Function reference • phyf

All functions

autoplot(<pf>): Make an automatic ggplot2 plot for a pf object

avonet: AVONET Bird Trait Data with Phylogeny

bird_beak_codes: Dataset of latent codes representing bird beak 3D shapes

ecoregion_ids: Ecoregion IDs

make_interp(): Make a phylogenetic interpolation pfc

mammal_biogeo: Terrestrial Mammal Bioegeography Data with Phylogeny

pf(): pf object constructor

pf_anc(): Return a pfc with ancestral features

pf_as_pf(): Convert an object to a pf object

pf_as_pfc(): Make a pfc object from a phylo object

pf_as_phylo(): Convert a pf or pfc object to a ape::phylo object

pf_as_sparse(): Convert a pf or pfc object to a sparse matrix representation.

pf_desc(): Return a pfc with descendent's features

pf_edge_apply(): Apply a function along edges within a pfc object

pf_edge_names(): Extract edge names from pfc object

pf_edge_segmentize(): Segments the edges of a phylogeny by splitting them at particular positions

pf_end_features(): Extract the features of the end edge of each phylogenetic flow

pf_ends(): Returns the end edge of each phylogenetic flow as a two-column tibble with start and end columns

pf_epoch_info(): Get edges and positions along edges where a set of epoch times intersect

pf_filter_with_mrca(): Filter descendents of a MRCA

pf_flow_cumsum(): Calculate the cumulative sum of features for each flow

pf_flow_sum(): Calculate the sum of features for each flow

pf_indexes(): Replace feature with edge index in a pfc

pf_internal() `pf_internal<-`() pf_terminal() `pf_terminal<-`(): Extract or assign into the internal or terminal edges of a pfc

pf_is_desc(): Return a logical vector determining if a flow's terminal node is a descendant of an edge.

pf_is_empty(): Test which elements of a pfc are empty

pf_is_tips(): Return a logical vector which is TRUE for the elements of a pfc whci reprsent tips of a phylogeny

pf_kronecker(): Calculate a kronecker product when a pfc is the multiplicand or the multiplier.

pf_labels(): Return a vector of labels for a pfc object

pf_mean_edge_features(): Extract mean edge features from pfc object

pf_mrca(): Return the edge leading up to the most recent common ancestor of a set of phylogenetic flows

pf_nedges(): Return the number of edges in a pfc

pf_nodes(): Get only the (internal) node elements of a pfc

pf_ones(): Replace features with ones

pf_path(): Extract pfp object from pfc, the paths of each flow from root to terminal node.

pf_phyloflow(): Extracts the phylogenetic flow column of an pf object

pf_position(): Replace feature with edge position in flow in a pfc

pf_row_kron(): Calculate a rowwise kronecker product when the multiplicand or multiplier is a pfc.

pf_scale_flow_sum(): Scale the phylogenetic flow features to a constant sum.

pf_second_order(): Calculate a 'second order' pfc, which represents summed branch length from each node to the terminal node along each flow. When used in modelling traits, a second order pfc implies that rates of evolution of the trait are themselves evolving according to Brownian motion.

pf_standardise(): Standardise the phylogenetic flow features to an implied typical variance of 1.

pf_tips(): Get only the tip elements of a pfc

pf_vcv(): Calculate phylogenetic variance covariance matrix from pfc

pf_zeros(): Replace features with zeros

pfc() pf_is_pfc(): Create a new phylogenetic flow collection object (pfc)

pfp() pf_is_pfp(): Create a new phylogenetic flow path object (pfp)

plant_fungus: Dataset of latent codes representing bird beak 3D shapes

plot(<pf>): Make a plot for a pf object

primate_diet: Primate Diet Diversity and Threat Status Data with Phylogeny

primate_diet_hierarchy: Primate Diet Items Hierarchy

primate_diet_refs: Primate Diet Data References

rpfc(): Generate a random tree and return it as a pfc object

vert_bmr: Vertebrate Base Metabolic Rates with Phylogeny