Entropy Partitioning to Measure Diversity

Documentation for package ‘divent’ version 0.5-2

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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