calculateSparsity {parafac4microbiome} | R Documentation |
Calculate sparsity across the feature mode of a multi-way array.
Description
Calculate sparsity across the feature mode of a multi-way array.
Usage
calculateSparsity(dataset, considerGroups = FALSE, groupVariable = "")
Arguments
dataset |
See Fujita2023, Shao2019 or vanderPloeg2024. |
considerGroups |
Consider subject groups in calculating sparsity (default FALSE) |
groupVariable |
Column name in dataset$mode1 that should be used to consider groups (default "") |
Value
Vector of sparsity fractions (N x J) where N is the number of groups and J is the number of features.
Examples
# No groups
sparsity = calculateSparsity(Fujita2023)
length(sparsity)
hist(sparsity)
# Consider groups
colnames(Shao2019$mode1)
sparsity = calculateSparsity(Shao2019, considerGroups=TRUE, groupVariable="Delivery_mode")
dim(sparsity)
hist(sparsity[1,])
hist(sparsity[2,])
[Package parafac4microbiome version 1.0.3 Index]