check_divent_args: check_divent_args
In divent: Entropy Partitioning to Measure Diversity

check_divent_args

R Documentation

check_divent_args

Description

Checks the arguments of a function of the package divent

Usage

check_divent_args(
  abd = NULL,
  abundances = NULL,
  alpha = NULL,
  as_numeric = NULL,
  bootstrap = NULL,
  check_arguments = NULL,
  correction = NULL,
  coverage_estimator = NULL,
  distances = NULL,
  distribution = NULL,
  estimator = NULL,
  fisher_alpha = NULL,
  gamma = NULL,
  global = NULL,
  jack_alpha = NULL,
  jack_max = NULL,
  k = NULL,
  level = NULL,
  n = NULL,
  n_simulations = NULL,
  normalize = NULL,
  orders = NULL,
  prob = NULL,
  prob_geom = NULL,
  probability_estimator = NULL,
  q = NULL,
  q_threshold = NULL,
  r = NULL,
  rate = NULL,
  richness_estimator = NULL,
  sample_coverage = NULL,
  sd_lnorm = NULL,
  show_progress = NULL,
  similarities = NULL,
  size = NULL,
  species_number = NULL,
  species_distribution = NULL,
  thomas_mu = NULL,
  thomas_scale = NULL,
  tree = NULL,
  use.names = NULL,
  unveiling = NULL,
  weights = NULL,
  w_max = NULL,
  w_mean = NULL,
  w_min = NULL,
  weibull_scale = NULL,
  weibull_shape = NULL,
  X = NULL,
  win = NULL
)

Arguments

`abd`	a numeric vector containing abundances.
`abundances`	an object of class abundances.
`alpha`	the risk level, 5% by default.
`as_numeric`	if `TRUE`, a number or a numeric vector is returned rather than a tibble.
`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.
`check_arguments`	if `TRUE`, the function arguments are verified. Should be set to `FALSE` to save time when the arguments have been checked elsewhere.
`correction`	the edge-effect correction to apply when estimating the number of neighbors.
`coverage_estimator`	an estimator of sample coverage used by coverage.
`distances`	a distance matrix or an object of class stats::dist.
`distribution`	The distribution of species abundances. May be "lnorm" (log-normal), "lseries" (log-series), "geom" (geometric) or "bstick" (broken stick).
`estimator`	an estimator of asymptotic entropy, diversity or richness.
`fisher_alpha`	Fisher's `\alpha` in the log-series distribution.
`gamma`	if `TRUE`, `\gamma` diversity, i.e. diversity of the metacommunity, is computed.
`global`	if `TRUE`, a global envelope sensu \insertCiteDuranton2005divent is calculated.
`jack_alpha`	the risk level, 5% by default, used to optimize the jackknife order.
`jack_max`	the highest jackknife order allowed. Default is 10.
`k`	the order of Hurlbert's diversity.
`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.
`n`	the number of observations.
`n_simulations`	the number of simulations used to estimate the confidence envelope.
`normalize`	if `TRUE`, phylogenetic is normalized: the height of the tree is set to 1.
`orders`	The orders of diversity.
`prob`	a numeric vector containing probabilities.
`prob_geom`	the proportion of resources taken by successive species of the geometric distribution.
`probability_estimator`	a string containing one of the possible estimators of the probability distribution (see probabilities). Used only for extrapolation.
`q`	a number: the order of diversity.
`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.
`r`	a vector of distances.
`rate`	the decay rate of the exponential similarity.
`richness_estimator`	an estimator of richness to evaluate the total number of species, see div_richness. used for interpolation and extrapolation.
`sample_coverage`	the sample coverage of `x` calculated elsewhere. Used to calculate the gamma diversity of meta-communities, see details.
`sd_lnorm`	the simulated log-normal distribution standard deviation. This is the standard deviation on the log scale.
`show_progress`	if TRUE, a progress bar is shown during long computations.
`similarities`	a similarity matrix, that can be obtained by fun_similarity. Its default value is the identity matrix.
`size`	the number of individuals to draw in each community.
`species_number`	the number of species.
`species_distribution`	an object of class species_distribution.
`thomas_mu`	in Thomas point patterns, the mean number of points per cluster. The intensity of the Poisson process of cluster centers is calculated as the number of points (`size`) per area divided by `thomas_mu`.
`thomas_scale`	in Thomas point patterns, the standard deviation of random displacement (along each coordinate axis) of a point from its cluster center.
`tree`	an ultrametric, phylogenetic tree. May be an object of class phylo_divent, ape::phylo, ade4::phylog or stats::hclust.
`use.names`	if `TRUE`, the names of the `species_distribution` are kept in the matrix or vector they are converted to.
`unveiling`	a string containing one of the possible unveiling methods to estimate the probabilities of the unobserved species (see probabilities). Used only for extrapolation.
`weights`	the weights of the sites of the species distributions.
`w_max`	the maximum weight in a uniform distribution.
`w_mean`	the mean weight in an exponential distribution (i.e. the negative of the inverse of the decay rate).
`w_min`	the minimum weight in a uniform, exponential or Weibull distribution.
`weibull_scale`	the scale parameter in a Weibull distribution.
`weibull_shape`	the shape parameter in a Weibull distribution.
`X`	a spatialized community (A dbmss::wmppp object with `PointType` values as species names.)
`win`	the window containing the point pattern. It is an spatstat.geom::owin object. Default is a 1x1 square.

Details

The function compares the arguments passed to its parent function to the type they should be and performs some extra tests, e.g. probabilities must be positive and sum to 1. It stops if an argument is not correct.

The function is always called without arguments. Its arguments exist only for documentation.