Package: phyf 0.0.0.9000

phyf: Phylogenetic Flow Objects for Easy Manipulation and Modelling of Data on Phylogenetic Trees and Graphs

The {phyf} package implements a tibble and vctrs based object for storing phylogenetic trees along with data. It is fast and flexible and directly produces data structures useful for phylogenetic modelling in the {fibre} package.

Authors:Russell Dinnage [aut, cre]

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phyf.pdf |phyf.html✨
phyf/json (API)

# Install 'phyf' in R:
install.packages('phyf', repos = c('https://rdinnager.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/rdinnager/phyf/issues

Datasets:

On CRAN:

4.49 score 1 stars 1 packages 51 scripts 52 exports 88 dependencies

Last updated 2 months agofrom:39f1c42a86. Checks:OK: 1 ERROR: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 24 2024
R-4.5-winERROROct 24 2024
R-4.5-linuxERROROct 24 2024
R-4.4-winERROROct 24 2024
R-4.4-macERROROct 24 2024
R-4.3-winERROROct 24 2024
R-4.3-macERROROct 24 2024

Exports:%>%autoplotfortifymake_interppfpf_ancpf_as_pfpf_as_pfcpf_as_pftibblepf_as_phylopf_as_sparsepf_descpf_edge_applypf_edge_namespf_edge_segmentizepf_end_featurespf_endspf_epoch_infopf_filter_with_mrcapf_flow_cumsumpf_flow_sumpf_indexespf_internalpf_internal<-pf_is_descpf_is_emptypf_is_pfcpf_is_pfppf_is_tipspf_kroneckerpf_labelspf_mean_edge_featurespf_mrcapf_nedgespf_nodespf_onespf_pathpf_phyloflowpf_positionpf_row_kronpf_scale_flow_sumpf_second_orderpf_standardisepf_terminalpf_terminal<-pf_tipspf_vcvpf_zerospfcpfc_from_pftibblepfprpfc

Dependencies:apeaplotassertthatclassclassIntcliclusterGenerationcodacodetoolscolorspacecombinatcpp11DBIDEoptimdigestdoParalleldplyre1071expmfansifarverfastmatchfmesherforeachfsgenericsggfunggplot2ggplotifyggtreegluegridGraphicsgtableigraphinlabruisobanditeratorsivsjsonliteKernSmoothlabelinglatticelazyevallifecyclemagrittrmapsMASSMatrixMatrixModelsmgcvmnormtmunsellnlmenumDerivoptimParallelpatchworkphangornphytoolspillarpkgconfigplyrproxypurrrquadprogR6RColorBrewerRcpprlangs2scalesscatterplot3dsfspstringistringrterratibbletidyrtidyselecttidytreetreeiounitsutf8vctrsviridisLitewithrwkyulab.utils

Getting Started with {phyf}

Rendered fromphyf.Rmdusingknitr::rmarkdownon Oct 24 2024.

Last update: 2022-11-12
Started: 2022-11-12

Tree Arithmetic with Phylogenetic Flows

Rendered fromphyf_arith.Rmdusingknitr::rmarkdownon Oct 24 2024.

Last update: 2022-10-16
Started: 2022-10-14

Readme and manuals

Help Manual

Help pageTopics
Make an automatic 'ggplot2' plot for a 'pf' objectautoplot.pf
AVONET Bird Trait Data with Phylogenyavonet
Dataset of latent codes representing bird beak 3D shapesbird_beak_codes
Ecoregion IDsecoregion_ids
Make a phylogenetic interpolation 'pfc'make_interp
Terrestrial Mammal Bioegeography Data with Phylogenymammal_biogeo
'pf' object constructorpf
Return a 'pfc' with ancestral featurespf_anc
Convert an object to a 'pf' objectpf_as_pf
Make a 'pfc' object from a 'phylo' objectpf_as_pfc
Convert pfc into a pftibblepf_as_pftibble
Convert a 'pf' or 'pfc' object to a 'ape::phylo' objectpf_as_phylo
Convert a 'pf' or 'pfc' object to a sparse matrix representation.pf_as_sparse
Return a 'pfc' with descendent's featurespf_desc
Apply a function along edges within a 'pfc' objectpf_edge_apply
Extract edge names from 'pfc' objectpf_edge_names
Segments the edges of a phylogeny by splitting them at particular positionspf_edge_segmentize
Extract the features of the end edge of each phylogenetic flowpf_end_features
Returns the end edge of each phylogenetic flow as a two-column tibble with start and end columnspf_ends
Get edges and positions along edges where a set of epoch times intersectpf_epoch_info
Filter descendents of a MRCApf_filter_with_mrca
Calculate the cumulative sum of features for each flowpf_flow_cumsum
Calculate the sum of features for each flowpf_flow_sum
Replace feature with edge index in a 'pfc'pf_indexes
Extract or assign into the internal or terminal edges of a 'pfc'pf_internal pf_internal<- pf_terminal pf_terminal<-
Return a logical vector determining if a flow's terminal node is a descendant of an edge.pf_is_desc
Test which elements of a pfc are emptypf_is_empty
Return a logical vector which is 'TRUE' for the elements of a 'pfc' whci reprsent tips of a phylogenypf_is_tips
Calculate a kronecker product when a 'pfc' is the multiplicand or the multiplier.pf_kronecker
Return a vector of labels for a 'pfc' objectpf_labels
Extract mean edge features from 'pfc' objectpf_mean_edge_features
Return the edge leading up to the most recent common ancestor of a set of phylogenetic flowspf_mrca
Return the number of edges in a 'pfc'pf_nedges
Get only the (internal) node elements of a 'pfc'pf_nodes
Replace features with onespf_ones
Extract 'pfp' object from 'pfc', the paths of each flow from root to terminal node.pf_path
Extracts the phylogenetic flow column of an 'pf' objectpf_phyloflow
Replace feature with edge position in flow in a 'pfc'pf_position
Calculate a rowwise kronecker product when the multiplicand or multiplier is a 'pfc'.pf_row_kron
Scale the phylogenetic flow features to a constant sum.pf_scale_flow_sum
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_second_order
Standardise the phylogenetic flow features to an implied typical variance of 1.pf_standardise
Get only the tip elements of a 'pfc'pf_tips
Calculate phylogenetic variance covariance matrix from 'pfc'pf_vcv
Replace features with zerospf_zeros
Create a new phylogenetic flow collection object ('pfc')pfc pf_is_pfc
Convert pftibble into a pfcpfc_from_pftibble
Create a new phylogenetic flow path object ('pfp')pfp pf_is_pfp
Dataset of latent codes representing bird beak 3D shapesplant_fungus
Make a plot for a 'pf' objectplot.pf
Primate Diet Diversity and Threat Status Data with Phylogenyprimate_diet
Primate Diet Items Hierarchyprimate_diet_hierarchy
Primate Diet Data Referencesprimate_diet_refs
Generate a random tree and return it as a 'pfc' objectrpfc
Vertebrate Base Metabolic Rates with Phylogenyvert_bmr