Entropy Partitioning to Measure Diversity


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Documentation for package ‘divent’ version 0.5-2

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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