check_divent_args {divent} | R Documentation |
check_divent_args
Description
Checks the arguments of a function of the package divent
Usage
check_divent_args(
abundances = NULL,
alpha = NULL,
as_numeric = NULL,
check_arguments = NULL,
coverage_estimator = NULL,
distances = NULL,
estimator = NULL,
gamma = NULL,
jack_alpha = NULL,
jack_max = NULL,
k = NULL,
level = NULL,
n_simulations = NULL,
normalize = NULL,
probability_estimator = NULL,
q = NULL,
rate = NULL,
richness_estimator = NULL,
sample_coverage = NULL,
show_progress = NULL,
similarities = NULL,
species_distribution = NULL,
tree = NULL,
use.names = NULL,
unveiling = NULL,
weights = NULL
)
Arguments
abundances |
An object of class abundances. |
alpha |
The risk level, 5% by default. |
as_numeric |
If |
check_arguments |
If |
coverage_estimator |
An estimator of sample coverage used by coverage. |
distances |
A distance matrix or an object of class stats::dist |
estimator |
An estimator of asymptotic entropy, diversity or richness. |
gamma |
If |
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 |
n_simulations |
The number of simulations used to estimate the confidence envelope. |
normalize |
If |
probability_estimator |
A string containing one of the possible estimators of the probability distribution (see probabilities). Used only for extrapolation. |
q |
The order of diversity. |
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 |
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. |
species_distribution |
An object of class species_distribution. |
tree |
An ultrametric, phylogenetic tree. May be an object of class phylo_divent, ape::phylo, ade4::phylog or stats::hclust. |
use.names |
if |
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. |
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.
Value
Returns TRUE
or stops if a problem is detected.