Updated dependencies and vignetter

Author: mcguinlu

DESCRIPTION

@@ -12,4 +12,4 @@ Encoding: UTF-8
 LazyData: true
 RoxygenNote: 6.1.1
 Imports:
-  tidyverse
+  ggplot2

R/rob_summary_plot.R

@@ -10,7 +10,6 @@ rob_summary <- function(data, tool, save = "No") {
 
 if (tool == "ROB2") {
     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"
@@ -23,9 +22,8 @@ if (tool == "ROB2") {
                                              domain, judgement,
                                              -Weight))
 
-    print("Data tidied")
-
     rob.tidy$judgement <- as.factor(rob.tidy$judgement)
+
     rob.tidy$domain <- as.factor(rob.tidy$domain)
 
     rob.tidy$domain <- factor(rob.tidy$domain,
@@ -81,7 +79,6 @@ if (tool == "ROBINS-I") {
     start <- 2
     end <- 9
     data.tmp <- data
-    print("Renaming columns...")
     names(data.tmp)[2] <- "Bias due to confounding"
     names(data.tmp)[3] <- "Bias due to selection of participants"
     names(data.tmp)[4] <- "Bias in classification of interventions"
@@ -94,7 +91,6 @@ if (tool == "ROBINS-I") {
                                                domain, judgement,
                                                start:end,
                                                -Weight))
-    print("Data tidied")
 
     rob.tidy$judgement <- as.factor(rob.tidy$judgement)
 
@@ -167,9 +163,7 @@ if (tool == "QUADAS-2") {
                                              domain, judgement,
                                              start:end,
                                              -Weight))
-  print("Data tidied")
-
-    rob.tidy$judgement <- as.factor(rob.tidy$judgement)
+  rob.tidy$judgement <- as.factor(rob.tidy$judgement)
 
     rob.tidy$domain <- as.factor(rob.tidy$domain)
 
@@ -227,7 +221,6 @@ if (tool == "QUADAS-2") {
     extension <- paste(save)
     filename <- paste(tool, "_summary_figure",extension, sep = "")
     ggplot2::ggsave(filename, width = 8, height = 2.41)
-    print("Figure saved")
   }
 
   return(plot)

robvis.Rproj

@@ -18,4 +18,4 @@ StripTrailingWhitespace: Yes
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
-PackageRoxygenize: rd,collate,namespace
+PackageRoxygenize: rd,collate,namespace,vignette

vignettes/Introduction to robvis.Rmd

@@ -1,44 +1,47 @@
 ---
 title: "Introduction to robvis"
-author: "LAM"
+author: "Luke A McGuinness"
 date: "`r Sys.Date()`"
 vignette: >
   %\VignetteIndexEntry{Introduction to robvis}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
-
 ```{r setup, include=FALSE}
 knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>",
   warning = FALSE,
   fig.width = 8,
   fig.height = 2.41)
-  library(tidyverse)
-library(robvis)
+  library(ggplot2)
+  library(robvis)
 ```
-## R Markdown
+## Introduction to robvis, a visualisation tool for risk-of-bias assessments
 
+The tool takes the summary table from risk-of-bias assessments, produces a summary plot (incorporating some measure of weighting for each study), and formats the plot by the tool used.
 
+### RoB2.0 tool for randomised controlled trials
 
 ```{r rob2summary}
-#Import data for ROB2.0 based risk-of-bias assessments
-
+# data_rob: example dataset for ROBINS-I tool
 # Produce barchart summarising risk of bias for each domain, weighted by study precision.
-robvis::rob_summary(robvis::data_rob, tool = "ROB2", save = "No")
+rob_summary(data_rob, tool = "ROB2", save = "No")
 ```
 
 Users can also produce summary plots for two other commonly used tools: ROBINS-I and QUADAS-2
 
+### ROBINS-I tool for non-randomised studies of interventions
 ```{r robinssummary}
-#Import data for ROB2.0 based risk-of-bias assessments
+# data_robins: example dataset for ROBINS-I tool
 # Produce barchart summarising risk of bias for each domain, weighted by study precision.
-robvis::rob_summary(data_robins, tool = "ROBINS-I", save = "No")
+rob_summary(data_robins, tool = "ROBINS-I", save = "No")
 ```
 
+
+### QUADAS-2 for diagnostic test accuracy studies
 ```{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")
+rob_summary(data_quadas, tool = "QUADAS-2", save = "No")
 ```