ROUT report cleaned up, outlier table and Q-valus added

dev/app.R

@@ -338,7 +338,8 @@ server <- function(input, output, session) {
           "Adjust the slider to mark the suspected outliers. Mostly, a Q-value of 2% is sufficient.",
           "If the general variability of the data is high, many datapoints will be flagged, also ones that are not deemed to be outliers",
           "An indicator for high variability is, when the Q-value needs to be increased above 5%, to flag suspected outliers.",
-          "Then, please re-consider, if the suspected outlier is not 'just' normal variability."
+          "Then, please re-consider, if the suspected outlier is not 'just' normal variability.",
+          tableOutput("ANOVA_ROUT")
           ),
           tabPanel(
             "parameter estimates",
@@ -576,13 +577,13 @@ server <- function(input, output, session) {
                 " CI for difference of slopes:",
                 tableOutput("SlopeDiffCIMeta"),
               )
-            ),
-            tabPanel(
-              "Report",
-              h4("Settings for report"),
-              downloadButton("downloadXLReportMeta", label = "Download PDF report", class = "butt"),
-              tags$style(type = "text/css", "#downloadXLReportMeta {background-color: orange; color: black;font-family: COurier New}"),
-            )
+            ) #,
+            # tabPanel(
+            #   "Report",
+            #   h4("Settings for report"),
+            #   downloadButton("downloadXLReportMeta", label = "Download PDF report", class = "butt"),
+            #   tags$style(type = "text/css", "#downloadXLReportMeta {background-color: orange; color: black;font-family: COurier New}"),
+            # )
           )
         )
         # )
@@ -822,6 +823,9 @@ server <- function(input, output, session) {
           ##### ROUT outlier testing ----
     #browser()
           if(!is.null(input$Qslider)) {
+            
+           
+            
               all_lROUT <- all_l[complete.cases(all_l),]
               colnames(all_lROUT) <- c("log_dose","sample","y","isRef","isSample","conc")
               res <- rout_4pl_potency(all_lROUT, Q=input$Qslider/100)
@@ -870,6 +874,9 @@ server <- function(input, output, session) {
               REP$ROUTplot <- ROUTplot
               
               ANOVA_ROUT <- ANOVA4plUnresfunc(ro_new = ro_newROUT)
+              output$ANOVA_ROUT <- renderTable({
+                ANOVA_ROUT
+              })
               REP$ANOVA_ROUT <- ANOVA_ROUT
               
               Limite <- list(
@@ -915,6 +922,8 @@ server <- function(input, output, session) {
               
               
               REP$BendsROUT <- BendsROUT
+              REP$Qslider <- input$Qslider
+              REP$OUTs_ <- OUTs_
             }          
 
   
@@ -2959,43 +2968,43 @@ server <- function(input, output, session) {
     
     #### download Meta 4PL report----
     
-    observeEvent(input$btn2, {
-      if(!Dat$FITsFlag) {
-        runjs("$('#downloadXLReportMeta')[0].click();")
-      } else {
-        showModal(modalDialog(
-          title = "No 4PL model to Download",
-          "Please select other data before download.",
-          easyClose = TRUE,
-          footer = NULL
-        ))
-      }
-    })
-    
-    output$downloadXLReportMeta <- downloadHandler(
-      filename = paste0("Report_4PLEvaluation", Dat$RepIdentifier, ".pdf"),
-      content = function(file) {
-        tpdr <- tempdir()
-        tempReport <- file.path(tpdr, "Doc_BioassayReport.Rmd")
-        file.copy("Doc_BioassayReport.Rmd", tempReport, overwrite = T)
-        
-        tempReportc <- file.path(tpdr, "logov2.png")
-        file.copy("logov2.png", tempReportc, overwrite = T)
-        
-        rmarkdown::render(tempReport,
-                          output_file = file,
-                          params = list(
-                            FileName = Dat$FileName,
-                            author = Dat$Author,
-                            NoP = Dat$NoP,
-                            Assay = Dat$Assay,
-                            REP = REP,
-                            coeffs = Dat$coeffs_UN
-                          ),
-                          envir = new.env(parent = globalenv())
-        )
-      }
-    )
+    # observeEvent(input$btn2, {
+    #   if(!Dat$FITsFlag) {
+    #     runjs("$('#downloadXLReportMeta')[0].click();")
+    #   } else {
+    #     showModal(modalDialog(
+    #       title = "No 4PL model to Download",
+    #       "Please select other data before download.",
+    #       easyClose = TRUE,
+    #       footer = NULL
+    #     ))
+    #   }
+    # })
+    # 
+    # output$downloadXLReportMeta <- downloadHandler(
+    #   filename = paste0("Report_4PLEvaluation", Dat$RepIdentifier, ".pdf"),
+    #   content = function(file) {
+    #     tpdr <- tempdir()
+    #     tempReport <- file.path(tpdr, "Doc_BioassayReport.Rmd")
+    #     file.copy("Doc_BioassayReport.Rmd", tempReport, overwrite = T)
+    #     
+    #     tempReportc <- file.path(tpdr, "logov2.png")
+    #     file.copy("logov2.png", tempReportc, overwrite = T)
+    #     
+    #     rmarkdown::render(tempReport,
+    #                       output_file = file,
+    #                       params = list(
+    #                         FileName = Dat$FileName,
+    #                         author = Dat$Author,
+    #                         NoP = Dat$NoP,
+    #                         Assay = Dat$Assay,
+    #                         REP = REP,
+    #                         coeffs = Dat$coeffs_UN
+    #                       ),
+    #                       envir = new.env(parent = globalenv())
+    #     )
+    #   }
+    # )
     
     
     #### download Wizard report ----