deprecate: Deprecated Methods

Description

Deprecated Methods

Usage

index_heterogeneity(object, ...)
# S4 method for ANY
index_heterogeneity(
  object,
  method = c("berger", "brillouin", "mcintosh", "shannon", "simpson")
)
index_evenness(object, ...)
# S4 method for ANY
index_evenness(
  object,
  method = c("shannon", "brillouin", "mcintosh", "simpson")
)
index_richness(object, ...)
# S4 method for ANY
index_richness(object, method = c("count", "margalef", "menhinick"))
index_composition(object, ...)
# S4 method for ANY
index_composition(
  object,
  method = c("chao1", "ace", "chao2", "ice"),
  unbiased = FALSE,
  improved = FALSE,
  k = 10
)
simulate_heterogeneity(object, ...)
bootstrap_heterogeneity(object, ...)
jackknife_heterogeneity(object, ...)
simulate_evenness(object, ...)
bootstrap_evenness(object, ...)
jackknife_evenness(object, ...)
simulate_richness(object, ...)
bootstrap_richness(object, ...)
jackknife_richness(object, ...)
# S4 method for CountMatrix
bootstrap_heterogeneity(
  object,
  method = c("berger", "brillouin", "mcintosh", "shannon", "simpson"),
  probs = c(0.05, 0.95),
  n = 1000,
  ...
)
# S4 method for CountMatrix
jackknife_heterogeneity(
  object,
  method = c("berger", "brillouin", "mcintosh", "shannon", "simpson"),
  ...
)
# S4 method for CountMatrix
simulate_heterogeneity(
  object,
  method = c("berger", "brillouin", "mcintosh", "shannon", "simpson"),
  quantiles = TRUE,
  level = 0.8,
  step = 1,
  n = 1000,
  progress = getOption("tabula.progress"),
  ...
)
# S4 method for CountMatrix
bootstrap_evenness(
  object,
  method = c("berger", "brillouin", "mcintosh", "shannon", "simpson"),
  probs = c(0.05, 0.95),
  n = 1000,
  ...
)
# S4 method for CountMatrix
jackknife_evenness(
  object,
  method = c("berger", "brillouin", "mcintosh", "shannon", "simpson"),
  ...
)
# S4 method for CountMatrix
simulate_evenness(
  object,
  method = c("shannon", "brillouin", "mcintosh", "simpson"),
  quantiles = TRUE,
  level = 0.8,
  step = 1,
  n = 1000,
  progress = getOption("tabula.progress"),
  ...
)
# S4 method for CountMatrix
bootstrap_richness(
  object,
  method = c("none", "margalef", "menhinick"),
  probs = c(0.05, 0.95),
  n = 1000,
  ...
)
# S4 method for CountMatrix
jackknife_richness(object, method = c("none", "margalef", "menhinick"), ...)
# S4 method for CountMatrix
simulate_richness(
  object,
  method = c("none", "margalef", "menhinick"),
  quantiles = TRUE,
  level = 0.8,
  step = 1,
  n = 1000,
  progress = getOption("tabula.progress"),
  ...
)

Arguments

object: A \(m \times p\) matrix of count data (typically a CountMatrix object).
...: Currently not used.
method: A character string specifying the index to be computed (see details). Any unambiguous substring can be given.
probs: A numeric vector of probabilities with values in \([0,1]\) (see stats::quantile()).
n: A non-negative integer giving the number of bootstrap replications.
quantiles: A logical scalar: should sample quantiles be used as confidence interval? If TRUE (the default), sample quantiles are used as described in Kintigh (1989), else quantiles of the normal distribution are used.
level: A length-one numeric vector giving the confidence level.
step: A non-negative integer giving the increment of the sample size. Only used if simulate is TRUE.
progress: A logical scalar: should a progress bar be displayed?
diag: A logical scalar indicating whether the diagonal of the matrix should be plotted. Only used if object is a symmetric matrix.
upper: A logical scalar indicating whether the upper triangle of the matrix should be plotted. Only used if object is a symmetric matrix.
lower: A logical scalar indicating whether the lower triangle of the matrix should be plotted. Only used if object is a symmetric matrix.

Author

N. Frerebeau