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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.
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.
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")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}.
This will run the default/stable version of rumiante:
As new modules are developed they can be found in the development app. This command will run the ruminate with any development modules enabled:
library(ruminate)
library(shiny)
runApp(system.file(package="ruminate","templates", "ruminate_devel.R"))If you are running this you should probably be using the development version off of github to make sure you have the latest version.
This kind of assumes a basic familiarity with Docker. Keep in mind that these containers are built for ‘x86’ images. Basically Intel/AMD cpus. This means that if you have a Mac with Apple Silicon (M1, M2,etc.) it may not work or the performance may not be that good.
This will pull container from docker and run it locally
docker pull johnmharrold/ruminate:latest
docker run -p 3838:3838 johnmharrold/ruminate:latest &If you want to create your own container you can do the following:
This will run the Docker image locally:
If everything worked you can then point your web browser to:
http://127.0.0.1:3838/This will push the image to DockerHub:
You can use this to pull the image from DockerHub:
If you want to deploy and customize ruminate, please see the Deployment vignette.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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