Skip to contents

Collect PC scores from PCA results

Source: R/stat_pca.R
collect.stat_pca.Rd

Extract PC scores from a PCA result and add them to a tibble.

Usage

# S3 method for class 'stat_pca'
collect(x, data = NULL, retain = NULL, fold = FALSE, ...)

Arguments

x

A stat_pca object

data

A tibble. If NULL, uses the original data from the PCA.

retain

How many PCs to retain:

  • NULL (default): All PCs

  • Integer (e.g., 5): First N PCs

  • Numeric 0-1 (e.g., 0.95): PCs explaining this proportion of variance

fold

How to add PC scores:

  • FALSE (default): Add as separate columns (PC1, PC2, ...)

  • TRUE: Fold into single list-column named "pca"

  • Character: Fold into single list-column with this name

...

Additional arguments (reserved)

Value

A tibble with PC scores added

Details

The retain parameter allows flexible selection of PCs:

  • retain = NULL: Keep all PCs

  • retain = 5: Keep first 5 PCs

  • retain = 0.95: Keep PCs explaining 95% of variance

  • retain = 1: Keep only PC1

When fold = TRUE or a character name, PC scores are stored as a list-column with class c("pca", "coe"), making them usable in downstream analyses.

Examples

if (FALSE) { # \dontrun{
pca <- boteft %>% stat_pca()

# Add all PCs
collect(pca)

# Add first 5 PCs
collect(pca, retain = 5)

# Add PCs explaining 95% variance
collect(pca, retain = 0.95)

# Fold into list-column
collect(pca, retain = 5, fold = TRUE)
collect(pca, retain = 5, fold = "pca_scores")
} # }