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ontophylo
View on CRAN: Click
here
Download and install ontophylo package within the R console
Install from CRAN:
install.packages("ontophylo")
Install from Github:
library("remotes")
install_github("cran/ontophylo")
Install by package version:
library("remotes")
install_version("ontophylo", "1.1.3")
Attach the package and use:
library("ontophylo")
Maintained by
Diego S. Porto
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2023-12-20
Latest Update: 2024-01-10
Description:
Provides new 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 vector images of the organisms of interest.
How to cite:
Diego S. Porto (2023). ontophylo: Ontology-Informed Phylogenetic Comparative Analyses. R package version 1.1.3, https://cran.r-project.org/web/packages/ontophylo. Accessed 31 Jan. 2025.
Previous versions and publish date:
1.1.2 (2023-12-20 17:30)
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imports, suggests or enhances
Complete documentation for ontophylo
Functions, R codes and Examples using
the ontophylo R package
Some associated functions: HAO . KDE_unnorm_trunc_Markov . KDE_unnormalized_scalar_Markov_kernel . MultiScale.simmap . RAC_query . add_noise_MD . add_pseudodata . anat_plot . color.bar . derivative_KDE . discr_Simmap . discr_Simmap_all . edge_profiles4plotting . edgeplot . estimate_band_W . estimate_edge_KDE . estimate_edge_KDE_Markov_kernel_unnorm . get_descendants_chars . get_path_edges . get_rough_state_cols . get_state . get_states_path . get_vector_ids_list . get_vector_ids_per_term . hym_annot . hym_graph . hym_hm . hym_img . hym_kde . hym_matrix . hym_nhpp . hym_stm . hym_stm_amalg . hym_stm_mds . hym_tree . integrate_edge_KDE . join_edges . list2edges . loess_smoothing_KDE . make_colors . make_colors_relative_scale . make_contMap_KDE . make_data_NHPP_KDE_Markov_kernel . make_data_NHPP_over_edge_MarkovKDE . make_pic . make_postPois_KDE . mds_plot . merge_branch_cat . merge_tree_cat . merge_tree_cat_list . normalize_KDE . pNHPP . paramo.list . paramo . path_hamming . path_hamming_over_all_edges . path_hamming_over_trees_KDE . posterior_lambda_KDE . posterior_lambda_KDE_Distr . read_Simmap_Rev . stack2 . stack_stm .
Some associated R codes: graphics_functions.R . morphospace_functions.R . nhpp_functions.R . ontophylo_data.R . paramo_functions.R . Full ontophylo package functions and examples
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