R/dashboardui_reunif.R
In Peccary-PMX/Peccary: PD and PK results
Defines functions
peccary_app3
go
pecc_ui_reunif
# library(shiny)
# library(shinydashboard)
#
#' @export
pecc_ui_reunif <- function(){dashboardPage(
# Header ------------------------------------------------------------------
dashboardHeader(title = "Peccary",
dropdownMenuOutput(outputId = "messages")
),
# Sidebar -----------------------------------------------------------------
dashboardSidebar(
sidebarMenu(
style = "overflow: visible",
menuItem("Project", tabName = "Welcome", icon = icon("Project")
# menuSubItem("Project", tabName = "", icon = icon("dashboard")),
),
menuItem("Pre-modelisation", icon = icon("bacon"), tabName = "Pre-modelisation",
menuSubItem("Datasets", tabName = "Datasets", icon = icon("dashboard")),
menuSubItem("Dataset explo", tabName = "datasetExplo", icon = icon("dashboard")),
menuSubItem("Graphical exploration", tabName = "graph", icon = icon("dashboard")),
menuSubItem("NCA", tabName = "NCA", icon = icon("dashboard")),
# menuSubItem("PKNCA", tabName = "PKNCA", icon = icon("dashboard")),
selectInput(inputId = "preloadeddataset", label = "Preloaded dataset", choices = c("Use external")),
# textInput("pathExplo", "Path of a dataset", value = ""),
textAreaInput("filterrExplo", "Filter", value = ""),
selectInput(inputId = "exploX", label = "X", choices = ""),
selectInput(inputId = "exploY", label = "Y", choices = "")
# actionButton("loadExplo", "Load"),
),
menuItem("Model building ", icon = icon("deSolve"), tabName = "deSolve"),
# menuItem("Run manager ", icon = icon("deSolve"), tabName = "runmanager"),
menuItem("Models analysis",icon = icon("deSolve"), tabName = "modelAnalysis",
textInput("path2", "Path to folder", value = "D:/Peccary/Exemple_demo"),
actionButton("folderupdate", "Go"),
selectInput(inputId = "subPath",multiple = F, label = "subPath", choices = "Root", selected = "subF"),
textInput("number", "Runs" ),
menuSubItem("Folder", tabName = "folder", icon = icon("dashboard")),
menuSubItem("Preds", tabName = "prediction", icon = icon("dashboard")),
menuSubItem("GOF", tabName = "GOF", icon = icon("dashboard")),
menuSubItem("Covariate", tabName = "covariate", icon = icon("dashboard")),
menuSubItem("Matrix", tabName = "matrix", icon = icon("dashboard")),
menuSubItem("iLL", tabName = "iLL", icon = icon("dashboard")),
menuSubItem("Sensitivity", tabName = "sensitivity", icon = icon("dashboard")),
menuSubItem("Forest", tabName = "forestPlot", icon = icon("dashboard")),
menuSubItem("VPC", tabName = "simulation", icon = icon("dashboard")),
menuSubItem("Plot saved", tabName = "rapports" , icon = icon("dashboard")),
actionButton("allplotbutton", "AllPlots"),
textInput(inputId = "gofunits_obs", label = "units obs"),
textInput(inputId = "gofunits_time", label = "units time"),
radioButtons("variable", "CovPrim:",
choices = "none"
# c( "none" = "none",
# "PRED" = "pred",
# "GOF" = "GOF",
# "RE_Boxplot" = "box",
# "RE_matrix" = "matrix")
),
radioButtons("variable2", "CovSec:",
choices = "none"
# c( "none" = "none",
# "PRED" = "pred",
# "GOF" = "GOF",
# "RE_Boxplot" = "box",
# "RE_matrix" = "matrix")
)
),
menuItem("Manual", tabName = "ManualFunc", icon = icon("deSolve")),
menuItem("vpc_pckg", tabName = "vpc_pckg", icon = icon("deSolve")),
menuItem("Report", tabName = "Report", icon = icon("deSolve")),
map(unique(gsub("(_serv)|(_ui)|(\\.R)", "", list.files("D:/Peccary/inst/Module"))), function(x){
menuItem(x, tabName = x, icon = icon("deSolve"))
}),
menuItem("Authors", tabName = "Authors", icon = icon("deSolve"))
)
),
dashboardBody(
useShinyjs(),
do.call(tabItems, append(list(
tabItem(tabName = "Welcome",
h2("Welcome to Peccary !", align = "center"),
br("With Peccary, pharmacometrics becomes simpler and faster"),
br("For tutorials, you can find:"),
"+", tags$a(href="https://github.com/Peccary-PMX/Peccary/releases/download/Doc/Peccary_Documentation.html", "a html document (click to download)", target="_blank" ),
br(),
"+", tags$a(href = "https://www.youtube.com/watch?v=d77c4v2_jcw", "Youtube videos (click to open)"),
h3("Load Project"),
br("First, do you have a Peccary project you want to load?"),
br(""),
selectInput(inputId = "recentprojectfile", label = "Previous Project", width ="800", choices = c("No Previous Project Available")),
actionButton("getpathProjectexisting", "or click to find a project file"),
br(""),
textInput(inputId = "Project_file", label = "Path to Project File", width = "800", value = ""),
br(""),
actionButton(inputId = "Project_load", label = "Load project"),
br("(if you want to change the loaded project, it is safier to restart Peccary Shiny App first)"),
br(""),
h3("Create Project"),
br("Otherwise, do you want to create one?"),
br(""),
actionButton("getpathProject", "click to find a path"),
textInput(inputId = "Project_file_create", label = "Set where to put the project", width = "800", value = "file:///D:/these/demo"),
# br("Do you want to create a complete project folder with subfolders? It will help you to store your files"),
# checkboxInput(inputId = "creation_folder_cb", label = "Yes, create folders and subfolders", value = T),
br("Click on the button below and let's start !"),
br(""),
actionButton(inputId = "Project_create", label = "Create project")
),
# Datasets handling -------------------------------------------------------
tabItem(tabName = "Datasets",
h2("Datasets Loading", align = "center"),
h3("Dataset loading and input settings"),
br("Here is the place where you can store your data files, make graphical exploration, NCA analysis and pre-modelling work !"),
br("First, let's look at wich data are available: "),
rHandsontableOutput(outputId = "datasets"),
br("If there is no data files, you can first try to upload the one in the 1_DATA folder "),
br(""),
actionButton(inputId = "load_data_folders", label = "Try automatic loading"),
br(""),
br("Otherwise, you can add manually a file or just temporary use:"),
br(""),
actionButton("getpathDataset", "click to find a path"),
textInput(inputId = "path_dataset_manual", label = "Add path to a dataset", width = "800"),
fluidRow(
div(style="display:inline-block; width: 100px;height: 75px;", selectInput("sepExplo", "Sep", choices = c("Space" = "", ";", ".", ","), selected = "Space")),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput("decExplo", "Dec", choices = c(".", ","), selected = ".")),
div(style="display:inline-block; width: 100px;height: 75px;", textInput("nastringExplo", "NA", value = ".")),
div(style="display:inline-block; width: 100px;height: 75px;", actionButton("addDataset", label = "add"))
),
br(""),
numericInput(inputId = "dataset_default", label = "Choose which dataset you want to open by default", value = 1),
br(""),
br("After additions, please make sure to save them"),
actionButton(inputId = "save_datasets", label = "Save modifications"),
h3("Dataset informations (column header)"),
br("here, you can simply fill the informations on the table above"),
fluidRow(
div(style="display:inline-block; width: 100px;height: 75px;", numericInput(inputId = "quicklookn", label = "Number of the dataset", value = 0, min = 0)),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "quicklooksep", label = "sep", choices = c("", " ", ";", ",", "."), selected = ";")),
div(style="display:inline-block; width: 100px;height: 75px;",selectInput(inputId = "quicklookdec", label = "dec", choices = c(""," ", ";", ",","."), selected = ".")),
div(style="display:inline-block; width: 100px;height: 75px;", textInput(inputId = "quicklookna", label = "na_string", value = ".")),
div(style="display:inline-block; width: 100px;height: 75px;", textInput(inputId = "quicklookx", label = "x", value = "")),
div(style="display:inline-block; width: 100px;height: 75px;",textInput(inputId = "quicklookxlabel", label = "x label", value = "")),
div(style="display:inline-block; width: 100px;height: 75px;",textInput(inputId = "quicklooky", label = "y", value = "")),
div(style="display:inline-block; width: 100px;height: 75px;",textInput(inputId = "quicklookylabel", label = "y label", value = "")),
div(style="display:inline-block; width: 400px;height: 75px;",textInput(inputId = "quicklookcomment", label = "comment", value = ".")),
# div(style="display:inline-block; width: 100px;height: 75px;",actionButton(inputId = "quicklookload", label = "load")),
div(style="display:inline-block; width: 100px;height: 75px;",actionButton(inputId = "quicklooksave", label = "Import"))
# div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "colourPred2", label = "COV", choices = "None"))
),
fluidRow(
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "IDheader", label = "ID", choices = c(""), selected = "")),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "IDheader2", label = "TIME", choices = c(""), selected = "")),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "OBSheader", label = "OBS", choices = c(""), selected = "")),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "AMTheader", label = "AMT", choices = c(""), selected = "")),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "ADMheader", label = "ADM", choices = c(""), selected = "")),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "RATEheader", label = "RATE", choices = c(""), selected = "")),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "EVIDheader", label = "EVID", choices = c(""), selected = "")),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "MDVheader", label = "MDV", choices = c(""), selected = "")),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "YTYPEheader", label = "YTYPE", choices = c(""), selected = "")),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "COVCONTheader", label = "cov.cont", choices = c(""), selected = "")),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "COVCATheader", label = "cov.cat", choices = c(""), selected = ""))
)
# selectInput(inputID = "headerEVID", label = "EVID"),
# selectInput(inputID = "headerMDV", label = "MDV"),
# selectInput(inputID = "headerYTYPE", label = "YTYPE"),
# selectInput(inputID = "headerCOVCONT", label = "cov.cont"),
# selectInput(inputID = "headerCOVCAT", label = "cov.cat"),
# rHandsontableOutput(outputId = "defineheader", height = 200),
# DT::dataTableOutput(outputId = "quicklookTable")
),
tabItem(tabName = "widgets",
h2("Widgets tab content"),
fluidRow(
box(plotOutput("plot1", height = 250)),
box(
title = "Controls",
sliderInput("slider", "Number of observations:", 1, 100, 50)
)
)
),
# Dataset exploration ---------------------------------------------------
tabItem(tabName = "datasetExplo",
div(style="display:inline-block; width: 300px;height: 75px;", selectInput(inputId = "dataexploVersion", label = "Version", choices = c(""), selected = "")),
div(style="display:inline-block; width: 75px;height: 75px;", actionButton(inputId = "dataexploLoad", label = "Load")),
div(style="display:inline-block; width: 300px;height: 75px;", textInput(inputId = "dataexplonewVersion", label = "Name")),
div(style="display:inline-block; width: 75px;height: 75px;", actionButton(inputId = "dataexploSave", label = "Save")),
textInput(inputId = "filtertableexplo", label = "Exploratory filter", value = ""),
fluidRow(
column(4,
textAreaInput(inputId = "tableExploManipulation", label = "Free Manipulation (temp being loaded dataset)", resize = "both", height = 180),
),
column(1,
br(""),
actionButton(inputId = "storemodif", label = "Store modif"),
br(""),
actionButton(inputId = "copymodif", label = "Create file with modif"),
# br(""),
# actionButton(inputId = "overwrite", label = "Overwrite original ds")
)
),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "groupbyCovExplo", label = "Extract cov by", multiple = T, choices = "")),
# div(style="display:inline-block; width: 150px;height: 75px;", checkboxInput(inputId = "covreduceExplo", label = "Cov reduce", value = T)),
actionButton(inputId = "abtableexplo", label = "Go"),
dataTableOutput("tableexplo"),
box(title = "table1", collapsible = T, collapsed = F,width = 1000,
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "table1reduceBy", label = "Reduce by", multiple = T, choices = "All")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "table1x", label = "In rows", multiple = T, choices = "")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "table1y", label = "In col", multiple = T, choices = "")),
div(style="display:inline-block; width: 150px;height: 75px;", actionButton(inputId = "table1go", label = "Go")),
tableOutput(outputId = "table1output"),
box(title = "Code", collapsible = T, collapsed = T, width = 400,
textAreaInput(inputId = "table1_code",label = "Code", width = "100%", height = 40)
)
),
box(title = "Count", collapsible = T, collapsed = T,width = 1000,
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "countwhat", label = "Count what", multiple = F, choices = "")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "countx", label = "Row", multiple = F, choices = "")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "county", label = "Col", multiple = F, choices = "")),
div(style="display:inline-block; width: 150px;height: 75px;", actionButton(inputId = "countgo", label = "Go")),
textOutput(outputId = "countbytext"),
rHandsontableOutput(outputId = "countoutput"),
box(title = "Code", collapsible = T, collapsed = T, width = 400,
textAreaInput(inputId = "count_code",label = "Code", width = "100%")
)
),
box(title = "plot cov", collapsible = T, collapsed = T,width = 1000,
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "plotcov_x", label = "covariate 1", multiple = F, choices = "")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "plotcov_y", label = "covariate 2", multiple = F, choices = "")),
div(style="display:inline-block; width: 150px;height: 75px;", actionButton(inputId = "plotcov_go", label = "Go")),
shinyjqui::jqui_resizable(plotOutput("plotcovplot", width = "800px", height = "600px")),
box(title = "Code", collapsible = T, collapsed = T, width = 400,
textAreaInput(inputId = "plotcov_code",label = "Code", width = "100%")
)
)
# actionButton("loadexplo", label = "Start"),
# fluidRow(
#
# div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "groupbyExplo", label = "Group by", multiple = T, choices = "")),
# div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "tableexploselected",label = "Table2", choices = c("tally", "distinct"))),
# div(style="display:inline-block; width: 150px;height: 75px;", actionButton(inputId = "launchtableexplo2", label = "Load second table"))
# ),
# dataTableOutput("tableexplo2"),
# fluidRow(
#
# div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "groupbyExplo3", label = "Variable one", choices = "")),
# div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "tableexploselected3",label = "Table3", choices = c("percentage","table1","detail" ))),
# div(style="display:inline-block; width: 150px;height: 75px;", actionButton(inputId = "launchtableexplo3", label = "Load third table"))
# ),
# dataTableOutput("tableexplo3")
),
# graph dataset -----------------------------------------------------------
tabItem(tabName = "graph",
conditionalPanel(
condition = 'input.exploPlotly == false',
shinyjqui::jqui_resizable(plotOutput("exploPlot", width = "800px", height = "700px"))
),
conditionalPanel(
condition = 'input.exploPlotly == true',
shinyjqui::jqui_resizable( plotlyOutput("exploPlotly", width = "800px", height = "700px"))
),
box(
rHandsontableOutput(outputId = "PlotexplorationSaved"),
actionButton(inputId = "pdfPLotExplo", label = "Pdf export"),
title = "Plots saved", collapsible = T, collapsed = F),
fluidRow(
div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = "exploPlotly", label = "Plotly", value = FALSE)),
div(style="display:inline-block; width: 250px;height: 75px;", textInput("secondFilter", "second Filter", value = "")),
div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = "allbackground", label = "grey_all", value = FALSE)),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "exploCol", label = "Col", choices = "")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "exploID", label = "Group", choices = "")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "exploShape", label = "Shape", choices = "")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "exploLty", label = "Lty", choices = "")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "exploWrap", label = "Wrap", choices = "")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "exploGrid", label = "Grid", choices = "")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "exploStand", label = "Standardization", choices = "")),
div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = "exploXlog", label = "Xlog", value = FALSE)),
div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = "exploYlog", label = "Ylog", value = TRUE)),
div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = "exploMedian", label = "Median", value = FALSE)),
div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = "exploNA", label = "Remove NA", value = TRUE)),
div(style="display:inline-block; width: 150px;height: 75px;", numericInput(inputId = "exploLOQ", label = "LOQ", value = -1, step = 1)),
# div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = "all_bkgrd", label = "bkgd", value = FALSE)),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput("scaleExplo", "Wrap scale",selected = "free", choices = c("fixed", "free", "free_x", "free_y"))),
div(style="display:inline-block; width: 150px;height: 75px;", textInput(inputId = "plotexploname", label = "Name")),
div(style="display:inline-block; width: 150px;height: 75px;", actionButton(inputId = "plotexplosaveaction",label = "Save"))
),
box(width = 1000,
div(style="display:inline-block; width: 150px;height: 75px;", numericInput(inputId = "exploPoint", label = "Point-Alpha", value = 1, min = 0, max = 1, step = 0.1)),
div(style="display:inline-block; width: 150px;height: 75px;", numericInput(inputId = "exploLine", label = "Line-Alpha", value = 1, min = 0, max = 1, step = 0.1)),
div(style="display:inline-block; width: 150px;height: 75px;", numericInput(inputId = "all_bkgrdalpha", label = "bckgd_alpha", min = 0, max = 1 , value = 0.3, step = 0.1)),
div(style="display:inline-block; width: 150px;height: 75px;", textInput("titleExplo", "Title", value = "")),
div(style="display:inline-block; width: 150px;height: 75px;", textInput("subtitleExplo", "subtitle", value = "")),
div(style="display:inline-block; width: 150px;height: 75px;", textInput("xlabsExplo", "xlabs", value = "")),
div(style="display:inline-block; width: 150px;height: 75px;", textInput("ylabsExplo", "ylabs", value = "")),
div(style="display:inline-block; width: 150px;height: 75px;", textInput("captionExplo", "caption", value = "")),
div(style="display:inline-block; width: 150px;height: 75px;", textInput("colLabExplo", "colLab", value = "")),
div(style="display:inline-block; width: 150px;height: 75px;", textInput("colValuesExplo", "colValues", value = "")),
div(style="display:inline-block; width: 150px;height: 75px;", textInput("shapeLabExplo", "shapeLab", value = "")),
div(style="display:inline-block; width: 150px;height: 75px;", textInput("shapeValuesExplo", "shapeValues", value = "")),
div(style="display:inline-block; width: 150px;height: 75px;", textInput("ltyLabExplo", "ltyLab", value = "")),
div(style="display:inline-block; width: 150px;height: 75px;", textInput("ltyValuesExplo", "ltyValues", value = "")),
div(style="display:inline-block; width: 150px;height: 75px;", numericInput(inputId = "sizeTextExplo", label = "Size Text", value = 15, step = 1)),
div(style="display:inline-block; width: 150px;height: 75px;", actionButton(inputId = "addlineexplo",label = "addline")),
div(style="display:inline-block; width: 150px;height: 75px;", actionButton(inputId = "removelineexplo",label = "removelin")),
rHandsontableOutput(outputId = "addlinesexploration"),
title = "More control",
collapsible = T, collapsed = T),
box(width = 1000,
textAreaInput(inputId = "codeexplopec", label = "Short Peccary Code ", height = 100,width = 1000),
textAreaInput(inputId = "codeexplo", label = "Peccary Independant Code", height = 300,width = 1000),
title = "R code", collapsible = T, collapsed = T)
),
# NCA ---------------------------------------------------------------------
tabItem(tabName = "NCA",
shinyjqui::jqui_resizable(plotOutput("plotNCAcov", width = "800px", height = "600px")),
box(
rHandsontableOutput(outputId = "NCASaved"),
actionButton(inputId = "pdfNCA", label = "NCA export"),
title = "Plots saved", collapsible = T, collapsed = F),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "pckgNCA", label = "Software", choices = c("Peccary", "pknca") )),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "groupNCA", label = "Group", choices = "", multiple = T)),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "covNCA", label = "Cov", choices = "")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "blqNCA", label = "BLQ", choices = "")),
# div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "evidNCA", label = "EVID", choices = "")),
div(style="display:inline-block; width: 150px;height: 75px;", numericInput(inputId = "Nsignif", label = "Nsignif", value = 3, min = 0, step = 1)),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "nca_admin", label = "Admin option", choices = c("None", "IVbolus -> backextrapolation", "Other -> add observation = 0 at time = 0"))),
div(style="display:inline-block; width: 150px;height: 75px;", numericInput(inputId = "auc_0_x", label = "AUC_0_x", value = 0, min = 0, step = 1)),
div(style="display:inline-block; width: 150px;height: 75px;", checkboxInput(inputId = "nca_forcecat", label = "ForceBoxplot", value = F)),
div(style="display:inline-block; width: 150px;height: 75px;", checkboxInput(inputId = "nca_teststat", label = "TestStat", value = T)),
div(style="display:inline-block; width: 150px;height: 75px;", checkboxInput(inputId = "nca_bxpltpoint", label = "ShowBPpoints", value = T)),
div(style="display:inline-block; width: 150px;height: 75px;", checkboxInput(inputId = "nca_corCI", label = "ShowCI", value = F)),
div(style="display:inline-block; width: 150px;height: 75px;", checkboxInput(inputId = "nca_corregline", label = "ShowRegLine", value = T)),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "nca_method_box", label = "Stat boxplot", choices = c("wilcox.test","t.test", "anova", "kruskal.test") )),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "nca_method_corr", label = "Stat correlation", choices = c("spearman","pearson", "kendall") )),
div(style="display:inline-block; width: 150px;height: 75px;", checkboxInput(inputId = "nca_xlog", label = "xlog", value = F)),
div(style="display:inline-block; width: 150px;height: 75px;", checkboxInput(inputId = "nca_ylog", label = "ylog", value = T)),
div(style="display:inline-block; width: 150px;height: 75px;", textInput(inputId = "nca_unitx", label = "Unit x ", value = "")),
div(style="display:inline-block; width: 150px;height: 75px;", textInput(inputId = "nca_unity", label = "Unit y ", value = "")),
div(style="display:inline-block; width: 150px;height: 75px;", textInput(inputId = "nca_labelx", label = "Label x ", value = "")),
div(style="display:inline-block; width: 150px;height: 75px;", textInput(inputId = "nca_labely", label = "Label y ", value = "")),
div(style="display:inline-block; width: 150px;height: 75px;", textInput(inputId = "nca_tabletitle", label = "Title", value = "")),
div(style="display:inline-block; width: 150px;height: 75px;", textInput(inputId = "nca_name", label = "Name ", value = "")),
div(style="display:inline-block; width: 150px;height: 75px;", actionButton(inputId = "nca_save", label = "Save")),
br(""),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "pknca_dose", label = "PKNCA Dose", choices = names(Theoph), selected = "Dose")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "pknca_ADM", label = "PKNCA EVID", choices = names(Theoph), selected = "Dose")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "pknca_route", label = "PKNCA route", choices = c("extravascular", "IV bolus", "IV perf (rate)", "IV perf (time perf)"), selected = "intravascular")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "pknca_rateduration", label = "RateDuration", choices =names(Theoph), selected = "Dose")),
br(""),
# selectInput(inputId = "nca_table_display", label = "Table type", choices = c("Individuals", "Per cov")),
br(""),
box(id = "boxpkncaparam", title = "Option of PKNCA package", width = 12, collapsible = T, collapsed = T,
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "pknca_auc.method", label = "auc.method", choices = c("lin up/log down", "linear"), selected = "lin up/log down")),
div(style="display:inline-block; width: 150px;height: 75px;", numericInput(inputId = "pknca_adj.r.squared.factor", label = "adj.r.squared.factor",value = 0.0001)),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "pknca_max.missing", label = "max.missing",selected = "drop", choices = "drop")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "pknca_conc.na", label = "conc.na",choices = c("drop", "keep"), selected = "drop" )),
div(style="display:inline-block; width: 150px;height: 75px;", checkboxInput(inputId = "pknca_first.tmax", label = "first.tmax",value = T)),
div(style="display:inline-block; width: 150px;height: 75px;", checkboxInput(inputId = "pknca_allow.tmax.in.half.life", label = "allow.tmax.in.half.life",value = F)),
div(style="display:inline-block; width: 150px;height: 75px;", numericInput(inputId = "pknca_min.hl.points", label = "min.hl.points",value = 3)),
div(style="display:inline-block; width: 150px;height: 75px;", numericInput(inputId = "pknca_min.span.ratio", label = "min.span.ratio",value = 2)),
div(style="display:inline-block; width: 150px;height: 75px;", numericInput(inputId = "pknca_max.aucinf.pext", label = "max.aucinf.pext",value = 20)),
div(style="display:inline-block; width: 150px;height: 75px;", numericInput(inputId = "pknca_min.hl.r.squared", label = "min.hl.r.squared",value = 0.9)),
br(""),
# br("See https://cran.r-project.org/web/packages/PKNCA/vignettes/Options-for-Controlling-PKNCA.html for an explenation of these options"),s
tags$a(href="https://cran.r-project.org/web/packages/PKNCA/vignettes/Options-for-Controlling-PKNCA.html", "See https://cran.r-project.org/web/packages/PKNCA/vignettes/Options-for-Controlling-PKNCA.html for an explenation of these options")
),
br(""),
br(""),
h3("Individual Values"),
DT::dataTableOutput("tableNCA"),
h3("Stat per cov"),
tableOutput("tableNCA2"),
box(title = "Code", collapsible = T, collapsed = T, width = 400,
fluidRow(
# div(style="display:inline-block; width: 300px;height: 75px;", textInput(inputId = "nca_path_export", "Path to export", value = "")),
# div(style="display:inline-block; width: 200px;height: 75px;", selectInput("nca_to_export", "What to export", choices = c("Individuals", "Per cov", "Both"))),
# div(style="display:inline-block; width: 100px;height: 75px;", actionButton("nca_export_go", "Launch")),
textAreaInput(inputId = "nca_code_peccdep",label = "Short Code Peccary", width = "100%",height = 100),
textAreaInput(inputId = "nca_code_peccindep",label = "Peccary Independent Code", width = "100%",height = 500)
)
)
),
# Model building -------------------------------------------------------------
tabItem(tabName = "deSolve",
fluidRow(
# div(style="display:inline-block; width: 200px;height: 75px;", textInput(inputId = "path_models", "File of models", value = "D:/these/Pecc_test")),
div(style="display:inline-block; width: 400px;height: 75px;", selectInput(inputId = "names_model", "Model", choices = "")),
div(style="display:inline-block; width: 100px;height: 75px;", actionButton(inputId = "load_model", "Load")),
div(style="display:inline-block; width: 200px;height: 75px;", textInput(inputId = "name_model", "Name to Save")),
div(style="display:inline-block; width: 100px;height: 75px;", actionButton(inputId = "save_model", "Save"))
# div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = "helpmodel", "display model helper"))
),
# box(title = "Covariate equations", collapsible = T, collapsed = T, width = 400,
# conditionalPanel('input.helpmodel == true',
# box(id = "helperModel", title = "helperModel",
# textInput(inputId = "nameLibOutput", label = "Desired Name", value = "auto",width = "50%"),
# textInput(inputId = "targetLibOutput", label = "Namelinks", value = "auto",width = "50%"),
# )),
# rHandsontableOutput(outputId= "modelLibInput"),
fluidRow(
column(6,
textAreaInput("mb_model", "Write your model (_plot & _output)", value = "",width = "500", height = "500")
) ,
column(6,
selectInput(multiple = T, inputId = "modelLibInput", "Library-input", choices = c("a", "b")),
textAreaInput("mb_model_cov", "Opti. covariate equations", value = "",width = "200", height = "200")
)
),
# box(title = "Model Librairies", collapsible = T, collapsed = T, width = 400,
#
# fluidRow(
#
# ),
#
# textAreaInput("mb_model_helper", "Proposition", value = "")
#
# ),
fluidRow(
div(style="display:inline-block; width: 100px;height: 75px;", actionButton("mb_load_model", "Load Model")),
div(style="display:inline-block; width: 200px;height: 75px;", checkboxInput("mb_load_cov", label = "Use covariate", value = F)),
div(style="display:inline-block; width: 100px;height: 75px;", actionButton("mb_add_event", "Add event")),
div(style="display:inline-block; width: 100px;height: 75px;", actionButton("mb_delete_event", "Delete event"))
),
fluidRow(
div(style="display:inline-block; width: 200px;height: 200px;", rHandsontableOutput("mb_state", width = 200, height = 200)),
div(style="display:inline-block; width: 200px;height: 200px;", rHandsontableOutput("mb_paramater", width = 200, height = 200)),
div(style="display:inline-block; width: 200px;height: 200px;", rHandsontableOutput("mb_event", width = 200, height = 200))
),
fluidRow(
div(style="display:inline-block; width: 520px;height: 200px;",rHandsontableOutput("mb_matrix", width = 500, height = 200)),
div(style="display:inline-block; width: 200px;height: 200px;", rHandsontableOutput("mb_output", width = 200, height = 200))
),
# div(style="display:inline-block; width: 150px;height: 75px;", actionButton("update_matrix", label = "update matrix")),
div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput("matrix_diag", label = "full matrix", value = T)),
div(style="display:inline-block; width: 200px;height: 75px;", selectInput("matrix_sd_var", label = "coded in", choices = c("sd", "var"), selected = "sd")),
div(style="display:inline-block; width: 100px;height: 75px;", actionButton("mb_output_add", label = "add output")),
div(style="display:inline-block; width: 150px;height: 75px;", actionButton("mb_output_remv", label = "remove output")),
div(style="display:inline-block; width: 200px;height: 75px;", selectInput("IDImpMod", "Id", choices = "Initial")),
div(style="display:inline-block; width: 300px;height: 75px;", checkboxInput("useImpData", "use imported data", value = F)),
# Import model -------------------------------------------------------------
#
# box(title = "Import model", collapsible = T, collapsed = T, width = 400,
#
# fluidRow(
# # div(style="display:inline-block; width: 300px;height: 75px;", textInput(inputId = "pathImpMod", "Path to the model", value = "file:///D:/these/Pecc_test/3_Models/1_Models/000_20_04_03/model_base.mlxtran")),
#
# # div(style="display:inline-block; width: 100px;height: 75px;", actionButton("launchImpMod", "Launch")),
# # div(style="display:inline-block; width: 100px;height: 75px;", actionButton("pdfImpData", "Launch pdf")),
# # div(style="display:inline-block; width: 100px;height: 75px;", actionButton("pdfImpData2", "Launch pdf"))
# # actionButton("mb_add_plot", "Add Plot"),
# # actionButton("mb_load_plot", "Load Plot"),
# # actionButton("mb_delete_plot", "Delete Plot"),
# # checkboxInput("mb_matrix_display", label = "Simulations", value = F)
# )
#
# ),
# plot & simulation -------------------------------------------------------
box(title = "Plot & Simulations", collapsible = T, collapsed = F, width = 400,
fluidRow(
# div(style="display:inline-block; width: 300px;height: 75px;", checkboxGroupInput("mb_display", "Plot-to-display", inline = T, choices = c(""))),
div(style="display:inline-block; width: 500px;height: 200px;", rHandsontableOutput("mb_display2", width = 300, height = 100)),
div(style="display:inline-block; width: 400px;height: 200px;", rHandsontableOutput("mb_plot_stat", width = 400, height = 100))
# div(style="display:inline-block; width: 50px;height: 75px;", checkboxInput(inputId = "mb_ylog", label = "y log", value = F)),
# div(style="display:inline-block; width: 50px;height: 75px;", checkboxInput(inputId = "mb_wrap", label = "Wrap", value = F))
# div(style="display:inline-block; width: 200px;height: 75px;", checkboxInput(inputId = "mb_add_point", label = "Add points explo", value = F))
),
fluidRow(
div(style="display:inline-block; width: 80px;", numericInput("mb_time_from", value = 0,label = "From")),
div(style="display:inline-block; width: 80px;", numericInput("mb_time_to", value = 100,label = "To")),
div(style="display:inline-block; width: 80px;", numericInput("mb_time_by", value = 1,label = "By")),
div(style="display:inline-block; width: 80px;", numericInput(inputId = "mb_nsimul", label = "N simul", value = 0)),
div(style="display:inline-block; width: 80px;", numericInput(inputId = "mb_minvaluesimul", label = "min value", value = 0)),
div(style="display:inline-block; width: 80px;", numericInput(inputId = "mb_maxvaluesimul", label = "max value", value = NA)),
div(style="display:inline-block; width: 80px;", selectInput("mb_ode_solver", "ODE solver", choices = c("deSolve", "RxODE"), selected = "RxODE", width = "80px")),
actionButton("mb_add_plot", "Add Plot"),
actionButton("mb_load_plot", "Load Plot"),
actionButton("mb_delete_plot", "Delete Plot"),
actionButton("mb_estimatePopParam", "Try estimation"),
checkboxInput("mb_add_error_plot", label = "Include error", value = F)
),
shinyjqui::jqui_resizable(plotOutput("mb_plot", width = "900px", height = "700px")),
box(textAreaInput(inputId = "Code_plot_sim", label = "", width = 500,height = 800, resize = "none"),title = "Code", collapsible = T, collapsed = T, width = 400)
),
# optimal design ----------------------------------------------------------
box(title = "Optimal Design", collapsible = T, collapsed = T, width = 1200,
fluidRow(
# div(style="display:inline-block; width: 300px;height: 200px;", textInput("samplingTime", label = "Sampling")),
div(style="display:inline-block; width: 1200px;height: 200px;",rHandsontableOutput("OD_sampling", width = 1200, height = 200)),
div(style="display:inline-block; width: 150px;height: 200px;", actionButton("OptimDesign_add", "Add line")),
div(style="display:inline-block; width: 150px;height: 200px;", actionButton("OptimDesign_delete", "Delete line")),
div(style="display:inline-block; width: 150px;height: 200px;", actionButton("OptimDesign", "Eval design"))
),
plotOutput("OptimPlot", width = "400px", height = "300px"),
textAreaInput(inputId = "Result_Optimal_Design", label = "", width = 500,height = 300, resize = "none"),
box(textAreaInput(inputId = "Code_Optimal_Design", label = "", width = 500,height = 300, resize = "none"),title = "Code", collapsible = T, collapsed = T, width = 400)
),
# Scheme model ------------------------------------------------------------
box(title = "Scheme of the model", collapsible = T, collapsed = T, width = 1200,
fluidRow(
# div(style="display:inline-block; width: 300px;height: 200px;", textInput("samplingTime", label = "Sampling")),
# div(style="display:inline-block; width: 1200px;height: 200px;",rHandsontableOutput("OD_sampling", width = 1200, height = 200)),
# div(style="display:inline-block; width: 150px;height: 200px;", actionButton("OptimDesign_add", "Add line")),
div(style="display:inline-block; width: 150px;height: 200px;", numericInput(inputId = "scheme_size", label = "Size", value = 0.9, min = 0, max = 1, step = 0.1)),
div(style="display:inline-block; width: 150px;height: 200px;", actionButton("scheme_launch", "Go"))
),
shinyjqui::jqui_resizable(plotOutput("scheme_plot", width = "1000px", height = "800px"))
# plotOutput("OptimPlot", width = "400px", height = "300px"),
# textAreaInput(inputId = "Result_Optimal_Design", label = "", width = 500,height = 300, resize = "none"),
# box(textAreaInput(inputId = "Code_Optimal_Design", label = "", width = 500,height = 300, resize = "none"),title = "Code", collapsible = T, collapsed = T, width = 400)
),
# nlmixr ------------------------------------------------------------------
box(title = "nlmixr", collapsible = T, collapsed = T, width = 400,
div(style="display:inline-block; width: 80px;", selectInput("nlmixr_methods", "methods", choices = c("saem", "focei", "nlme"), selected = "saem", width = "80px")),
div(style="display:inline-block; width: 50px;height: 75px;", actionButton("nlmixr_translate", "Generate code")),
textAreaInput("nlmixr_result",label = "", height = 500),
div(style="display:inline-block; width: 200px;height: 75px;", textInput(inputId = "nlmixr_path", "Path_to_save", value = "D:/Peccary_Annexe/Exemple_demo/nlmixr_test")),
# div(style="display:inline-block; width: 400px;height: 75px;", textInput("nlmixr_path", label = "Path", value = "D:/Peccary/Exemple_demo/saemix_test")),
div(style="display:inline-block; width: 100px;height: 75px;", actionButton("nlmixr_go", "Estimate"))
),
# monolix launcher --------------------------------------------------------
box(title = "Monolix", collapsible = T, collapsed = T, width = 400,
div(style="display:inline-block; width: 200px;height: 75px;", actionButton("ode_modelsave_monolix", "Generate Mlxtran")),
div(style="display:inline-block; width: 200px;height: 75px;", textInput("ode_projectpath_monolix", label = "Monolix project path", value = "")),
div(style="display:inline-block; width: 200px;height: 75px;", actionButton("launch_monolix", label = "Launch Monolix")),
div(style="display:inline-block; width: 400px;height: 75px;", textInput("monolix_filter", label = "Additional Filter", value = "")),
div(style="display:inline-block; width: 400px;height: 75px;", textInput("monolix_description", label = "Additional Filter", value = "")),
tabBox(
title = "Monolix launcher",
# The id lets us use input$tabset1 on the server to find the current tab
id = "tabset1", height = "750px",
tabPanel("Model file",
actionButton("ode_trigger_monolix", "Launch ode translation"),
textAreaInput("ode_output", "Model", value = "", width = "400", height = "500" ) # , div(style="display:inline-block; width: 1000px;height: 700px;",
),
tabPanel("NMLXTRAN",
actionButton(inputId = "nmlxtran_launch", label = "launch"),
textAreaInput("nmlxtran_output", "Model", value = "", width = "400", height = "500" ))
)
),
# nonmem code -------------------------------------------------------------
box(title = "NONMEM", collapsible = T, collapsed = T, width = 400,
# div(style="display:inline-block; width: 250px;height: 75px;", selectInput("ode_input", "Exporte software",choices = c("NONMEM", "Monolix"), selected = "NONMEM")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput("ode_baselines2", "Baseline parameters",choices = "", selected = "", multiple = T)),
div(style="display:inline-block; width: 50px;height: 75px;", checkboxInput(inputId = "ode_mu", label = "mu-ref", value = T)),
div(style="display:inline-block; width: 50px;height: 75px;", checkboxInput(inputId = "ode_blq", label = "BLQ", value = F)),
div(style="display:inline-block; width: 50px;height: 75px;", actionButton("ode_trigger_nonmem", "Launch ode translation")),
# tabBox(
# title = "Nonmem launcher",
# The id lets us use input$tabset1 on the server to find the current tab
# id = "tabset1", height = "750px",
# tabPanel("Nonmem", "First tab content",
textAreaInput("ode_output_nonmem", "Model", value = "", width = "400", height = "700" ) # , div(style="display:inline-block; width: 1000px;height: 700px;",
# ),
# tabPanel("CTRLFILE", "Tab content 2")
# )
),
box(title = "ADAPT", collapsible = T, collapsed = T, width = 400,
div(style="display:inline-block; width: 50px;height: 75px;", actionButton("ode_trigger_adapt", "Launch ADAPT translation")),
textAreaInput("ode_output_adapt", "Model", value = "", width = "400", height = "700" ) # , div(style="display:inline-block; width: 1000px;height: 700px;",
)
# box(title = "saemix", collapsible = T, collapsed = T, width = 400,
#
# div(style="display:inline-block; width: 400px;height: 75px;", textInput("saemix_path", label = "Path", value = "D:/Peccary/Exemple_demo/saemix_test")),
# div(style="display:inline-block; width: 50px;height: 75px;", actionButton("saemix_go", "Go")),
# div(style="display:inline-block; width: 400px;height: 400px;", textAreaInput("nlmixr_result",label = ""))
#
# )
# conditionalPanel(condition = 'input.model_sections == "Monolix_Launcher"',
#
# shinyTree("tree", stripes = TRUE, multiple = TRUE, animation = TRUE, contextmenu = TRUE)
# )
),
# folder ------------------------------------------------------------------
tabItem(tabName = "folder",
textOutput(outputId = "namecurrendfolder"),
# conditionalPanel(
# condition = 'input.path2 != ""',
# tableOutput("table"),
# ),
div(style = 'overflow-x: scroll', tableOutput('table')),
# conditionalPanel(
# condition = 'input.path2 != ""',
tableOutput("runscompar")
# )
),
# prediction --------------------------------------------------------------
tabItem(tabName = "prediction",
checkboxInput(
inputId = 'interactivePreds', label = 'Interactive figure', value = FALSE
),
conditionalPanel(
condition = 'input.interactivePreds == true',
plotlyOutput('PredIndiInteractive',width = "1000px", height = "800px" )
),
conditionalPanel(
condition = 'input.interactivePreds == false',
conditionalPanel(
condition = 'input.path2 != ""',
shinyjqui::jqui_resizable( plotOutput('PredIndi', width = "1000px", height = "800px"))
) ),
conditionalPanel(
condition = 'input.path2 != ""',
fluidRow(
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "whichFunctionPred",label = "Function", choices = "Default", selected = "Default")),
div(style="display:inline-block; width: 100px;height: 75px;", textInput("numberPred2", "Runs" )),
# div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = "singmult", label = "S/M", value = TRUE)),
div(style="display:inline-block; width: 100px;height: 75px;", numericInput(inputId = "nIndPred2", label = "n",value = 20, min = 1)),
div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = "logPred2", label = "ylog", value = TRUE)),
div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = "logxPred2", label = "xlog", value = FALSE)),
div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = "PredPred2", label = "Pred", value = TRUE)),
div(style="display:inline-block; width: 150px;height: 75px;", checkboxInput(inputId = "freeSalePred2", label = "Free Scales", value = TRUE)),
div(style="display:inline-block; width: 300px;height: 75px;", textInput(inputId = "filterID2", label = "Filter")),
div(style="display:inline-block; width: 300px;height: 75px;", actionButton(inputId = "updatePred", label = "Update PLot")),
div(style="display:inline-block; width: 100px;height: 75px;", numericInput(inputId = "lowerlimitPred", label = "low limit",value = NA)),
div(style="display:inline-block; width: 100px;height: 75px;", numericInput(inputId = "upperlimitPred", label = "high limit",value = NA)),
div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = "extrVal", label = "Extr. Value", value = F)),
div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = "stratTypePred", label = "strat", value = F)),
div(style="display:inline-block; width: 100px;height: 75px;", textInput(inputId = "xlabPred", label = "xlab", value = "")),
div(style="display:inline-block; width: 100px;height: 75px;", textInput(inputId = "ylabPred", label = "ylab", value = ""))
# div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "colourPred2", label = "COV", choices = "None"))
)
),
conditionalPanel(
condition = 'input.path2 != ""',
fluidRow(
div(style="display:inline-block; width: 150px;height: 75px;", actionButton("savePRED", "Save Plot")),
div(style="display:inline-block; width: 800px;height: 75px;", textInput("commPRED", "Commentary (new line with three spaces)" ))
)
),
conditionalPanel(
condition = 'input.path2 != ""',
tableOutput("covPRED")
),
conditionalPanel(
condition = 'input.path2 != ""',
tableOutput("table2")
)
),
# gof ---------------------------------------------------------------------
tabItem( tabName = 'GOF',
radioButtons(inputId = 'radioGOF', label = "", choices = c("Single Static", "Single Dynamic", "Multiple Static"), inline = T),
# fluidRow(
# div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = 'interactive', label = 'Interactive figure', value = FALSE )),
# div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = 'multiGOFcheck', label = '', value = FALSE ))
# ),
#
conditionalPanel(
condition = 'input.radioGOF == "Single Dynamic"',
plotlyOutput('GOFinteractivePlot',width = "1000px", height = "700px" )
),
conditionalPanel(
condition = 'input.radioGOF == "Single Static"',
conditionalPanel(
condition = 'input.path2 != ""',
shinyjqui::jqui_resizable( plotOutput('GOFstaticPlot', width = "1000px", height = "700px"))
)),
conditionalPanel(
condition = 'input.radioGOF == "Multiple Static"',
shinyjqui::jqui_resizable(plotOutput('multiGOFplot', width = "1000px", height = "700px"))
),
fluidRow(
div(style="display:inline-block; width: 100px;height: 75px;", textInput("nGOF", "Runs" )),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "covPrimGOF", label = "Prim.Cov", choices = "")),
div(style="display:inline-block; width: 150px;height: 75px;", checkboxInput(inputId = "colcov", label = "Col Cov", value = FALSE)),
div(style="display:inline-block; width: 300px;height: 75px;", textInput(inputId = "filterGOF", label = "Filter")),
div(style="display:inline-block; width: 150px;height: 75px;", checkboxInput(inputId = "remBLQGOF", label = "Remove BLQ", value = TRUE)),
div(style="display:inline-block; width: 300px;height: 75px;", actionButton(inputId = "updateGOF", label = "Update")),
div(style="display:inline-block; width: 150px;height: 75px;", textInput(inputId = "SelectGOF", label = "SelectGOF")),
div(style="display:inline-block; width: 150px;height: 75px;", checkboxInput(inputId = "gofxlog", label = "xlog", value = TRUE)),
div(style="display:inline-block; width: 150px;height: 75px;", checkboxInput(inputId = "gofylog", label = "ylog", value = TRUE)),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "gofmethods", label = "method smooth",choices = c("auto", "none", "lm", "glm", "gam", "loess"), selected = "auto")),
div(style="display:inline-block; width: 150px;height: 75px;", textInput(inputId = "goftitle", label = "Title"))
),
fluidRow(
div(style="display:inline-block; width: 150px;height: 75px;", actionButton("saveGOF", "Save plot")),
div(style="display:inline-block; width: 800px;height: 75px;", textInput("commGOF", "Commentary (new line with three spaces)" ))
),
conditionalPanel(
condition = 'input.path2 != ""',
tableOutput("covGOF")
),
div(style="display:inline-block; width: 150px;height: 75px;", textInput(inputId = "SelectmultiGOF", label = "Filter table below")),
radioButtons(inputId = "ArrangeGOF", label = "", choices = c( "name", "run", "COV"), inline = T),
conditionalPanel(
condition = 'input.path2 != ""',
tableOutput("multiGOF")
)
),
# covariate ---------------------------------------------------------------
tabItem( tabName = "covariate",
conditionalPanel(
condition = 'input.path2 != ""',
shinyjqui::jqui_resizable( plotOutput("multiBox", width = "1000px", height = "600px"))
),
fluidRow(
div(style="display:inline-block; width: 100px;height: 75px;", textInput("nBoxPlots", "Runs" )),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "covPrimBP2", label = "Prim.Cov", choices = "None")),
div(style="display:inline-block; width: 150px;height: 75px;", checkboxInput(inputId = "pointBP2", label = "Points", value = FALSE)),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "boxplottest", label = "Pvalue test",choices = c("t.test", "wilcox.test", "anova", "kruskal.test" ), selected = "anova"))
# div(style="display:inline-block; width: 150px;height: 75px;", checkboxInput(inputId = "dissociateBP2", label = "Dissociated", value = FALSE))
),
fluidRow(
div(style="display:inline-block; width: 150px;height: 75px;", actionButton("saveBP", "Save plot")),
div(style="display:inline-block; width: 800px;height: 75px;", textInput("commBP", "Commentary (new line with three spaces)" ))
),
conditionalPanel(
condition = 'input.path2 != ""',
tableOutput("covBP"))
,
conditionalPanel(
condition = 'input.path2 != ""',
tableOutput("table4"))
),
# matrix ------------------------------------------------------------------
tabItem( tabName = "matrix",
radioButtons(inputId = 'radioMatrix', label = "", choices = c("Single", "Multiple Run"), inline = T),
conditionalPanel(
condition = 'input.radioMatrix == "Multiple Run"',
shinyjqui::jqui_resizable(plotOutput("matrixMultiPlot", width = "1000px", height = "600px"))
),
conditionalPanel(
condition = 'input.radioMatrix == "Single"',
conditionalPanel(
condition = 'input.path2 != ""',
shinyjqui::jqui_resizable(plotOutput("matrix", width = "1000px", height = "600px"))
)
),
fluidRow(
div(style="display:inline-block; width: 100px;height: 75px;", textInput("nmatrix", "Runs" )),
div(style="display:inline-block; width: 100px;height: 75px;", textInput("matrixfilter", "Filter" )),
div(style="display:inline-block; width: 150px;height: 75px;", radioButtons(inputId = "ArrangeMatrix", label = "", choices = c( "name", "run"), inline = T))
# div(style="display:inline-block; width: 150px;height: 75px;", checkboxInput(inputId = "pointBP2", label = "Points", value = FALSE))
# div(style="display:inline-block; width: 150px;height: 75px;", checkboxInput(inputId = "dissociateBP2", label = "Dissociated", value = FALSE))
),
fluidRow(
div(style="display:inline-block; width: 150px;height: 75px;", actionButton("saveMATRIX", "Save plot")),
div(style="display:inline-block; width: 800px;height: 75px;", textInput("commMATRIX", "Commentary (new line with three spaces)" ))
),
# radioButtons(inputId = "ArrangeMatrix", label = "", choices = c("run", "COV", "name"), inline = T),
conditionalPanel(
condition = 'input.path2 != ""',
tableOutput("multiMatrix"))
# tableOutput("table4")
),
# ############################## ill #######################
tabItem( tabName = "iLL",
conditionalPanel(
condition = 'input.path2 != ""',
shinyjqui::jqui_resizable(plotOutput("iLL", width = "1000px", height = "600px"))
),
fluidRow(
div(style="display:inline-block; width: 100px;height: 75px;", textInput("niLL", "Runs" )),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "covPrimiLL", label = "Prim.Cov", choices = "None")),
# div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "covPrimBP2", label = "Prim.Cov", choices = "None")),
div(style="display:inline-block; width: 150px;height: 75px;", checkboxInput(inputId = "HistoiLL", label = "Histogram", value = FALSE))
# div(style="display:inline-block; width: 150px;height: 75px;", checkboxInput(inputId = "dissociateBP2", label = "Dissociated", value = FALSE))
),
fluidRow(
div(style="display:inline-block; width: 150px;height: 75px;", actionButton("saveILL", "Save plot")),
div(style="display:inline-block; width: 800px;height: 75px;", textInput("commILL", "Commentary (new line with three spaces)" ))
)
# tableOutput("table4")
),
# Manual plpot ------------------------------------------------------------
tabItem( tabName = "ManualFunc",
fluidRow(
# div(style="display:inline-block; width: 150px;height: 75px;", actionButton("saveSENS", "Save plot")),
div(style="display:inline-block; width: 800px;height: 75px;", textInput("fileManualPLot",label = "file",value = "D:/these/Pecc_test/3_Models/1_Models/pecc_func.R" )),
div(style="display:inline-block; width: 800px;height: 75px;", selectInput("selectManualFunction", label = "Function", choices = "wait")),
rHandsontableOutput("argManualFunction"),
div(style="display:inline-block; width: 800px;height: 75px;", actionButton("ManualPlotGo","Go !"))
),
shinyjqui::jqui_resizable( plotOutput("ManualPlotPlot", width = "900px", height = "900px"))
),
# ############################## sensititivity #######################
tabItem( tabName = "sensitivity",
conditionalPanel(
condition = 'input.path2 != ""',
tableOutput("table5")),
fluidRow(column(4, wellPanel(selectInput("parSens", "Parameter", choices = "")))),
fluidRow(
div(style="display:inline-block; width: 150px;height: 75px;", actionButton("saveSENS", "Save plot")),
div(style="display:inline-block; width: 800px;height: 75px;", textInput("commSENS", "Commentary (new line with three spaces)" ))
),
conditionalPanel(
condition = 'input.path2 != ""',
plotOutput("sensitivity", width = "1500px", height = "900px"))
),
# saved plot --------------------------------------------------------------
tabItem(tabName = "rapports",
tableOutput("savedPlotsTable"),
fluidRow(
div(style="display:inline-block; width: 150px;height: 75px;", actionButton("savedUpdate", "Update saved list")),
div(style="display:inline-block; width: 100px;height: 75px;", numericInput(inputId = "saved_n_to_display", label = "ID to display", value = 0)),
actionButton("pdfplots", "Export Saved Plots")
),
plotOutput("saved_displayed", width = "1000px", height = "600px")
),
# VPC perso---------------------------------------------------------------------
tabItem(tabName = "simulation",
fluidRow(
div(style="display:inline-block; width: 300px;height: 75px;", textInput("pathVPC", "Path of a dataset", value = "")),
div(style="display:inline-block; width: 50px;height: 75px;", selectInput("sepVPC", "Sep", choices = c("", ";", ".", ","), selected = "")),
div(style="display:inline-block; width: 50px;height: 75px;", selectInput("decVPC", "Dec", choices = c(".", ","), selected = ".")),
div(style="display:inline-block; width: 50px;height: 75px;", textInput("nastringVPC", "NA", value = "")),
div(style="display:inline-block; width: 50px;height: 75px;", checkboxInput(inputId = "headerVPC", label = "header", value = F))
),
fluidRow(
div(style="display:inline-block; width: 300px;height: 75px;", textInput("nameVPC", "Names of column", value = "")),
div(style="display:inline-block; width: 50px;height: 75px;", actionButton(inputId = "loadVPC", label = "load file"))
),
conditionalPanel(
condition = 'input.radioVPC == "Visual Predicted Check"',
plotOutput("VPCPlot", width = "800px", height = "700px")),
conditionalPanel(
condition = 'input.radioVPC == "Prediction Distributions"',
plotOutput("PDPlot", width = "800px", height = "700px")),
div(style="display:inline-block; width: 500px;height: 75px;", radioButtons(inline = T , inputId = 'radioVPC', label = "", choices = c("Visual Predicted Check", "Prediction Distributions"))),
fluidRow(
div(style="display:inline-block; width: 300px;height: 75px;", textInput("filterrVPC", "Filter", value = "")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "VPCX", label = "X", choices = "")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "VPCY", label = "Y", choices = "")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "VPCsim", label = "sim", choices = "")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "VPCobs", label = "obs", choices = "")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "VPCtype", label = "type", choices = c("Conf Int VPC" = "CI", "scatter VPC" = "scatter"))),
div(style="display:inline-block; width: 150px;height: 75px;", textInput("VPCquantile", "Quantiles", value = "5 50 95")),
div(style="display:inline-block; width: 150px;height: 75px;", numericInput(inputId = "VPCCIpct", label = "Confidence Intervale", value = 5, min = 0, max = 49, step = 1)),
# div(style="display:inline-block; width: 150px;height: 75px;", numericInput(inputId = "VPCLine", label = "Line-Alpha", value = 1, min = 0, max = 1, step = 0.1)),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "VPCCOV", label = "Covariate", choices = "", multiple = T)),
# div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = "VPCXlog", label = "Xlog", value = FALSE)),
div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = "VPCYlog", label = "Ylog", value = TRUE)),
# div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = "VPCMedian", label = "Median", value = FALSE)),
# div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = "VPCNA", label = "Remove NA", value = FALSE)),
div(style="display:inline-block; width: 150px;height: 75px;", numericInput(inputId = "VPCLOQ", label = "LOQ obs", value = 0, step = 1)),
div(style="display:inline-block; width: 150px;height: 75px;", numericInput(inputId = "VPCYMIN", label = "ymin", value = 0, step = 1)),
div(style="display:inline-block; width: 150px;height: 75px;", textInput("VPCxlabel", "xlabel", value = "Time")),
div(style="display:inline-block; width: 150px;height: 75px;", textInput("VPCylabel", "ylabel", value = "Concentration")),
div(style="display:inline-block; width: 150px;height: 75px;", numericInput(inputId = "VPCsizeText", label = "Text size", value = 20, step = 1)),
div(style="display:inline-block; width: 50px;height: 75px;", actionButton(inputId = "launchVPC", label = "create VPC"))
)
),
# forest ------------------------------------------------------------------
tabItem(tabName = "forestPlot",
fluidRow(
div(style="display:inline-block; width: 100px;height: 75px;", textInput("nForest", "Runs" )),
div(style="display:inline-block; width: 100px;height: 75px;", actionButton("mb_load_forest_run", "Prefill w run")),
div(style="display:inline-block; width: 100px;height: 75px;", actionButton("mb_add_forest", "Add line")),
div(style="display:inline-block; width: 100px;height: 75px;", actionButton("mb_delete_forestt", "Delete line")),
div(style="display:inline-block; width: 150px;height: 75px;", actionButton(inputId = "forest_go", label = "Go"))
),
rHandsontableOutput("table_forest"),
shinyjqui::jqui_resizable(plotOutput("forestPlot", width = "1000px", height = "700px")),
box(width = 1000,
textAreaInput(inputId = "codeforestpec", label = "Short Peccary Code ", height = 100,width = 1000),
textAreaInput(inputId = "codeforest", label = "Peccary Independant Code", height = 300,width = 1000),
title = "R code", collapsible = T, collapsed = T)
),
# VPC package---------------------------------------------------------------------
tabItem(tabName = "vpc_pckg",
plotOutput("vpc_pckg_plot", width = "700px", height = "700px"),
box(collapsible = T, collapsed = F,width = 12,
div(style="display:inline-block; width: 400px;height: 75px;", textInput(inputId = "vpc_pckg_simdata", label = "Path sim")),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "vpc_pckg_simdata_ID", label = "ID", choices = c(""), selected = "")),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "vpc_pckg_simdata_REP", label = "REP", choices = c(""), selected = "")),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "vpc_pckg_simdata_TIME", label = "TIME", choices = c(""), selected = "")),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "vpc_pckg_simdata_PRED", label = "PRED", choices = c(""), selected = "")),
div(style="display:inline-block; width: 400px;height: 75px;", textInput(inputId = "vpc_pckg_obsdata", label = "Path obs")),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "vpc_pckg_obsdata_ID", label = "ID", choices = c(""), selected = "")),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "vpc_pckg_obsdata_TIME", label = "TIME", choices = c(""), selected = "")),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "vpc_pckg_obsdata_DV", label = "DV", choices = c(""), selected = "")),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "vpc_pckg_obsdata_MDV", label = "MDV", choices = c(""), selected = ""))
),
div(style="display:inline-block; width: 100px;height: 75px;", actionButton(inputId = "vpc_pckg_go", label = "create VPC")),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "vpc_pckg_bins", label = "Bins", choices = c("jenks", "density", "time", "data", "none", "pretty"), selected = "jenks")),
div(style="display:inline-block; width: 100px;height: 75px;", numericInput(inputId = "vpc_pckg_n_bins", label = "n_bins", value = 0)),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "vpc_pckg_bin_mid", label = "bin_mid", choices = c("mean", "middle"), selected = "mean")),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "vpc_pckg_software", label = "software", choices = c("auto", "nonmem", "phoenix"), selected = "auto")),
div(style="display:inline-block; width: 400px;height: 75px;", selectInput(inputId = "vpc_pckg_show", label = "show", choices = c("obs_dv", "obs_ci", "pi", "pi_as_area","pi_ci", "obs_median","sim_median","sim_median_ci" ), selected = c("obs_dv", "obs_ci", "pi_ci", "obs_median","sim_median_ci"), multiple = T)),
div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = "vpc_pckg_pred_corr", label = "pred_corr", value = F)),
div(style="display:inline-block; width: 150px;height: 75px;", numericInput(inputId = "vpc_pckg_pred_corr_lower_bnd", label = "pred_corr_lower_bnd",value = 0)),
div(style="display:inline-block; width: 100px;height: 75px;", numericInput(inputId = "vpc_pckg_pi_low", label = "pi_low",value = 0.05)),
div(style="display:inline-block; width: 100px;height: 75px;", numericInput(inputId = "vpc_pckg_pi_high", label = "pi_high",value = 0.95)),
div(style="display:inline-block; width: 100px;height: 75px;", numericInput(inputId = "vpc_pckg_ci_low", label = "ci_low",value = 0.05)),
div(style="display:inline-block; width: 100px;height: 75px;", numericInput(inputId = "vpc_pckg_ci_high", label = "ci_high",value = 0.95)),
div(style="display:inline-block; width: 100px;height: 75px;", numericInput(inputId = "vpc_pckg_uloq", label = "uloq",value = NA)),
div(style="display:inline-block; width: 100px;height: 75px;", numericInput(inputId = "vpc_pckg_lloq", label = "lloq",value = NA)),
div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = "vpc_pckg_log_y", label = "log_y", value = F)),
div(style="display:inline-block; width: 100px;height: 75px;", numericInput(inputId = "vpc_pckg_log_y_min", label = "log_y_min",value = 0.001)),
div(style="display:inline-block; width: 100px;height: 75px;", textInput(inputId = "vpc_pckg_xlab", label = "xlab")),
div(style="display:inline-block; width: 100px;height: 75px;", textInput(inputId = "vpc_pckg_ylab", label = "ylab")),
div(style="display:inline-block; width: 100px;height: 75px;", textInput(inputId = "vpc_pckg_title", label = "title")),
div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = "vpc_pckg_smooth", label = "smooth", value = T)),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "vpc_pckg_facet", label = "facet", choices = c("wrap", "columns", "rows"), selected = "wrap")),
textAreaInput(inputId = "vpc_pckg_code", label = "Code")
),
# Report ------------------------------------------------------------------
tabItem(tabName = "Report",
div(style="display:inline-block; width: 300px;height: 75px;", selectInput(inputId = "reportVersion", label = "Report Version", choices = c(""), selected = "")),
div(style="display:inline-block; width: 75px;height: 75px;", actionButton(inputId = "reportLoad", label = "Load")),
div(style="display:inline-block; width: 300px;height: 75px;", textInput(inputId = "reportnewVersion", label = "Name")),
div(style="display:inline-block; width: 75px;height: 75px;", actionButton(inputId = "reportSave", label = "Save")),
box(title = "Prototype", collapsible = T, collapsed = T,width = 12,
div(style="display:inline-block; width: 400px;height: 75px;", textInput(inputId = "reportTemplatePath", label = "Prototype File", value = "D:/Peccary/inst/Report/templateReport.txt")),
div(style="display:inline-block; width: 200px;height: 75px;", actionButton(inputId = "reportTemplateLaunch", label = "Load Template"))
),
box(title = "Free introduction", collapsible = T, collapsed = T,width = 12,
textAreaInput(inputId = "Report_introduction", label = "Introduction")
),
box(title = "Project Presentation / Bibliographie", collapsible = T, collapsed = T,width = 12,
# div(style="display:inline-block; width: 600px;height: 100px;", selectInput(inputId = "reportDatasetInfo", label = "Info on", choices = c(""), selected = "", multiple = T)),
textAreaInput(inputId = "Report_biblio", label = "Project Presentation")
),
box(title = "Dataset information", collapsible = T, collapsed = T,width = 12,
div(style="display:inline-block; width: 600px;height: 100px;", selectInput(inputId = "reportDatasetInfo", label = "Info on", choices = c(""), selected = "", multiple = T)),
textAreaInput(inputId = "Report_dataset", label = "Dataset information")
),
box(title = "Pre-modeling", collapsible = T, collapsed = T,width = 12,
div(style="display:inline-block; width: 600px;height: 100px;", selectInput(inputId = "reportDataExploSelect", label = "DataExplo", choices = c(""), selected = "", multiple = T)),
div(style="display:inline-block; width: 600px;height: 100px;", selectInput(inputId = "reportPlotExploSelect", label = "PlotExplo", choices = c(""), selected = "", multiple = T)),
textAreaInput(inputId = "Report_premodeling", label = "Output")
),
box(title = "Modeling", collapsible = T, collapsed = T,width = 12,
div(style="display:inline-block; width: 400px;height: 100px;", selectInput(inputId = "reportModelEq", label = "model", choices = c(""), selected = "", multiple = T)),
textAreaInput(inputId = "Report_modeling", label = "Output")
),
box(title = "Final run", collapsible = T, collapsed = T,width = 12,
div(style="display:inline-block; width: 600px;height: 100px;", textInput(inputId = "reportRunfinalpat", label = "Run final", value = "")),
textAreaInput(inputId = "Report_run", label = "Output")
),
box(title = "Simulation", collapsible = T, collapsed = T,width = 12,
div(style="display:inline-block; width: 400px;height: 100px;", selectInput(inputId = "reportModelSimul", label = "model", choices = c(""), selected = "", multiple = T)),
textAreaInput(inputId = "Report_simulation", label = "Output")
),
box(title = "Export report", background="blue", collapsible = T, collapsed = T,width = 12,
div(style="display:inline-block; width: 300px;height: 100px;", textInput(inputId = "exportReportPath", label = "Output path", value = "D:/Peccary/Exemple_demo/report/demo")),
div(style="display:inline-block; width: 75px;height: 100px;", selectInput(inputId = "exportReportFormat", label = "Format", choices = c("word", "html", "pdf"), selected = "word", multiple = F)),
div(style="display:inline-block; width: 200px;height: 75px;", actionButton(inputId = "exportReportGo", label = "Load Template")),
box(title = "Options", collapsible = T, background="blue", collapsed = T,
div(style="display:inline-block; width: 150px;height: 75px;", textInput(inputId = "exportReportTitle", label = "Title", value = "UCART19")),
div(style="display:inline-block; width: 150px;height: 75px;", textInput(inputId = "exportReportAuthor", label = "Author", value = "Thibaud Derippe")),
div(style="display:inline-block; width: 150px;height: 75px;", textInput(inputId = "exportReportBibPath", label = "Bib path (optional)", value = "D:/Peccary/Exemple_demo/report/These_Peccary.bib")),
div(style="display:inline-block; width: 150px;height: 75px;", textInput(inputId = "exportReportCSLPath", label = "CSL path (optional)", value = "D:/Peccary/Exemple_demo/report/elsevier-vancouver.csl"))
)
)
),
# Authors ------------------------------------------------------------------
tabItem(tabName = "Authors",
h2("Authors", align = "center"),
br("Peccary aims to be a collaborative project where anyone can add or modify functionnalities."),
h3("List of all Peccary contributors (alphabetical order)"),
br(""),
br(HTML("<b><u>Aziz Ouerdani</b></u>: improved 3SetReplace_NONMEM_Run.R file")),
br(HTML("<b><u>Blaise Pasquiers</b></u>: provide lots of feedback and improvement thoughts")),
br(HTML("<b><u>Christelle Rodrigues</b></u>: wrote indiv_plot_christelle.R (additional function)")),
br(HTML("<b><u>Thibaud Derippe</b></u>: designed and wrote the first Peccary version (more than 50 files, including the Shiny App)")),
br(""),
br("")
)
), map(unique(gsub("(_serv)|(_ui)|(\\.R)", "", list.files("D:/Peccary/inst/Module"))), function(x){
eval(parse_expr(paste(readLines(file.path("D:/Peccary/inst/Module", paste0(x,"_ui.R"))), collapse = "")))
#
# print(class(eval(parse_expr(paste0(x,"_ui")))))
# return(eval(parse_expr(paste0(x,"_ui"))))
}))
)
# tabItems(
# Project load/creation ---------------------------------------------------
# for(a in unique(gsub("(_serv)|(_ui)|(\\.R)", "", list.files("D:/Peccary/inst/Module")))){
#
# eval(parse_expr(paste(readLines(file.path("D:/Peccary/inst/Module", paste0(a,"_ui.R"))), collapse = "")))
#
# }
# eval(map(unique(gsub("(_serv)|(_ui)|(\\.R)", "", list.files("D:/Peccary/inst/Module"))), function(x){
#
# parse_expr(paste(readLines(file.path("D:/Peccary/inst/Module", paste0(x,"_ui.R"))), collapse = ""))
# #
# # print(class(eval(parse_expr(paste0(x,"_ui")))))
# # return(eval(parse_expr(paste0(x,"_ui"))))
# })[[1]])
### don't touch
# )## end tab items
)
)
}
go <- function() shinyApp(pecc_ui_reunif, pecc_server_reunif_test)
#' @export
peccary_app3 <- function(){
rm(InfoModelPecc, envir = global_env())
shinyApp(pecc_ui_reunif(), pecc_server_reunif)
}
Peccary-PMX/Peccary documentation built on Jan. 17, 2024, 9:27 p.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions peccary_app3 go pecc_ui_reunif
# library(shiny)
# library(shinydashboard)
#
#' @export
pecc_ui_reunif <- function(){dashboardPage(
# Header ------------------------------------------------------------------
dashboardHeader(title = "Peccary",
dropdownMenuOutput(outputId = "messages")
),
# Sidebar -----------------------------------------------------------------
dashboardSidebar(
sidebarMenu(
style = "overflow: visible",
menuItem("Project", tabName = "Welcome", icon = icon("Project")
# menuSubItem("Project", tabName = "", icon = icon("dashboard")),
),
menuItem("Pre-modelisation", icon = icon("bacon"), tabName = "Pre-modelisation",
menuSubItem("Datasets", tabName = "Datasets", icon = icon("dashboard")),
menuSubItem("Dataset explo", tabName = "datasetExplo", icon = icon("dashboard")),
menuSubItem("Graphical exploration", tabName = "graph", icon = icon("dashboard")),
menuSubItem("NCA", tabName = "NCA", icon = icon("dashboard")),
# menuSubItem("PKNCA", tabName = "PKNCA", icon = icon("dashboard")),
selectInput(inputId = "preloadeddataset", label = "Preloaded dataset", choices = c("Use external")),
# textInput("pathExplo", "Path of a dataset", value = ""),
textAreaInput("filterrExplo", "Filter", value = ""),
selectInput(inputId = "exploX", label = "X", choices = ""),
selectInput(inputId = "exploY", label = "Y", choices = "")
# actionButton("loadExplo", "Load"),
),
menuItem("Model building ", icon = icon("deSolve"), tabName = "deSolve"),
# menuItem("Run manager ", icon = icon("deSolve"), tabName = "runmanager"),
menuItem("Models analysis",icon = icon("deSolve"), tabName = "modelAnalysis",
textInput("path2", "Path to folder", value = "D:/Peccary/Exemple_demo"),
actionButton("folderupdate", "Go"),
selectInput(inputId = "subPath",multiple = F, label = "subPath", choices = "Root", selected = "subF"),
textInput("number", "Runs" ),
menuSubItem("Folder", tabName = "folder", icon = icon("dashboard")),
menuSubItem("Preds", tabName = "prediction", icon = icon("dashboard")),
menuSubItem("GOF", tabName = "GOF", icon = icon("dashboard")),
menuSubItem("Covariate", tabName = "covariate", icon = icon("dashboard")),
menuSubItem("Matrix", tabName = "matrix", icon = icon("dashboard")),
menuSubItem("iLL", tabName = "iLL", icon = icon("dashboard")),
menuSubItem("Sensitivity", tabName = "sensitivity", icon = icon("dashboard")),
menuSubItem("Forest", tabName = "forestPlot", icon = icon("dashboard")),
menuSubItem("VPC", tabName = "simulation", icon = icon("dashboard")),
menuSubItem("Plot saved", tabName = "rapports" , icon = icon("dashboard")),
actionButton("allplotbutton", "AllPlots"),
textInput(inputId = "gofunits_obs", label = "units obs"),
textInput(inputId = "gofunits_time", label = "units time"),
radioButtons("variable", "CovPrim:",
choices = "none"
# c( "none" = "none",
# "PRED" = "pred",
# "GOF" = "GOF",
# "RE_Boxplot" = "box",
# "RE_matrix" = "matrix")
),
radioButtons("variable2", "CovSec:",
choices = "none"
# c( "none" = "none",
# "PRED" = "pred",
# "GOF" = "GOF",
# "RE_Boxplot" = "box",
# "RE_matrix" = "matrix")
)
),
menuItem("Manual", tabName = "ManualFunc", icon = icon("deSolve")),
menuItem("vpc_pckg", tabName = "vpc_pckg", icon = icon("deSolve")),
menuItem("Report", tabName = "Report", icon = icon("deSolve")),
map(unique(gsub("(_serv)|(_ui)|(\\.R)", "", list.files("D:/Peccary/inst/Module"))), function(x){
menuItem(x, tabName = x, icon = icon("deSolve"))
}),
menuItem("Authors", tabName = "Authors", icon = icon("deSolve"))
)
),
dashboardBody(
useShinyjs(),
do.call(tabItems, append(list(
tabItem(tabName = "Welcome",
h2("Welcome to Peccary !", align = "center"),
br("With Peccary, pharmacometrics becomes simpler and faster"),
br("For tutorials, you can find:"),
"+", tags$a(href="https://github.com/Peccary-PMX/Peccary/releases/download/Doc/Peccary_Documentation.html", "a html document (click to download)", target="_blank" ),
br(),
"+", tags$a(href = "https://www.youtube.com/watch?v=d77c4v2_jcw", "Youtube videos (click to open)"),
h3("Load Project"),
br("First, do you have a Peccary project you want to load?"),
br(""),
selectInput(inputId = "recentprojectfile", label = "Previous Project", width ="800", choices = c("No Previous Project Available")),
actionButton("getpathProjectexisting", "or click to find a project file"),
br(""),
textInput(inputId = "Project_file", label = "Path to Project File", width = "800", value = ""),
br(""),
actionButton(inputId = "Project_load", label = "Load project"),
br("(if you want to change the loaded project, it is safier to restart Peccary Shiny App first)"),
br(""),
h3("Create Project"),
br("Otherwise, do you want to create one?"),
br(""),
actionButton("getpathProject", "click to find a path"),
textInput(inputId = "Project_file_create", label = "Set where to put the project", width = "800", value = "file:///D:/these/demo"),
# br("Do you want to create a complete project folder with subfolders? It will help you to store your files"),
# checkboxInput(inputId = "creation_folder_cb", label = "Yes, create folders and subfolders", value = T),
br("Click on the button below and let's start !"),
br(""),
actionButton(inputId = "Project_create", label = "Create project")
),
# Datasets handling -------------------------------------------------------
tabItem(tabName = "Datasets",
h2("Datasets Loading", align = "center"),
h3("Dataset loading and input settings"),
br("Here is the place where you can store your data files, make graphical exploration, NCA analysis and pre-modelling work !"),
br("First, let's look at wich data are available: "),
rHandsontableOutput(outputId = "datasets"),
br("If there is no data files, you can first try to upload the one in the 1_DATA folder "),
br(""),
actionButton(inputId = "load_data_folders", label = "Try automatic loading"),
br(""),
br("Otherwise, you can add manually a file or just temporary use:"),
br(""),
actionButton("getpathDataset", "click to find a path"),
textInput(inputId = "path_dataset_manual", label = "Add path to a dataset", width = "800"),
fluidRow(
div(style="display:inline-block; width: 100px;height: 75px;", selectInput("sepExplo", "Sep", choices = c("Space" = "", ";", ".", ","), selected = "Space")),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput("decExplo", "Dec", choices = c(".", ","), selected = ".")),
div(style="display:inline-block; width: 100px;height: 75px;", textInput("nastringExplo", "NA", value = ".")),
div(style="display:inline-block; width: 100px;height: 75px;", actionButton("addDataset", label = "add"))
),
br(""),
numericInput(inputId = "dataset_default", label = "Choose which dataset you want to open by default", value = 1),
br(""),
br("After additions, please make sure to save them"),
actionButton(inputId = "save_datasets", label = "Save modifications"),
h3("Dataset informations (column header)"),
br("here, you can simply fill the informations on the table above"),
fluidRow(
div(style="display:inline-block; width: 100px;height: 75px;", numericInput(inputId = "quicklookn", label = "Number of the dataset", value = 0, min = 0)),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "quicklooksep", label = "sep", choices = c("", " ", ";", ",", "."), selected = ";")),
div(style="display:inline-block; width: 100px;height: 75px;",selectInput(inputId = "quicklookdec", label = "dec", choices = c(""," ", ";", ",","."), selected = ".")),
div(style="display:inline-block; width: 100px;height: 75px;", textInput(inputId = "quicklookna", label = "na_string", value = ".")),
div(style="display:inline-block; width: 100px;height: 75px;", textInput(inputId = "quicklookx", label = "x", value = "")),
div(style="display:inline-block; width: 100px;height: 75px;",textInput(inputId = "quicklookxlabel", label = "x label", value = "")),
div(style="display:inline-block; width: 100px;height: 75px;",textInput(inputId = "quicklooky", label = "y", value = "")),
div(style="display:inline-block; width: 100px;height: 75px;",textInput(inputId = "quicklookylabel", label = "y label", value = "")),
div(style="display:inline-block; width: 400px;height: 75px;",textInput(inputId = "quicklookcomment", label = "comment", value = ".")),
# div(style="display:inline-block; width: 100px;height: 75px;",actionButton(inputId = "quicklookload", label = "load")),
div(style="display:inline-block; width: 100px;height: 75px;",actionButton(inputId = "quicklooksave", label = "Import"))
# div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "colourPred2", label = "COV", choices = "None"))
),
fluidRow(
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "IDheader", label = "ID", choices = c(""), selected = "")),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "IDheader2", label = "TIME", choices = c(""), selected = "")),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "OBSheader", label = "OBS", choices = c(""), selected = "")),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "AMTheader", label = "AMT", choices = c(""), selected = "")),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "ADMheader", label = "ADM", choices = c(""), selected = "")),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "RATEheader", label = "RATE", choices = c(""), selected = "")),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "EVIDheader", label = "EVID", choices = c(""), selected = "")),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "MDVheader", label = "MDV", choices = c(""), selected = "")),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "YTYPEheader", label = "YTYPE", choices = c(""), selected = "")),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "COVCONTheader", label = "cov.cont", choices = c(""), selected = "")),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "COVCATheader", label = "cov.cat", choices = c(""), selected = ""))
)
# selectInput(inputID = "headerEVID", label = "EVID"),
# selectInput(inputID = "headerMDV", label = "MDV"),
# selectInput(inputID = "headerYTYPE", label = "YTYPE"),
# selectInput(inputID = "headerCOVCONT", label = "cov.cont"),
# selectInput(inputID = "headerCOVCAT", label = "cov.cat"),
# rHandsontableOutput(outputId = "defineheader", height = 200),
# DT::dataTableOutput(outputId = "quicklookTable")
),
tabItem(tabName = "widgets",
h2("Widgets tab content"),
fluidRow(
box(plotOutput("plot1", height = 250)),
box(
title = "Controls",
sliderInput("slider", "Number of observations:", 1, 100, 50)
)
)
),
# Dataset exploration ---------------------------------------------------
tabItem(tabName = "datasetExplo",
div(style="display:inline-block; width: 300px;height: 75px;", selectInput(inputId = "dataexploVersion", label = "Version", choices = c(""), selected = "")),
div(style="display:inline-block; width: 75px;height: 75px;", actionButton(inputId = "dataexploLoad", label = "Load")),
div(style="display:inline-block; width: 300px;height: 75px;", textInput(inputId = "dataexplonewVersion", label = "Name")),
div(style="display:inline-block; width: 75px;height: 75px;", actionButton(inputId = "dataexploSave", label = "Save")),
textInput(inputId = "filtertableexplo", label = "Exploratory filter", value = ""),
fluidRow(
column(4,
textAreaInput(inputId = "tableExploManipulation", label = "Free Manipulation (temp being loaded dataset)", resize = "both", height = 180),
),
column(1,
br(""),
actionButton(inputId = "storemodif", label = "Store modif"),
br(""),
actionButton(inputId = "copymodif", label = "Create file with modif"),
# br(""),
# actionButton(inputId = "overwrite", label = "Overwrite original ds")
)
),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "groupbyCovExplo", label = "Extract cov by", multiple = T, choices = "")),
# div(style="display:inline-block; width: 150px;height: 75px;", checkboxInput(inputId = "covreduceExplo", label = "Cov reduce", value = T)),
actionButton(inputId = "abtableexplo", label = "Go"),
dataTableOutput("tableexplo"),
box(title = "table1", collapsible = T, collapsed = F,width = 1000,
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "table1reduceBy", label = "Reduce by", multiple = T, choices = "All")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "table1x", label = "In rows", multiple = T, choices = "")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "table1y", label = "In col", multiple = T, choices = "")),
div(style="display:inline-block; width: 150px;height: 75px;", actionButton(inputId = "table1go", label = "Go")),
tableOutput(outputId = "table1output"),
box(title = "Code", collapsible = T, collapsed = T, width = 400,
textAreaInput(inputId = "table1_code",label = "Code", width = "100%", height = 40)
)
),
box(title = "Count", collapsible = T, collapsed = T,width = 1000,
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "countwhat", label = "Count what", multiple = F, choices = "")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "countx", label = "Row", multiple = F, choices = "")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "county", label = "Col", multiple = F, choices = "")),
div(style="display:inline-block; width: 150px;height: 75px;", actionButton(inputId = "countgo", label = "Go")),
textOutput(outputId = "countbytext"),
rHandsontableOutput(outputId = "countoutput"),
box(title = "Code", collapsible = T, collapsed = T, width = 400,
textAreaInput(inputId = "count_code",label = "Code", width = "100%")
)
),
box(title = "plot cov", collapsible = T, collapsed = T,width = 1000,
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "plotcov_x", label = "covariate 1", multiple = F, choices = "")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "plotcov_y", label = "covariate 2", multiple = F, choices = "")),
div(style="display:inline-block; width: 150px;height: 75px;", actionButton(inputId = "plotcov_go", label = "Go")),
shinyjqui::jqui_resizable(plotOutput("plotcovplot", width = "800px", height = "600px")),
box(title = "Code", collapsible = T, collapsed = T, width = 400,
textAreaInput(inputId = "plotcov_code",label = "Code", width = "100%")
)
)
# actionButton("loadexplo", label = "Start"),
# fluidRow(
#
# div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "groupbyExplo", label = "Group by", multiple = T, choices = "")),
# div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "tableexploselected",label = "Table2", choices = c("tally", "distinct"))),
# div(style="display:inline-block; width: 150px;height: 75px;", actionButton(inputId = "launchtableexplo2", label = "Load second table"))
# ),
# dataTableOutput("tableexplo2"),
# fluidRow(
#
# div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "groupbyExplo3", label = "Variable one", choices = "")),
# div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "tableexploselected3",label = "Table3", choices = c("percentage","table1","detail" ))),
# div(style="display:inline-block; width: 150px;height: 75px;", actionButton(inputId = "launchtableexplo3", label = "Load third table"))
# ),
# dataTableOutput("tableexplo3")
),
# graph dataset -----------------------------------------------------------
tabItem(tabName = "graph",
conditionalPanel(
condition = 'input.exploPlotly == false',
shinyjqui::jqui_resizable(plotOutput("exploPlot", width = "800px", height = "700px"))
),
conditionalPanel(
condition = 'input.exploPlotly == true',
shinyjqui::jqui_resizable( plotlyOutput("exploPlotly", width = "800px", height = "700px"))
),
box(
rHandsontableOutput(outputId = "PlotexplorationSaved"),
actionButton(inputId = "pdfPLotExplo", label = "Pdf export"),
title = "Plots saved", collapsible = T, collapsed = F),
fluidRow(
div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = "exploPlotly", label = "Plotly", value = FALSE)),
div(style="display:inline-block; width: 250px;height: 75px;", textInput("secondFilter", "second Filter", value = "")),
div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = "allbackground", label = "grey_all", value = FALSE)),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "exploCol", label = "Col", choices = "")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "exploID", label = "Group", choices = "")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "exploShape", label = "Shape", choices = "")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "exploLty", label = "Lty", choices = "")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "exploWrap", label = "Wrap", choices = "")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "exploGrid", label = "Grid", choices = "")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "exploStand", label = "Standardization", choices = "")),
div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = "exploXlog", label = "Xlog", value = FALSE)),
div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = "exploYlog", label = "Ylog", value = TRUE)),
div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = "exploMedian", label = "Median", value = FALSE)),
div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = "exploNA", label = "Remove NA", value = TRUE)),
div(style="display:inline-block; width: 150px;height: 75px;", numericInput(inputId = "exploLOQ", label = "LOQ", value = -1, step = 1)),
# div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = "all_bkgrd", label = "bkgd", value = FALSE)),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput("scaleExplo", "Wrap scale",selected = "free", choices = c("fixed", "free", "free_x", "free_y"))),
div(style="display:inline-block; width: 150px;height: 75px;", textInput(inputId = "plotexploname", label = "Name")),
div(style="display:inline-block; width: 150px;height: 75px;", actionButton(inputId = "plotexplosaveaction",label = "Save"))
),
box(width = 1000,
div(style="display:inline-block; width: 150px;height: 75px;", numericInput(inputId = "exploPoint", label = "Point-Alpha", value = 1, min = 0, max = 1, step = 0.1)),
div(style="display:inline-block; width: 150px;height: 75px;", numericInput(inputId = "exploLine", label = "Line-Alpha", value = 1, min = 0, max = 1, step = 0.1)),
div(style="display:inline-block; width: 150px;height: 75px;", numericInput(inputId = "all_bkgrdalpha", label = "bckgd_alpha", min = 0, max = 1 , value = 0.3, step = 0.1)),
div(style="display:inline-block; width: 150px;height: 75px;", textInput("titleExplo", "Title", value = "")),
div(style="display:inline-block; width: 150px;height: 75px;", textInput("subtitleExplo", "subtitle", value = "")),
div(style="display:inline-block; width: 150px;height: 75px;", textInput("xlabsExplo", "xlabs", value = "")),
div(style="display:inline-block; width: 150px;height: 75px;", textInput("ylabsExplo", "ylabs", value = "")),
div(style="display:inline-block; width: 150px;height: 75px;", textInput("captionExplo", "caption", value = "")),
div(style="display:inline-block; width: 150px;height: 75px;", textInput("colLabExplo", "colLab", value = "")),
div(style="display:inline-block; width: 150px;height: 75px;", textInput("colValuesExplo", "colValues", value = "")),
div(style="display:inline-block; width: 150px;height: 75px;", textInput("shapeLabExplo", "shapeLab", value = "")),
div(style="display:inline-block; width: 150px;height: 75px;", textInput("shapeValuesExplo", "shapeValues", value = "")),
div(style="display:inline-block; width: 150px;height: 75px;", textInput("ltyLabExplo", "ltyLab", value = "")),
div(style="display:inline-block; width: 150px;height: 75px;", textInput("ltyValuesExplo", "ltyValues", value = "")),
div(style="display:inline-block; width: 150px;height: 75px;", numericInput(inputId = "sizeTextExplo", label = "Size Text", value = 15, step = 1)),
div(style="display:inline-block; width: 150px;height: 75px;", actionButton(inputId = "addlineexplo",label = "addline")),
div(style="display:inline-block; width: 150px;height: 75px;", actionButton(inputId = "removelineexplo",label = "removelin")),
rHandsontableOutput(outputId = "addlinesexploration"),
title = "More control",
collapsible = T, collapsed = T),
box(width = 1000,
textAreaInput(inputId = "codeexplopec", label = "Short Peccary Code ", height = 100,width = 1000),
textAreaInput(inputId = "codeexplo", label = "Peccary Independant Code", height = 300,width = 1000),
title = "R code", collapsible = T, collapsed = T)
),
# NCA ---------------------------------------------------------------------
tabItem(tabName = "NCA",
shinyjqui::jqui_resizable(plotOutput("plotNCAcov", width = "800px", height = "600px")),
box(
rHandsontableOutput(outputId = "NCASaved"),
actionButton(inputId = "pdfNCA", label = "NCA export"),
title = "Plots saved", collapsible = T, collapsed = F),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "pckgNCA", label = "Software", choices = c("Peccary", "pknca") )),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "groupNCA", label = "Group", choices = "", multiple = T)),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "covNCA", label = "Cov", choices = "")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "blqNCA", label = "BLQ", choices = "")),
# div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "evidNCA", label = "EVID", choices = "")),
div(style="display:inline-block; width: 150px;height: 75px;", numericInput(inputId = "Nsignif", label = "Nsignif", value = 3, min = 0, step = 1)),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "nca_admin", label = "Admin option", choices = c("None", "IVbolus -> backextrapolation", "Other -> add observation = 0 at time = 0"))),
div(style="display:inline-block; width: 150px;height: 75px;", numericInput(inputId = "auc_0_x", label = "AUC_0_x", value = 0, min = 0, step = 1)),
div(style="display:inline-block; width: 150px;height: 75px;", checkboxInput(inputId = "nca_forcecat", label = "ForceBoxplot", value = F)),
div(style="display:inline-block; width: 150px;height: 75px;", checkboxInput(inputId = "nca_teststat", label = "TestStat", value = T)),
div(style="display:inline-block; width: 150px;height: 75px;", checkboxInput(inputId = "nca_bxpltpoint", label = "ShowBPpoints", value = T)),
div(style="display:inline-block; width: 150px;height: 75px;", checkboxInput(inputId = "nca_corCI", label = "ShowCI", value = F)),
div(style="display:inline-block; width: 150px;height: 75px;", checkboxInput(inputId = "nca_corregline", label = "ShowRegLine", value = T)),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "nca_method_box", label = "Stat boxplot", choices = c("wilcox.test","t.test", "anova", "kruskal.test") )),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "nca_method_corr", label = "Stat correlation", choices = c("spearman","pearson", "kendall") )),
div(style="display:inline-block; width: 150px;height: 75px;", checkboxInput(inputId = "nca_xlog", label = "xlog", value = F)),
div(style="display:inline-block; width: 150px;height: 75px;", checkboxInput(inputId = "nca_ylog", label = "ylog", value = T)),
div(style="display:inline-block; width: 150px;height: 75px;", textInput(inputId = "nca_unitx", label = "Unit x ", value = "")),
div(style="display:inline-block; width: 150px;height: 75px;", textInput(inputId = "nca_unity", label = "Unit y ", value = "")),
div(style="display:inline-block; width: 150px;height: 75px;", textInput(inputId = "nca_labelx", label = "Label x ", value = "")),
div(style="display:inline-block; width: 150px;height: 75px;", textInput(inputId = "nca_labely", label = "Label y ", value = "")),
div(style="display:inline-block; width: 150px;height: 75px;", textInput(inputId = "nca_tabletitle", label = "Title", value = "")),
div(style="display:inline-block; width: 150px;height: 75px;", textInput(inputId = "nca_name", label = "Name ", value = "")),
div(style="display:inline-block; width: 150px;height: 75px;", actionButton(inputId = "nca_save", label = "Save")),
br(""),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "pknca_dose", label = "PKNCA Dose", choices = names(Theoph), selected = "Dose")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "pknca_ADM", label = "PKNCA EVID", choices = names(Theoph), selected = "Dose")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "pknca_route", label = "PKNCA route", choices = c("extravascular", "IV bolus", "IV perf (rate)", "IV perf (time perf)"), selected = "intravascular")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "pknca_rateduration", label = "RateDuration", choices =names(Theoph), selected = "Dose")),
br(""),
# selectInput(inputId = "nca_table_display", label = "Table type", choices = c("Individuals", "Per cov")),
br(""),
box(id = "boxpkncaparam", title = "Option of PKNCA package", width = 12, collapsible = T, collapsed = T,
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "pknca_auc.method", label = "auc.method", choices = c("lin up/log down", "linear"), selected = "lin up/log down")),
div(style="display:inline-block; width: 150px;height: 75px;", numericInput(inputId = "pknca_adj.r.squared.factor", label = "adj.r.squared.factor",value = 0.0001)),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "pknca_max.missing", label = "max.missing",selected = "drop", choices = "drop")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "pknca_conc.na", label = "conc.na",choices = c("drop", "keep"), selected = "drop" )),
div(style="display:inline-block; width: 150px;height: 75px;", checkboxInput(inputId = "pknca_first.tmax", label = "first.tmax",value = T)),
div(style="display:inline-block; width: 150px;height: 75px;", checkboxInput(inputId = "pknca_allow.tmax.in.half.life", label = "allow.tmax.in.half.life",value = F)),
div(style="display:inline-block; width: 150px;height: 75px;", numericInput(inputId = "pknca_min.hl.points", label = "min.hl.points",value = 3)),
div(style="display:inline-block; width: 150px;height: 75px;", numericInput(inputId = "pknca_min.span.ratio", label = "min.span.ratio",value = 2)),
div(style="display:inline-block; width: 150px;height: 75px;", numericInput(inputId = "pknca_max.aucinf.pext", label = "max.aucinf.pext",value = 20)),
div(style="display:inline-block; width: 150px;height: 75px;", numericInput(inputId = "pknca_min.hl.r.squared", label = "min.hl.r.squared",value = 0.9)),
br(""),
# br("See https://cran.r-project.org/web/packages/PKNCA/vignettes/Options-for-Controlling-PKNCA.html for an explenation of these options"),s
tags$a(href="https://cran.r-project.org/web/packages/PKNCA/vignettes/Options-for-Controlling-PKNCA.html", "See https://cran.r-project.org/web/packages/PKNCA/vignettes/Options-for-Controlling-PKNCA.html for an explenation of these options")
),
br(""),
br(""),
h3("Individual Values"),
DT::dataTableOutput("tableNCA"),
h3("Stat per cov"),
tableOutput("tableNCA2"),
box(title = "Code", collapsible = T, collapsed = T, width = 400,
fluidRow(
# div(style="display:inline-block; width: 300px;height: 75px;", textInput(inputId = "nca_path_export", "Path to export", value = "")),
# div(style="display:inline-block; width: 200px;height: 75px;", selectInput("nca_to_export", "What to export", choices = c("Individuals", "Per cov", "Both"))),
# div(style="display:inline-block; width: 100px;height: 75px;", actionButton("nca_export_go", "Launch")),
textAreaInput(inputId = "nca_code_peccdep",label = "Short Code Peccary", width = "100%",height = 100),
textAreaInput(inputId = "nca_code_peccindep",label = "Peccary Independent Code", width = "100%",height = 500)
)
)
),
# Model building -------------------------------------------------------------
tabItem(tabName = "deSolve",
fluidRow(
# div(style="display:inline-block; width: 200px;height: 75px;", textInput(inputId = "path_models", "File of models", value = "D:/these/Pecc_test")),
div(style="display:inline-block; width: 400px;height: 75px;", selectInput(inputId = "names_model", "Model", choices = "")),
div(style="display:inline-block; width: 100px;height: 75px;", actionButton(inputId = "load_model", "Load")),
div(style="display:inline-block; width: 200px;height: 75px;", textInput(inputId = "name_model", "Name to Save")),
div(style="display:inline-block; width: 100px;height: 75px;", actionButton(inputId = "save_model", "Save"))
# div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = "helpmodel", "display model helper"))
),
# box(title = "Covariate equations", collapsible = T, collapsed = T, width = 400,
# conditionalPanel('input.helpmodel == true',
# box(id = "helperModel", title = "helperModel",
# textInput(inputId = "nameLibOutput", label = "Desired Name", value = "auto",width = "50%"),
# textInput(inputId = "targetLibOutput", label = "Namelinks", value = "auto",width = "50%"),
# )),
# rHandsontableOutput(outputId= "modelLibInput"),
fluidRow(
column(6,
textAreaInput("mb_model", "Write your model (_plot & _output)", value = "",width = "500", height = "500")
) ,
column(6,
selectInput(multiple = T, inputId = "modelLibInput", "Library-input", choices = c("a", "b")),
textAreaInput("mb_model_cov", "Opti. covariate equations", value = "",width = "200", height = "200")
)
),
# box(title = "Model Librairies", collapsible = T, collapsed = T, width = 400,
#
# fluidRow(
#
# ),
#
# textAreaInput("mb_model_helper", "Proposition", value = "")
#
# ),
fluidRow(
div(style="display:inline-block; width: 100px;height: 75px;", actionButton("mb_load_model", "Load Model")),
div(style="display:inline-block; width: 200px;height: 75px;", checkboxInput("mb_load_cov", label = "Use covariate", value = F)),
div(style="display:inline-block; width: 100px;height: 75px;", actionButton("mb_add_event", "Add event")),
div(style="display:inline-block; width: 100px;height: 75px;", actionButton("mb_delete_event", "Delete event"))
),
fluidRow(
div(style="display:inline-block; width: 200px;height: 200px;", rHandsontableOutput("mb_state", width = 200, height = 200)),
div(style="display:inline-block; width: 200px;height: 200px;", rHandsontableOutput("mb_paramater", width = 200, height = 200)),
div(style="display:inline-block; width: 200px;height: 200px;", rHandsontableOutput("mb_event", width = 200, height = 200))
),
fluidRow(
div(style="display:inline-block; width: 520px;height: 200px;",rHandsontableOutput("mb_matrix", width = 500, height = 200)),
div(style="display:inline-block; width: 200px;height: 200px;", rHandsontableOutput("mb_output", width = 200, height = 200))
),
# div(style="display:inline-block; width: 150px;height: 75px;", actionButton("update_matrix", label = "update matrix")),
div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput("matrix_diag", label = "full matrix", value = T)),
div(style="display:inline-block; width: 200px;height: 75px;", selectInput("matrix_sd_var", label = "coded in", choices = c("sd", "var"), selected = "sd")),
div(style="display:inline-block; width: 100px;height: 75px;", actionButton("mb_output_add", label = "add output")),
div(style="display:inline-block; width: 150px;height: 75px;", actionButton("mb_output_remv", label = "remove output")),
div(style="display:inline-block; width: 200px;height: 75px;", selectInput("IDImpMod", "Id", choices = "Initial")),
div(style="display:inline-block; width: 300px;height: 75px;", checkboxInput("useImpData", "use imported data", value = F)),
# Import model -------------------------------------------------------------
#
# box(title = "Import model", collapsible = T, collapsed = T, width = 400,
#
# fluidRow(
# # div(style="display:inline-block; width: 300px;height: 75px;", textInput(inputId = "pathImpMod", "Path to the model", value = "file:///D:/these/Pecc_test/3_Models/1_Models/000_20_04_03/model_base.mlxtran")),
#
# # div(style="display:inline-block; width: 100px;height: 75px;", actionButton("launchImpMod", "Launch")),
# # div(style="display:inline-block; width: 100px;height: 75px;", actionButton("pdfImpData", "Launch pdf")),
# # div(style="display:inline-block; width: 100px;height: 75px;", actionButton("pdfImpData2", "Launch pdf"))
# # actionButton("mb_add_plot", "Add Plot"),
# # actionButton("mb_load_plot", "Load Plot"),
# # actionButton("mb_delete_plot", "Delete Plot"),
# # checkboxInput("mb_matrix_display", label = "Simulations", value = F)
# )
#
# ),
# plot & simulation -------------------------------------------------------
box(title = "Plot & Simulations", collapsible = T, collapsed = F, width = 400,
fluidRow(
# div(style="display:inline-block; width: 300px;height: 75px;", checkboxGroupInput("mb_display", "Plot-to-display", inline = T, choices = c(""))),
div(style="display:inline-block; width: 500px;height: 200px;", rHandsontableOutput("mb_display2", width = 300, height = 100)),
div(style="display:inline-block; width: 400px;height: 200px;", rHandsontableOutput("mb_plot_stat", width = 400, height = 100))
# div(style="display:inline-block; width: 50px;height: 75px;", checkboxInput(inputId = "mb_ylog", label = "y log", value = F)),
# div(style="display:inline-block; width: 50px;height: 75px;", checkboxInput(inputId = "mb_wrap", label = "Wrap", value = F))
# div(style="display:inline-block; width: 200px;height: 75px;", checkboxInput(inputId = "mb_add_point", label = "Add points explo", value = F))
),
fluidRow(
div(style="display:inline-block; width: 80px;", numericInput("mb_time_from", value = 0,label = "From")),
div(style="display:inline-block; width: 80px;", numericInput("mb_time_to", value = 100,label = "To")),
div(style="display:inline-block; width: 80px;", numericInput("mb_time_by", value = 1,label = "By")),
div(style="display:inline-block; width: 80px;", numericInput(inputId = "mb_nsimul", label = "N simul", value = 0)),
div(style="display:inline-block; width: 80px;", numericInput(inputId = "mb_minvaluesimul", label = "min value", value = 0)),
div(style="display:inline-block; width: 80px;", numericInput(inputId = "mb_maxvaluesimul", label = "max value", value = NA)),
div(style="display:inline-block; width: 80px;", selectInput("mb_ode_solver", "ODE solver", choices = c("deSolve", "RxODE"), selected = "RxODE", width = "80px")),
actionButton("mb_add_plot", "Add Plot"),
actionButton("mb_load_plot", "Load Plot"),
actionButton("mb_delete_plot", "Delete Plot"),
actionButton("mb_estimatePopParam", "Try estimation"),
checkboxInput("mb_add_error_plot", label = "Include error", value = F)
),
shinyjqui::jqui_resizable(plotOutput("mb_plot", width = "900px", height = "700px")),
box(textAreaInput(inputId = "Code_plot_sim", label = "", width = 500,height = 800, resize = "none"),title = "Code", collapsible = T, collapsed = T, width = 400)
),
# optimal design ----------------------------------------------------------
box(title = "Optimal Design", collapsible = T, collapsed = T, width = 1200,
fluidRow(
# div(style="display:inline-block; width: 300px;height: 200px;", textInput("samplingTime", label = "Sampling")),
div(style="display:inline-block; width: 1200px;height: 200px;",rHandsontableOutput("OD_sampling", width = 1200, height = 200)),
div(style="display:inline-block; width: 150px;height: 200px;", actionButton("OptimDesign_add", "Add line")),
div(style="display:inline-block; width: 150px;height: 200px;", actionButton("OptimDesign_delete", "Delete line")),
div(style="display:inline-block; width: 150px;height: 200px;", actionButton("OptimDesign", "Eval design"))
),
plotOutput("OptimPlot", width = "400px", height = "300px"),
textAreaInput(inputId = "Result_Optimal_Design", label = "", width = 500,height = 300, resize = "none"),
box(textAreaInput(inputId = "Code_Optimal_Design", label = "", width = 500,height = 300, resize = "none"),title = "Code", collapsible = T, collapsed = T, width = 400)
),
# Scheme model ------------------------------------------------------------
box(title = "Scheme of the model", collapsible = T, collapsed = T, width = 1200,
fluidRow(
# div(style="display:inline-block; width: 300px;height: 200px;", textInput("samplingTime", label = "Sampling")),
# div(style="display:inline-block; width: 1200px;height: 200px;",rHandsontableOutput("OD_sampling", width = 1200, height = 200)),
# div(style="display:inline-block; width: 150px;height: 200px;", actionButton("OptimDesign_add", "Add line")),
div(style="display:inline-block; width: 150px;height: 200px;", numericInput(inputId = "scheme_size", label = "Size", value = 0.9, min = 0, max = 1, step = 0.1)),
div(style="display:inline-block; width: 150px;height: 200px;", actionButton("scheme_launch", "Go"))
),
shinyjqui::jqui_resizable(plotOutput("scheme_plot", width = "1000px", height = "800px"))
# plotOutput("OptimPlot", width = "400px", height = "300px"),
# textAreaInput(inputId = "Result_Optimal_Design", label = "", width = 500,height = 300, resize = "none"),
# box(textAreaInput(inputId = "Code_Optimal_Design", label = "", width = 500,height = 300, resize = "none"),title = "Code", collapsible = T, collapsed = T, width = 400)
),
# nlmixr ------------------------------------------------------------------
box(title = "nlmixr", collapsible = T, collapsed = T, width = 400,
div(style="display:inline-block; width: 80px;", selectInput("nlmixr_methods", "methods", choices = c("saem", "focei", "nlme"), selected = "saem", width = "80px")),
div(style="display:inline-block; width: 50px;height: 75px;", actionButton("nlmixr_translate", "Generate code")),
textAreaInput("nlmixr_result",label = "", height = 500),
div(style="display:inline-block; width: 200px;height: 75px;", textInput(inputId = "nlmixr_path", "Path_to_save", value = "D:/Peccary_Annexe/Exemple_demo/nlmixr_test")),
# div(style="display:inline-block; width: 400px;height: 75px;", textInput("nlmixr_path", label = "Path", value = "D:/Peccary/Exemple_demo/saemix_test")),
div(style="display:inline-block; width: 100px;height: 75px;", actionButton("nlmixr_go", "Estimate"))
),
# monolix launcher --------------------------------------------------------
box(title = "Monolix", collapsible = T, collapsed = T, width = 400,
div(style="display:inline-block; width: 200px;height: 75px;", actionButton("ode_modelsave_monolix", "Generate Mlxtran")),
div(style="display:inline-block; width: 200px;height: 75px;", textInput("ode_projectpath_monolix", label = "Monolix project path", value = "")),
div(style="display:inline-block; width: 200px;height: 75px;", actionButton("launch_monolix", label = "Launch Monolix")),
div(style="display:inline-block; width: 400px;height: 75px;", textInput("monolix_filter", label = "Additional Filter", value = "")),
div(style="display:inline-block; width: 400px;height: 75px;", textInput("monolix_description", label = "Additional Filter", value = "")),
tabBox(
title = "Monolix launcher",
# The id lets us use input$tabset1 on the server to find the current tab
id = "tabset1", height = "750px",
tabPanel("Model file",
actionButton("ode_trigger_monolix", "Launch ode translation"),
textAreaInput("ode_output", "Model", value = "", width = "400", height = "500" ) # , div(style="display:inline-block; width: 1000px;height: 700px;",
),
tabPanel("NMLXTRAN",
actionButton(inputId = "nmlxtran_launch", label = "launch"),
textAreaInput("nmlxtran_output", "Model", value = "", width = "400", height = "500" ))
)
),
# nonmem code -------------------------------------------------------------
box(title = "NONMEM", collapsible = T, collapsed = T, width = 400,
# div(style="display:inline-block; width: 250px;height: 75px;", selectInput("ode_input", "Exporte software",choices = c("NONMEM", "Monolix"), selected = "NONMEM")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput("ode_baselines2", "Baseline parameters",choices = "", selected = "", multiple = T)),
div(style="display:inline-block; width: 50px;height: 75px;", checkboxInput(inputId = "ode_mu", label = "mu-ref", value = T)),
div(style="display:inline-block; width: 50px;height: 75px;", checkboxInput(inputId = "ode_blq", label = "BLQ", value = F)),
div(style="display:inline-block; width: 50px;height: 75px;", actionButton("ode_trigger_nonmem", "Launch ode translation")),
# tabBox(
# title = "Nonmem launcher",
# The id lets us use input$tabset1 on the server to find the current tab
# id = "tabset1", height = "750px",
# tabPanel("Nonmem", "First tab content",
textAreaInput("ode_output_nonmem", "Model", value = "", width = "400", height = "700" ) # , div(style="display:inline-block; width: 1000px;height: 700px;",
# ),
# tabPanel("CTRLFILE", "Tab content 2")
# )
),
box(title = "ADAPT", collapsible = T, collapsed = T, width = 400,
div(style="display:inline-block; width: 50px;height: 75px;", actionButton("ode_trigger_adapt", "Launch ADAPT translation")),
textAreaInput("ode_output_adapt", "Model", value = "", width = "400", height = "700" ) # , div(style="display:inline-block; width: 1000px;height: 700px;",
)
# box(title = "saemix", collapsible = T, collapsed = T, width = 400,
#
# div(style="display:inline-block; width: 400px;height: 75px;", textInput("saemix_path", label = "Path", value = "D:/Peccary/Exemple_demo/saemix_test")),
# div(style="display:inline-block; width: 50px;height: 75px;", actionButton("saemix_go", "Go")),
# div(style="display:inline-block; width: 400px;height: 400px;", textAreaInput("nlmixr_result",label = ""))
#
# )
# conditionalPanel(condition = 'input.model_sections == "Monolix_Launcher"',
#
# shinyTree("tree", stripes = TRUE, multiple = TRUE, animation = TRUE, contextmenu = TRUE)
# )
),
# folder ------------------------------------------------------------------
tabItem(tabName = "folder",
textOutput(outputId = "namecurrendfolder"),
# conditionalPanel(
# condition = 'input.path2 != ""',
# tableOutput("table"),
# ),
div(style = 'overflow-x: scroll', tableOutput('table')),
# conditionalPanel(
# condition = 'input.path2 != ""',
tableOutput("runscompar")
# )
),
# prediction --------------------------------------------------------------
tabItem(tabName = "prediction",
checkboxInput(
inputId = 'interactivePreds', label = 'Interactive figure', value = FALSE
),
conditionalPanel(
condition = 'input.interactivePreds == true',
plotlyOutput('PredIndiInteractive',width = "1000px", height = "800px" )
),
conditionalPanel(
condition = 'input.interactivePreds == false',
conditionalPanel(
condition = 'input.path2 != ""',
shinyjqui::jqui_resizable( plotOutput('PredIndi', width = "1000px", height = "800px"))
) ),
conditionalPanel(
condition = 'input.path2 != ""',
fluidRow(
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "whichFunctionPred",label = "Function", choices = "Default", selected = "Default")),
div(style="display:inline-block; width: 100px;height: 75px;", textInput("numberPred2", "Runs" )),
# div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = "singmult", label = "S/M", value = TRUE)),
div(style="display:inline-block; width: 100px;height: 75px;", numericInput(inputId = "nIndPred2", label = "n",value = 20, min = 1)),
div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = "logPred2", label = "ylog", value = TRUE)),
div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = "logxPred2", label = "xlog", value = FALSE)),
div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = "PredPred2", label = "Pred", value = TRUE)),
div(style="display:inline-block; width: 150px;height: 75px;", checkboxInput(inputId = "freeSalePred2", label = "Free Scales", value = TRUE)),
div(style="display:inline-block; width: 300px;height: 75px;", textInput(inputId = "filterID2", label = "Filter")),
div(style="display:inline-block; width: 300px;height: 75px;", actionButton(inputId = "updatePred", label = "Update PLot")),
div(style="display:inline-block; width: 100px;height: 75px;", numericInput(inputId = "lowerlimitPred", label = "low limit",value = NA)),
div(style="display:inline-block; width: 100px;height: 75px;", numericInput(inputId = "upperlimitPred", label = "high limit",value = NA)),
div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = "extrVal", label = "Extr. Value", value = F)),
div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = "stratTypePred", label = "strat", value = F)),
div(style="display:inline-block; width: 100px;height: 75px;", textInput(inputId = "xlabPred", label = "xlab", value = "")),
div(style="display:inline-block; width: 100px;height: 75px;", textInput(inputId = "ylabPred", label = "ylab", value = ""))
# div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "colourPred2", label = "COV", choices = "None"))
)
),
conditionalPanel(
condition = 'input.path2 != ""',
fluidRow(
div(style="display:inline-block; width: 150px;height: 75px;", actionButton("savePRED", "Save Plot")),
div(style="display:inline-block; width: 800px;height: 75px;", textInput("commPRED", "Commentary (new line with three spaces)" ))
)
),
conditionalPanel(
condition = 'input.path2 != ""',
tableOutput("covPRED")
),
conditionalPanel(
condition = 'input.path2 != ""',
tableOutput("table2")
)
),
# gof ---------------------------------------------------------------------
tabItem( tabName = 'GOF',
radioButtons(inputId = 'radioGOF', label = "", choices = c("Single Static", "Single Dynamic", "Multiple Static"), inline = T),
# fluidRow(
# div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = 'interactive', label = 'Interactive figure', value = FALSE )),
# div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = 'multiGOFcheck', label = '', value = FALSE ))
# ),
#
conditionalPanel(
condition = 'input.radioGOF == "Single Dynamic"',
plotlyOutput('GOFinteractivePlot',width = "1000px", height = "700px" )
),
conditionalPanel(
condition = 'input.radioGOF == "Single Static"',
conditionalPanel(
condition = 'input.path2 != ""',
shinyjqui::jqui_resizable( plotOutput('GOFstaticPlot', width = "1000px", height = "700px"))
)),
conditionalPanel(
condition = 'input.radioGOF == "Multiple Static"',
shinyjqui::jqui_resizable(plotOutput('multiGOFplot', width = "1000px", height = "700px"))
),
fluidRow(
div(style="display:inline-block; width: 100px;height: 75px;", textInput("nGOF", "Runs" )),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "covPrimGOF", label = "Prim.Cov", choices = "")),
div(style="display:inline-block; width: 150px;height: 75px;", checkboxInput(inputId = "colcov", label = "Col Cov", value = FALSE)),
div(style="display:inline-block; width: 300px;height: 75px;", textInput(inputId = "filterGOF", label = "Filter")),
div(style="display:inline-block; width: 150px;height: 75px;", checkboxInput(inputId = "remBLQGOF", label = "Remove BLQ", value = TRUE)),
div(style="display:inline-block; width: 300px;height: 75px;", actionButton(inputId = "updateGOF", label = "Update")),
div(style="display:inline-block; width: 150px;height: 75px;", textInput(inputId = "SelectGOF", label = "SelectGOF")),
div(style="display:inline-block; width: 150px;height: 75px;", checkboxInput(inputId = "gofxlog", label = "xlog", value = TRUE)),
div(style="display:inline-block; width: 150px;height: 75px;", checkboxInput(inputId = "gofylog", label = "ylog", value = TRUE)),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "gofmethods", label = "method smooth",choices = c("auto", "none", "lm", "glm", "gam", "loess"), selected = "auto")),
div(style="display:inline-block; width: 150px;height: 75px;", textInput(inputId = "goftitle", label = "Title"))
),
fluidRow(
div(style="display:inline-block; width: 150px;height: 75px;", actionButton("saveGOF", "Save plot")),
div(style="display:inline-block; width: 800px;height: 75px;", textInput("commGOF", "Commentary (new line with three spaces)" ))
),
conditionalPanel(
condition = 'input.path2 != ""',
tableOutput("covGOF")
),
div(style="display:inline-block; width: 150px;height: 75px;", textInput(inputId = "SelectmultiGOF", label = "Filter table below")),
radioButtons(inputId = "ArrangeGOF", label = "", choices = c( "name", "run", "COV"), inline = T),
conditionalPanel(
condition = 'input.path2 != ""',
tableOutput("multiGOF")
)
),
# covariate ---------------------------------------------------------------
tabItem( tabName = "covariate",
conditionalPanel(
condition = 'input.path2 != ""',
shinyjqui::jqui_resizable( plotOutput("multiBox", width = "1000px", height = "600px"))
),
fluidRow(
div(style="display:inline-block; width: 100px;height: 75px;", textInput("nBoxPlots", "Runs" )),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "covPrimBP2", label = "Prim.Cov", choices = "None")),
div(style="display:inline-block; width: 150px;height: 75px;", checkboxInput(inputId = "pointBP2", label = "Points", value = FALSE)),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "boxplottest", label = "Pvalue test",choices = c("t.test", "wilcox.test", "anova", "kruskal.test" ), selected = "anova"))
# div(style="display:inline-block; width: 150px;height: 75px;", checkboxInput(inputId = "dissociateBP2", label = "Dissociated", value = FALSE))
),
fluidRow(
div(style="display:inline-block; width: 150px;height: 75px;", actionButton("saveBP", "Save plot")),
div(style="display:inline-block; width: 800px;height: 75px;", textInput("commBP", "Commentary (new line with three spaces)" ))
),
conditionalPanel(
condition = 'input.path2 != ""',
tableOutput("covBP"))
,
conditionalPanel(
condition = 'input.path2 != ""',
tableOutput("table4"))
),
# matrix ------------------------------------------------------------------
tabItem( tabName = "matrix",
radioButtons(inputId = 'radioMatrix', label = "", choices = c("Single", "Multiple Run"), inline = T),
conditionalPanel(
condition = 'input.radioMatrix == "Multiple Run"',
shinyjqui::jqui_resizable(plotOutput("matrixMultiPlot", width = "1000px", height = "600px"))
),
conditionalPanel(
condition = 'input.radioMatrix == "Single"',
conditionalPanel(
condition = 'input.path2 != ""',
shinyjqui::jqui_resizable(plotOutput("matrix", width = "1000px", height = "600px"))
)
),
fluidRow(
div(style="display:inline-block; width: 100px;height: 75px;", textInput("nmatrix", "Runs" )),
div(style="display:inline-block; width: 100px;height: 75px;", textInput("matrixfilter", "Filter" )),
div(style="display:inline-block; width: 150px;height: 75px;", radioButtons(inputId = "ArrangeMatrix", label = "", choices = c( "name", "run"), inline = T))
# div(style="display:inline-block; width: 150px;height: 75px;", checkboxInput(inputId = "pointBP2", label = "Points", value = FALSE))
# div(style="display:inline-block; width: 150px;height: 75px;", checkboxInput(inputId = "dissociateBP2", label = "Dissociated", value = FALSE))
),
fluidRow(
div(style="display:inline-block; width: 150px;height: 75px;", actionButton("saveMATRIX", "Save plot")),
div(style="display:inline-block; width: 800px;height: 75px;", textInput("commMATRIX", "Commentary (new line with three spaces)" ))
),
# radioButtons(inputId = "ArrangeMatrix", label = "", choices = c("run", "COV", "name"), inline = T),
conditionalPanel(
condition = 'input.path2 != ""',
tableOutput("multiMatrix"))
# tableOutput("table4")
),
# ############################## ill #######################
tabItem( tabName = "iLL",
conditionalPanel(
condition = 'input.path2 != ""',
shinyjqui::jqui_resizable(plotOutput("iLL", width = "1000px", height = "600px"))
),
fluidRow(
div(style="display:inline-block; width: 100px;height: 75px;", textInput("niLL", "Runs" )),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "covPrimiLL", label = "Prim.Cov", choices = "None")),
# div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "covPrimBP2", label = "Prim.Cov", choices = "None")),
div(style="display:inline-block; width: 150px;height: 75px;", checkboxInput(inputId = "HistoiLL", label = "Histogram", value = FALSE))
# div(style="display:inline-block; width: 150px;height: 75px;", checkboxInput(inputId = "dissociateBP2", label = "Dissociated", value = FALSE))
),
fluidRow(
div(style="display:inline-block; width: 150px;height: 75px;", actionButton("saveILL", "Save plot")),
div(style="display:inline-block; width: 800px;height: 75px;", textInput("commILL", "Commentary (new line with three spaces)" ))
)
# tableOutput("table4")
),
# Manual plpot ------------------------------------------------------------
tabItem( tabName = "ManualFunc",
fluidRow(
# div(style="display:inline-block; width: 150px;height: 75px;", actionButton("saveSENS", "Save plot")),
div(style="display:inline-block; width: 800px;height: 75px;", textInput("fileManualPLot",label = "file",value = "D:/these/Pecc_test/3_Models/1_Models/pecc_func.R" )),
div(style="display:inline-block; width: 800px;height: 75px;", selectInput("selectManualFunction", label = "Function", choices = "wait")),
rHandsontableOutput("argManualFunction"),
div(style="display:inline-block; width: 800px;height: 75px;", actionButton("ManualPlotGo","Go !"))
),
shinyjqui::jqui_resizable( plotOutput("ManualPlotPlot", width = "900px", height = "900px"))
),
# ############################## sensititivity #######################
tabItem( tabName = "sensitivity",
conditionalPanel(
condition = 'input.path2 != ""',
tableOutput("table5")),
fluidRow(column(4, wellPanel(selectInput("parSens", "Parameter", choices = "")))),
fluidRow(
div(style="display:inline-block; width: 150px;height: 75px;", actionButton("saveSENS", "Save plot")),
div(style="display:inline-block; width: 800px;height: 75px;", textInput("commSENS", "Commentary (new line with three spaces)" ))
),
conditionalPanel(
condition = 'input.path2 != ""',
plotOutput("sensitivity", width = "1500px", height = "900px"))
),
# saved plot --------------------------------------------------------------
tabItem(tabName = "rapports",
tableOutput("savedPlotsTable"),
fluidRow(
div(style="display:inline-block; width: 150px;height: 75px;", actionButton("savedUpdate", "Update saved list")),
div(style="display:inline-block; width: 100px;height: 75px;", numericInput(inputId = "saved_n_to_display", label = "ID to display", value = 0)),
actionButton("pdfplots", "Export Saved Plots")
),
plotOutput("saved_displayed", width = "1000px", height = "600px")
),
# VPC perso---------------------------------------------------------------------
tabItem(tabName = "simulation",
fluidRow(
div(style="display:inline-block; width: 300px;height: 75px;", textInput("pathVPC", "Path of a dataset", value = "")),
div(style="display:inline-block; width: 50px;height: 75px;", selectInput("sepVPC", "Sep", choices = c("", ";", ".", ","), selected = "")),
div(style="display:inline-block; width: 50px;height: 75px;", selectInput("decVPC", "Dec", choices = c(".", ","), selected = ".")),
div(style="display:inline-block; width: 50px;height: 75px;", textInput("nastringVPC", "NA", value = "")),
div(style="display:inline-block; width: 50px;height: 75px;", checkboxInput(inputId = "headerVPC", label = "header", value = F))
),
fluidRow(
div(style="display:inline-block; width: 300px;height: 75px;", textInput("nameVPC", "Names of column", value = "")),
div(style="display:inline-block; width: 50px;height: 75px;", actionButton(inputId = "loadVPC", label = "load file"))
),
conditionalPanel(
condition = 'input.radioVPC == "Visual Predicted Check"',
plotOutput("VPCPlot", width = "800px", height = "700px")),
conditionalPanel(
condition = 'input.radioVPC == "Prediction Distributions"',
plotOutput("PDPlot", width = "800px", height = "700px")),
div(style="display:inline-block; width: 500px;height: 75px;", radioButtons(inline = T , inputId = 'radioVPC', label = "", choices = c("Visual Predicted Check", "Prediction Distributions"))),
fluidRow(
div(style="display:inline-block; width: 300px;height: 75px;", textInput("filterrVPC", "Filter", value = "")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "VPCX", label = "X", choices = "")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "VPCY", label = "Y", choices = "")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "VPCsim", label = "sim", choices = "")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "VPCobs", label = "obs", choices = "")),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "VPCtype", label = "type", choices = c("Conf Int VPC" = "CI", "scatter VPC" = "scatter"))),
div(style="display:inline-block; width: 150px;height: 75px;", textInput("VPCquantile", "Quantiles", value = "5 50 95")),
div(style="display:inline-block; width: 150px;height: 75px;", numericInput(inputId = "VPCCIpct", label = "Confidence Intervale", value = 5, min = 0, max = 49, step = 1)),
# div(style="display:inline-block; width: 150px;height: 75px;", numericInput(inputId = "VPCLine", label = "Line-Alpha", value = 1, min = 0, max = 1, step = 0.1)),
div(style="display:inline-block; width: 150px;height: 75px;", selectInput(inputId = "VPCCOV", label = "Covariate", choices = "", multiple = T)),
# div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = "VPCXlog", label = "Xlog", value = FALSE)),
div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = "VPCYlog", label = "Ylog", value = TRUE)),
# div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = "VPCMedian", label = "Median", value = FALSE)),
# div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = "VPCNA", label = "Remove NA", value = FALSE)),
div(style="display:inline-block; width: 150px;height: 75px;", numericInput(inputId = "VPCLOQ", label = "LOQ obs", value = 0, step = 1)),
div(style="display:inline-block; width: 150px;height: 75px;", numericInput(inputId = "VPCYMIN", label = "ymin", value = 0, step = 1)),
div(style="display:inline-block; width: 150px;height: 75px;", textInput("VPCxlabel", "xlabel", value = "Time")),
div(style="display:inline-block; width: 150px;height: 75px;", textInput("VPCylabel", "ylabel", value = "Concentration")),
div(style="display:inline-block; width: 150px;height: 75px;", numericInput(inputId = "VPCsizeText", label = "Text size", value = 20, step = 1)),
div(style="display:inline-block; width: 50px;height: 75px;", actionButton(inputId = "launchVPC", label = "create VPC"))
)
),
# forest ------------------------------------------------------------------
tabItem(tabName = "forestPlot",
fluidRow(
div(style="display:inline-block; width: 100px;height: 75px;", textInput("nForest", "Runs" )),
div(style="display:inline-block; width: 100px;height: 75px;", actionButton("mb_load_forest_run", "Prefill w run")),
div(style="display:inline-block; width: 100px;height: 75px;", actionButton("mb_add_forest", "Add line")),
div(style="display:inline-block; width: 100px;height: 75px;", actionButton("mb_delete_forestt", "Delete line")),
div(style="display:inline-block; width: 150px;height: 75px;", actionButton(inputId = "forest_go", label = "Go"))
),
rHandsontableOutput("table_forest"),
shinyjqui::jqui_resizable(plotOutput("forestPlot", width = "1000px", height = "700px")),
box(width = 1000,
textAreaInput(inputId = "codeforestpec", label = "Short Peccary Code ", height = 100,width = 1000),
textAreaInput(inputId = "codeforest", label = "Peccary Independant Code", height = 300,width = 1000),
title = "R code", collapsible = T, collapsed = T)
),
# VPC package---------------------------------------------------------------------
tabItem(tabName = "vpc_pckg",
plotOutput("vpc_pckg_plot", width = "700px", height = "700px"),
box(collapsible = T, collapsed = F,width = 12,
div(style="display:inline-block; width: 400px;height: 75px;", textInput(inputId = "vpc_pckg_simdata", label = "Path sim")),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "vpc_pckg_simdata_ID", label = "ID", choices = c(""), selected = "")),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "vpc_pckg_simdata_REP", label = "REP", choices = c(""), selected = "")),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "vpc_pckg_simdata_TIME", label = "TIME", choices = c(""), selected = "")),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "vpc_pckg_simdata_PRED", label = "PRED", choices = c(""), selected = "")),
div(style="display:inline-block; width: 400px;height: 75px;", textInput(inputId = "vpc_pckg_obsdata", label = "Path obs")),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "vpc_pckg_obsdata_ID", label = "ID", choices = c(""), selected = "")),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "vpc_pckg_obsdata_TIME", label = "TIME", choices = c(""), selected = "")),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "vpc_pckg_obsdata_DV", label = "DV", choices = c(""), selected = "")),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "vpc_pckg_obsdata_MDV", label = "MDV", choices = c(""), selected = ""))
),
div(style="display:inline-block; width: 100px;height: 75px;", actionButton(inputId = "vpc_pckg_go", label = "create VPC")),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "vpc_pckg_bins", label = "Bins", choices = c("jenks", "density", "time", "data", "none", "pretty"), selected = "jenks")),
div(style="display:inline-block; width: 100px;height: 75px;", numericInput(inputId = "vpc_pckg_n_bins", label = "n_bins", value = 0)),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "vpc_pckg_bin_mid", label = "bin_mid", choices = c("mean", "middle"), selected = "mean")),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "vpc_pckg_software", label = "software", choices = c("auto", "nonmem", "phoenix"), selected = "auto")),
div(style="display:inline-block; width: 400px;height: 75px;", selectInput(inputId = "vpc_pckg_show", label = "show", choices = c("obs_dv", "obs_ci", "pi", "pi_as_area","pi_ci", "obs_median","sim_median","sim_median_ci" ), selected = c("obs_dv", "obs_ci", "pi_ci", "obs_median","sim_median_ci"), multiple = T)),
div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = "vpc_pckg_pred_corr", label = "pred_corr", value = F)),
div(style="display:inline-block; width: 150px;height: 75px;", numericInput(inputId = "vpc_pckg_pred_corr_lower_bnd", label = "pred_corr_lower_bnd",value = 0)),
div(style="display:inline-block; width: 100px;height: 75px;", numericInput(inputId = "vpc_pckg_pi_low", label = "pi_low",value = 0.05)),
div(style="display:inline-block; width: 100px;height: 75px;", numericInput(inputId = "vpc_pckg_pi_high", label = "pi_high",value = 0.95)),
div(style="display:inline-block; width: 100px;height: 75px;", numericInput(inputId = "vpc_pckg_ci_low", label = "ci_low",value = 0.05)),
div(style="display:inline-block; width: 100px;height: 75px;", numericInput(inputId = "vpc_pckg_ci_high", label = "ci_high",value = 0.95)),
div(style="display:inline-block; width: 100px;height: 75px;", numericInput(inputId = "vpc_pckg_uloq", label = "uloq",value = NA)),
div(style="display:inline-block; width: 100px;height: 75px;", numericInput(inputId = "vpc_pckg_lloq", label = "lloq",value = NA)),
div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = "vpc_pckg_log_y", label = "log_y", value = F)),
div(style="display:inline-block; width: 100px;height: 75px;", numericInput(inputId = "vpc_pckg_log_y_min", label = "log_y_min",value = 0.001)),
div(style="display:inline-block; width: 100px;height: 75px;", textInput(inputId = "vpc_pckg_xlab", label = "xlab")),
div(style="display:inline-block; width: 100px;height: 75px;", textInput(inputId = "vpc_pckg_ylab", label = "ylab")),
div(style="display:inline-block; width: 100px;height: 75px;", textInput(inputId = "vpc_pckg_title", label = "title")),
div(style="display:inline-block; width: 100px;height: 75px;", checkboxInput(inputId = "vpc_pckg_smooth", label = "smooth", value = T)),
div(style="display:inline-block; width: 100px;height: 75px;", selectInput(inputId = "vpc_pckg_facet", label = "facet", choices = c("wrap", "columns", "rows"), selected = "wrap")),
textAreaInput(inputId = "vpc_pckg_code", label = "Code")
),
# Report ------------------------------------------------------------------
tabItem(tabName = "Report",
div(style="display:inline-block; width: 300px;height: 75px;", selectInput(inputId = "reportVersion", label = "Report Version", choices = c(""), selected = "")),
div(style="display:inline-block; width: 75px;height: 75px;", actionButton(inputId = "reportLoad", label = "Load")),
div(style="display:inline-block; width: 300px;height: 75px;", textInput(inputId = "reportnewVersion", label = "Name")),
div(style="display:inline-block; width: 75px;height: 75px;", actionButton(inputId = "reportSave", label = "Save")),
box(title = "Prototype", collapsible = T, collapsed = T,width = 12,
div(style="display:inline-block; width: 400px;height: 75px;", textInput(inputId = "reportTemplatePath", label = "Prototype File", value = "D:/Peccary/inst/Report/templateReport.txt")),
div(style="display:inline-block; width: 200px;height: 75px;", actionButton(inputId = "reportTemplateLaunch", label = "Load Template"))
),
box(title = "Free introduction", collapsible = T, collapsed = T,width = 12,
textAreaInput(inputId = "Report_introduction", label = "Introduction")
),
box(title = "Project Presentation / Bibliographie", collapsible = T, collapsed = T,width = 12,
# div(style="display:inline-block; width: 600px;height: 100px;", selectInput(inputId = "reportDatasetInfo", label = "Info on", choices = c(""), selected = "", multiple = T)),
textAreaInput(inputId = "Report_biblio", label = "Project Presentation")
),
box(title = "Dataset information", collapsible = T, collapsed = T,width = 12,
div(style="display:inline-block; width: 600px;height: 100px;", selectInput(inputId = "reportDatasetInfo", label = "Info on", choices = c(""), selected = "", multiple = T)),
textAreaInput(inputId = "Report_dataset", label = "Dataset information")
),
box(title = "Pre-modeling", collapsible = T, collapsed = T,width = 12,
div(style="display:inline-block; width: 600px;height: 100px;", selectInput(inputId = "reportDataExploSelect", label = "DataExplo", choices = c(""), selected = "", multiple = T)),
div(style="display:inline-block; width: 600px;height: 100px;", selectInput(inputId = "reportPlotExploSelect", label = "PlotExplo", choices = c(""), selected = "", multiple = T)),
textAreaInput(inputId = "Report_premodeling", label = "Output")
),
box(title = "Modeling", collapsible = T, collapsed = T,width = 12,
div(style="display:inline-block; width: 400px;height: 100px;", selectInput(inputId = "reportModelEq", label = "model", choices = c(""), selected = "", multiple = T)),
textAreaInput(inputId = "Report_modeling", label = "Output")
),
box(title = "Final run", collapsible = T, collapsed = T,width = 12,
div(style="display:inline-block; width: 600px;height: 100px;", textInput(inputId = "reportRunfinalpat", label = "Run final", value = "")),
textAreaInput(inputId = "Report_run", label = "Output")
),
box(title = "Simulation", collapsible = T, collapsed = T,width = 12,
div(style="display:inline-block; width: 400px;height: 100px;", selectInput(inputId = "reportModelSimul", label = "model", choices = c(""), selected = "", multiple = T)),
textAreaInput(inputId = "Report_simulation", label = "Output")
),
box(title = "Export report", background="blue", collapsible = T, collapsed = T,width = 12,
div(style="display:inline-block; width: 300px;height: 100px;", textInput(inputId = "exportReportPath", label = "Output path", value = "D:/Peccary/Exemple_demo/report/demo")),
div(style="display:inline-block; width: 75px;height: 100px;", selectInput(inputId = "exportReportFormat", label = "Format", choices = c("word", "html", "pdf"), selected = "word", multiple = F)),
div(style="display:inline-block; width: 200px;height: 75px;", actionButton(inputId = "exportReportGo", label = "Load Template")),
box(title = "Options", collapsible = T, background="blue", collapsed = T,
div(style="display:inline-block; width: 150px;height: 75px;", textInput(inputId = "exportReportTitle", label = "Title", value = "UCART19")),
div(style="display:inline-block; width: 150px;height: 75px;", textInput(inputId = "exportReportAuthor", label = "Author", value = "Thibaud Derippe")),
div(style="display:inline-block; width: 150px;height: 75px;", textInput(inputId = "exportReportBibPath", label = "Bib path (optional)", value = "D:/Peccary/Exemple_demo/report/These_Peccary.bib")),
div(style="display:inline-block; width: 150px;height: 75px;", textInput(inputId = "exportReportCSLPath", label = "CSL path (optional)", value = "D:/Peccary/Exemple_demo/report/elsevier-vancouver.csl"))
)
)
),
# Authors ------------------------------------------------------------------
tabItem(tabName = "Authors",
h2("Authors", align = "center"),
br("Peccary aims to be a collaborative project where anyone can add or modify functionnalities."),
h3("List of all Peccary contributors (alphabetical order)"),
br(""),
br(HTML("<b><u>Aziz Ouerdani</b></u>: improved 3SetReplace_NONMEM_Run.R file")),
br(HTML("<b><u>Blaise Pasquiers</b></u>: provide lots of feedback and improvement thoughts")),
br(HTML("<b><u>Christelle Rodrigues</b></u>: wrote indiv_plot_christelle.R (additional function)")),
br(HTML("<b><u>Thibaud Derippe</b></u>: designed and wrote the first Peccary version (more than 50 files, including the Shiny App)")),
br(""),
br("")
)
), map(unique(gsub("(_serv)|(_ui)|(\\.R)", "", list.files("D:/Peccary/inst/Module"))), function(x){
eval(parse_expr(paste(readLines(file.path("D:/Peccary/inst/Module", paste0(x,"_ui.R"))), collapse = "")))
#
# print(class(eval(parse_expr(paste0(x,"_ui")))))
# return(eval(parse_expr(paste0(x,"_ui"))))
}))
)
# tabItems(
# Project load/creation ---------------------------------------------------
# for(a in unique(gsub("(_serv)|(_ui)|(\\.R)", "", list.files("D:/Peccary/inst/Module")))){
#
# eval(parse_expr(paste(readLines(file.path("D:/Peccary/inst/Module", paste0(a,"_ui.R"))), collapse = "")))
#
# }
# eval(map(unique(gsub("(_serv)|(_ui)|(\\.R)", "", list.files("D:/Peccary/inst/Module"))), function(x){
#
# parse_expr(paste(readLines(file.path("D:/Peccary/inst/Module", paste0(x,"_ui.R"))), collapse = ""))
# #
# # print(class(eval(parse_expr(paste0(x,"_ui")))))
# # return(eval(parse_expr(paste0(x,"_ui"))))
# })[[1]])
### don't touch
# )## end tab items
)
)
}
go <- function() shinyApp(pecc_ui_reunif, pecc_server_reunif_test)
#' @export
peccary_app3 <- function(){
rm(InfoModelPecc, envir = global_env())
shinyApp(pecc_ui_reunif(), pecc_server_reunif)
}
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