Use RevBayes with a Graphical Interface


Graphical User Interfaces


There are two main graphical user interfaces (GUIs) that can be used with RevBayes. Below, installation instructions are listed for both.

Jupyter Notebook


First, download and install Python 3 and the Jupyter Notebook. Installation instructions are available from the Jupyter Development team here.

Now, use the Downloads page to find RevBayes compilation instructions for your operating system. When building RevBayes, substitute

./build.sh -jupyter true

for the normal build step. This will generate an rb-jupyter executeable. Add this executeable to your system path.

Finally, clone the RevBayes Jupyter Kernel.

git clone https://github.com/revbayes/revbayes_kernel.git

Change directories into the revbayes_kernel directory and use

sudo python3 setup.py install
python3 -m revbayes_kernel.install
pip3 install metakernel

to deploy the kernel. Now, when launching a Jupyter Notebook, RevBayes should be an available language when starting a notebook. You can check the installation by executing the revbayes_mcmc_demo.ipynb found in the revbayes_kernel directory.

Examples of RevNotebooks can be found in the RevNotebook repository.

RStudio


Compile or download RevBayes as appropriate for your system above. Add RevBayes to your system path.

Download R and RStudio. Once these are downloaded, start RStudio. Install the remotes package. We will also install the package usethis to aid with installation:

install.packages("remotes")
install.packages("usethis")

Use remotes to install RevKnitr:

remotes::install_github("revbayes/Revticulate")

Once installation is complete, type

library(Revticulate)

in a markdown chunk or in the console. This will prompt Revticulate to open your .Renviron file. You will use this to place the path to RevBayes in the Renviron, providing R with the location of RevBayes so that Revticulate may execute code using it. You will enter into the file the location of RevBayes on your hard drive. For example, if I have RevBayes installed in my software directory, this will be:

rb=/Users/software/rb

Now, you may use RevBayes in either KnitR or console. For examples of RevBayes used via Revticulate, see the Revticulate website.