Updating paper title. Dropping CI calibration from sensitivity analysis.

thehyve · Apr 9, 2018 · 42a8bd6 · 42a8bd6
1 parent d131a32
commit 42a8bd6
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Showing 3 changed files with 19 additions and 16 deletions.
diff --git a/SystematicEvidence/plots.R b/SystematicEvidence/plots.R
@@ -80,19 +80,23 @@ plotPs <- function(ps, target, comparator) {
   return(plot)
 }
 
-plotForest <- function(estimate) {
+plotForest <- function(estimate, showCalibrated = TRUE) {
   d1 <- data.frame(logRr = estimate$logRr,
                    logLb95Rr = log(estimate$ci95lb),
                    logUb95Rr = log(estimate$ci95ub),
                    database = estimate$db,
                    type = "Uncalibrated")
+  if (showCalibrated) {
   d2 <- data.frame(logRr = estimate$calLogRr,
                    logLb95Rr = log(estimate$calCi95lb),
                    logUb95Rr = log(estimate$calCi95ub),
                    database = estimate$db,
                    type = "Calibrated")
 
   d <- rbind(d1, d2)
+  } else {
+    d <- d1
+  }
   d$significant <- d$logLb95Rr > 0 | d$logUb95Rr < 0
 
   breaks <- c(0.25, 0.5, 1, 2, 4, 6, 8, 10)

diff --git a/SystematicEvidence/server.R b/SystematicEvidence/server.R
@@ -241,7 +241,7 @@ shinyServer(function(input, output) {
   output$sensitivityAnalysisPlot <- renderPlot({
     sensitivityAnalysis <- sensitivityAnalysis()
     if (is.null(sensitivityAnalysis)) return(NULL)
-    plotForest(sensitivityAnalysis)
+    plotForest(sensitivityAnalysis, showCalibrated = FALSE)
   })
 
   output$sensitivityAnalysisTable <-  renderTable({
@@ -267,18 +267,18 @@ shinyServer(function(input, output) {
                  ", p = ",
                  formatC(estimate$p, digits = 2, format = "f"),
                  ")")
-    calHr <- paste0(formatC(estimate$calRr, digits = 2, format = "f"), 
-                    " (95% CI: ",
-                    formatC(estimate$calCi95lb, digits = 2, format = "f"), 
-                    "-",
-                    formatC(estimate$calCi95ub, digits = 2, format = "f"), 
-                    ", p = ",
-                    formatC(estimate$calP, digits = 2, format = "f"),
-                    ")")
+    # calHr <- paste0(formatC(estimate$calRr, digits = 2, format = "f"), 
+    #                 " (95% CI: ",
+    #                 formatC(estimate$calCi95lb, digits = 2, format = "f"), 
+    #                 "-",
+    #                 formatC(estimate$calCi95ub, digits = 2, format = "f"), 
+    #                 ", p = ",
+    #                 formatC(estimate$calP, digits = 2, format = "f"),
+    #                 ")")
     p(HTML(paste0("Using an intent-to-treat  instead of a per-protocol analysis, when comparing the risk of ", point$outcomeName, " between new users of ", point$targetName, 
                   " and ", point$comparatorName, " in the ", point$db, 
                   " database, the estimated <b>uncalibrated hazard ratio</b> was <b>",hr,
-                  "</b>, the estimated <b>calibrated hazard ratio</b> was <b>", calHr, "</b>.")))
+                  "</b>.")))
   })
 
   # Literature --------------------------------------------------------------

diff --git a/SystematicEvidence/ui.R b/SystematicEvidence/ui.R
@@ -1,7 +1,7 @@
 library(shiny)
 
 shinyUI(fluidPage(style = 'width:1000px;',
-  titlePanel("Supplementary data for 'Improving reproducibility using high-throughput observational studies with empirical calibration: comparing all depression treatments'"),
+  titlePanel("Supplementary data for 'Improving reproducibility using high-throughput observational studies with empirical calibration'"),
   tabsetPanel(
     tabPanel("Systematically generated evidence",
              fluidRow(
@@ -70,8 +70,7 @@ shinyUI(fluidPage(style = 'width:1000px;',
                                  div(strong("Table S1.2."),"Counts of subjects, person-days and outcomes in the target and comparator population.")),
                           column(4, 
                                  plotOutput("sensitivityAnalysisPlot", height = "200px"),
-                                 div(strong("Figure S1.6."),"Hazard ratios and confidence intervals (CI) across the databases, both
-                                     calibrated (top) and uncalibrated (bottom). Blue indicates the CI includes one, orange indicates
+                                 div(strong("Figure S1.6."),"Hazard ratios and confidence intervals (CI) across the databases. Blue indicates the CI includes one, orange indicates
                                      the CI does not include one."))
                         )
                )
@@ -104,8 +103,8 @@ shinyUI(fluidPage(style = 'width:1000px;',
              br(),
              p("Supplementary data for:"),
              p("Schuemie MJ, Ryan PB, Hripcsak G, Madigan D, Suchard MA,", 
-               em("A systematic approach to improving the reliability and scale of evidence from health care data."), 
-               ", ...")
+               em("Improving reproducibility using high-throughput observational studies with empirical calibration."), 
+               ", Phil. Trans. R. Soc. A, 2018")
     )
   )
 )