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.
| 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. | |
HSAr |
Automates the delineation of hospital service areas (HSAs). Previous methods rely extensively on manual, subjective decisions regarding to which HSA a given unit should be assigned. This package provides a method to construct contiguous HSAs using spatial shapefiles and source-destination patient flow data. | |
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. | |
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. | |
SwissASR |
Completing the SwissEthics Annual Safety Report can be tiresome. This package eases the pain by providing an automated method to fill it out. |
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")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
The package logo was created with
ggplot2 and
hexSticker.