Package: clustra 0.2.1

George Ostrouchov

clustra: Clustering Longitudinal Trajectories

Clusters longitudinal trajectories over time (can be unequally spaced, unequal length time series and/or partially overlapping series) on a common time axis. Performs k-means clustering on a single continuous variable measured over time, where each mean is defined by a thin plate spline fit to all points in a cluster. Distance is MSE across trajectory points to cluster spline. Provides graphs of derived cluster splines, silhouette plots, and Adjusted Rand Index evaluations of the number of clusters. Scales well to large data with multicore parallelism available to speed computation.

Authors:George Ostrouchov [aut, cre], David Gagnon [aut], Hanna Gerlovin [aut], Chen Wei-Chen [ctb], Schmidt Drew [ctb], Oak Ridge National Laboratory [cph], U.S. Department of Veteran's Affairs [fnd]

clustra_0.2.1.tar.gz
clustra_0.2.1.zip(r-4.5)clustra_0.2.1.zip(r-4.4)clustra_0.2.1.zip(r-4.3)
clustra_0.2.1.tgz(r-4.4-any)clustra_0.2.1.tgz(r-4.3-any)
clustra_0.2.1.tar.gz(r-4.5-noble)clustra_0.2.1.tar.gz(r-4.4-noble)
clustra_0.2.1.tgz(r-4.4-emscripten)clustra_0.2.1.tgz(r-4.3-emscripten)
clustra.pdf |clustra.html✨
clustra/json (API)
NEWS

# Install 'clustra' in R:
install.packages('clustra', repos = c('https://go-ski.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/mvp-champion/clustra/issues

Datasets:
  • bp10k - Simulated blood pressure data

On CRAN:

11 exports 1.47 score 7 dependencies 6 scripts 360 downloads

Last updated 8 months agofrom:eb32d08772. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 30 2024
R-4.5-winOKAug 30 2024
R-4.5-linuxOKAug 30 2024
R-4.4-winOKAug 30 2024
R-4.4-macOKAug 30 2024
R-4.3-winOKAug 30 2024
R-4.3-macOKAug 30 2024

Exports:clustraclustra_randclustra_sildeltimedeltimeTgen_traj_dataplot_sampleplot_silhouetteplot_smoothsrand_plottrajectories

Dependencies:data.tablelatticeMASSMatrixmgcvMixSimnlme

clustra: clustering trajectories

George Ostrouchov, Hanna Gerlovin, and David Gagnon

Rendered fromclustra_vignette.Rmdusingknitr::rmarkdownon Aug 30 2024.

Last update: 2023-10-16
Started: 2020-11-11

clustra: Graphics with BP Data

Nimish Adhikari, George Ostrouchov, Hanna Gerlovin, and David Gagnon

Rendered fromclustra_bp_vignette.Rmdusingknitr::rmarkdownon Aug 30 2024.

Last update: 2024-01-11
Started: 2023-10-04

Readme and manuals

Help Manual

Help pageTopics
clustra-packageclustra-package
allpair_RandIndex: helper for replicated cluster comparisonallpair_RandIndex
Simulated blood pressure databp10k
Checks if non-empty groups have enough data for spline fit degrees of freedom.check_df
Cluster longitudinal trajectories over timeclustra
clustra_rand: Rand Index cluster evaluationclustra_rand
clustra_sil: Prepare silhouette plot data for several k or for a previous clustra runclustra_sil
Timing functiondeltime deltimeT
Data Generatorsgen_traj_data
gendatagendata
Function to test information criteria. Not exported and used by internal function 'kchoose'.ic_fun
A test function to evaluate information criteria for several k values. Not exported and only for debugging internal use.kchoose
Various Loss functions used internally by clustramae_g mme_g mse_g mxe_g
Generates data for one 'id'oneid
Plots a sample of ids in a small mutiples layoutplot_sample
Plots a list item, a silhouette, from the result of 'clustra_sil' along with the average silhouette value. Typically used via 'lapply(list, plot_silhouette)'plot_silhouette
plot_smoothsplot_smooths
Function to predict for new data based on fitted gam object.pred_g
Matrix plot of Rand Index comparison of replicated clustersrand_plot
Function to assign starting groups.start_groups
Fits a thin plate spline to a single group with 'bam'.tps_g
Function to run trajectories inside mclapply with one core.traj_rep
Cluster longitudinal trajectories over time.trajectories
xit_reportxit_report