LUPINE for longitudinal data

LUPINE for longitudinal data

Usage

LUPINE_t(
  data,
  day_index,
  num_lags = 999,
  excluded_taxa = NULL,
  is.transformed = FALSE,
  lib_size = NULL,
  ncomp = 1
)

Arguments

data

A 3D array of counts or transformed data with dimensions samples x taxa x time points

day_index

The index of the time point for which the correlations are calculated

num_lags

The number of previous time points to be used for the calculation of the correlation

excluded_taxa

A list of taxa to be excluded at each time point

is.transformed

A logical indicating whether the data is transformed or not

lib_size

A matrix of library sizes for each sample and time point

ncomp

The number of components to use for dimensionality reduction

Value

A list of correlations and p-values