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robvis

Project Status: Active – The project has reached a stable, usable state and is being actively developed. CRAN Badge. CRAN Downloads.
R build status Codecov test coverage
DOI metaverse Identifier

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

The robvis package takes the summary table from risk-of-bias assessments and produces plots formatted according to the assessment tool used.

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

2. rob_traffic_light()

Returns a ggplot object displaying a “traffic light plot”, displaying the risk of bias judgment in each domain for each study.

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

trafficlight_rob

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.

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()
#> Note: the "ROB2-Cluster" template is only available for the rob_traffic_light() function.
#> [1] "ROB2"         "ROB2-Cluster" "ROBINS-I"     "QUADAS-2"     "QUIPS"       
#> [6] "Generic"

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")

And to define your own colour scheme:

rob_summary(
  data = data_rob2,
  tool = "ROB2",
  colour = c("#f442c8",
             "#bef441",
             "#000000",
             "#d16684")
)

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.

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

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:

library(ggplot2)

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

Examples of robvis in published papers

See more 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.

Research notice

Please note that this repository is participating in a study into sustainability of open source projects. Data will be gathered about this repository for approximately the next 12 months, starting from June 2021.

Data collected will include number of contributors, number of PRs, time taken to close/merge these PRs, and issues closed.

For more information, please visit the informational page or download the participant information sheet.