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.