philips-labs / demo-clustering-longitudinal-data

Supplementary materials for the manuscript "Clustering of longitudinal data: A tutorial on a variety of approaches" by N. G. P. Den Teuling, S.C. Pauws, and E.R. van den Heuvel (2021)

This repository contains the R scripts used in the analysis of the case study of the manuscript.

Useful links

• MixTVEM source code used in the MixTVEM demo analysis - https://github.com/dziakj1/MixTVEM
• lcmm R package, used for estimating GMM and GBTM - https://cran.r-project.org/package=lcmm
• kml R package, used for estimating KmL - https://cran.r-project.org/package=kml
• mclust R package, used for estimating LLPA - https://cran.r-project.org/package=mclust
• latrend R package: The longitudinal clustering framework that we have created, originating from the learnings of this work - https://github.com/philips-software/latrend

Getting started

1. Either load the Rstudio project file demo.Rproj, or start an R session with the working directory set to the root repository directory.
2. Install required packages and dependencies

install.packages(c("assertthat", "data.table", "ggdendro", "ggplot2", "IMIFA", "kml", "lcmm", "lpSolve", "magrittr", "MASS", "matrixStats", "mclust", "nlme", "scales"), dependencies = TRUE)

3. In case you want to run the MixTVEM analysis, you'll need to fetch MixTVEM.R from https://github.com/dziakj1/MixTVEM

You should now be able to run any of the analysis scripts.