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tempted (version 0.1.1)

Temporal Tensor Decomposition, a Dimensionality Reduction Tool for Longitudinal Multivariate Data

Description

TEMPoral TEnsor Decomposition (TEMPTED), is a dimension reduction method for multivariate longitudinal data with varying temporal sampling. It formats the data into a temporal tensor and decomposes it into a summation of low-dimensional components, each consisting of a subject loading vector, a feature loading vector, and a continuous temporal loading function. These loadings provide a low-dimensional representation of subjects or samples and can be used to identify features associated with clusters of subjects or samples. TEMPTED provides the flexibility of allowing subjects to have different temporal sampling, so time points do not need to be binned, and missing time points do not need to be imputed.

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install.packages('tempted')

Monthly Downloads

117

Version

0.1.1

License

GPL-3

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Maintainer

Pixu Shi

Last Published

May 9th, 2024

Functions in tempted (0.1.1)

tempted

Decomposition of temporal tensor
tdenoise

Calculate the de-noised temporal tensor
svd_centralize

Remove the mean structure of the temporal tensor
processed_table

Central-log-ratio (clr) transformed OTU table from the ECAM data
plot_feature_summary

Plot nonparametric smoothed mean and error bands of features versus time
format_tempted

Format data table into the input of tempted
bernoulli_kernel

Caculate the Bernoulli kernel
plot_metafeature

Plot nonparametric smoothed mesan and error bands of meta features versus time
est_test_subject

Estimate subject loading of testing data
plot_time_loading

Plot the temporal loading functions
aggregate_feature

Aggregate features using feature loadings
count_table

OTU read count table from the ECAM data
meta_table

Meta data table from the ECAM data
tempted_all

Run all major functions of tempted
reconstruct

Reconstruct tensor from low dimensional components
ratio_feature

Take log ratio of the abundance of top features over bottom features