RProj deleted

.Rproj.user/1804966C/assistant_options

@@ -1,4 +0,0 @@
-assistant="default"
-chat_provider="default"
-copilot_enabled="-1"
-copilot_indexing_enabled="-1"

.Rproj.user/1804966C/build_options

@@ -1,7 +0,0 @@
-auto_roxygenize_for_build_and_reload="1"
-auto_roxygenize_for_build_package="1"
-auto_roxygenize_for_check="1"
-live_preview_website="0"
-makefile_args=""
-preview_website="1"
-website_output_format="all"

.Rproj.user/1804966C/pcs/files-pane.pper

@@ -1,9 +0,0 @@
-{
-    "sortOrder": [
-        {
-            "columnIndex": 2,
-            "ascending": true
-        }
-    ],
-    "path": "~/plateflow/NewApp"
-}

.Rproj.user/1804966C/pcs/source-pane.pper

@@ -1,3 +0,0 @@
-{
-    "activeTab": 3
-}

.Rproj.user/1804966C/pcs/windowlayoutstate.pper

@@ -1,14 +0,0 @@
-{
-    "left": {
-        "splitterpos": 349,
-        "topwindowstate": "NORMAL",
-        "panelheight": 872,
-        "windowheight": 910
-    },
-    "right": {
-        "splitterpos": 493,
-        "topwindowstate": "NORMAL",
-        "panelheight": 872,
-        "windowheight": 910
-    }
-}

.Rproj.user/1804966C/pcs/workbench-pane.pper

@@ -1,6 +0,0 @@
-{
-    "TabSet1": 0,
-    "TabSet2": 3,
-    "TabZoom": {},
-    "Sidebar": 0
-}

.Rproj.user/1804966C/rmd-outputs

@@ -1,5 +0,0 @@
-
-
-
-
-

.Rproj.user/1804966C/rstudio-prefs.json

@@ -1,3 +0,0 @@
-{
-    "file_monitor_use_gitignore": true
-}

.Rproj.user/1804966C/saved_source_markers

@@ -1 +0,0 @@
-{"active_set":"","sets":[]}

.Rproj.user/1804966C/sources/prop/0498AE4A

@@ -1,6 +0,0 @@
-{
-    "source_window_id": "",
-    "Source": "Source",
-    "cursorPosition": "149,33",
-    "scrollLine": "0"
-}

.Rproj.user/1804966C/sources/prop/1F7C96C9

@@ -1,7 +0,0 @@
-{
-    "tempName": "Untitled1",
-    "source_window_id": "",
-    "Source": "Source",
-    "cursorPosition": "53,0",
-    "scrollLine": "32"
-}

.Rproj.user/1804966C/sources/prop/2E42830B

@@ -1,8 +0,0 @@
-{
-    "source_window_id": "",
-    "Source": "Source",
-    "cursorPosition": "2155,38",
-    "scrollLine": "2145",
-    "docOutlineVisible": "1",
-    "docOutlineSize": "118"
-}

.Rproj.user/1804966C/sources/prop/690ECC06

@@ -1,6 +0,0 @@
-{
-    "source_window_id": "",
-    "Source": "Source",
-    "cursorPosition": "43,17",
-    "scrollLine": "18"
-}

.Rproj.user/1804966C/sources/prop/75D6CC68

@@ -1,7 +0,0 @@
-{
-    "tempName": "Untitled1",
-    "source_window_id": "",
-    "Source": "Source",
-    "cursorPosition": "53,0",
-    "scrollLine": "32"
-}

.Rproj.user/1804966C/sources/prop/D28532A3

@@ -1,7 +0,0 @@
-{
-    "source_window_id": "",
-    "Source": "Source",
-    "docOutlineVisible": "1",
-    "cursorPosition": "470,1",
-    "scrollLine": "456"
-}

.Rproj.user/1804966C/sources/prop/E0EFE663

@@ -1,6 +0,0 @@
-{
-    "source_window_id": "",
-    "Source": "Source",
-    "cursorPosition": "917,0",
-    "scrollLine": "911"
-}

.Rproj.user/1804966C/sources/prop/INDEX

@@ -1,7 +0,0 @@
-~%2Fplateflow%2FNewApp%2Fapp.R="2E42830B"
-~%2Fplateflow%2Fwizard%2Fserver.R="D28532A3"
-~%2Fplateflow%2Fwizard%2Fui.R="0498AE4A"
-~%2Fplateflow%2FwizardNew%2FDataGenerator.R="75D6CC68"
-~%2Fplateflow%2FwizardNew%2FUntitled.R="1F7C96C9"
-~%2Fplateflow%2FwizardNew%2Fserver.R="E0EFE663"
-~%2Fplateflow%2FwizardNew%2Fui.R="690ECC06"

.Rproj.user/1804966C/sources/session-c8f70505/00336B5B

@@ -1,26 +0,0 @@
-{
-    "id": "00336B5B",
-    "path": "~/plateflow/wizard/ui.R",
-    "project_path": null,
-    "type": "r_source",
-    "hash": "0",
-    "contents": "",
-    "dirty": false,
-    "created": 1777315188063.0,
-    "source_on_save": false,
-    "relative_order": 3,
-    "properties": {
-        "source_window_id": "",
-        "Source": "Source",
-        "cursorPosition": "149,33",
-        "scrollLine": "0"
-    },
-    "folds": "",
-    "lastKnownWriteTime": 1776610618,
-    "encoding": "UTF-8",
-    "collab_server": "",
-    "source_window": "",
-    "last_content_update": 1776610618,
-    "read_only": false,
-    "read_only_alternatives": []
-}

.Rproj.user/1804966C/sources/session-c8f70505/00336B5B-contents

@@ -1,277 +0,0 @@
-library(shiny)
-library(shinyjs)
-library(shinyAce)
-library(bslib)
-
-version <- "1.0.0"
-
-function(req) {
-  fluidPage(
-    useShinyjs(),
-    titlePanel("Dilution Wizard"),
-    tags$head(tags$style((".shiny-notification {position: fixed; top: 20%;left: 50%; margin-top: -100px; 
-                          margin-left: -250px; color: blue;font-size: 20px; font-style: italic;}")),
-      tabsetPanel(id="toptab",
-          tabPanel("Data entry",
-                   wellPanel(
-                     fluidRow(
-                       tags$head(tags$style(HTML("label {font-size:80%;margin-bottom: 3px;margin-top: 3px;}"))),
-                       column(2,
-                              tags$image(src="logo.png", class="adv_logo"),
-                              h4("upload EXCEL"),
-                              fileInput(inputId = "iFile", label = "", accept="ms-excel"),
-                              uiOutput(outputId = "sheetName"),
-                              div(checkboxInput("PureErr", "Should pure error be used for calculation of CIs?", FALSE),
-                                  style = "font-size: 24px !important;color: red"),
-                              verbatimTextOutput("stats"),
-                              h5("\n\n\n Author: Franz Innerbichler, InnerAnalytics")),
-                       div(id="parameter",
-                           column(1,style = "background: lightgrey",
-                                  #actionButton("StartCalc", "Click, when calculations to be started"),
-                                  h4("curve settings"),
-                                  numericInput("lowAsymptREF", "lower asymptote REF",10,step=1,min=0),
-                                  numericInput("lowAsymptTEST", "lower asymptote TEST",10,step=1,min=0),
-                                  numericInput("uppAsymptREF", "upper asymptote REF",110,step=1,min=0),
-                                  numericInput("uppAsymptTEST", "upper asymptote TEST",110,step=1,min=0)
-                                  ),
-                           column(1,style = "background: lightgrey",
-                                  numericInput("slopeREF", "slope REF",1,step=0.1,min=-10),
-                                  numericInput("slopeTEST", "slope TEST",1,step=0.1,min=-10),
-                                  numericInput("EC50", "EC50 REF",-3.5),
-                                  numericInput("potDiff", "potency difference",0)
-                           ),
-                           column(1,style = "background: lightgreen",
-                                  h4("dilutions"),
-                                  numericInput("CONC1", "highest concentration",0.3, min=-3.5),
-                                  numericInput("CONC2", "2nd concentration",0.15),
-                                  numericInput("CONC3", "3rd concentration",0.075),
-                                  numericInput("CONC4", "4th concentration",0.0375),
-                                  numericInput("CONC5", "5th concentration",0.01875),
-                                  
-                                  numericInput("CONC6", "6th concentration",0.00938)
-                           ),
-                           column(1,style = "background: lightgreen",
-                               
-                                  numericInput("CONC7", "7th concentration",0.00469),
-                                  numericInput("CONC8", "8thd concentration",0.00235),
-                                  numericInput("CONC9", "9thd concentration",NA),
-                                  numericInput("CONC10", "10th concentration",NA),
-                                  numericInput("CONC11", "11th concentration",NA),
-                                  
-                                  numericInput("CONC12", "lowest concentration",NA)
-                           ),
-                           column(1,style = "background: lightblue",
-                                  h4("geometric dilution scheme"),
-                                  numericInput("ConcStart", "starting concentration",NA),
-                                  numericInput("dilutionFac", "dilution factor",NA),
-                                  numericInput("NoDil", "no. of dilutions",NA),
-                                  numericInput("NoDilSer", "no. of dil. series",NA),
-                                  verbatimTextOutput("dilutions")
-                           ),
-                           column(4,
-                                  h4("log-dilution scheme"),
-                                  verbatimTextOutput("logdil"),
-                                  h4("User help"),
-                                  h5("If new dilutions are entered, please adjust EC50 to avoid calculation errors"))
-                           )
-                     )
-                   )),
-                   
-                   #### XLSX diagnostics ----
-                   tabPanel ("XLSX diagnostics",
-                             tags$style(HTML("pre { color: black; background-color: #FFE1FF; 
-                                             font-family: 'Helvetica Neue', Helvetica, Arial, sans-serif;font-size: 12px;} ")),
-                             wellPanel(
-                               fluidRow(
-                                 column(2, 
-                                        h5("Diagnostics only shown if EXCEL is uploaded"),
-                                        htmlOutput("PureErrW2"), 
-                                        tags$head(tags$style("#PureErrW2{color: red;
-                                                             font-size: 16px;
-                                                             font_style: italic;}")),
-                                        tableOutput("FileSAmpl"),
-                                        downloadButton("downloadXLReport", label="Download PDF report", class="butt"),
-                                        tags$style(type="text/css","#downloadXLReport {background-color: orange; color: black;font-family: COurier New}"),
-                                        plotOutput("relpotTestPlot", width="300px", height="150px"),
-                                        h4("Akaike Information Criterion"),
-                                        tableOutput("AIC"),
-                                        h5("First row: restricted model; 2nd row: unrestricted model"),
-                                        h5("Smaller values of AIC indicate better fit to the data"),
-                                        tableOutput("VarDiagn")
-                                        ),
-                                 column(4,
-                                        plotOutput("XLplot"),
-                                        column(6,
-                                               br(),
-                                               "Regression results restricted",
-                                               tableOutput("coeffs_r"),
-                                               "Bend points restricted",
-                                               tableOutput("coeffs_r2")),
-                                       column(6,
-                                              br(),
-                                              "Regression results unrestricted",
-                                              tableOutput("coeffs_unr"))),
-                                 column(4,
-                                        plotOutput("diagnplot"),
-                                        column(6,
-                                               tableOutput("logcoeffs_r"),
-                                               tableOutput("coeffs_unr2")),
-                                               column(6,
-                                                      tableOutput("logcoeffs_unr"))),
-                                 column(2,
-                                        tableOutput("ANOVAXLS"),
-                                        DT::renderDataTable("EQtests"))
-                             )
-                             )),
-                   #### 4pl fits ----
-                   tabPanel("4pl-fit",
-                             wellPanel(
-                               fluidRow(
-                                 column(6,
-                                        tags$style(span(htmlOutput("PureErrW3"), style="color: red")),
-                                                   htmlOutput("PureErrW3"),
-                                                   tags$head(tags$style("#PureErrW2{color: red;
-                                                             font-size: 16px;
-                                                             font_style: italic;}")),
-                                                   plotOutput("plot"),
-                                                   DT::dataTableOutput("pottab4pl"),
-                                                                       "Footnote: test performed on absolute CIs."),
-                                 column(6,
-                                        DT::dataTableOutput("secondary"), # SSTs
-                                        h5("*...The estimate for F-test on regression and on non-linearity is the p-value"),
-                                        h5("F-test on regression passes if F-value > F-crit and thus p < 0.05"),
-                                        h5("F-test on non-linearity passes if F-value < F-crit and thus p > 0.05"),
-                                        h5("Test results outcome: 0 ... test passed (for EQ tests: CI within limits);
-                                           1 ... test failed (for EQ tests CI not within limits);
-                                           -1 ... calculations unbound/denominator too close to 0"),
-                                        #plotOutput("CIplot, height=50%")
-                                        )                  
-                                 ))
-                               ),
-                   #### Linear PLA ----
-                   tabPanel("Linear PLA",
-                            wellPanel(
-                              fluidRow(
-                                column(6,
-                                       htmlOutput("PureErrW3"),
-                                       tags$head(tags$style("#PureErrW2{color: red;
-                                                             font-size: 16px;
-                                                             font_style: italic;}")),
-                                       plotOutput("plotLin"),
-                                       "Delta method is used for potency CIs",
-                                       DT::dataTableOutput("pottab"),
-                                       h4("Unrestricted linear model (SSSI):"),
-                                       tableOutput("SummaryModABu"),
-                                       h4("Restricted linear model (CSSI):"),
-                                       tableOutput("SummaryModAB")),
-                                column(3,
-                                       h3("Tests for linear PLA):"),
-                                       DT::dataTableOutput("TESTSlin"),
-                                       h5("The estimate is the p-value of the test"),
-                                       h5("F-tests on regression, significance of slopes, and preparation need to have a p-value <0.05 to pass"),
-                                       h5("All other tests pass if p-value > 0.05"),
-                                       "SST CI for difference of slopes:",
-                                       tableOutput("SlopeDiffCI")),
-                                column(3,
-                                       h3("ANOVA for parallel line assay"),
-                                       DT::dataTableOutput("ANOVAlin"))
-                              )
-                            )),
-                   #### Dilution simulator ----
-                   tabPanel("Dilution simulator",
-                            wellPanel(
-                              fluidRow(
-                                column(4,
-                                       h3("Confidence intervals"),
-                                       tableOutput("CIs"),
-                                       "The confidence intrval table is interaactive for changes in: variability slider (%SD), potency of test-slider,
-                                       and 'Adjust the dilutions'-slider",
-                                       tableOutput("optimalDils"),
-                                       selectInput(inputId="scenario", label= "Select an 'optimal' scenario:", choices = c("scenario 2","scenario 3","scenario 6","steep slope"))),
-                                column(5,
-                                       plotOutput("plotfordilutions"),
-                                       h4("in grey: most extreme bend point lines of theoretical samples with 50% and 200% potency"),
-                                       sliderInput("dilslider", "Adjust the dilutions(+-change in %)", min = -100,max=100, value=0, step=1, round=0),
-                                       checkboxInput("fixupper","Fix highest concentration (if unticked, the center is fixed)",FALSE),
-                                       h5("Dilution factors"),
-                                       tableOutput("adjlogdil"),
-                                       "Short guidance: wider dilution ranges increase the CIs of rel. potency, and decrease the CIs of upper and lower asymptote ratios, as well as Hill's slope ratios", br(),
-                                       "Narrower dilution ranges decrease the CIs of rel. potency, and increase the CIs of upper and lower asymptote ratios, ands Hill's slope ratios",),
-                                column(3,
-                                       h3("Bend points"),
-                                       tableOutput("bps"),
-                                       tableOutput("extremebps"),
-                                       h4("Explanation of the plots")
-                                       )
-                              )
-                            )),
-                   #### EQ limits simulation ----
-                   tabPanel("EQ-limit simulatioin",
-                            wellPanel(
-                              fluidRow(
-                                column(1, style="background: lightblue",
-                                       numericInput("simN","number of datasets to simulate", 100, step=10, min=10, max=1000),
-                                       numericInput("lowQuant", "lower quantile", 1, min = 0.01,max=20),
-                                       numericInput("uppQuant", "upper quantile", 99, min = 801,max=99.99),
-                                       actionButton('goSim', "Start simulation",class="btn-success")
-                                       ),
-                                column(4,
-                                       h4("estimation of EACs for slope ratio, dynamic range-ratio, upper asymptote ratio, and potency"),
-                                       plotOutput("plotHistuAs", width = "1400px", height = "400px"))
-                              )
-                            )),
-                   #### Documentation ----
-                   tabPanel("Documentation",
-                            h4("Information on dilution setting"),
-                            "(for details see:", a(href="ADONIS.pdf","Whitepaper", download=NA, target="_blank"),")",tags$br(),
-                            "Bend points are calculated according to following formula:",
-                            withMathJax(" $$bp_{1/2} = \\pm\\frac{1.31696}{Hill's slope}$$"))),
-                             
-   #### setting lower panel ----
-   wellPanel(
-     fluidRow(
-       column(2,
-              h3("Settings"),
-              helpText("Vary the slider to see the effect of special cause"),
-              sliderInput("sdfac","Variability as % of lower to upper asymptote", max=10, value=3, min=0.1, step=0.1),
-              checkboxInput("heterosked","heteroskedastic noise", FALSE),
-              sliderInput("potencydiff","potency of test (%)", max=200, min=50, value=100, step=1),
-              sliderInput("outlL","outlier in lower asymptote",  min=0, max=1.5, value=0, step=0.1),
-              sliderInput("outlM","outlier in mid part",   min=0, max=1.5,value=0, step=0.1),
-              sliderInput("outlU","outlier in upper asymptote",   min=0, max=1.5,value=0, step=0.1)
-              ),
-       column(1,
-              tags$table(id="dose-table",
-                         numericInput("lEACdiffla","lower EAC for diff. of LA", -0.175, step=0.001),
-                         numericInput("uEACdiffla","upper EAC for diff. of LA", 0.189, step=0.001),
-                         numericInput("lEACratiola","lower EAC ratio of LAs", 0.005, step=0.001),
-                         numericInput("uEACratiola","upper EAC for ratio of LAs", 100, step=1),
-                         
-                         numericInput("lEACratioSlope","lower EAC for ratio of slopes", 0.55, step=0.01),
-                         numericInput("uEACratioSlope","upper EAC for ratio of slopes", 1.84, step=0.1),
-                         numericInput("lEACratioua","lower EAC for ratio of UAs", 0.75, step=0.1),
-                         numericInput("uEACratioua","upper EAC for ratio of UAs", 1.33, step=0.1),
-                         numericInput("lowerPot","lower EAC for potency", 75, step=1),
-                         numericInput("upperPot","upper EAC for potency", 133, step=1),
-                         numericInput("lEACratioAdiff","lower EAC of ratio of asymptote differences", 0.75, step=0.01),
-                         numericInput("uEACratioAdiff","upper EAC of ratio of asymptote differences", 1.33, step=0.01)
-                         )),
-       column(4,
-              "4 PL ANOVA unrestricted",
-              DT::dataTableOutput("ANOVA"),
-              h5("Please note that for the CIs of rel. potency the RSS of the restricted model is used"),
-              h5("RSS ... 'Residual error' in the SumSquares column"),
-              h5("MSE ... 'Residual error' in the MSs column"),
-              h5("SSE ... 'Pure error' in the SumSquares column"),
-              h5("RMSE ... Square root of the 'Residual Error' in the MS column"),
-              verbatimTextOutput("RMSE")
-              ),
-       column(5,
-              DT::dataTableOutput("Conctab"))
-     )
-   )
-                   
-                   
-                   )
-  )
-}

.Rproj.user/1804966C/sources/session-c8f70505/2D702BEF

@@ -1,27 +0,0 @@
-{
-    "id": "2D702BEF",
-    "path": "~/plateflow/wizard/server.R",
-    "project_path": null,
-    "type": "r_source",
-    "hash": "0",
-    "contents": "",
-    "dirty": false,
-    "created": 1777235022084.0,
-    "source_on_save": false,
-    "relative_order": 2,
-    "properties": {
-        "source_window_id": "",
-        "Source": "Source",
-        "docOutlineVisible": "1",
-        "cursorPosition": "470,1",
-        "scrollLine": "456"
-    },
-    "folds": "",
-    "lastKnownWriteTime": 1777235902,
-    "encoding": "UTF-8",
-    "collab_server": "",
-    "source_window": "",
-    "last_content_update": 1777235902359,
-    "read_only": false,
-    "read_only_alternatives": []
-}

.Rproj.user/1804966C/sources/session-c8f70505/47543094

@@ -1,28 +0,0 @@
-{
-    "id": "47543094",
-    "path": "~/plateflow/NewApp/app.R",
-    "project_path": "app.R",
-    "type": "r_source",
-    "hash": "2785151077",
-    "contents": "",
-    "dirty": false,
-    "created": 1777232335294.0,
-    "source_on_save": false,
-    "relative_order": 3,
-    "properties": {
-        "source_window_id": "",
-        "Source": "Source",
-        "cursorPosition": "2155,38",
-        "scrollLine": "2145",
-        "docOutlineVisible": "1",
-        "docOutlineSize": "118"
-    },
-    "folds": "",
-    "lastKnownWriteTime": 1777839495,
-    "encoding": "UTF-8",
-    "collab_server": "",
-    "source_window": "",
-    "last_content_update": 1777839495532,
-    "read_only": false,
-    "read_only_alternatives": []
-}

.Rproj.user/1804966C/sources/session-c8f70505/A4E06B42-contents

@@ -1,51 +0,0 @@
-#
-# This is a Shiny web application. You can run the application by clicking
-# the 'Run App' button above.
-#
-# Find out more about building applications with Shiny here:
-#
-#    https://shiny.posit.co/
-#
-
-library(shiny)
-
-# Define UI for application that draws a histogram
-ui <- fluidPage(
-
-    # Application title
-    titlePanel("Old Faithful Geyser Data"),
-
-    # Sidebar with a slider input for number of bins 
-    sidebarLayout(
-        sidebarPanel(
-            sliderInput("bins",
-                        "Number of bins:",
-                        min = 1,
-                        max = 50,
-                        value = 30)
-        ),
-
-        # Show a plot of the generated distribution
-        mainPanel(
-           plotOutput("distPlot")
-        )
-    )
-)
-
-# Define server logic required to draw a histogram
-server <- function(input, output) {
-
-    output$distPlot <- renderPlot({
-        # generate bins based on input$bins from ui.R
-        x    <- faithful[, 2]
-        bins <- seq(min(x), max(x), length.out = input$bins + 1)
-
-        # draw the histogram with the specified number of bins
-        hist(x, breaks = bins, col = 'darkgray', border = 'white',
-             xlab = 'Waiting time to next eruption (in mins)',
-             main = 'Histogram of waiting times')
-    })
-}
-
-# Run the application 
-shinyApp(ui = ui, server = server)

.Rproj.user/1804966C/sources/session-c8f70505/AFA288F2

@@ -1,27 +0,0 @@
-{
-    "id": "AFA288F2",
-    "path": "~/plateflow/wizardNew/DataGenerator.R",
-    "project_path": null,
-    "type": "r_source",
-    "hash": "0",
-    "contents": "",
-    "dirty": false,
-    "created": 1777554257099.0,
-    "source_on_save": false,
-    "relative_order": 4,
-    "properties": {
-        "tempName": "Untitled1",
-        "source_window_id": "",
-        "Source": "Source",
-        "cursorPosition": "53,0",
-        "scrollLine": "32"
-    },
-    "folds": "",
-    "lastKnownWriteTime": 1777557164,
-    "encoding": "UTF-8",
-    "collab_server": "",
-    "source_window": "",
-    "last_content_update": 1777557164367,
-    "read_only": false,
-    "read_only_alternatives": []
-}

.Rproj.user/1804966C/sources/session-c8f70505/AFA288F2-contents

@@ -1,54 +0,0 @@
-Calc_DilRes <- function(as=3, bs=1, cs=-4, ds=10, at=3, bt=1,  dt=10,r=0.0001,ct=cs-r,
-                        sd_fac=0.1, gt=1, gs=1, log_conc,
-                        heteroNoise=FALSE, noDilSeries, noDils) {
-  yAxfac <- (ds-as)
-  log_dose <- log_conc
-  isRef <- rep(c(1,0),1,each=length(log_conc)*noDilSeries)
-  isSample <- rep(c(0,1),1,each=length(log_conc)*noDilSeries)
-  browser()  
-  av <- as*isRef + at*isSample + (ds*isRef + dt*isSample - as*isRef - at*isSample)/
-    (1+isRef*exp(bs*(cs - log_dose)) + isSample*exp(bt*(ct-log_dose)))
-  if (heteroNoise) {
-    # heterosc noise
-    ro_jit <- matrix(unlist(map(av, function(x) x+rnorm(1,0,x*sd_fac/100))), nrow=noDils, ncol=noDilSeries*2)
-  } else {
-    # homosc noise
-    ro_jit <- matrix(unlist(map(av, function(x) x+rnorm(1,0,sd_fac*yAxfac/100))), nrow=noDils, ncol=noDilSeries*2)
-  }
-  ro_jit <- abs(ro_jit)
-  
-  ro_jit2 <- cbind(ro_jit, log_dose)
-  if (noDilSeries==3) {
-    colnames(ro_jit2) <- c("R_dil1","R_dil2","R_dil3","T_dil1","T_dil2","T_dil3", "log_dose")
-  } else {
-    colnames(ro_jit2) <- c("R_dil1","R_dil2","T_dil1","T_dil2", "log_dose")
-  }
-  return(ro_jit2)
-}
-
-library(openxlsx)
-Conc <- 9*1/(3^(1:11))
-Conc_ <- c(9, Conc)
-
-ro_new <- list()
-ro_new[[1]] <- Calc_DilRes(as=1000, bs=-2, cs=-4, ds=10000, at=1000, bt=-2,  dt=10000, log_conc = log(Conc_),
-                      sd_fac=3.3,
-                      # auslenkU=outlierU,
-                      # auslenkM=outlierM,
-                      # auslenkL=outlierL,
-                      heteroNoise = F, noDilSeries = 2, noDils = 12)
-ro_new[[2]] <- Calc_DilRes(as=1000, bs=-2, cs=-4, ds=10000, at=1000, bt=-2, dt=10000, log_conc = log(Conc_),
-                      sd_fac=3.3,r=0.1,
-                      # auslenkU=outlierU,
-                      # auslenkM=outlierM,
-                      # auslenkL=outlierL,
-                      heteroNoise = F, noDilSeries = 2, noDils = 12)
-ro_new[[3]] <- Calc_DilRes(as=1000, bs=-2, cs=-4, ds=10000, at=1000, bt=-2, dt=10000, log_conc = log(Conc_),
-                      sd_fac=3.2, r=-0.3,
-                      # auslenkU=outlierU,
-                      # auslenkM=outlierM,
-                      # auslenkL=outlierL,
-                      heteroNoise = F, noDilSeries = 2, noDils = 12)
-
-write.xlsx(ro_new, "~/plateflow/wizard/Tests3Plates.xlsx")
-

.Rproj.user/1804966C/sources/session-c8f70505/E68D9B8B-contents

@@ -1,45 +0,0 @@
-
-library(shiny)
-library(shinydashboard)
-library(fontawesome)
-
-ui <- dashboardPage(
-  dashboardHeader("wizard"),
-    dashboardSidebar(
-      sidebarMenu(
-      img(src="logo.png", width=230),
-        menuItem("Home", tabName="home", icon=icon("home")),
-        menuItem("Data template", tabName = "template", icon=icon("table"),
-                 menuSubItem( tags$li(a("EXCEL File",  target="self",href="TestFIle.xlsx")))
-                 ),
-        menuItem("User Manual /Validation", tabName = "manual", icon=icon("book"),
-                 menuSubItem(icon = NULL, tags$li(a("Document",  target="self",href="UserManual.pdf")))
-        ),
-        menuItem("EXCEL upload", tabName="Dataupload", icon=icon("magnet", lib="glyphicon")),
-        menuItem("4PL + report", tabName="4PL", icon=icon("chart-line", lib="font-awesome")),
-        menuItem("Linear regression + report", tabName="pla", icon=icon("pencil", lib="glyphicon")),
-        menuItem("Wizard", tabName="wizard", icon=icon("chart-column", lib="font-awesome")),
-        menuItem("Documentation", tabName="documentation", icon=icon("chart-area", lib="font-awesome"))
-      ),
-      tags$footer(HTML(paste("Owned by",tags$strong(tags$u("InnerAnalytics")), paste(rep("&nbsp",9), collapse=""),
-                             "Developer:", paste(rep("&nbsp",9), collapse=""),
-                              "Host on:", paste(rep("&nbsp",9), collapse=""),
-                             "Version:")),
-                  align="left", style=
-                    "position:fixed; bottom_=;;width=100%; background: #7FAEFF; font-family: Times New Roman; font-size:100%;
-                  padding: 5px; color:#990000; box-sizing: border-box; z-index: 1000;")
-    ),
-    dashboardBody(
-      fluidPage(
-        tabItems(
-          tabItem(tabName = "home", htmlOutput("homePage")),
-          tabItem(tabName = "Datapload", uiOutput("Dataupload")),
-          tabItem(tabName = "fourPL", uiOutput("fourPL")),
-          tabItem(tabName = "pla", uiOutput("pla")),
-          tabItem(tabName = "wizard", uiOutput("wizard"))
-
-        )
-
-    )
-  ) , skin="blue"
-)

.Rproj.user/shared/notebooks/paths

@@ -1,5 +0,0 @@
-/Users/franzinnerbichler/plateflow/NewApp/app.R="232C6386"
-/Users/franzinnerbichler/plateflow/wizardNew/DataGenerator.R="038FF5B5"
-/Users/franzinnerbichler/plateflow/wizardNew/Untitled.R="405C9157"
-/Users/franzinnerbichler/plateflow/wizardNew/server.R="710F8608"
-/Users/franzinnerbichler/plateflow/wizardNew/ui.R="CB737866"

.gitignore

@@ -0,0 +1,5 @@
+.Rproj.user
+.Rproj
+.Rhistory
+.RData
+.Ruserdata

app.R

@@ -2164,7 +2164,8 @@ server <- function(input, output, session) {
     
     # tab <- sim2()
     if (is.character(tab)) stop(tab)
-    browser()  
+    #browser() 
+    log_conc <- tab$log_dose
     noDilSer = (ncol(tab)-1)/2
     noDil <- nrow(tab)
     Conctab <- perConcTab(tab, noDilSer) 
@@ -2173,11 +2174,11 @@ server <- function(input, output, session) {
     slopeSt <- slopeTe <- matrix(NA, nrow=noDil-2,ncol=2)
     for (i in 1:(noDil-2)) {
       avs <- Conctab[noDilSer+1,]
-      threes <- data.frame(lnC=log(Conc[i:(i+2)]), resp=avs[i:(i+2)])
+      threes <- data.frame(lnC=log_conc[i:(i+2)], resp=avs[i:(i+2)])
       lm3St <- lm(resp ~ lnC, data=threes)
       slopeSt[i,] <- lm3St$coefficients
       avt <- Conctab[noDilSer*2+4,]
-      threet <- data.frame(lnC=log(Conc[i:(i+2)]), resp=avt[i:(i+2)])
+      threet <- data.frame(lnC=log_conc[i:(i+2)], resp=avt[i:(i+2)])
       lm3Te <- lm(resp ~ lnC, data=threet)
       slopeTe[i,] <- lm3Te$coefficients
     }
@@ -2185,9 +2186,9 @@ server <- function(input, output, session) {
     indS <- which(abs(slopeSt[,2]) == max(abs(slopeSt[,2])))
     indT <- which(abs(slopeTe[,2]) == max(abs(slopeTe[,2])))
 
-    pl_ <- slopeSt[indS,1]+slopeSt[indS,2]*log(Conc)
+    pl_ <- slopeSt[indS,1]+slopeSt[indS,2]*log_conc
-    pl_T <- slopeTe[indT,1]+slopeTe[indT,2]*log(Conc)
+    pl_T <- slopeTe[indT,1]+slopeTe[indT,2]*log_conc
-    pl_df <- data.frame(lnC=log(Conc), plotS=pl_, plotT=pl_T)
+    pl_df <- data.frame(lnC=log_conc, plotS=pl_, plotT=pl_T)
 
     all_l <- melt(data.frame(tab), id.vars="log_dose",variable.name="replname",value.name="readout")
     isRef <- rep(c(1,0), 1,each=nrow(all_l)/2)
@@ -2240,9 +2241,9 @@ server <- function(input, output, session) {
 # fit intercept for test and ref and common slope
     
 
-    pl_restS <- sum_mLin$coefficients[1,1] + sum_mLin$coefficients[2,1]*log(Conc)
+    pl_restS <- sum_mLin$coefficients[1,1] + sum_mLin$coefficients[2,1]*log_conc
-    pl_restT <- sum_mLin$coefficients[1,1] + sum_mLin$coefficients[3,1] + sum_mLin$coefficients[2,1]*log(Conc)
+    pl_restT <- sum_mLin$coefficients[1,1] + sum_mLin$coefficients[3,1] + sum_mLin$coefficients[2,1]*log_conc
-    pl_rest <- data.frame(lnC=log(Conc), plotS=pl_restS, plotT=pl_restT)
+    pl_rest <- data.frame(lnC=log_conc, plotS=pl_restS, plotT=pl_restT)
 
     pr2 <- p + geom_line(data=pl_rest,aes(x=lnC,y=plotS),color="#4545BA",
                          inherit.aes = F) +
@@ -2285,9 +2286,9 @@ server <- function(input, output, session) {
     indS <- which(abs(slopeSt[,2]) == max(abs(slopeSt[,2])))
     indT <- which(abs(slopeTe[,2]) == max(abs(slopeTe[,2])))
     
-    pl_ <- slopeSt[indS,1]+slopeSt[indS,2]*log(Conc)
+    pl_ <- slopeSt[indS,1]+slopeSt[indS,2]*log_conc
-    pl_T <- slopeTe[indT,1]+slopeTe[indT,2]*log(Conc)
+    pl_T <- slopeTe[indT,1]+slopeTe[indT,2]*log_conc
-    pl_df <- data.frame(lnC=log(Conc), plotS=pl_, plotT=pl_T)
+    pl_df <- data.frame(lnC=log_conc, plotS=pl_, plotT=pl_T)
     
     all_l <- melt(data.frame(tab), id.vars="log_dose",variable.name="replname",value.name="readout")
     isRef <- rep(c(1,0), 1,each=nrow(all_l)/2)
@@ -2338,9 +2339,9 @@ server <- function(input, output, session) {
     # alternativ: modAB <- lm(readout ~ log_dose+isSample, circle)
     sum_mLin <- summary(mLin)
     
-    pl_restS <- sum_mLin$coefficients[1,1] + sum_mLin$coefficients[2,1]*log(Conc)
+    pl_restS <- sum_mLin$coefficients[1,1] + sum_mLin$coefficients[2,1]*log_conc
-    pl_restT <- sum_mLin$coefficients[1,1] + sum_mLin$coefficients[3,1] + sum_mLin$coefficients[2,1]*log(Conc)
+    pl_restT <- sum_mLin$coefficients[1,1] + sum_mLin$coefficients[3,1] + sum_mLin$coefficients[2,1]*log_conc
-    pl_rest <- data.frame(lnC=log(Conc), plotS=pl_restS, plotT=pl_restT)
+    pl_rest <- data.frame(lnC=log_conc, plotS=pl_restS, plotT=pl_restT)
     
     pr2 <- p + geom_line(data=pl_rest,aes(x=lnC,y=plotS),color="blue",
                          inherit.aes = F) +