latrend

The package is described in detail in the pre-print available at https://arxiv.org/abs/2402.14621

Features

  • Unified cluster analysis, independent of the underlying algorithms used. Enabling users to compare the performance of various longitudinal cluster methods on the case study at hand.
  • Supports many different methods for longitudinal clustering out of the box (see the list of supported packages below).
  • The framework consists of extensible S4 methods based on an abstract model class, enabling rapid prototyping of new cluster methods or model specifications.
  • Standard plotting tools for model evaluation across methods (e.g., trajectories, cluster trajectories, model fit, metrics)
  • Support for many cluster metrics through the packages clusterCrit, mclustcomp, and igraph.
  • The structured and unified analysis approach enables simulation studies for comparing methods.
  • Standardized model validation for all methods through bootstrapping or k-fold cross-validation.

See the release notes page for the latest updates.

Installation

The latest release of latrend can be installed from CRAN by running:

install.packages("latrend")

It can also be installed from Github directly using:

remotes::install_github('philips-software/latrend', ref = remotes::github_release())
# include vignettes
remotes::install_github('philips-software/latrend', ref = remotes::github_release(), build_vignettes = TRUE)

Usage

Load and view example data.

data(latrendData)
head(latrendData)
options(latrend.id = "Id", latrend.time = "Time")
plotTrajectories(latrendData, response = "Y")
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Cluster the trajectories and plot the results.

kmlMethod <- lcMethodKML("Y", nClusters = 3)
model <- latrend(kmlMethod, data = latrendData)
summary(model)
plot(model)
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Identify solutions for 1 to 5 clusters.

kmlMethods <- lcMethods(kmlMethod, nClusters = 1:5)
models <- latrendBatch(kmlMethods, data = latrendData)

Determine the number of clusters through one or more internal cluser metrics.

metric(models, c("WMAE", "BIC"))
plotMetric(models, c("Dunn", "ASW", "WMAE", "WRSS", "BIC", "estimationTime"))
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Supported packages

The latrend package provides interfaces to the relevant methods for longitudinal clustering for the following packages: * akmedoids * crimCV * dtwclust * fda * flexmix * funFEM * kml * lcmm * mclust * mixAK * mixtools

Contributing

We appreciate any contributions in the form of ideas, feature requests, bug reports, bug fixes, documentation improvements, code reformatting, and code submissions. Please see the Contributing guide.