Package: ontophylo 1.0.0

ontophylo: Ontology-Informed Phylogenetic Comparative Analyses

This package provides new phylogenetic tools for analyzing discrete trait data integrating bio-ontologies and phylogenetics. It expands on the previous work of Tarasov et al. (2019). The PARAMO pipeline allows to reconstruct ancestral phenomes treating groups of morphological traits as a single complex character. The pipeline incorporates knowledge from ontologies during the amalgamation of individual character stochastic maps. Here we expand the current PARAMO functionality by adding new statistical methods for inferring evolutionary phenome dynamics using non-homogeneous Poisson process (NHPP). The new functionalities include: (1) reconstruction of evolutionary rate shifts of phenomes across lineages and time; (2) reconstruction of morphospace dynamics through time; and (3) estimation of rates of phenome evolution at different levels of anatomical hierarchy (e.g., entire body or specific regions only). The package also includes user-friendly tools for visualizing evolutionary rates of different anatomical regions using PNG vector images of the organisms of interest.

Authors:Diego S. Porto [aut, cre], Sergei Tarasov [aut]

ontophylo_1.0.0.tar.gz


ontophylo_1.0.0.tar.gz(r-4.4-noble)
ontophylo_1.0.0.tgz(r-4.4-emscripten)ontophylo_1.0.0.tgz(r-4.3-emscripten)
ontophylo.pdf |ontophylo.html✨
ontophylo/json (API)

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

Peer review:

Bug tracker:https://github.com/diegosasso/ontophylo/issues

Datasets:

    On CRAN:

    40 exports 0.83 score 62 dependencies 8 scripts 156 downloads

    Last updated 10 months agofrom:49565f518d. Checks:OK: 1. Indexed: yes.

    TargetResultDate
    Doc / VignettesOKAug 24 2024

    Exports:add_noise_MDadd_pseudodataanat_plotcolor.barderivative_KDEdiscr_Simmapdiscr_Simmap_alledge_profiles4plottingedgeplotestimate_band_Westimate_edge_KDEestimate_edge_KDE_Markov_kernel_unnormget_descendants_charsget_rough_state_colsget_vector_ids_listget_vector_ids_per_termintegrate_edge_KDElist2edgesloess_smoothing_KDEmake_colorsmake_colors_relative_scalemake_contMap_KDEmake_data_NHPP_KDE_Markov_kernelmake_picmake_postPois_KDEmds_plotmerge_branch_catmerge_tree_catmerge_tree_cat_listMultiScale.simmapnormalize_KDEparamoparamo.listpath_hamming_over_all_edgespath_hamming_over_trees_KDEpNHPPposterior_lambda_KDEposterior_lambda_KDE_DistrRAC_queryread_Simmap_Rev

    Dependencies:apecliclusterGenerationcodacodetoolscolorspacecombinatcpp11DEoptimdigestdoParalleldplyrexpmfANCOVAfansifarverfastmatchforeachgenericsggplot2gluegtableigraphisobanditeratorslabelinglatticelifecyclemagrittrmapsMASSMatrixmgcvmnormtmunsellnlmenumDerivontologyIndexoptimParallelphangornphytoolspillarpkgconfigpurrrquadprogR6RColorBrewerRcpprlangscalesscatterplot3dstringdiststringistringrtibbletidyrtidyselecttruncnormutf8vctrsviridisLitewithr

    Readme and manuals

    Help Manual

    Help pageTopics
    Adding noise to MDS from one stochastic character mapadd_noise_MD
    Add pseudodataadd_pseudodata
    Plot Pictureanat_plot
    Color barcolor.bar
    Calculate KDE derivative over edgesderivative_KDE
    Reading unsummarized simmap for one treediscr_Simmap
    Reading unsummarized simmap for a list of treesdiscr_Simmap_all
    Make edge profiles for plottingedge_profiles4plotting
    Plot edge profiles and contMapedgeplot
    Estimate bandwidthestimate_band_W
    Estimate the normalized Markov KDEestimate_edge_KDE
    Estimate the unnormalized Markov KDEestimate_edge_KDE_Markov_kernel_unnorm
    Get characters that are the descendants of a selected ontology termget_descendants_chars
    Get edges IDs from root to a given node.get_path_edges
    Multiple character state colorsget_rough_state_cols
    Get state information about a given path.get_states_path
    Wrapper for getting vector layer IDs for multiple termsget_vector_ids_list
    Get vector layer IDs for single termget_vector_ids_per_term
    Calculate KDE integral over edgesintegrate_edge_KDE
    Join neighboring edges in edge profiles.join_edges
    KDE for unnormalized Markov kernel vectorized.KDE_unnorm_trunc_Markov
    KDE for unnormalized Markov kernel.KDE_unnormalized_scalar_Markov_kernel
    Convert list to edge matrixlist2edges
    Get loess smoothing for the unnormalized Markov KDEloess_smoothing_KDE
    Make color palette for image plottingmake_colors
    Make color palette for image plotting with relative scalemake_colors_relative_scale
    Make contMap KDE objectmake_contMap_KDE
    Get NHPP data for all edges (Markov KDE)make_data_NHPP_KDE_Markov_kernel
    Get NHPP data for a given edge (Markov KDE)make_data_NHPP_over_edge_MarkovKDE
    Assign colors to picture ID layersmake_pic
    Make posterior distribution of NHPPmake_postPois_KDE
    Plot morphospace from MDSmds_plot
    Merge state bins over branchmerge_branch_cat
    Merge state bins over a treemerge_tree_cat
    Merge state bins over a tree listmerge_tree_cat_list
    Multidimensional scaling of character states from one stochastic character mapMultiScale.simmap
    Normalize loess smoothingnormalize_KDE
    PARAMOparamo
    Stack multiple discrete stochastic character map listsparamo.list
    Path hammingpath_hamming
    Hamming distances for a treepath_hamming_over_all_edges
    Hamming distances for a list of treespath_hamming_over_trees_KDE
    Phylogenetic Non-Homogeneous Poisson Process (pNHPP) methodpNHPP
    Get analytical posteriorposterior_lambda_KDE
    Get distributions of analytical posteriorposterior_lambda_KDE_Distr
    Retrieve all characters under a given set of termsRAC_query
    Reading stochastic character maps file from ReVBayesread_Simmap_Rev
    Stack two discrete stochastic character maps.stack_stm
    Stack two discrete stochastic character map lists; x and y are the list of state names (i.e. maps).stack2