Fix git issues

Author: mcguinlu

.gitignore

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 /*.png
 *.xlsx
 R/rob_paired_plot.R
-README.md
-man/figures/robplot*

README.md

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+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+# robvis <img src="man/figures/robvis_hex_box.png" align="right" width="18%" height="18%" />
+
+[![Project Status: Active – The project has reached a stable, usable
+state and is being actively
+developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
+[![CRAN
+Badge.](https://www.r-pkg.org/badges/version-ago/robvis)](https://CRAN.R-project.org/package=robvis)
+[![CRAN
+Downloads.](https://cranlogs.r-pkg.org/badges/last-month/robvis)](https://CRAN.R-project.org/package=robvis)
+<br> [![R build
+status](https://github.com/mcguinlu/robvis/workflows/R-CMD-check/badge.svg)](https://github.com/mcguinlu/robvis/actions)
+[![Codecov test
+coverage](https://codecov.io/gh/mcguinlu/robvis/branch/master/graph/badge.svg)](https://codecov.io/gh/mcguinlu/robvis?branch=master)
+<br>
+[![DOI](https://img.shields.io/static/v1.svg?label=Publication&message=10.1002/jrsm.1411&color=informational)](https://doi.org/10.1002/jrsm.1411)
+[![metaverse
+Identifier](https://img.shields.io/static/v1.svg?label=Part%20of%20the&message=metaverse&color=informational)](https://www.github.com/rmetaverse/metaverse)
+
+**UPDATE**: `robvis` now exists as a
+[web-app](https://mcguinlu.shinyapps.io/robvis), 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:
+
+``` r
+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:
+
+``` r
+install.packages("robvis")
+```
+
+### Load data
+
+To load your own data from a .csv file:
+
+``` r
+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](https://github.com/mcguinlu/robvis/blob/master/data_raw/data_rob2.csv)),
+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. \[*Note: the
+defaults used in this function have changed from their original
+settings, so that a un-weighted barplot is now produced by default. See
+the NEWS.md file for further information.*\]
+
+``` r
+summary_rob <- rob_summary(data = data_rob2, tool = "ROB2")
+
+summary_rob
+```
+
+<div style="text-align:center">
+
+<img src=man/figures/robplot1.png 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
+```
+
+<div style="text-align:center">
+
+<img src=man/figures/robplot2.png 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).
+
+``` r
+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:
+
+``` r
+rob_summary(data = data_rob2,
+            tool = "ROB2",
+            colour = "colourblind")
+```
+
+<div style="text-align:center">
+
+<img src=man/figures/robplot3.png 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")
+)
+```
+
+<div style="text-align:center">
+
+<img src=man/figures/robplot4.png 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
+```
+
+<div style="text-align:center">
+
+<img src=man/figures/robplot5.png width="70%" height="70%"/>
+
+</div>
+
+``` r
+rob_traffic_light(data = data_rob2[1:6],
+                  tool = "ROB2",
+                  overall = FALSE)
+```
+
+<div style="text-align:center">
+
+<img src=man/figures/robplot6.png 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")
+```
+
+<div style="text-align:center">
+
+<img src=man/figures/robplot7.png width="70%" height="70%"/>
+
+</div>
+
+## Examples of `robvis` in published papers
+
+  - Perivoliotis, Konstantinos, et al. “[Comparing the efficacy and
+    safety of laparoscopic and robotic adrenalectomy: a meta-analysis
+    and trial sequential
+    analysis.](https://link.springer.com/article/10.1007/s00423-020-01860-9)”
+    Langenbeck’s Archives of Surgery (2020): 1-11.
+  - Adile, Ashley A., et al. “[Salvage therapy for progressive,
+    treatment-refractory or recurrent pediatric medulloblastoma: a
+    systematic review
+    protocol.](https://systematicreviewsjournal.biomedcentral.com/articles/10.1186/s13643-020-01307-8)”
+    Systematic Reviews 9.1 (2020): 1-9.
+  - Tanneru, Karthik, et al. “[Meta-analysis and systematic review of
+    intermediate-term follow-up of prostatic urethral lift for benign
+    prostatic
+    hyperplasia.](https://link.springer.com/article/10.1007/s11255-020-02408-y)”
+    International Urology and Nephrology (2020): 1-10.
+  - Veloso, Andreia, et al.. “[Effectiveness of Cognitive Training for
+    School-Aged Children and Adolescents With Attention
+    Deficit/Hyperactivity Disorder: A Systematic
+    Review.](https://www.frontiersin.org/articles/10.3389/fpsyg.2019.02983/full)”
+    Frontiers in Psychology 10 (2020): 2983.
+  - Simillis, Constantinos, et al. “[Postoperative chemotherapy improves
+    survival in patients with resected high‐risk stage II colorectal
+    cancer: results of a systematic review and
+    meta‐analysis.](https://onlinelibrary.wiley.com/doi/pdf/10.1111/codi.14994)”
+    Colorectal Disease (2020).
+  - Habadi, Mohammed Ibrahim, et al. “[Prevalence of Panic Disorders in
+    the Primary Health Care Setting: A Systematic Review and
+    Meta-Analysis.](https://www.ecronicon.com/ecmi/pdf/prevalence-of-panic-disorders-in-the-primary-health-care-setting-a-systematic-review-and-meta-analysis.pdf)”
+    EC Microbiology 16.1 (2019): 01-09.
+  - Gibb, Kate, et al. “[The consistent burden in published estimates of
+    delirium occurrence in medical inpatients over four decades: a
+    systematic review and meta-analysis
+    study.](https://www.medrxiv.org/content/medrxiv/early/2019/08/29/19005165.full.pdf)”
+    medRxiv (2019): 19005165.
+
+See more
+[here](https://scholar.google.com/scholar?cites=12564214960529060925&as_sdt=2005&sciodt=0,5&hl=en).
+
+## Code of conduct
+
+Please note that the ‘robvis’ project is released with a [Contributor
+Code of
+Conduct](https://github.com/mcguinlu/robvis/blob/master/CODE_OF_CONDUCT.md).
+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](https://github.com/mcguinlu/robvis/blob/master/LICENSE)
+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](https://bookdown.org/MathiasHarrer/Doing_Meta_Analysis_in_R/plotting-the-summary.html)”
+    guide, so I would like to acknowledge the authors here.
+  - [Emily Kothe](https://github.com/ekothe) for help in fixing
+    `ggplot2` coding issues.
+  - [Eliza Grames](https://github.com/elizagrames) 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](https://sustainable-open-science-and-software.github.io/) or
+download the [participant information
+sheet](https://sustainable-open-science-and-software.github.io/assets/PIS_sustainable_software.pdf).