In mcguinlu/robvis: Visualize the Results of Risk-of-Bias (ROB) Assessments

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-", 
  out.width = "90%",
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fig_count <- 1

robvis

UPDATE: robvis now exists as a web-app, aimed at those who are not familiar with R or who want to explore the package's functionality before installing it locally.

Description

library(robvis)

The robvis (Risk-Of-Bias VISualization) package facilitates the rapid production of publication-quality risk-of-bias assessment figures, correctly formatted according to the assessment tool used.

The motivation for this package is more fully described in the (open access) article introducing the tool, available here.

Getting started

Install the development version which contains new functionality and a range of bug fixes:

install.packages("devtools")
devtools::install_github("mcguinlu/robvis")

To update the package, run the install_github("mcguinlu/robvis") command again.

If you wish to use the older CRAN version of the package, use the following command:

install.packages("robvis")

Load data

To load your own data from a .csv file:

mydata <- read.csv("path/to/mydata.csv", header = TRUE)

To help users explore robvis, we have included example datasets in the package, one for each of the tool templates that currently exist within the package. The data_rob2 dataset (view it here), which contains example risk-of-bias assessments performed using the RoB2.0 tool for randomized controlled trials, is used to create the plots in subsequent sections.

Create plots

The package contains two plotting functions:

1. rob_summary()

Returns a ggplot object displaying a bar-chart of the risk of bias of included studies across the domains of the specified tool. [Note: the defaults used in this function have changed from their original settings, so that a un-weighted barplot is now produced by default. See the NEWS.md file for further information.]

summary_rob <- rob_summary(data = data_rob2, tool = "ROB2")

summary_rob

``` {r, echo = FALSE} plot <- rob_summary(data = data_rob2, tool = "ROB2") file = paste0("man/figures/robplot",fig_count,".png") rob_save(plot, file) fig_count <- fig_count + 1

<div style="text-align:center"><img src=`r file` width="70%" height="70%"/></div>



#### 2. rob_traffic_light()
Returns a ggplot object displaying a ["traffic light plot"](https://handbook-5-1.cochrane.org/chapter_8/figure_8_6_c_example_of_a_risk_of_bias_summary_figure.htm), displaying the risk of bias judgment in each domain for each study.

```r
trafficlight_rob <- rob_traffic_light(data = data_rob2,
                                      tool = "ROB2",
                                      psize = 10)

trafficlight_rob

``` {r, echo = FALSE} plot <- rob_traffic_light(data = data_rob2, tool = "ROB2", psize = 10) file = paste0("man/figures/robplot",fig_count,".png") rob_save(plot, file) fig_count <- fig_count + 1

<div style="text-align:center"><img src=`r file` width="70%" height="70%"/></div>

### Other functions

#### rob_save()
Pass the `robvis` to this function, along with a destination file, to save your risk-of-bias plots using sensible defaults.

```r
rob_save(trafficlight_rob, "rob_fig.png")

rob_tools()

Outputs a list of the risk of bias assessment tools for which a template currently exists in rob_summary(). We expect this list to be updated in the near future to include tools such as ROBIS (tool for assessing risk of bias in systematic reviews).

rob_tools()

Advanced usage

Change the colour scheme

The colour argument of both plotting functions allows users to select from two predefined colour schemes ("cochrane" or "colourblind") or to define their own palette by providing a vector of hex codes.

For example, to use the predefined "colourblind" palette:

rob_summary(data = data_rob2,
            tool = "ROB2",
            colour = "colourblind")

``` {r, echo = FALSE} plot <- rob_summary(data = data_rob2, tool = "ROB2", colour = "colourblind") file = paste0("man/figures/robplot",fig_count,".png") rob_save(plot, file) fig_count <- fig_count + 1

<div style="text-align:center"><img src=`r file` width="70%" height="70%"/></div>

And to define your own colour scheme:
```r
rob_summary(
  data = data_rob2,
  tool = "ROB2",
  colour = c("#f442c8",
             "#bef441",
             "#000000",
             "#d16684")
)

``` {r, echo = FALSE} plot <- rob_summary(data = data_rob2, tool = "ROB2", colour = c("#f442c8", "#bef441", "#000000", "#d16684")) file = paste0("man/figures/robplot",fig_count,".png") rob_save(plot, file) fig_count <- fig_count + 1

<div style="text-align:center"><img src=`r file` width="70%" height="70%"/></div>

### No "Overall" judgement

By default, both functions include an "Overall" risk of bias domain. To prevent this, remove the overall column from your dataset and set `overall = FALSE`.

```r
summary_rob <- rob_summary(data = data_rob2[1:6], tool = "ROB2", overall = FALSE)
summary_rob

``` {r, echo = FALSE} plot <- rob_summary(data = data_rob2[1:6], tool = "ROB2", overall = FALSE) file = paste0("man/figures/robplot",fig_count,".png") rob_save(plot, file) fig_count <- fig_count + 1

<div style="text-align:center"><img src=`r file` width="70%" height="70%"/></div>

```r
rob_traffic_light(data = data_rob2[1:6],
                  tool = "ROB2",
                  overall = FALSE)

``` {r, echo = FALSE} plot <- rob_traffic_light(data = data_rob2[1:6], tool = "ROB2", overall = FALSE) file = paste0("man/figures/robplot",fig_count,".png") rob_save(plot, file) fig_count <- fig_count + 1

<div style="text-align:center"><img src=`r file` width="70%" height="70%"/></div>

### Editing the plots
Finally, because the output (`summary_rob` and `trafficlight_rob` in the examples above) is a ggplot2 object, it is easy to adjust the plot to your own preferences.

For example, to add a title:
```r
library(ggplot2)

rob_summary(data = data_rob2, tool = "ROB2") +
  ggtitle("Summary of RoB 2.0 assessments")

{r, echo = FALSE} plot <- rob_summary(data = data_rob2, tool = "ROB2") + ggplot2::ggtitle("Summary of RoB2.0 assessments") file = paste0("man/figures/robplot",fig_count,".png") rob_save(plot, file) fig_count <- fig_count + 1

r file width="70%" height="70%"/>

Examples of robvis in published papers

To date, robvis has been cited in more than 1500 academic articles - these can be explored here.

Code of conduct

Please note that the 'robvis' project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

License

This project is licensed under the MIT License - see the LICENSE.md file for details.

Acknowledgments

• The rob_summary() function was based on code forwarded by a colleague. I recently discovered that this code was adapted from that presented in the wonderful "Doing Meta-Analysis in R" guide, so I would like to acknowledge the authors here.
• Emily Kothe for help in fixing ggplot2 coding issues.
• Eliza Grames for creating the robvis hex sticker.

mcguinlu/robvis documentation built on July 4, 2023, 11:15 p.m.