R: Entropy Partitioning to Measure Diversity

# Entropy Partitioning to Measure Diversity

## Documentation for package ‘divent’ version 0.5-4

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A C D E F I L M N P R S

divent-package | divent

## -- A --

abd_freq_count | Abundance Frequency Count of a Community
abd_species | Abundances of Communities
abd_sum | Abundances of Communities
abundances | Species Distributions
accum_div_phylo | Phylogenetic Diversity Accumulation of a Community
accum_div_phylo.abundances | Phylogenetic Diversity Accumulation of a Community
accum_div_phylo.numeric | Phylogenetic Diversity Accumulation of a Community
accum_ent_phylo | Phylogenetic Diversity Accumulation of a Community
accum_ent_phylo.abundances | Phylogenetic Diversity Accumulation of a Community
accum_ent_phylo.numeric | Phylogenetic Diversity Accumulation of a Community
accum_hill | Diversity Accumulation of a Community
accum_hill.abundances | Diversity Accumulation of a Community
accum_hill.numeric | Diversity Accumulation of a Community
accum_mixing | Spatial Diversity Accumulation of a Community
accum_sp | Spatial Accumulation of Diversity
accum_sp_diversity | Spatial Accumulation of Diversity
accum_sp_entropy | Spatial Accumulation of Diversity
accum_sp_hill | Spatial Diversity Accumulation of a Community
accum_sp_mixing | Spatial Accumulation of Diversity
accum_sp_tsallis | Spatial Diversity Accumulation of a Community
accum_tsallis | Diversity Accumulation of a Community
accum_tsallis.abundances | Diversity Accumulation of a Community
accum_tsallis.numeric | Diversity Accumulation of a Community
alphahull | alpha-shape calculation
as.double.species_distribution | Species Distributions
as.matrix.species_distribution | Species Distributions
as.numeric.species_distribution | Species Distributions
as_abundances | Species Distributions
as_abundances.character | Species Distributions
as_abundances.data.frame | Species Distributions
as_abundances.factor | Species Distributions
as_abundances.matrix | Species Distributions
as_abundances.numeric | Species Distributions
as_abundances.wmppp | Species Distributions
as_phylo_divent | Class phylo_divent
as_probabilities | Species Distributions
as_probabilities.character | Species Distributions
as_probabilities.data.frame | Species Distributions
as_probabilities.factor | Species Distributions
as_probabilities.matrix | Species Distributions
as_probabilities.numeric | Species Distributions
as_probabilities.wmppp | Species Distributions
as_species_distribution | Species Distributions
as_species_distribution.character | Species Distributions
as_species_distribution.data.frame | Species Distributions
as_species_distribution.factor | Species Distributions
as_species_distribution.matrix | Species Distributions
as_species_distribution.numeric | Species Distributions
as_species_distribution.wmppp | Species Distributions
autoplot.accumulation | Plot Accumulation Objects
autoplot.accum_sp | Spatial Accumulation of Diversity
autoplot.profile | Plot Profile Objects
autoplot.species_distribution | Plot Profile Objects
autoplot.wmppp | ggplot method to plot wmppp objects

## -- C --

coverage | Sample Coverage of a Community
coverage.abundances | Sample Coverage of a Community
coverage.numeric | Sample Coverage of a Community
coverage_to_size | Sample Coverage of a Community
coverage_to_size.abundances | Sample Coverage of a Community
coverage_to_size.numeric | Sample Coverage of a Community

## -- D --

divent | divent
div_gen_simpson | Generalized Simpson's Diversity
div_gen_simpson.numeric | Generalized Simpson's Diversity
div_gen_simpson.species_distribution | Generalized Simpson's Diversity
div_hill | Hill number of a Community
div_hill.numeric | Hill number of a Community
div_hill.species_distribution | Hill number of a Community
div_hurlbert | Hurlbert Diversity of a Community
div_hurlbert.numeric | Hurlbert Diversity of a Community
div_hurlbert.species_distribution | Hurlbert Diversity of a Community
div_part | Diversity partition
div_pd | Faith's Phylogenetic Diversity of a Community
div_pd.numeric | Faith's Phylogenetic Diversity of a Community
div_pd.species_distribution | Faith's Phylogenetic Diversity of a Community
div_phylo | Phylogenetic Diversity of a Community
div_phylo.numeric | Phylogenetic Diversity of a Community
div_phylo.species_distribution | Phylogenetic Diversity of a Community
div_richness | Number of Species of a Community
div_richness.numeric | Number of Species of a Community
div_richness.species_distribution | Number of Species of a Community
div_similarity | Similarity-Based Diversity of a Community
div_similarity.numeric | Similarity-Based Diversity of a Community
div_similarity.species_distribution | Similarity-Based Diversity of a Community

## -- E --

ent_allen | Allen et al.'s Phylogenetic Entropy of a Community
ent_allen.numeric | Allen et al.'s Phylogenetic Entropy of a Community
ent_allen.species_distribution | Allen et al.'s Phylogenetic Entropy of a Community
ent_gen_simpson | Generalized Simpson's Entropy
ent_gen_simpson.numeric | Generalized Simpson's Entropy
ent_gen_simpson.species_distribution | Generalized Simpson's Entropy
ent_hurlbert | Hurlbert Entropy of a Community
ent_hurlbert.numeric | Hurlbert Entropy of a Community
ent_hurlbert.species_distribution | Hurlbert Entropy of a Community
ent_phylo | Phylogenetic Entropy of a Community
ent_phylo.numeric | Phylogenetic Entropy of a Community
ent_phylo.species_distribution | Phylogenetic Entropy of a Community
ent_rao | Rao's Quadratic Entropy of a Community
ent_rao.numeric | Rao's Quadratic Entropy of a Community
ent_rao.species_distribution | Rao's Quadratic Entropy of a Community
ent_shannon | Shannon's Entropy of a Community
ent_shannon.numeric | Shannon's Entropy of a Community
ent_shannon.species_distribution | Shannon's Entropy of a Community
ent_similarity | Similarity-Based Entropy of a Community
ent_similarity.numeric | Similarity-Based Entropy of a Community
ent_similarity.species_distribution | Similarity-Based Entropy of a Community
ent_simpson | Simpson's Entropy of a Community
ent_simpson.numeric | Simpson's Entropy of a Community
ent_simpson.species_distribution | Simpson's Entropy of a Community
ent_sp_simpson | Spatially Explicit Simpson's Entropy
ent_sp_simpsonEnvelope | Spatially Explicit Simpson's Entropy
ent_tsallis | Tsallis Entropy of a Community
ent_tsallis.numeric | Tsallis Entropy of a Community
ent_tsallis.species_distribution | Tsallis Entropy of a Community
exp_q | Deformed exponential
e_n_q | Grassberger's expectation of n^q

## -- F --

fit_rac | Fit a distribution
fit_rac.numeric | Fit a distribution
fit_rac.species_distribution | Fit a distribution
fun_ordinariness | Functional ordinariness of a community
fun_similarity | Functional similarity

## -- I --

is_abundances | Species Distributions
is_phylo_divent | Class phylo_divent
is_probabilities | Species Distributions
is_species_distribution | Species Distributions

## -- L --

ln_q | Deformed logarithm

## -- M --

metacommunity | Aggregate communities into a metacommunity
metacommunity.abundances | Aggregate communities into a metacommunity
metacommunity.matrix | Aggregate communities into a metacommunity
mock_3sp | Mock data
mock_3sp_abd | Mock data
mock_3sp_dist | Mock data
mock_3sp_tree | Mock data

## -- N --

non_species_columns | Non-Species columns

## -- P --

paracou_6 | Paracou plot 6
paracou_6_abd | Paracou plot 6
paracou_6_fundist | Functional distances between Paracou plot 6 species
paracou_6_taxo | Taxonomy of Paracou plot 6 species
paracou_6_wmppp | Paracou plot 6
phylo_divent | Class phylo_divent
plot.accum_sp | Spatial Accumulation of Diversity
plot.phylo_divent | Plot phylo_divent Objects
plot.species_distribution | Plot Profile Objects
plot_map | Spatial Accumulation of Diversity
probabilities | Probabilities of Species
probabilities.abundances | Probabilities of Species
probabilities.numeric | Probabilities of Species
prob_species | Abundances of Communities
profile_hill | Diversity Profile of a Community
profile_hill.numeric | Diversity Profile of a Community
profile_hill.species_distribution | Diversity Profile of a Community
profile_phylo | Phylogenetic Diversity Profile of a Community
profile_phylo.numeric | Phylogenetic Diversity Profile of a Community
profile_phylo.species_distribution | Phylogenetic Diversity Profile of a Community
profile_similarity | Similarity-Based Diversity Profile of a Community
profile_similarity.numeric | Similarity-Based Diversity Profile of a Community
profile_similarity.species_distribution | Similarity-Based Diversity Profile of a Community

## -- R --

rcommunity | Random communities
rlseries | Log-Series Distribution
rspcommunity | Random communities

## -- S --

species_distribution | Species Distributions