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Calculate Principal Component Analysis Scores not including depth statistics

Source: R/6_pca_results.R
pca_scores.Rd

This function extracts the PCA scores from the PCA results and plots the loadings. This function is to be use on output from the pca_data() function not including depth statistics.

Usage

pca_scores(
  pc_results = results,
  plot_loadings = TRUE,
  every_nth = 12,
  output = FALSE,
  output_folder = NULL,
  verbose = FALSE
)

Arguments

pc_results

PCA class object containing the output from the 'pca_results()' function.

plot_loadings

TRUE or FALSE. Plot PC loadings figures. Default TRUE.

every_nth

Numeric. Sequence of labels to show on mean power plot. Default is 12.

output

Logical. If TRUE, output is saved to output_folder. Defaults to FALSE.

output_folder

Output folder path. If output = TRUE, output_folder must be provided. Defaults to NULL.

verbose

Logical. If TRUE, progress messages are shown. Defaults to FALSE.

Value

A data frame of pc scores containing one column for each Principal Component kept. If processing just one tag, the attribute 'unique_tag_ID' is given to the data frame with the tag_ID. Plots the PC loadings for each row of pc_data

Examples

# Set file path
filepath <- system.file("extdata", package = "FishDiveR")

# Load pc_results
pc_results <- readRDS(file.path(filepath, "data/4_PCA/pc_results.rds"))

# Run pca_scores function
pc_scores <- pca_scores(
  pc_results = pc_results,
  plot_loadings = FALSE,
  every_nth = 12,
  output = TRUE,
  output_folder = tempdir(),
  verbose = TRUE
)
#> Output file: /tmp/RtmpTKWEE7/data/4_PCA/pc_scores.rds