RAVE:Install

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RAVE logo R Analysis and Visualization of iEEG


Install RAVE

Simplified Mac Install

Click here to download the Mac installation script.

This script has been tested with the current Mac operating system, Catalina (Mac OSX 10.15).

  1. After download, find the file "rave-installer-macosx.command.zip" in the "Downloads" folder.
  2. If it has not automatically been unzipped, double-click to extract the file named "rave-installer-macosx.command".
  3. To run the the commands in the script, right click (with no right mouse button, hold down the control key on the keyboard and click the mouse button or trackpad) on the file to bring up an actions menu and select the first choice, "Open". The warning "rave-installer-macosx.command is from an unidentified developer. Are you sure you want to open it?" will be presented, choose "Open" to proceed. If "Open" is not shown (only "OK") you may have left-clicked instead of right-clicked on the installer script. Select "OK" and try again.

The script installs R, RStudio, RAVE and all dependencies including the 3D Viewer, the N27 brain and demo data. You will be asked various "Do you accept this license?"-type questions along the way. The installer will place a "RAVE" icon on your desktop. Double-click the icon to launch RAVE.

Full Installation Guide For Any Platform

  1. Install the prerequisites. The most common installation problem is that the prerequisites are not installed. For instance, RAVE requires the latest versions of R (>= 3.6.0) and RStudio. Trying to install RAVE on older versions of R and RStudio will lead to unpredictable error messages.
  2. Open the RStudio application using the desktop shortcut. In Mac OSX, RStudio can be found in the Applications folder. Copy and paste the following commands (one at a time) into the RStudio console to install the current version of RAVE. Answer "Yes" to any questions that appear. In the case of errors, relaunch RStudio and repeat the commands.
 install.packages('devtools')
 devtools::install_github('beauchamplab/rave')

An error will be generated if XCode (for Mac) or RTools (for Windows) is not installed. Return to previous step, "install prerequisites". Next, install other packages needed by RAVE. If asked to compile packages from source, choose "no".

 rave::check_dependencies()

This step may fail on Windows. If so, run

 remotes::install_github("dipterix/dipsaus", upgrade = FALSE, force = FALSE, quiet = FALSE)

Ensure that all available RAVE modules are accessible

 rave::arrange_modules(TRUE, TRUE)

Check if template brain is installed.

 threeBrain::download_N27(make_default = TRUE)

Docker (special-purpose containerized installation)

Docker creates a "virtual machine" within which other software, such as RAVE, runs. This can be useful if you wish to distribute or create archival copies of RAVE, for instance to create a snapshot of software+data for uploading to a repository when a manuscript is published.For more information, see the GitHub Rave Docker page.

RAVE-within-Docker is not recommended for day-to-day (production) usage as performance is worse and usage is more complex. For most use case, we recommend installing RAVE using the steps above.

Checking installation

After installing or updating RAVE, quit and restart RStudio before continuing. To start RAVE, type (or copy and paste) the following command into the RStudio console:

 rave::start_rave()

A new web browser window should open showing the RAVE splash screen and the current version number (e.g. 1.0). If RAVE data is not in the default location, point RAVE to it with

rave::rave_options()

Updating RAVE

To update existing installations of RAVE, first check for newer versions of RStudio (start RStudio, "Help"/"Check for Updates") and R (start R, "R"/"Check For R Updates"). Quit and restart as RStudio is unable to update packages that are in use. Then, run the following commands.

 rave::check_dependencies()

If updating fails, use the following command to reinstall.

 install.packages(c("startup", "rstudioapi"))
 install.packages(c(
   'threeBrain', 'dipsaus', 'rutabaga', 'ravebuiltins', 'rave'
 ), repo = c(
   'CRAN' = "https://cran.rstudio.com/",
   'dipterix' = "https://dipterix.github.io/drat/"
 )); rstudioapi::restartSession()

Note that for major updates of R (e.g. R 3.X to 4.X) RAVE will need to be completely reinstalled: all packages must be reloaded and rave_options() reset.

Additional Demo data

RAVE includes time series data from one subject for single subject processing and collated data from many subjects for learning group analysis. Additional time series data can be obtained with

 rave::download_sample_data('XX')

Where XX is one of the following: KC, YAB, YAD, YAF, YAH, YAI, YAJ, YAK (~ 1GB per subject). For sample data included with RAVE, XX is 'DemoSubject' and '_group_data'.

Experimental RAVE

For the latest experimental features, install the development build. Check GitHub for latest versioning information.

devtools::install_github('beauchamplab/ravebuiltins@migrate2')
devtools::install_github('beauchamplab/rave@dev-1.1')
devtools::install_github('dipterix/threeBrain')
devtools::install_github('dipterix/dipsaus')

if asked

 These packages have more recent versions available. It is recommended to update all of them. Which would you like to update?

Type

 3: None

Restart the RStudio session after installing the new version.