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The goal of ruminate is to facilitate exploration of pharmacometrics data. This is done by creating a Shiny interface to different tools for data transformation (dplyr and tidyr), plotting (ggplot2), and noncompartmental analysis (PKNCA). These results can be reported in Excel, Word or PowerPoint. The state of the app can be saved and loaded at a later date. When saved, a script is generated to reproduce the different actions in the Shiny interface.

Deployed example in the cloud

You can point your web browser to runrumiate.ubiquity.tools and try the development version of ruminate. Keep in mind this is a public server. No data is tracked or kept, but it is open to the public. So be careful about uploading confidential data. Also know this is a single instance and if many people are using it at once it can be slow.

Local installation

From CRAN

You can install the released version of rumiante from CRAN with:

# General dependencies:
install.packages("clipr")
install.packages("gridExtra")
install.packages("prompter")
install.packages("readxl")
install.packages("shinydashboard")
install.packages("ubiquity")

# Dependencies for the MB and CTS modules
install.packages("nlmixr2lib")
install.packages("nonmem2rx")
install.packages("rxode2")

# Actual package
install.packages("ruminate")

Development version

You can install the development version from GitHub with the following:

# Installing devtools if it's not already installed
if(system.file(package="devtools") == ""){
  install.packages("devtools") 
}

# General dependencies:
install.packages("clipr")
install.packages("gridExtra")
install.packages("prompter")
install.packages("readxl")
install.packages("shinydashboard")
install.packages("ubiquity")

# Dependencies for the MB and CTS modules
install.packages("nlmixr2lib")
install.packages("nonmem2rx")
install.packages("rxode2")

devtools::install_github("john-harrold/onbrand",  dependencies=TRUE)
devtools::install_github("john-harrold/formods",  dependencies=TRUE)
devtools::install_github("john-harrold/ruminate")

Note that because ruminate depends on formods and onbrand you will need to first install the development versions of onbrand and formods.

Running in ruminate

In RStudio

In a Docker container

Note this uses an x86 image. So it will only work on Intel or AMD cpus. This means that you wont get very far with an M1 mac. If you want, you can download the Docker file here. This will build the docker image from the repository on GitHub.

docker build -t ruminate --no-cache  https://raw.githubusercontent.com/john-harrold/ruminate/main/inst/docker/local_container

This will run the Docker image locally:

docker run --name ruminate --rm -p 3838:3838 ruminate

If everything worked you can then point your web browser to:

http://127.0.0.1:3838/

This will push the image to DockerHub:

docker tag ruminate <username>/ruminate:latest
docker push <username>/ruminate:latest

You can use this to pull the image from DockerHub:

docker pull <username>/ruminate:latest