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#' Diversity measures implemented
#'
#' The diversity functions offered in \code{abdiv} are organized based on the
#' function signature.
#' @format Four objects of class \code{character}.
#' @details
#' The following character vectors are provided:
#' \describe{
#' \item{\code{alpha_diversities}}{
#' All non-phylogenetic alpha diversity measures. These functions take a
#' single numeric vector as an argument.}
#' \item{\code{beta_diversities}}{
#' All non-phylogenetic beta diversity measures. These functions take two
#' numeric vectors as arguments.}
#' \item{\code{phylogenetic_alpha_diversities}}{
#' There is only one phylogenetic alpha diversity measure implemented, but
#' we use the plural to be consistent with the other vectors. This function
#' takes a numeric vector, a phylogenetic tree object, and optionally a
#' character vector of species labels.}
#' \item{\code{phylogenetic_beta_diversities}}{
#' Phylogenetic measures of beta diversity. These functions take two
#' numeric vectors, a phylogenetic tree object, and optionally a
#' character vector of species labels.}
#' }
#' @name diversity_measures
NULL
#' @rdname diversity_measures
#' @export
alpha_diversities <- sort(c(
"berger_parker_d", "brillouin_d", "dominance", "heip_e", "invsimpson",
"kempton_taylor_q", "margalef", "mcintosh_d", "mcintosh_e", "menhinick",
"pielou_e", "richness", "shannon", "simpson", "simpson_e", "strong"))
#' @rdname diversity_measures
#' @export
beta_diversities <- sort(c(
# From beta.R
"euclidean", "rms_distance", "chord", "hellinger", "geodesic_metric",
"kullback_leibler_divergence", "manhattan", "mean_character_difference",
"modified_mean_character_difference", "canberra",
"clark_coefficient_of_divergence", "chebyshev", "correlation_distance",
"cosine_distance", "bray_curtis", "weighted_kulczynski_second", "minkowski",
"morisita", "horn_morisita", "binomial_deviance", "cy_dissimilarity",
"ruzicka", "jaccard", "sorenson", "kulczynski_first", "kulczynski_second",
"rogers_tanimoto", "russel_rao", "sokal_michener", "sokal_sneath",
"yule_dissimilarity", "hamming",
# From beta_components.R
"jaccard_turnover", "jaccard_nestedness",
"sorenson_turnover", "sorenson_nestedness",
"bray_curtis_balanced", "bray_curtis_gradient",
"ruzicka_balanced", "ruzicka_gradient"))
#' @rdname diversity_measures
#' @export
phylogenetic_alpha_diversities <- c("faith_pd")
#' @rdname diversity_measures
#' @export
phylogenetic_beta_diversities <- sort(c(
# From unifrac.R
"unweighted_unifrac", "weighted_unifrac", "weighted_normalized_unifrac",
"variance_adjusted_unifrac", "generalized_unifrac", "information_unifrac",
# From beta_components.R
"unweighted_unifrac_turnover", "unweighted_unifrac_nestedness",
"phylosor_turnover", "phylosor_nestedness"))
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