Update app.R

app.R

@@ -85,7 +85,7 @@ baseR_generate_randomizations <- function(n_units, n_treated, X, accept_prob, ra
     base_assign <- c(rep(1, n_treated), rep(0, n_units - n_treated))
     
     # shuffle in R
-    # We'll store T2's in chunks to reduce memory overhead
+    # We'll store T^2's in chunks to reduce memory overhead
     batch_count <- ceiling(max_draws / batch_size)
     all_assign <- list()
     all_T2 <- numeric(0)
@@ -230,7 +230,7 @@ ui <- dashboardPage(
                                       "Exact"        = "exact"),
                           selected = "monte_carlo"),
               numericInput("accept_prob", "Acceptance Probability (stringency)", 
-                           value = 0.05, min = 0.0001, max = 1),
+                           value = 0.01, min = 0.0001, max = 1),
               conditionalPanel(
                 condition = "input.random_type == 'monte_carlo'",
                 numericInput("max_draws", "Max Draws (MC)", value = 1e5, min = 1e3),
@@ -241,12 +241,19 @@ ui <- dashboardPage(
           
           box(width = 8, title = "Summary of Accepted Randomizations",
               status = "info", solidHeader = TRUE,
+              
+              # First row of boxes: accepted randomizations and min balance measure
+              fluidRow(
+                column(width = 6, valueBoxOutput("n_accepted_box", width = 12)),
+                column(width = 6, valueBoxOutput("balance_min_box", width = 12))
+              ),
+              
+              # Second row of boxes: fastrerandomize time & base R time
               fluidRow(
-                valueBoxOutput("n_accepted_box", width = 4),
-                valueBoxOutput("balance_min_box", width = 4),
-                valueBoxOutput("fastrerand_time_box", width = 4),
-                valueBoxOutput("baseR_time_box", width = 4)
+                column(width = 6, valueBoxOutput("fastrerand_time_box", width = 12)),
+                column(width = 6, valueBoxOutput("baseR_time_box", width = 12))
               ),
+              
               br(),
               plotOutput("balance_hist", height = "250px")
           )
@@ -287,12 +294,19 @@ ui <- dashboardPage(
           ),
           
           box(width = 8, title = "Test Results", status = "info", solidHeader = TRUE,
+              
+              # First row: p-value and observed effect
+              fluidRow(
+                column(width = 6, valueBoxOutput("pvalue_box", width = 12)),
+                column(width = 6, valueBoxOutput("tauobs_box", width = 12))
+              ),
+              
+              # Second row: fastrerandomize test time & base R test time
               fluidRow(
-                valueBoxOutput("pvalue_box", width = 4),
-                valueBoxOutput("tauobs_box", width = 4),
-                valueBoxOutput("fastrerand_test_time_box", width = 4),
-                valueBoxOutput("baseR_test_time_box", width = 4)
+                column(width = 6, valueBoxOutput("fastrerand_test_time_box", width = 12)),
+                column(width = 6, valueBoxOutput("baseR_test_time_box", width = 12))
               ),
+              
               uiOutput("fi_text"),
               br(),
               plotOutput("test_plot", height = "280px")
@@ -361,53 +375,56 @@ server <- function(input, output, session) {
            "Number treated cannot exceed total units.")
     )
     
-    # =========== 1) fastrerandomize generation timing ===========
-    t0_fast <- Sys.time()
-    out <- tryCatch({
-      generate_randomizations(
-        n_units                  = nrow(X_data()),
-        n_treated                = input$n_treated,
-        X                        = X_data(),
-        randomization_accept_prob= input$accept_prob,
-        randomization_type       = input$random_type,
-        max_draws                = if (input$random_type == "monte_carlo") input$max_draws else NULL,
-        batch_size               = if (input$random_type == "monte_carlo") input$batch_size else NULL,
-        verbose                  = FALSE
-      )
-    }, error = function(e) e)
-    t1_fast <- Sys.time()
-    
-    if (inherits(out, "error")) {
-      showNotification(paste("Error generating randomizations (fastrerandomize):", out$message), type = "error")
-      RerandResult(NULL)
-    } else {
-      RerandResult(out)
-    }
-    fastrand_time(difftime(t1_fast, t0_fast, units = "secs"))
-    
-    # =========== 2) base R generation timing ===========
-    t0_base <- Sys.time()
-    out_base <- tryCatch({
-      baseR_generate_randomizations(
-        n_units    = nrow(X_data()),
-        n_treated  = input$n_treated,
-        X          = X_data(),
-        accept_prob= input$accept_prob,
-        random_type= input$random_type,
-        max_draws  = if (input$random_type == "monte_carlo") input$max_draws else NULL,
-        batch_size = if (input$random_type == "monte_carlo") input$batch_size else NULL
-      )
-    }, error = function(e) e)
-    t1_base <- Sys.time()
-    
-    if (inherits(out_base, "error")) {
-      showNotification(paste("Error generating randomizations (base R):", out_base$message), type = "error")
-      RerandResult_base(NULL)
-    } else {
-      RerandResult_base(out_base)
-    }
-    baseR_time(difftime(t1_base, t0_base, units = "secs"))
-    
+    # ------------------ COMPUTING RESULTS TOGGLE ------------------
+    withProgress(message = "Computing results...", value = 0, {
+      
+      # =========== 1) fastrerandomize generation timing ===========
+      t0_fast <- Sys.time()
+      out <- tryCatch({
+        generate_randomizations(
+          n_units                  = nrow(X_data()),
+          n_treated                = input$n_treated,
+          X                        = X_data(),
+          randomization_accept_prob= input$accept_prob,
+          randomization_type       = input$random_type,
+          max_draws                = if (input$random_type == "monte_carlo") input$max_draws else NULL,
+          batch_size               = if (input$random_type == "monte_carlo") input$batch_size else NULL,
+          verbose                  = FALSE
+        )
+      }, error = function(e) e)
+      t1_fast <- Sys.time()
+      
+      if (inherits(out, "error")) {
+        showNotification(paste("Error generating randomizations (fastrerandomize):", out$message), type = "error")
+        RerandResult(NULL)
+      } else {
+        RerandResult(out)
+      }
+      fastrand_time(difftime(t1_fast, t0_fast, units = "secs"))
+      
+      # =========== 2) base R generation timing ===========
+      t0_base <- Sys.time()
+      out_base <- tryCatch({
+        baseR_generate_randomizations(
+          n_units    = nrow(X_data()),
+          n_treated  = input$n_treated,
+          X          = X_data(),
+          accept_prob= input$accept_prob,
+          random_type= input$random_type,
+          max_draws  = if (input$random_type == "monte_carlo") input$max_draws else NULL,
+          batch_size = if (input$random_type == "monte_carlo") input$batch_size else NULL
+        )
+      }, error = function(e) e)
+      t1_base <- Sys.time()
+      
+      if (inherits(out_base, "error")) {
+        showNotification(paste("Error generating randomizations (base R):", out_base$message), type = "error")
+        RerandResult_base(NULL)
+      } else {
+        RerandResult_base(out_base)
+      }
+      baseR_time(difftime(t1_base, t0_base, units = "secs"))
+    })
   })
   
   # Summaries of accepted randomizations
@@ -521,64 +538,68 @@ server <- function(input, output, session) {
   baseR_test_time <- reactiveVal(NULL)
   
   observeEvent(input$run_randtest_btn, {
-    req(RerandResult())
-    rr <- RerandResult()
-    req(rr$randomizations)
-    if (is.null(Y_data())) {
-      showNotification("No outcome data Y found. Upload or simulate first.", type="error")
-      return(NULL)
-    }
-    
-    obsW  <- rr$randomizations[1, ]
-    obsY  <- Y_data()
-    
-    # =========== 1) fastrerandomize randomization_test timing ===========
-    t0_testfast <- Sys.time()
-    outTest <- tryCatch({
-      randomization_test(
-        obsW      = obsW,
-        obsY      = obsY,
-        candidate_randomizations = rr$randomizations,
-        findFI    = input$findFI
-      )
-    }, error=function(e) e)
-    t1_testfast <- Sys.time()
-    
-    if (inherits(outTest, "error")) {
-      showNotification(paste("Error in randomization_test (fastrerandomize):", outTest$message), type="error")
-      RandTestResult(NULL)
-    } else {
-      RandTestResult(outTest)
-    }
-    fastrand_test_time(difftime(t1_testfast, t0_testfast, units = "secs"))
-    
-    # =========== 2) base R randomization test timing ===========
-    # We must also have the base R set of randomizations
-    req(RerandResult_base())
-    rr_base <- RerandResult_base()
-    if (is.null(rr_base$randomizations) || nrow(rr_base$randomizations) < 1) {
-      showNotification("No base R randomizations found. Cannot run base R test.", type = "error")
-      RandTestResult_base(NULL)
-      return(NULL)
-    }
-    
-    t0_testbase <- Sys.time()
-    outTestBase <- tryCatch({
-      baseR_randomization_test(
-        obsW    = obsW,
-        obsY    = obsY,
-        allW    = rr_base$randomizations
-      )
-    }, error = function(e) e)
-    t1_testbase <- Sys.time()
-    
-    if (inherits(outTestBase, "error")) {
-      showNotification(paste("Error in randomization_test (base R):", outTestBase$message), type="error")
-      RandTestResult_base(NULL)
-    } else {
-      RandTestResult_base(outTestBase)
-    }
-    baseR_test_time(difftime(t1_testbase, t0_testbase, units = "secs"))
+    # ------------------ COMPUTING RESULTS TOGGLE ------------------
+    withProgress(message = "Computing results...", value = 0, {
+      
+      req(RerandResult())
+      rr <- RerandResult()
+      req(rr$randomizations)
+      if (is.null(Y_data())) {
+        showNotification("No outcome data Y found. Upload or simulate first.", type="error")
+        return(NULL)
+      }
+      
+      obsW  <- rr$randomizations[1, ]
+      obsY  <- Y_data()
+      
+      # =========== 1) fastrerandomize randomization_test timing ===========
+      t0_testfast <- Sys.time()
+      outTest <- tryCatch({
+        randomization_test(
+          obsW      = obsW,
+          obsY      = obsY,
+          candidate_randomizations = rr$randomizations,
+          findFI    = input$findFI
+        )
+      }, error=function(e) e)
+      t1_testfast <- Sys.time()
+      
+      if (inherits(outTest, "error")) {
+        showNotification(paste("Error in randomization_test (fastrerandomize):", outTest$message), type="error")
+        RandTestResult(NULL)
+      } else {
+        RandTestResult(outTest)
+      }
+      fastrand_test_time(difftime(t1_testfast, t0_testfast, units = "secs"))
+      
+      # =========== 2) base R randomization test timing ===========
+      # We must also have the base R set of randomizations
+      req(RerandResult_base())
+      rr_base <- RerandResult_base()
+      if (is.null(rr_base$randomizations) || nrow(rr_base$randomizations) < 1) {
+        showNotification("No base R randomizations found. Cannot run base R test.", type = "error")
+        RandTestResult_base(NULL)
+        return(NULL)
+      }
+      
+      t0_testbase <- Sys.time()
+      outTestBase <- tryCatch({
+        baseR_randomization_test(
+          obsW    = obsW,
+          obsY    = obsY,
+          allW    = rr_base$randomizations
+        )
+      }, error = function(e) e)
+      t1_testbase <- Sys.time()
+      
+      if (inherits(outTestBase, "error")) {
+        showNotification(paste("Error in randomization_test (base R):", outTestBase$message), type="error")
+        RandTestResult_base(NULL)
+      } else {
+        RandTestResult_base(outTestBase)
+      }
+      baseR_test_time(difftime(t1_testbase, t0_testbase, units = "secs"))
+    })
   })
   
   # Display p-value and observed tau (from the fastrerandomize test)