plotVIP: Plot Variable Influence on Projection

In pcvr: Plant Phenotyping and Bayesian Statistics

Plot Variable Influence on Projection

Description

This function is used to visualize variable influence on projection (vip) from a plsr model.

Usage

plotVIP(plsrObject, i = 1, mean = FALSE, removePattern = ".*_")

Arguments

plsrObject	Output from pcv.plsr
i	An index from the plsrObject to use if the plsrObject contains models for several outcomes. Can be a name or a position. Defaults to 1.
mean	Logical, should the mean be plotted (TRUE) or should the components be shown individually (FALSE, the default).
removePattern	A pattern to remove to make the wavelength column into a numeric.

Value

A ggplot showing variable influence on projection

Examples

if (rlang::is_installed("pls")) {
  dists <- list(
    rlnorm = list(meanlog = log(40), sdlog = 0.5),
    rlnorm = list(meanlog = log(60), sdlog = 0.35)
  )
  mv <- mvSim(
    dists = dists, n_samples = 100, counts = 1000,
    min_bin = 1, max_bin = 180, wide = TRUE
  )
  sv <- growthSim("logistic",
    n = 5, t = 20,
    params = list("A" = c(200, 160), "B" = c(13, 11), "C" = c(3, 3.5))
  )
  d <- cbind(sv, mv[, -1])
  x <- pcv.plsr(df = d, resps = "y", spectra = grepl("^sim_", colnames(d)))
  plotVIP(x)
}

pcvr documentation built on April 16, 2025, 5:12 p.m.