the data files needed to run this package are too large to be uploaded but are available on my github (https://github.com/nam32/treeOptAndComTools) under the folder “r_data” please download the folder and place it within treeOptAndComTools folder please also be aware that some vignettes functions in this package are dependent on functions from https://github.com/aidanmacnamara/epiChoose
treeOptAndComTools package can be compiled by: 1.) downloading the folder and open it in RStudio. Set the working directory to the folder by: Session -> Set Working Directory -> set accordingly (or using setwd("") command)
2.) type "install.packages("treeOptAndComTools")" into RStudio Console
3.) please download all required packages
The exploration of the data, clustering methods and integration methods can be found in the vignettes file.
please fill in the correct directory in the function 'load()' of each ‘.R’ file in the vignettes folder