Skip to contents

ps_pca

ps_pca.Rd

Compute and plot principal components after standardizing the data

Usage

ps_pca(
  doc = "ps_pca",
  data,
  ID = " ",
  GroupVar,
  Groups,
  AnalyticVars,
  ScreePlot = FALSE,
  BoxPlots = FALSE,
  pcPlot = TRUE,
  PlotPoints = TRUE,
  PlotEllipses = TRUE,
  PlotHull = FALSE,
  PlotMedians = FALSE,
  Ellipses = c(0.95, 0.99),
  PlotColors = TRUE,
  legendLoc = "topright",
  Colors = c("red", "black", "blue", "green", "purple"),
  Identify = FALSE,
  digits = 3,
  Seed = 11111,
  folder = " "
)

Arguments

doc

A string with documentation in the list returned, default is the function name

data

A matrix or data frame containing the data to be analyzed

ID

An optional name for an ID, default is " " if no ID

GroupVar

The name for variable defining grouping; a variable name is required

Groups

Character-valued defining the values of the group variable for which plots are to be done. Options are a vector of values; "All" (use all groups). One of these is required

AnalyticVars

A vector of names (character values) of analytic results

ScreePlot

Logical, if TRUE create a scree plot, default is FALSE

BoxPlots

Logical, if TRUE, create box plots of the first two components, default is FALSE

pcPlot

Logical, if TRUE (the default), create the plot of the first two components

PlotPoints

Logical, if TRUE (the default) and pcPlot=TRUE, plot the points for the first two components

PlotEllipses

Logical, if TRUE (the default), plot the confidence ellipse or ellipses for each group

PlotHull

Logical, if TRUE, plot the convex hull for each group, default is FALSE

PlotMedians

Logical, if TRUE, plot the symbol for each group at the median point for that group, default is FALSE

Ellipses

A value or vector of proportions for confidence ellipses; default is c(.95,.99) to produce 95% and 99% confidence ellipses

PlotColors

Logical. If TRUE, use list of colors in Colors for points; if F, plot points as black

legendLoc

Character, location of legend for a plot with points; default is "topright", alternatives are combinations of "top", "bottom", "right", "left"

Colors

A vector of color names; default is a vector with five names

Identify

Logical. If TRUE, the user can identify points of interest in plots; information on these points is saved to a file; default is FALSE

digits

The number of significant digits to return in objects in data frames, default is 3

Seed

If not NA, the seed for the random number generator used if missing data are imputed; default is 11111

folder

The path to the folder in which data frames will be saved; default is " "

Value

The function produces a plot of the first two principal components, the contents of which are defined by the arguments PlotPoints, PlotEllipses, PlotHull, and PlotMedians. A scree plot and box plots are produced if requested. The function returns a list with the following components:

  • usage: A string with the contents of the argument doc, the date run, the version of R used

  • dataUsed: The contents of the argument data restricted to the groups used

  • dataNA: A data frame with observations containing a least one missing value for an analysis variable, NA if no missing values

  • params: A list with the values of the arguments for grouping, logical parameters, Ellipses, and Colors

  • analyticVars: A vector with the value of the argument AnalyticVars

  • ellipse_pct: The value of the argument Ellipses

  • variances: A data frame including the percent of variation explained by each principal component and the cumulative percent explained

  • weights: A data frame with the principal component weights for each observation

  • Predicted: A data frame with the predicted values for each principal component, plus the value of Groups and an integer GroupIndex (with values 1:number of Groups)

  • DataPlusPredicted: A data frame with the data used to compute the principal components, plus GroupIndex (as defined above) and predicted values for each principal component

  • dataCheck: If Identify=TRUE, a data frame with the observations in dataUsed identified as of interest

  • location: The value of the parameter folder

Details

If Identify=TRUE, the user must interact with each plot (or pane, if there is more than one pane on a plot). To identify a point, place the cursor as close as possible to the point and left click; repeat if desired. To go to the next pane, right click and select "Stop" in base R; click on "Finish" in the plot pane in Rstudio.

Examples

data(ObsidianSources)
analyticVars<-c("Rb","Sr","Y","Zr","Nb")
save_pca <- ps_pca(data=ObsidianSources, ID="ID", GroupVar="Code",
Groups="All", AnalyticVars=analyticVars)