ChemoSpec2D: calcLvls – R documentation

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calcLvls

Calculate Levels for Contour and Image Type Plots

Description

Given a matrix or vector input, this function will assist in selecting levels for preparing contour and image type plots. For instance, levels can be spaced evenly, logrithmically, exponentially or using a cumulative distribution function. NA values are ignored.

Usage

calcLvls(
  M,
  n = 10,
  mode = "even",
  lambda = 1.5,
  base = 2,
  showHist = FALSE,
  ...
)

Arguments

`M`	A numeric matrix or vector.
`n`	An integer giving the number of levels desired: For `mode = "even"` `n` evenly spaced levels are returned. For `mode = "ecdf"`, `n` should be one or more values in the interval [0...1]. For instance, a value of 0.6 corresponds to a single level in which 60 percent of the matrix values are below, and 40 percent above. For all other values of `mode`, `n` is used internally as `floor(n/2)` and the result eventually doubled in order to give a symmetric set of levels. In addition, only the positive or negative levels may be selected, leaving you with `floor(n/2)/2` levels.
`mode`	Character. One of `"even"`, `"log"`, `"exp"`, `"ecdf"`, `"posexp"`, `"negexp"`, `"poslog"`, `"neglog"` or `NMR`. `"even"` will create evenly spaced levels. `"log"` will create levels which are more closely spaced at the high values, while `"exp"` does the opposite. The pos- or neg- versions select just the positive or negative values. `"ecdf"` computes levels at the requested quantiles of the matrix. `NMR` uses `exp`, `lambda = 2.0` and `n = 32`. It also removes the four values closest to zero, where the data may be primarily noise.
`lambda`	Numeric. A non-zero exponent used with `method = "exp"` and relatives. Higher values push the levels toward zero.
`base`	Integer. The base used with `method = "log"` and relatives.
`showHist`	Logical. Shall a histogram be drawn showing the location of the chosen levels?
`...`	Arguments to be passed downstream.

Value

A numeric vector giving the levels.

Author(s)

Bryan A. Hanson, DePauw University. hanson@depauw.edu

Examples

set.seed(9)
MM <- matrix(runif(100, -1, 1), nrow = 10) # test data
tsts <- c("even", "log", "poslog", "exp", "posexp", "ecdf", "NMR")
for (i in 1:length(tsts)) {
  nl <- 20
  if (tsts[i] == "ecdf") nl <- seq(0.1, 0.9, 0.1)
  levels <- calcLvls(
    M = MM, n = nl, mode = tsts[i],
    showHist = TRUE, main = tsts[i]
  )
}

ChemoSpec2D

Exploratory Chemometrics for 2D Spectroscopy

v0.4.187

GPL-3

Authors

Bryan A. Hanson [aut, cre] (<https://orcid.org/0000-0003-3536-8246>)

Initial release

2021-03-15