CTU Berns R Package universe

R package universes are similar a bit like mini-CRANs. ‘The system automatically tracks registered git repositories containing R packages, builds binaries for Windows and MacOS, renders vignettes, and makes all data available through dashboards, feeds and APIs on personal subdomains’.

CTU Berns universe is here.

Packages in the universe

package	description	status
accrualPlot	Tracking accrual in clinical trials is important for trial success. If accrual is too slow, the trial will take too long and be too expensive. If accrual is much faster than expected, time sensitive tasks such as the writing of statistical analysis plans might need to be rushed. ‘accrualPlot’ provides functions to aid the tracking of accrual and predict when a trial will reach it’s intended sample size.
btabler	There are a number of packages for creating LaTeX tables from R, but they lack feature like merging cells. btabler provides a function to do just that.
CTUtemplate	Templates and functions for use in CTU Bern.
kpitools	Assessing performance of clinical trials can assist identify problems earlier in the trial than might be possible without it and help to improve trial quality. Tools for the creating performance indicator reports are however uncommon. ‘kpitools’ aims to provide tools to create such reports.
presize	Bland (2009) doi:10.1136/bmj.b3985 recommended to base study sizes on the width of the confidence interval rather the power of a statistical test. The goal of ‘presize’ is to provide functions for such precision based sample size calculations. For a given sample size, the functions will return the precision (width of the confidence interval), and vice versa.
redcaptools	Tools for exporting and working with REDCap data (e.g. adding labels, formatting dates).
secuTrialR	Seamless and standardized interaction with data exported from the clinical data management system (CDMS) ‘secuTrial’https://www.secutrial.com. The primary data export the package works with is a standard non-rectangular export.
sse	Provides functions to evaluate user-defined power functions for a parameter range, and draws a sensitivity plot. It also provides a resampling procedure for semi-parametric sample size estimation and methods for adding information to a Sweave report.
svn	Get information on SVN repositories through R. Explore file status, commit logs etc.
SwissASR	Completing the SwissEthics Annual Safety Report can be tiresome. This package eases the pain by providing an automated method to fill it out.
unibeCols	The University of Bern has a set of corporate design colours. This package has functions that contain them.
validation	The validation platform consists of three GitHub repositories, one of which hosts this package. The others host tests for specific packages, and a location to reports the results of tests and validations. This package provides tools to work with that data.

For users…

All vignettes are accessible via the articles button on the universe page.

To use the universe, in R, do the following, which adds the universe to your list of repos (when installing packages, R will cycle through the repos until it finds the appropriate package)…

options(repos = c(CTU = "https://ctu-bern.r-universe.dev",
                  CRAN = "https://cran.rstudio.com/"))

It is then possible to install universe packages as if they were CRAN packages…

install.packages("accrualPlot")

Alternatively, you can install without setting the option:

install.packages("accrualPlot", repos = "https://ctu-bern.r-universe.dev")

For maintainers…

A dashboard of the included packages and build status can be found here.

Briefly, packages should be added to packages.json. They are then tracked on r-universe and built each hour. See here for further details of universes

Acknowledgements

The package logo was created with ggplot2 and hexSticker.