tabby2

A friendly user tool for visualizing state level TB predictions and interventions.

Online at https://ppmltools.org/tabby2

Installation and Setup

Clone the project

git clone git@github.com:ppml/tabby2.git

Note that tabby2 makes use of Cario, a library in R which depends on having a few packages available.

On Debian based Linuxs this means having the following packages installed:

sudo apt install libgtk2.0-dev libcairo2-dev xvfb xauth xfonts-base libxt-dev

Now we can go ahead and install the R package dependencies:

# move into our project on terminal:
cd tabby2/
git checkout beta/
R

# in R:
devtools::install_deps("utilities/")
devtools::install_deps("tabby1utilities/")

We will also need MITUS, the model of tuberculosis that Tabby2 renders the outcomes of.

# in terminal 
cd .. # clone MITUS next to tabby2, or any other directory works fine too
git clone git@github.com:PPML/MITUS.git
cd MITUS/
R

# in R: 
devtools::install("./", dependencies=TRUE)

We also need the package MITUSCalibPlots, which handles the generation of calibration plots from stored data in the MITUS package.

# in terminal 
cd .. # clone MITUS_Calib_Plots next to tabby2, or any other directory works fine too
git clone git@github.com:PPML/MITUS_Calib_Plots.git
cd MITUS_Calib_Plots/
R

# in R: 
devtools::install("./", dependencies=TRUE)

We also need the tabus package, the package which does fast reshaping of outcomes from MITUS for plotting with ggplot2.

# in terminal 
cd .. # clone reshape_mitus_results_for_tabby2 next to tabby2, or any other directory works fine too
git clone git@github.com:ppml/reshape_mitus_results_for_tabby.git
cd reshape_mitus_results_for_tabby/
R

# in R: 
devtools::install("./", dependencies=TRUE)

Now we can run Tabby2

# in terminal 
cd ../
cd tabby2/
R

# in R: 
shiny::runApp()