deprecate: Deprecated Methods
In tesselle/tabula: Analysis and Visualization of Archaeological Count Data

deprecate

R Documentation

Deprecated Methods

Description

Deprecated Methods

Usage

index_heterogeneity(object, ...)

## S4 method for signature 'ANY'
index_heterogeneity(
  object,
  method = c("berger", "brillouin", "mcintosh", "shannon", "simpson")
)

index_evenness(object, ...)

## S4 method for signature 'ANY'
index_evenness(
  object,
  method = c("shannon", "brillouin", "mcintosh", "simpson")
)

index_richness(object, ...)

## S4 method for signature 'ANY'
index_richness(object, method = c("count", "margalef", "menhinick"))

index_composition(object, ...)

## S4 method for signature '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 signature 'CountMatrix'
bootstrap_heterogeneity(
  object,
  method = c("berger", "brillouin", "mcintosh", "shannon", "simpson"),
  probs = c(0.05, 0.95),
  n = 1000,
  ...
)

## S4 method for signature 'CountMatrix'
jackknife_heterogeneity(
  object,
  method = c("berger", "brillouin", "mcintosh", "shannon", "simpson"),
  ...
)

## S4 method for signature '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 signature 'CountMatrix'
bootstrap_evenness(
  object,
  method = c("berger", "brillouin", "mcintosh", "shannon", "simpson"),
  probs = c(0.05, 0.95),
  n = 1000,
  ...
)

## S4 method for signature 'CountMatrix'
jackknife_evenness(
  object,
  method = c("berger", "brillouin", "mcintosh", "shannon", "simpson"),
  ...
)

## S4 method for signature '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 signature 'CountMatrix'
bootstrap_richness(
  object,
  method = c("none", "margalef", "menhinick"),
  probs = c(0.05, 0.95),
  n = 1000,
  ...
)

## S4 method for signature 'CountMatrix'
jackknife_richness(object, method = c("none", "margalef", "menhinick"), ...)

## S4 method for signature '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 x 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.