profile_hill: Diversity Profile of a Community
In divent: Entropy Partitioning to Measure Diversity

profile_hill

R Documentation

Diversity Profile of a Community

Description

Calculate the diversity profile of a community, i.e. diversity (Hill numbers) against its order.

Usage

profile_hill(x, orders = seq(from = 0, to = 2, by = 0.1), ...)

## S3 method for class 'numeric'
profile_hill(
  x,
  orders = seq(from = 0, to = 2, by = 0.1),
  estimator = c("UnveilJ", "ChaoJost", "ChaoShen", "GenCov", "Grassberger", "Holste",
    "Marcon", "UnveilC", "UnveiliC", "ZhangGrabchak", "naive"),
  level = NULL,
  probability_estimator = c("Chao2015", "Chao2013", "ChaoShen", "naive"),
  unveiling = c("geometric", "uniform", "none"),
  richness_estimator = c("jackknife", "iChao1", "Chao1", "naive"),
  jack_alpha = 0.05,
  jack_max = 10,
  coverage_estimator = c("ZhangHuang", "Chao", "Turing", "Good"),
  q_threshold = 10,
  sample_coverage = NULL,
  as_numeric = FALSE,
  n_simulations = 0,
  alpha = 0.05,
  bootstrap = c("Chao2015", "Marcon2012", "Chao2013"),
  show_progress = TRUE,
  ...,
  check_arguments = TRUE
)

## S3 method for class 'species_distribution'
profile_hill(
  x,
  orders = seq(from = 0, to = 2, by = 0.1),
  estimator = c("UnveilJ", "ChaoJost", "ChaoShen", "GenCov", "Grassberger", "Holste",
    "Marcon", "UnveilC", "UnveiliC", "ZhangGrabchak", "naive"),
  level = NULL,
  probability_estimator = c("Chao2015", "Chao2013", "ChaoShen", "naive"),
  unveiling = c("geometric", "uniform", "none"),
  richness_estimator = c("jackknife", "iChao1", "Chao1", "naive"),
  jack_alpha = 0.05,
  jack_max = 10,
  coverage_estimator = c("ZhangHuang", "Chao", "Turing", "Good"),
  q_threshold = 10,
  gamma = FALSE,
  n_simulations = 0,
  alpha = 0.05,
  bootstrap = c("Chao2015", "Marcon2012", "Chao2013"),
  show_progress = TRUE,
  ...,
  check_arguments = TRUE
)

Arguments

`x`	An object, that may be a numeric vector containing abundances or probabilities, or an object of class abundances or probabilities.
`orders`	The orders of diversity used to build the profile.
`...`	Unused.
`estimator`	An estimator of entropy.
`level`	the level of interpolation or extrapolation. It may be a sample size (an integer) or a sample coverage (a number between 0 and 1). If not `NULL`, the asymptotic `estimator` is ignored.
`probability_estimator`	a string containing one of the possible estimators of the probability distribution (see probabilities). Used only for extrapolation.
`unveiling`	a string containing one of the possible unveiling methods to estimate the probabilities of the unobserved species (see probabilities). Used only for extrapolation.
`richness_estimator`	an estimator of richness to evaluate the total number of species, see div_richness. used for interpolation and extrapolation.
`jack_alpha`	the risk level, 5% by default, used to optimize the jackknife order.
`jack_max`	the highest jackknife order allowed. Default is 10.
`coverage_estimator`	an estimator of sample coverage used by coverage.
`q_threshold`	the value of `q` above which diversity is computed directly with the naive estimator `(\sum{p_s^q}^{\frac{1}{(1-q)}}`, without computing entropy. When `q` is great, the exponential of entropy goes to `0^{\frac{1}{(1-q)}}`, causing rounding errors while the naive estimator of diversity is less and less biased.
`sample_coverage`	the sample coverage of `x` calculated elsewhere. Used to calculate the gamma diversity of meta-communities, see details.
`as_numeric`	if `TRUE`, a number or a numeric vector is returned rather than a tibble.
`n_simulations`	The number of simulations used to estimate the confidence envelope of the profile.
`alpha`	The risk level, 5% by default, of the confidence envelope of the profile.
`bootstrap`	the method used to obtain the probabilities to generate bootstrapped communities from observed abundances. If "Marcon2012", the probabilities are simply the abundances divided by the total number of individuals \insertCiteMarcon2012adivent. If "Chao2013" or "Chao2015" (by default), a more sophisticated approach is used (see as_probabilities) following \insertCiteChao2013;textualdivent or \insertCiteChao2015;textualdivent.
`show_progress`	if TRUE, a progress bar is shown during long computations.
`check_arguments`	if `TRUE`, the function arguments are verified. Should be set to `FALSE` to save time when the arguments have been checked elsewhere.
`gamma`	if `TRUE`, `\gamma` diversity, i.e. diversity of the metacommunity, is computed.

Details

A bootstrap confidence interval can be produced by simulating communities (their number is n_simulations) with rcommunity and calculating their profiles. Simulating communities implies a downward bias in the estimation: rare species of the actual community may have abundance zero in simulated communities. Simulated diversity values are recentered so that their mean is that of the actual community.

Value

A tibble with the site names, the estimators used and the estimated diversity at each order. This is an object of class "profile" that can be plotted.