiny::textInput(inputId = "volume_sd51_2",
label = "V1 Std.err")))})
output$comp2_5_2<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "alpha_mean51_2",
label = "alpha Estimate")),
shiny::column(6,shiny::textInput(inputId = "alpha_sd51_2",
label = "alpha Std.err")))})
output$comp2_5_3<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "beta_mean51_2",
label = "beta Estimate")),
shiny::column(6,shiny::textInput(inputId = "beta_sd51_2",
label = "beta Std.err")))})
output$comp2_5_4<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "k21_mean51_2",
label = "k21 Estimate")),
shiny::column(6,shiny::textInput(inputId = "k21_sd51_2",
label = "k21 Std.err")))})
output$comp3_5_1<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "volume_mean51_3",
label = "V1 Estimate")),
shiny::column(6,shiny::textInput(inputId = "volume_sd51_3",
label = "V1 Std.err")))})
output$comp3_5_2<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "alpha_mean51_3",
label = "alpha Estimate")),
shiny::column(6,shiny::textInput(inputId = "alpha_sd51_3",
label = "alpha Std.err")))})
output$comp3_5_3<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "beta_mean51_3",
label = "beta Estimate")),
shiny::column(6,shiny::textInput(inputId = "beta_sd51_3",
label = "beta Std.err")))})
output$comp3_5_4<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "gamma_mean51_3",
label = "gamma Estimate")),
shiny::column(6,shiny::textInput(inputId = "gamma_sd51_3",
label = "gamma Std.err")))})
output$comp3_5_5<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "k21_mean51_3",
label = "k21 Estimate")),
shiny::column(6,shiny::textInput(inputId = "k21_sd51_3",
label = "k21 Std.err")))})
output$comp3_5_6<-shiny::renderUI({
shiny::fluidRow(shiny::column(6,
shiny::textInput(inputId = "k31_mean51_3",
label = "k31 Estimate")),
shiny::column(6,shiny::textInput(inputId = "k31_sd51_3",
label = "k31 Std.err")))})
###################### covariance ######################
######################One compartment######################
output$v1alpha_5<-shiny::renderUI({
shiny::textInput(inputId = "v1alpha_5",
label = "Cov(V1,alpha)", value = 0)})
######################Two compartment######################
output$v1beta_5<-shiny::renderUI({
shiny::textInput(inputId = "v1beta_5",
label = "Cov(V1,beta)", value = 0)})
output$v1k21_5<-shiny::renderUI({
shiny::textInput(inputId = "v1k21_5",
label = "Cov(V1,k21)", value = 0)})
output$alphabeta_5<-shiny::renderUI({
shiny::textInput(inputId = "alphabeta_5",
label = "Cov(alpha,beta)", value = 0)})
output$alphak21_5<-shiny::renderUI({
shiny::textInput(inputId = "alphak21_5",
label = "Cov(alpha,k21)", value = 0)})
output$betak21_5<-shiny::renderUI({
shiny::textInput(inputId = "betak21_5",
label = "Cov(beta,k21)", value = 0)})
######################Three compartment######################
output$v1gamma_5<-shiny::renderUI({
shiny::textInput(inputId = "v1gamma_5",
label = "Cov(V1,gamma)", value = 0)})
output$v1k31_5<-shiny::renderUI({
shiny::textInput(inputId = "v1k31_5",
label = "Cov(V1,k31)", value = 0)})
output$alphagamma_5<-shiny::renderUI({
shiny::textInput(inputId = "alphagamma_5",
label = "Cov(alpha,gamma)", value = 0)})
output$alphak31_5<-shiny::renderUI({
shiny::textInput(inputId = "alphak31_5",
label = "Cov(alpha,k31)", value = 0)})
output$betagamma_5<-shiny::renderUI({
shiny::textInput(inputId = "betagamma_5",
label = "Cov(beta,gamma)", value = 0)})
output$betak31_5<-shiny::renderUI({
shiny::textInput(inputId = "betak31_5",
label = "Cov(beta,k31)", value = 0)})
output$gammak21_5<-shiny::renderUI({
shiny::textInput(inputId = "gammak21_5",
label = "Cov(gamma,k21)", value = 0)})
output$gammak31_5<-shiny::renderUI({
shiny::textInput(inputId = "gammak31_5",
label="Cov(gamma,k31)", value=0)})
output$k21k31_5<-shiny::renderUI({
shiny::textInput(inputId = "k21k31_5",
label="Cov(k21,k31)", value = 0)})
###########################################################
#########################Results###########################
###########################################################
######################One compartment######################
result5_1<-shiny::reactive({
V1<-as.numeric(input$volume_mean51_1)
V1.sd<-as.numeric(input$volume_sd51_1)
alpha<-as.numeric(input$alpha_mean51_1)
alpha.sd<-as.numeric(input$alpha_sd51_1)
V1alpha<-as.numeric(input$v1alpha_5)
OneComp_Volume_Exponent(V1,alpha,V1.sd,alpha.sd,covar=c(V1alpha))})
output$T5_1<-shiny::renderTable({
Label<-c("Volume","","Clearnace","Micro Rate Constant",
"Exponent","Half-lives",
"True Coeffficient","Fractional Coefficient")
T5.1<-data.frame(Label,result5_1())
colnames(T5.1)[1]<-""
T5.1},align="?",digits=4,rownames=FALSE)
total5_1<-shiny::reactive({result5_1()})
fileext5 <- shiny::reactive({switch(input$type5,
"Excel (CSV)" = "csv",
"Text (tab separated)" = "tab",
"Text (Space Separated)" = "txt")})
output$downloadData5_1<-shiny::downloadHandler(
filename = function() {
paste("one_compartment_sheet5", fileext5(), sep = ".")},
content = function(file){
sep.t=switch(fileext5(),
csv=",",
tab="\t",
txt=" ")
utils::write.table(total5_1(), file, sep = sep.t,
row.names = FALSE,col.names = TRUE)})
######################Two compartment######################
result5_2<-shiny::reactive({
V1<-as.numeric(input$volume_mean51_2)
alpha<-as.numeric(input$alpha_mean51_2)
beta<-as.numeric(input$beta_mean51_2)
k21<-as.numeric(input$k21_mean51_2)
V1.sd<-as.numeric(input$volume_sd51_2)
alpha.sd<-as.numeric(input$alpha_sd51_2)
beta.sd<-as.numeric(input$beta_sd51_2)
k21.sd<-as.numeric(input$k21_sd51_2)
V1alpha<-as.numeric(input$v1alpha_5)
V1beta<-as.numeric(input$v1beta_5)
V1k21<-as.numeric(input$v1k21_5)
alphabeta<-as.numeric(input$alphabeta_5)
alphak21<-as.numeric(input$alphak21_5)
betak21<-as.numeric(input$betak21_5)
TwoComp_Volume_Exponent(V1,alpha,beta,k21,V1.sd,alpha.sd,beta.sd,k21.sd,
covar=c(V1alpha,V1beta,V1k21,alphabeta,alphak21,betak21)) })
output$T5_2<-shiny::renderTable({
Label<-c("Volume","","","Clearnace","",
"Micro Rate Constant","","",
"Exponent","","Half-lives","",
"True Coeffficient","","Fractional Coefficient","")
T5.2<-data.frame(Label,result5_2())
colnames(T5.2)[1]<-""
T5.2},align="?",digits=4,rownames=FALSE)
total5_2<-shiny::reactive({ result5_2()})
output$downloadData5_2<-shiny::downloadHandler(
filename = function() {
paste("two_compartment_sheet5", fileext5(), sep = ".")},
content = function(file){
sep.t=switch(fileext5(),
csv=",",
tab="\t",
txt=" ")
utils::write.table(total5_2(), file, sep = sep.t,
row.names = FALSE,col.names = TRUE)})
######################Three compartment######################
result5_3<-shiny::reactive({
V1<-as.numeric(input$volume_mean51_3)
alpha<-as.numeric(input$alpha_mean51_3)
beta<-as.numeric(input$beta_mean51_3)
gamma<-as.numeric(input$gamma_mean51_3)
k21<-as.numeric(input$k21_mean51_3)
k31<-as.numeric(input$k31_mean51_3)
V1.sd<-as.numeric(input$volume_sd51_3)
alpha.sd<-as.numeric(input$alpha_sd51_3)
beta.sd<-as.numeric(input$beta_sd51_3)
gamma.sd<-as.numeric(input$gamma_sd51_3)
k21.sd<-as.numeric(input$k21_sd51_3)
k31.sd<-as.numeric(input$k31_sd51_3)
V1alpha<-as.numeric(input$v1alpha_5);
V1beta<-as.numeric(input$v1beta_5)
V1gamma<-as.numeric(input$v1gamma_5);
V1k21<-as.numeric(input$v1k21_5)
V1k31<-as.numeric(input$v1k31_5);
alphabeta<-as.numeric(input$alphabeta_5)
alphagamma<-as.numeric(input$alphagamma_5)
alphak21<-as.numeric(input$alphak21_5)
alphak31<-as.numeric(input$alphak31_5)
betagamma<-as.numeric(input$betagamma_5)
betak21<-as.numeric(input$betak21_5)
betak31<-as.numeric(input$betak31_5)
gammak21<-as.numeric(input$gammak21_5)
gammak31<-as.numeric(input$gammak31_5)
k21k31<-as.numeric(input$k21k31_5)
ThreeComp_Volume_Exponent(V1,alpha,beta,gamma,k21,k31,
V1.sd,alpha.sd,beta.sd,gamma.sd,
k21.sd,k31.sd,covar=c(V1alpha,V1beta,V1gamma,V1k21,V1k31,alphabeta,
alphagamma,alphak21,alphak31,betagamma,betak21,betak31,gammak21,
gammak31,k21k31))})
output$T5_3<-shiny::renderTable({
Label<-c("Volume","","","","Clearnace","","",
"Micro Rate Constant","","","","",
"Exponent","","","Half-lives","","",
"True Coeffficient","","","Fractional Coefficient","","")
T5.3<-data.frame(Label,result3_3())
colnames(T5.3)[1]<-""
T5.3},align="?",digits=4,rownames=FALSE)
total5_3<-shiny::reactive({ result5_3()})
output$downloadData5_3<-shiny::downloadHandler(
filename = function() {
paste("three_compartment_sheet5", fileext5(), sep = ".")},
content = function(file){
sep.t=switch(fileext5(),
csv=",",
tab="\t",
txt=" ")
utils::write.table(total5_3(), file, sep = sep.t,
row.names = FALSE,col.names = TRUE)})
Dataset<-shiny::reactive({
if(is.null(input$inputfile)){return(data.frame())}
outputData<-data.frame(do.call("read.csv",
list(input$inputfile$datapath)))
return(outputData)})
output$choose_PK<-shiny::renderUI({
if(is.null(input$inputfile))
return()
if(identical(Dataset(),'')||identical(Dataset(),data.frame()))
return(NULL)
PKconverter.env$outputData<-Dataset()
PKconverter.env$labelList<-switch(
paste(input$modelF1,input$modelF2,sep="-"),
"one-M1"=c("V1","Cl1"),
"one-M2"=c("V1","k10"),
"one-M3"=c("Cl1","t_alpha"),
"one-M4"=c("True_A","alpha"),
"one-M5"=c("V1","alpha"),
"two-M1"=c("V1","V2","Cl1","Cl2"),
"two-M2"=c("V1","k10","k12","k21"),
"two-M3"=c("V1","Cl1","t_alpha","t_beta"),
"two-M4"=c("True_A","True_B","alpha","beta"),
"two-M5"=c("V1","k21","alpha","beta"),
"three-M1"=c("V1","V2","V3","Cl1","Cl2","Cl3"),
"three-M2"=c("V1","k10","k12","k21","k13","k31"),
"three-M3"=c("V1","Cl1","t_alpha","t_beta","t_gamma"),
"three-M4"=c("True_A","True_B","True_C","alpha","beta","gamma"),
"three-M5"=c("V1","k21","k31","alpha","beta","gamma"))
PKconverter.env$labelList<-c("ID",PKconverter.env$labelList)
MakeSelectList<-function(X=1){
shiny::selectInput(paste0("PK",as.character(X)),
label=PKconverter.env$labelList[X],
choices=c("",colnames(PKconverter.env$outputData)),
selected="")
}
WidgetVector<-shiny::reactive({
n<-length(PKconverter.env$labelList)
lapply(X=1:n,FUN=MakeSelectList)
})
output$choose_PK<-shiny::renderUI({
if(is.null(input$inputfile)|is.null(PKconverter.env$outputData)){
return()
} else{
shiny::tagList(WidgetVector())}})})
output$ShowResult<-shiny::renderTable({
if(is.null(input$inputfile)) return()
if(identical(Dataset(),'')||identical(Dataset(),data.frame()))
return(NULL)
if(length(PKconverter.env$labelList)==0) return()
if(length(input[["PK1"]])==0) return()
n<-length(PKconverter.env$labelList)
if(input[[paste0("PK",n)]]=="") return()
param.list<-rep("",n)
for(i in 1:n){
param.list[i]<-input[[paste0("PK",i)]]
}
PKconverter.env$param.list<-param.list
sel.data<-PKconverter.env$outputData[,param.list]
colnames(sel.data)<-PKconverter.env$labelList
modelF<-paste(input$modelF1,input$modelF2,sep="-")
tot.result<-NULL
if(input$modelF1=="one"){
for(i in 1:nrow(sel.data)){
if(input$modelF2=="M1"){
temp.result<-OneComp_Volume_Clearance(sel.data[i,2],
sel.data[i,3])
} else if(input$modelF2=="M2"){
temp.result<-OneComp_Volume_RateConstant(sel.data[i,2],
sel.data[i,3])
} else if(input$modelF2=="M3"){
temp.result<-OneComp_Volume_Clearance_HalfLife(sel.data[i,2],
sel.data[i,3])
} else if(input$modelF2=="M4"){
temp.result<-OneComp_Coefficient_Exponent(sel.data[i,2],
sel.data[i,3])
} else if(input$modelF2=="M5"){
temp.result<-OneComp_Volume_Exponent(sel.data[i,2],
sel.data[i,3])
}
tot.result<-rbind(tot.result,c(i,temp.result[,2]))
if(i==1) colnames(tot.result)<-c("ID",rownames(temp.result))
}
} else if(input$modelF1=="two"){
for(i in 1:nrow(sel.data)){
if(input$modelF2=="M1"){
temp.result<-TwoComp_Volume_Clearance(sel.data[i,2],
sel.data[i,3],sel.data[i,4],sel.data[i,5])
} else if(input$modelF2=="M2"){
print(c(input$modelF1,input$modelF2))
temp.result<-TwoComp_Volume_RateConstant(sel.data[i,2],
sel.data[i,3],sel.data[i,4],sel.data[i,5])
print(temp.result)
} else if(input$modelF2=="M3"){
temp.result<-TwoComp_Volume_Clearance_HalfLife(sel.data[i,2],
sel.data[i,3],sel.data[i,4],sel.data[i,5])
} else if(input$modelF2=="M4"){
temp.result<-TwoComp_Coefficient_Exponent(sel.data[i,2],
sel.data[i,3],sel.data[i,4],sel.data[i,5])
} else if(input$modelF2=="M5"){
temp.result<-TwoComp_Volume_Exponent(sel.data[i,2],sel.data[i,3],
sel.data[i,4],sel.data[i,5])
}
tot.result<-rbind(tot.result,c(i,temp.result[,2]))
if(i==1) colnames(tot.result)<-c("ID",rownames(temp.result))
}
} else if(input$modelF1=="three"){
for(i in 1:nrow(sel.data)){
if(input$modelF2=="M1"){
temp.result<-ThreeComp_Volume_Clearance(sel.data[i,2],
sel.data[i,3],sel.data[i,4],
sel.data[i,5],sel.data[i,6],sel.data[i,7])
} else if(input$modelF2=="M2"){
temp.result<-ThreeComp_Volume_RateConstant(sel.data[i,2],
sel.data[i,3],sel.data[i,4],
sel.data[i,5],sel.data[i,6],sel.data[i,7])
} else if(input$modelF2=="M3"){
temp.result<-ThreeComp_Volume_Clearance_HalfLife(sel.data[i,2],
sel.data[i,3],sel.data[i,4],
sel.data[i,5],sel.data[i,6],sel.data[i,7])
} else if(input$modelF2=="M4"){
temp.result<-ThreeComp_Coefficient_Exponent(sel.data[i,2],
sel.data[i,3],sel.data[i,4],
sel.data[i,5],sel.data[i,6],sel.data[i,7])
} else if(input$modelF2=="M5"){
temp.result<-ThreeComp_Volume_Exponent(sel.data[i,2],
sel.data[i,3],sel.data[i,4],
sel.data[i,5],sel.data[i,6],sel.data[i,7])
}
tot.result<-rbind(tot.result,c(i,temp.result[,2]))
if(i==1) colnames(tot.result)<-c("ID",rownames(temp.result))}}
out<-tot.result
PKconverter.env$tot.result<-tot.result})
output$SaveIndivResult<-shiny::downloadHandler(
filename = function() {
paste("IndivParam.csv")},
content = function(file){
utils::write.table(PKconverter.env$tot.result, file, sep = ",",
row.names = FALSE,col.names = TRUE)})
}#end server
)#end App
shiny::runApp(PK_app,launch.browser=TRUE)
}
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