updated databaseIds and names, fixed blinding bug

Covid19EstimationHydroxychloroquine/global.R

@@ -33,9 +33,7 @@ loadFile <- function(file, removePart) {
   camelCaseName <- SqlRender::snakeCaseToCamelCase(tableName)
   if (!(tableName %in% splittableTables)) {
     newData <- readRDS(file.path(dataFolder, file))
-
     colnames(newData) <- SqlRender::snakeCaseToCamelCase(colnames(newData))
-
     if (exists(camelCaseName, envir = .GlobalEnv)) {
       existingData <- get(camelCaseName, envir = .GlobalEnv)
       newData <- rbind(existingData, newData)

Covid19EstimationHydroxychloroquine/ui.R

@@ -3,7 +3,7 @@ library(DT)
 
 shinyUI(
   fluidPage(style = "width:1500px;",
-            titlePanel(paste("Safety of hydroxychloroquine with azythromycin: a multi-national study", if(blind) "***Blinded***" else "")),
+            titlePanel(paste("Safety of hydroxychloroquine alone and in combination with azithromycin: a multi-national study", if(blind) "***Blinded***" else "")),
             tags$head(tags$style(type = "text/css", "
              #loadmessage {
                                  position: fixed;
@@ -29,9 +29,9 @@ shinyUI(
                                  HTML("<br/>"),
                                  HTML("<p>Below is the abstract of the manuscript that summarizes the findings:</p>"),
                                  HTML("<p><strong>Background:</strong> Hydroxychloroquine has recently received Emergency Use Authorization by the FDA and is currently prescribed in combination with azithromycin for COVID-19 pneumonia. We studied the safety of hydroxychloroquine, alone and in combination with azithromycin.</strong></p>"),
-                                 HTML("<p><strong>Methods:</strong> New user cohort studies were conducted including 16 severe adverse events (SAEs). Rheumatoid arthritis patients aged 18+ and initiating hydroxychloroquine were compared to those initiating sulfasalazine and followed up over 30 days. Self-controlled case series (SCCS) were conducted to further establish safety in wider populations. Separately, SAEs associated  with hydroxychloroquine-azithromycin (compared to hydroxychloroquine-amoxicillin) were studied. Data comprised 14 sources of claims data or electronic medical records from Germany, Japan, Netherlands, Spain, UK, and USA. Propensity score stratification and calibration using negative control outcomes were used to address confounding. Cox models were fitted to estimate calibrated hazard ratios (CalHRs) according to drug use. Estimates were pooled where I2<40%.</p>"),
-                                 HTML("<p><strong>Results:</strong> Overall, 956,374 and 310,350 users of hydroxychloroquine and sulfasalazine, and 323,122 and 351,956 users of hydroxychloroquine-azithromycin and hydroxychloroquine-amoxicillin were included. No excess risk of SAEs was identified when 30-day hydroxychloroquine and sulfasalazine use were compared. SCCS confirmed these findings. However, when azithromycin was added to hydroxychloroquine, we observed an increased risk of 30-day cardiovascular mortality (CalHR 2.19 [95% CI 1.22-3.94]), chest pain/angina (CalHR 1.15 [95% CI 1.05-1.26]), and heart failure (CalHR 1.22 [95% CI 1.02-1.45]).</p>"),
-                                 HTML("<p><strong>Conclusions:</strong> Short-term hydroxychloroquine treatment is safe, but addition of azithromycin may induce heart failure and cardiovascular mortality, potentially due to synergistic effects on QT length. We call for caution if such combination is to be used in the management of Covid-19.</p>"),
+                                 HTML("<p><strong>Methods:</strong> New user cohort studies were conducted including 16 severe adverse events (SAEs). Rheumatoid arthritis patients aged 18+ and initiating hydroxychloroquine were compared to those initiating sulfasalazine and followed up over 30 days. Self-controlled case series (SCCS) were conducted to further establish safety in wider populations. Separately, SAEs associated with hydroxychloroquine-azithromycin (compared to hydroxychloroquine-amoxicillin) were studied. Data comprised 14 sources of claims data or electronic medical records from Germany, Japan, Netherlands, Spain, UK, and USA. Propensity score stratification and calibration using negative control outcomes were used to address confounding. Cox models were fitted to estimate calibrated hazard ratios (CalHRs) according to drug use. Estimates were pooled where I2<40%.</p>"),
+                                 HTML("<p><strong>Findings:</strong> Overall, 956,374 and 310,350 users of hydroxychloroquine and sulfasalazine, and 323,122 and 351,956 users of hydroxychloroquine-azithromycin and hydroxychloroquine-amoxicillin were included. No excess risk of SAEs was identified when 30-day hydroxychloroquine and sulfasalazine use were compared. SCCS confirmed these findings. However, when azithromycin was added to hydroxychloroquine, we observed an increased risk of 30-day cardiovascular mortality (CalHR 2.19 [95% CI 1.22-3.94]), chest pain/angina (CalHR 1.15 [1.05-1.26]), and heart failure (CalHR 1.22 [1.02-1.45]). Cardiovascular mortality was also increased in long term on-treatment analysis of hydroxychloroquine versus sulfasalazine (CalHR 1.65 [1.12-2.44]).</p>"),
+                                 HTML("<p><strong>Interpretation:</strong> Hydroxychloroquine treatment appears safe during the 30 days post-initiation in rheumatoid arthritis, but combination use of hydroxychloroquine and azithromycin may induce heart failure and cardiovascular mortality.  Extended use of hydroxychloroquine may increase mortality risk in RA. Given that hydroxychloroquine, alone and in combination with azithromycin, is being actively considered for treatment in COVID-19, we call for caution and careful consideration about the benefit-risk trade-off of the uncertain efficacy and this identified risk when managing patients with COVID-19.</p>"),
                                  HTML("<br/>"),
                                  HTML("<p>Below are links for study-related artifacts that have been made available as part of this study:</p>"),
                                  HTML("<ul>"),