plotBar produces a Bertin or a Ford (battleship curve) diagram.

plotBar(object, ...)

plotMatrix(object, ...)

plotRank(object, ...)

plotSpot(object, ...)

seriate(object, subset, ...)

refine(object, ...)

diversity(object, ...)

evenness(object, ...)

richness(object, ...)

# S4 method for CountMatrix
refine(object, cutoff, n = 1000, axes = c(1, 2), ...)

# S4 method for DateModel
refine(object, method = c("jackknife", "bootstrap"), n = 1000, ...)

# S4 method for CountMatrix
plotBar(object, level = FALSE, EPPM = FALSE, center = TRUE, horizontal = FALSE)

# S4 method for AbundanceMatrix
plotBar(object, level = FALSE, EPPM = FALSE, center = TRUE, horizontal = FALSE)

# S4 method for CountMatrix
plotMatrix(object, PVI = FALSE)

# S4 method for AbundanceMatrix
plotMatrix(object, PVI = FALSE)

# S4 method for IncidenceMatrix
plotMatrix(object)

# S4 method for CountMatrix
plotRank(object, PVI = FALSE)

# S4 method for AbundanceMatrix
plotRank(object, PVI = FALSE)

# S4 method for CountMatrix
plotSpot(object, threshold = NULL)

# S4 method for AbundanceMatrix
plotSpot(object, threshold = NULL)

# S4 method for SimilarityMatrix
plotSpot(object)

# S4 method for OccurrenceMatrix
plotSpot(object)

# S4 method for CountMatrix,missing
seriate(
  object,
  method = c("correspondance", "reciprocal"),
  EPPM = FALSE,
  margin = c(1, 2),
  stop = 100,
  ...
)

# S4 method for IncidenceMatrix,missing
seriate(
  object,
  method = c("correspondance", "reciprocal"),
  margin = c(1, 2),
  stop = 100,
  ...
)

# S4 method for CountMatrix,BootCA
seriate(object, subset, margin = c(1, 2), ...)

# S4 method for CountMatrix
diversity(
  object,
  method = c("berger", "brillouin", "mcintosh", "shannon", "simpson"),
  simplify = FALSE,
  ...
)

# S4 method for CountMatrix
evenness(
  object,
  method = c("brillouin", "mcintosh", "shannon", "simpson"),
  simplify = FALSE,
  ...
)

# S4 method for CountMatrix
richness(
  object,
  method = c("ace", "chao1", "margalef", "menhinick", "none"),
  unbiased = FALSE,
  improved = FALSE,
  k = 10,
  simplify = FALSE
)

# S4 method for IncidenceMatrix
richness(
  object,
  method = c("chao2", "ice"),
  unbiased = FALSE,
  improved = FALSE,
  k = 10,
  simplify = FALSE
)

Arguments

object

An object.

...

Further arguments to be passed to internal methods.

subset

A BootCA object giving the subset of object to be used.

cutoff

A function that takes a numeric vector as argument and returns a single numeric value.

n

A non-negative integer giving the number of partial bootstrap replications.

axes

A numeric vector giving the subscripts of the CA axes to use.

method

A character string specifying the method to be used. This must be one of "reciprocal", "correspondence". Any unambiguous substring can be given.

level

A length-one numeric vector giving the confidence level to be drawn.

EPPM

A logical scalar: should the seriation be computed on EPPM instead of raw data?

center

A logical scalar: should the bar plot be centered? The default, TRUE, produces a Ford diagram, otherwise it produces a Bertin diagram.

horizontal

A logical scalar: should the bar plot be horizontal? The default, FALSE, means variables in rows and cases in columns (i.e. Bertin diagram). Only used if center is FALSE.

PVI

A logical scalar: should the PVI be drawn instead of frequencies (see details)?

margin

A numeric vector giving the subscripts which the rearrangement will be applied over: 1 indicates rows, 2 indicates columns, c(1, 2) indicates rows then columns, c(2, 1) indicates columns then rows.

stop

A length-one numeric vector giving the stopping rule (i.e. maximum number of iterations) to avoid infinite loop.

simplify

A logical scalar: should the result be simplified to a matrix? The default value, FALSE, returns a list.

unbiased

A logical scalar. Should the bias-corrected estimator be used? Only used with "chao1" or "chao2" (improved) estimator.

improved

A logical scalar. Should the improved estimator be used? Only used with "chao1" or "chao2".

k

A length-one numeric vector giving the threshold between rare/infrequent and abundant/frequent species. Only used if method is "ace" or "ice".

log

A character string which contains "x" if the x axis is to be logarithmic, "y" if the y axis is to be logarithmic and "xy" or "yx" if both axes are to be logarithmic (base 10).

facet

A logical scalar: should a matrix of panels defined by case/sample be drawn?

sample

A length-one numeric vector giving the sub-sample size.