Tendril v2.0.4

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Compute and Display Tendril Plots

Compute the coordinates to produce a tendril plot. In the tendril plot, each tendril (branch) represents a type of events, and the direction of the tendril is dictated by on which treatment arm the event is occurring. If an event is occurring on the first of the two specified treatment arms, the tendril bends in a clockwise direction. If an event is occurring on the second of the treatment arms, the tendril bends in an anti-clockwise direction. Ref: Karpefors, M and Weatherall, J., "The Tendril Plot - a novel visual summary of the incidence, significance and temporal aspects of adverse events in clinical trials" - JAMIA 2018; 25(8): 1069-1073 <doi:10.1093/jamia/ocy016>.

Readme

Tendril plot package v2.0.4

R library for tendril plotting between two treatments.

Download

The package can be downloaded as a .tar.gz from the appropriate release page

Installation

In RStudio (for end-users)

The package can be installed with RStudio in Tools -> Install Packages -> Install from package archive file

In a packrat environment (for developers)

You can ensure that tendril is installed in an isolated packrat environment. This is only required if you want to keep its installation isolated and you don't have access to the dependencies in your normal working environment

OSX Mojave

To install the dependencies in your packrat environment on OSX you will need clang with OpenMP support. Unfortunately Mojave does not ship with it.

  1. open /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
  2. Install homebrew from https://brew.sh/
  3. Install the required packages to compile Tendril dependencies
    brew install gfortran
    brew install llvm
    brew install boost
    brew install libomp
  1. add this to ~/.R/Makevars
    CC=/usr/local/opt/llvm/bin/clang
    CXX=/usr/local/opt/llvm/bin/clang++
    CXX11=/usr/local/opt/llvm/bin/clang++
    CXX14=/usr/local/opt/llvm/bin/clang++
    CXX17=/usr/local/opt/llvm/bin/clang++
    CXX1X=/usr/local/opt/llvm/bin/clang++
    LDFLAGS=-L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib
    CFLAGS=-I/usr/local/opt/llvm/include
    CPPFLAGS=-I/usr/local/opt/llvm/include
  1. Type

    make env

Functions in Tendril

Name Description
TendrilData Example dataframe in package Tendril.
plot.TendrilPerm Plot TendrilPerm
plot_timeseries Plot time series
Tendril Tendril
Tendril.perm.res Example object Tendril as generated by Tendril() and Tendril.perm().
plot.Tendril Plot Tendril
TendrilPerm Tendril permutations
SubjList Example of SubjList in package Tendril.
Tendril.res Example object Tendril as generated by Tendril().
Rotations Example of Rotations in package Tendril.
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Vignettes of Tendril

Name
TendrilUsage.Rmd
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Details

Type Package
License GPL-2
URL https://github.com/Karpefors/Tendril
BugReports https://github.com/Karpefors/Tendril/issues
Encoding UTF-8
LazyData true
RoxygenNote 6.1.1
VignetteBuilder knitr
NeedsCompilation no
Packaged 2020-02-03 08:51:46 UTC; ktwg434
Repository CRAN
Date/Publication 2020-02-11 11:00:02 UTC

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