Package index • tidydiversity

Community data

as_community() community_wide() community_long(): Tidy community data
tidy(<td_estimate>) tidy(<td_standardise>) tidy(<td_rarefy>) tidy(<td_boot>) tidy(<td_beta_pair>) glance(<td_coverage>) add_site_data(): Tidy and model-ready output

png_ants: Ants at nutrient baits along Mt Wilhelm, Papua New Guinea
png_tree_ants: Tree-nesting ants in rainforest plots at three elevations, Papua New Guinea
png_frogs: Frogs along the Mt Wilhelm elevational gradient, Papua New Guinea
wanang_butterflies: Butterflies in the Wanang forest dynamics plot, Papua New Guinea
wanang_caterpillars: Caterpillars reared from trees in primary and secondary forest at Wanang
portal_rodents: Rodent captures at the Portal Project, Arizona

beta_pair() beta_multi(): Partition beta diversity into turnover and nestedness
beta_hill(): Coverage-standardised beta diversity with Hill numbers
beta_hill_pair(): Pairwise Hill-number dissimilarity
beta_decay(): Distance decay of similarity
beta_decay_model(): Fit and test a distance-decay model
beta_dist(): Pairwise dissimilarity as a distance matrix
beta_permanova() beta_dispersion(): PERMANOVA and dispersion tests on community composition
beta_welch(): Welch-type PERMANOVA robust to unequal dispersion
beta_indicator(): Indicator species analysis

ord_fit(): Ordination of community data
ord_test(): Permutation tests for constrained ordinations
ord_select(): Forward selection of explanatory variables
ord_varpart(): Variation partitioning
autoplot(<td_ordination>): Plot an ordination
tidy(<td_ordination>) glance(<td_ordination>): Tidy and glance methods for ordinations

trait_dist(): Trait dissimilarity between species
trait_cwm(): Community-weighted mean traits
trait_cwm_test(): Test CWM-environment relationships with the max test
trait_fd_indices(): Classic functional diversity indices
trait_rao(): Rao's quadratic entropy: alpha, beta and gamma functional diversity
trait_ses(): Standardised effect sizes from null models
trait_itv(): Intra- and interspecific trait variability
trait_fourth_corner(): Fourth-corner analysis
trait_tpd() trait_tpd_dissim(): Functional diversity from trait probability densities
phylo_signal(): Phylogenetic signal of traits
phylo_dist(): Phylogenetic distances between species
phylo_combine_dist(): Combine functional and phylogenetic distances
data_aravo(): Alpine plant communities with traits (aravo) in long format

autoplot(<td_rarefy>) autoplot(<td_standardise>) autoplot(<td_beta_decay>) autoplot(<td_hill>) autoplot(<td_estimate>) autoplot(<td_coverage>) autoplot(<td_beta_pair>) autoplot(<td_beta_hill_pair>) autoplot(<td_beta_multi>) autoplot(<td_beta_hill>) autoplot(<td_dispersion>) autoplot(<td_completeness>) autoplot(<td_evenness>): Plot tidydiversity results
theme_tidydiversity() plot_palette() scale_colour_tidydiversity() scale_fill_tidydiversity(): Publication theme and colour palettes
plot_venn(): Venn diagram of species shared between groups
plot_phylo(): Plot a phylogeny with species abundances and phylogenetic diversity
plot_trait_space(): Plot functional trait space
plot_panel(): Combine plots into a publication figure
plot_save(): Save a figure at journal sizes
div_table(): Publication-ready tables

tidy(<td_estimate>) tidy(<td_standardise>) tidy(<td_rarefy>) tidy(<td_boot>) tidy(<td_beta_pair>) glance(<td_coverage>) add_site_data(): Tidy and model-ready output
model_group_folds(): Grouped cross-validation folds for community data
model_case_weights(): Precision weights from estimated diversity
step_hill(): Hill number features in a recipe

model_count() tidy(<td_count_model>) glance(<td_count_model>): Overdispersed count and proportion models (aods3-free)
plot_partial() plot_surface(): Partial-effect and two-predictor surface plots (visreg / plotmo style)

stems_as_trees() stems_abundance() stems_basal_area() stems_size_class() stems_demography() stems_as_community(): ForestGEO-style stem and tree census verbs