enveomics.R (version 1.9.1)

enve.prefscore: Enveomics: Pref Score

Description

Estimate preference score of species based on occupancy in biased sample sets

Usage

enve.prefscore(
  x,
  set,
  ignore = NULL,
  signif.thr,
  plot = TRUE,
  col.above = rgb(148, 17, 0, maxColorValue = 255),
  col.equal = rgb(189, 189, 189, maxColorValue = 255),
  col.below = rgb(47, 84, 150, maxColorValue = 255),
  ...
)

Value

Returns a named vector of preference scores.

Arguments

x

Occupancy matrix (logical or numeric binary) with species as rows and samples as columns

set

Vector indicating samples in the test set. It can be any selection vector: boolean (same length as the number of columns in x), or numeric or character vector with indexes of the x columns.

ignore

Vector indicating species to ignore. It can be any selection vector with respect to the rows in x (see set).

signif.thr

Absolute value of the significance threshold

plot

Indicates if a plot should be generated

col.above

Color for points significantly above zero

col.equal

Color for points not significantly different from zero

col.below

Color for points significantly below zero

...

Any additional parameters supported by plot

Author

Luis M. Rodriguez-R [aut, cre]