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Author: mcguinlu

R/rob_summary_plot.R

@@ -7,50 +7,36 @@
 #' @export
 
 rob_summary <- function(data, tool, save = "No") {
-  #End column depends on number of domains in tool (end <- no. of domains + 1)
-  if (tool == "ROBINS-I") {
-    end <- 8
-  }
-  if (tool == "QUADAS-2") {
-    end <- 5
-  }
 
 if (tool == "ROB2") {
-    start <- 2
-    end <- 6
     data.tmp <- data
     print("Renaming columns...")
     names(data.tmp)[2] <- "Bias due to randomisation"
     names(data.tmp)[3] <- "Bias due to deviations from intended intervention"
     names(data.tmp)[4] <- "Bias due to missing data"
     names(data.tmp)[5] <- "Bias due to outcome measurement"
     names(data.tmp)[6] <- "Bias due to selection of reported result"
+    names(data.tmp)[7] <- "Weight"
+    data.tmp <- data.tmp[,c(2:7)]
 
     rob.tidy <- suppressWarnings(tidyr::gather(data.tmp,
                                              domain, judgement,
-                                             start:end))
-    print("Data tidied")
+                                             -Weight))
 
-    # rob.tidy <-
+    print("Data tidied")
 
     rob.tidy$judgement <- as.factor(rob.tidy$judgement)
     rob.tidy$domain <- as.factor(rob.tidy$domain)
 
-    # rob.tidy$domain <- as.factor(rob.tidy$domain)
-
-    # rob.tidy$domain <- factor(rob.tidy$domain,
-    #                                   levels(rob.tidy$domain)[c(5, 2, 3, 1, 4)])
-
     rob.tidy$domain <- factor(rob.tidy$domain,
-                                      levels(rob.tidy$domain)[c(5, 2, 3, 1, 4)])
-
+                                      levels(rob.tidy$domain)[c(5, 3, 2, 1, 4)])
 
     rob.tidy$judgement <- factor(rob.tidy$judgement,
                                  levels(rob.tidy$judgement)[c(1, 3, 2)])
 
     plot <- ggplot2::ggplot(data = rob.tidy) +
       geom_bar(
-        mapping = aes(x = domain, fill = judgement),
+        mapping = aes(x = domain, fill = judgement,weight = Weight),
         width = 0.7,
         position = "fill",
         color = "black"
@@ -93,7 +79,7 @@ if (tool == "ROB2") {
 
 if (tool == "ROBINS-I") {
     start <- 2
-    end <- 8
+    end <- 9
     data.tmp <- data
     print("Renaming columns...")
     names(data.tmp)[2] <- "Bias due to confounding"
@@ -106,8 +92,8 @@ if (tool == "ROBINS-I") {
 
     rob.tidy <- suppressWarnings(tidyr::gather(data.tmp,
                                                domain, judgement,
-                                               start:end))
-
+                                               start:end,
+                                               -Weight))
     print("Data tidied")
 
     rob.tidy$judgement <- as.factor(rob.tidy$judgement)
@@ -169,7 +155,7 @@ if (tool == "ROBINS-I") {
 
 if (tool == "QUADAS-2") {
   start <- 2
-  end <- 5
+  end <- 6
   data.tmp <- data
   print("Renaming columns...")
   names(data.tmp)[2] <- "Patient selection"
@@ -179,7 +165,8 @@ if (tool == "QUADAS-2") {
 
   rob.tidy <- suppressWarnings(tidyr::gather(data.tmp,
                                              domain, judgement,
-                                             start:end))
+                                             start:end,
+                                             -Weight))
   print("Data tidied")
 
     rob.tidy$judgement <- as.factor(rob.tidy$judgement)
@@ -204,13 +191,14 @@ if (tool == "QUADAS-2") {
       scale_fill_manual(
         "Risk of Bias",
         values = c(
-          "Low" = "#66c2a5",
+          "High" = "#fc8d62",
           "Some concerns" = "#808080",
-          "High" = "#fc8d62"
+          "Low" = "#66c2a5"
         ),
-        labels = c("  Low risk of bias   ",
-                   "  Some concerns      ",
-                   "  High risk of bias  ")
+        labels = c(
+          "  High risk of bias   ",
+          "  Some concerns      ",
+          "  Low risk of bias  ")
       ) +
       scale_y_continuous(labels = scales::percent) +
       theme(

R/traffic_light_plot.R

@@ -0,0 +1,13 @@
+Study,D1,D2,D3,D4,Weight
+Study 1,Low,Low,Low,Low,33.33333333
+Study 2,Some concerns,Low,Low,Low,33.33333333
+Study 3,Some concerns,Low,Some concerns,Low,0.142857143
+Study 4,Low,Low,High,Low,9.090909091
+Study 5,High,High,Low,Low,12.5
+Study 6,Low,High,Some concerns,Low,25
+Study 7,Low,Some concerns,Some concerns,High,200
+Study 8,Low,Some concerns,Low,Low,11.11111111
+Study 9,Low,Low,High,Low,1.111111111
+Study 10,Some concerns,Low,Low,High,33.33333333
+Study 11,Some concerns,High,Some concerns,Low,0.142857143
+Study 12,Low,Low,Low,Low,9.090909091

data/data_quadas.csv

@@ -0,0 +1,10 @@
+Study,D1,D2,D3,D4,D5,Weight
+Study 1,Low,Low,Low,Low,Low,33.33333333
+Study 2,Some concerns,Low,Low,Low,Low,33.33333333
+Study 3,Some concerns,Low,Some concerns,Low,Low,0.142857143
+Study 4,Low,Low,High,Low,Some concerns,9.090909091
+Study 5,High,High,Low,Low,Some concerns,12.5
+Study 6,Low,High,Some concerns,Low,Low,25
+Study 7,Low,Some concerns,Some concerns,High,Low,200
+Study 8,Low,Some concerns,Low,Low,Low,11.11111111
+Study 9,Low,Low,High,Low,Low,1.111111111

data/data_quadas.rda

@@ -0,0 +1,13 @@
+Study,D1,D2,D3,D4,D5,D6,D7,Weight
+Study 1,Critical,Low,Critical,Critical,Low,Low,High,33.33333333
+Study 2,Some concerns,Low,Low,Critical,Low,Some concerns,Low,33.33333333
+Study 3,Some concerns,Low,Some concerns,Critical,Critical,Low,High,0.142857143
+Study 4,Low,Low,High,Critical,Some concerns,Low,Critical,9.090909091
+Study 5,High,High,Low,Low,Some concerns,Low,Some concerns,12.5
+Study 6,Critical,High,Some concerns,Critical,Critical,Some concerns,High,25
+Study 7,Critical,Some concerns,Some concerns,High,Critical,High,High,200
+Study 8,Critical,Some concerns,Low,Low,Low,Low,Critical,11.11111111
+Study 9,Critical,Low,High,Low,Low,High,Low,1.111111111
+Study 10,Some concerns,Low,Critical,High,Some concerns,Some concerns,High,0.142857143
+Study 11,Some concerns,High,Some concerns,Critical,High,Low,Critical,9.090909091
+Study 12,Critical,Critical,Low,Critical,Critical,Critical,Critical,12.5

data/data_rob.csv

@@ -14,20 +14,31 @@ knitr::opts_chunk$set(
   comment = "#>",
   warning = FALSE,
   fig.width = 8,
-  fig.height = 2.41,
+  fig.height = 2.41)
   library(tidyverse)
-)
+library(robvis)
 ```
 ## R Markdown
 
-This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
 
-When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
 
-```{r robsummary}
-#Import data 
-data_rob <- read.csv("../data/data_rob.csv", header = TRUE)
+```{r rob2summary}
+#Import data for ROB2.0 based risk-of-bias assessments
 
-# Produce summary barchart, detailing % of included studies that were at a given risk of bias for a certain domain of the RoB2.0 tool.
-robvis::rob_summary(data_rob, tool = "ROB2", save = "No")
+# Produce barchart summarising risk of bias for each domain, weighted by study precision.
+robvis::rob_summary(robvis::data_rob, tool = "ROB2", save = "No")
+```
+
+Users can also produce summary plots for two other commonly used tools: ROBINS-I and QUADAS-2
+
+```{r robinssummary}
+#Import data for ROB2.0 based risk-of-bias assessments
+# Produce barchart summarising risk of bias for each domain, weighted by study precision.
+robvis::rob_summary(data_robins, tool = "ROBINS-I", save = "No")
+```
+
+```{r quadassummary}
+#Import data for ROB2.0 based risk-of-bias assessments
+# Produce barchart summarising risk of bias for each domain, weighted by study precision.
+robvis::rob_summary(data_quadas, tool = "QUADAS-2", save = "No")
 ```