vegan - Community Ecology Package
Ordination methods, diversity analysis and other functions for community and vegetation ecologists.
Last updated 9 days ago
ecological-modellingecologyordination
436 stars 11.05 score 7 dependencies 411 dependentsbrms - Bayesian Regression Models using 'Stan'
Fit Bayesian generalized (non-)linear multivariate multilevel models using 'Stan' for full Bayesian inference. A wide range of distributions and link functions are supported, allowing users to fit -- among others -- linear, robust linear, count data, survival, response times, ordinal, zero-inflated, hurdle, and even self-defined mixture models all in a multilevel context. Further modeling options include both theory-driven and data-driven non-linear terms, auto-correlation structures, censoring and truncation, meta-analytic standard errors, and quite a few more. In addition, all parameters of the response distribution can be predicted in order to perform distributional regression. Prior specifications are flexible and explicitly encourage users to apply prior distributions that actually reflect their prior knowledge. Models can easily be evaluated and compared using several methods assessing posterior or prior predictions. References: Bürkner (2017) <doi:10.18637/jss.v080.i01>; Bürkner (2018) <doi:10.32614/RJ-2018-017>; Bürkner (2021) <doi:10.18637/jss.v100.i05>; Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>.
Last updated 10 days ago
bayesian-inferencebrmsmultilevel-modelsstanstatistical-models
1.3k stars 10.50 score 73 dependencies 28 dependents![](https://github.com/KlausVigo/phangorn/raw/HEAD/man/figures/logo.png)
phangorn - Phylogenetic Reconstruction and Analysis
Allows for estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation (Schliep 2011). Offers methods for tree comparison, model selection and visualization of phylogenetic networks as described in Schliep et al. (2017).
Last updated 23 hours ago
phylogenetic-analysisphylogenetics
199 stars 8.93 score 37 dependencies 137 dependentsdendextend - Extending 'dendrogram' Functionality in R
Offers a set of functions for extending 'dendrogram' objects in R, letting you visualize and compare trees of 'hierarchical clusterings'. You can (1) Adjust a tree's graphical parameters - the color, size, type, etc of its branches, nodes and labels. (2) Visually and statistically compare different 'dendrograms' to one another.
Last updated 7 months ago
148 stars 8.91 score 30 dependencies 146 dependentstaxize - Taxonomic Information from Around the Web
Interacts with a suite of web 'APIs' for taxonomic tasks, such as getting database specific taxonomic identifiers, verifying species names, getting taxonomic hierarchies, fetching downstream and upstream taxonomic names, getting taxonomic synonyms, converting scientific to common names and vice versa, and more.
Last updated 2 months ago
taxonomybiologynomenclaturejsonapiwebapi-clientidentifiersspeciesnamesapi-wrapperbiodiversitydarwincoredatataxize
264 stars 7.24 score 121 dependencies 29 dependentstidytree - A Tidy Tool for Phylogenetic Tree Data Manipulation
Phylogenetic tree generally contains multiple components including node, edge, branch and associated data. 'tidytree' provides an approach to convert tree object to tidy data frame as well as provides tidy interfaces to manipulate tree data.
Last updated 22 hours ago
phylogenetic-treetidyversetree-data
49 stars 7.16 score 32 dependencies 117 dependentsgeomorph - Geometric Morphometric Analyses of 2D and 3D Landmark Data
Read, manipulate, and digitize landmark data, generate shape variables via Procrustes analysis for points, curves and surfaces, perform shape analyses, and provide graphical depictions of shapes and patterns of shape variation.
Last updated 1 months ago
73 stars 6.87 score 55 dependencies 6 dependentspicante - Integrating Phylogenies and Ecology
Functions for phylocom integration, community analyses, null-models, traits and evolution. Implements numerous ecophylogenetic approaches including measures of community phylogenetic and trait diversity, phylogenetic signal, estimation of trait values for unobserved taxa, null models for community and phylogeny randomizations, and utility functions for data input/output and phylogeny plotting. A full description of package functionality and methods are provided by Kembel et al. (2010) <doi:10.1093/bioinformatics/btq166>.
Last updated 1 years ago
32 stars 6.74 score 11 dependencies 15 dependentsphylolm - Phylogenetic Linear Regression
Provides functions for fitting phylogenetic linear models and phylogenetic generalized linear models. The computation uses an algorithm that is linear in the number of tips in the tree. The package also provides functions for simulating continuous or binary traits along the tree. Other tools include functions to test the adequacy of a population tree.
Last updated 9 months ago
30 stars 5.54 score 11 dependencies 11 dependentsrotl - Interface to the 'Open Tree of Life' API
An interface to the 'Open Tree of Life' API to retrieve phylogenetic trees, information about studies used to assemble the synthetic tree, and utilities to match taxonomic names to 'Open Tree identifiers'. The 'Open Tree of Life' aims at assembling a comprehensive phylogenetic tree for all named species.
Last updated 1 years ago
metadataropensciphylogeneticsindependant-contrastsbiodiversitypeer-reviewedphylogenytaxonomy
39 stars 5.25 score 26 dependencies 31 dependentsphylobase - Base Package for Phylogenetic Structures and Comparative Data
Provides a base S4 class for comparative methods, incorporating one or more trees and trait data.
Last updated 6 months ago
phylogenetics
17 stars 5.15 score 49 dependencies 19 dependentsphylosignal - Exploring the Phylogenetic Signal in Continuous Traits
A collection of tools to explore the phylogenetic signal in univariate and multivariate data. The package provides functions to plot traits data against a phylogenetic tree, different measures and tests for the phylogenetic signal, methods to describe where the signal is located and a phylogenetic clustering method.
Last updated 10 months ago
16 stars 4.62 score 90 dependenciesDAMOCLES - Dynamic Assembly Model of Colonization, Local Extinction and Speciation
Simulates and computes (maximum) likelihood of a dynamical model of community assembly that takes into account phylogenetic history.
Last updated 3 years ago
1 stars 4.39 score 101 dependenciesgeiger - Analysis of Evolutionary Diversification
Methods for fitting macroevolutionary models to phylogenetic trees Pennell (2014) <doi:10.1093/bioinformatics/btu181>.
Last updated 1 years ago
22 stars 4.29 score 57 dependencies 29 dependentsmvMORPH - Multivariate Comparative Tools for Fitting Evolutionary Models to Morphometric Data
Fits multivariate (Brownian Motion, Early Burst, ACDC, Ornstein-Uhlenbeck and Shifts) models of continuous traits evolution on trees and time series. 'mvMORPH' also proposes high-dimensional multivariate comparative tools (linear models using Generalized Least Squares and multivariate tests) based on penalized likelihood. See Clavel et al. (2015) <DOI:10.1111/2041-210X.12420>, Clavel et al. (2019) <DOI:10.1093/sysbio/syy045>, and Clavel & Morlon (2020) <DOI:10.1093/sysbio/syaa010>.
Last updated 4 months ago
17 stars 4.03 score 59 dependencies 2 dependentsstrap - Stratigraphic Tree Analysis for Palaeontology
Functions for the stratigraphic analysis of phylogenetic trees.
Last updated 3 months ago
1 stars 3.96 score 7 dependencies 3 dependentsRNeXML - Semantically Rich I/O for the 'NeXML' Format
Provides access to phyloinformatic data in 'NeXML' format. The package should add new functionality to R such as the possibility to manipulate 'NeXML' objects in more various and refined way and compatibility with 'ape' objects.
Last updated 3 months ago
metadatanexmlphylogeneticslinked-data
13 stars 3.94 score 38 dependencies 20 dependentsOUwie - Analysis of Evolutionary Rates in an OU Framework
Estimates rates for continuous character evolution under Brownian motion and a new set of Ornstein-Uhlenbeck based Hansen models that allow both the strength of the pull and stochastic motion to vary across selective regimes. Beaulieu et al (2012).
Last updated 3 months ago
8 stars 3.74 score 87 dependenciesTreeDist - Calculate and Map Distances Between Phylogenetic Trees
Implements measures of tree similarity, including information-based generalized Robinson-Foulds distances (Phylogenetic Information Distance, Clustering Information Distance, Matching Split Information Distance; Smith 2020) <doi:10.1093/bioinformatics/btaa614>; Jaccard-Robinson-Foulds distances (Bocker et al. 2013) <doi:10.1007/978-3-642-40453-5_13>, including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>; the Matching Split Distance (Bogdanowicz & Giaro 2012) <doi:10.1109/TCBB.2011.48>; Maximum Agreement Subtree distances; the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the Nearest Neighbour Interchange (NNI) distance, approximated per Li et al. (1996) <doi:10.1007/3-540-61332-3_168>. Includes tools for visualizing mappings of tree space (Smith 2022) <doi:10.1093/sysbio/syab100>, for identifying islands of trees (Silva and Wilkinson 2021) <doi:10.1093/sysbio/syab015>, for calculating the median of sets of trees, and for computing the information content of trees and splits.
Last updated 2 days ago
phylogeneticstree-distancephylogenetic-treestree-distancestrees
28 stars 3.68 score 48 dependencies 5 dependentsdispRity - Measuring Disparity
A modular package for measuring disparity (multidimensional space occupancy). Disparity can be calculated from any matrix defining a multidimensional space. The package provides a set of implemented metrics to measure properties of the space and allows users to provide and test their own metrics. The package also provides functions for looking at disparity in a serial way (e.g. disparity through time) or per groups as well as visualising the results. Finally, this package provides several statistical tests for disparity analysis.
Last updated 2 months ago
disparityecologymultidimensionalitypalaeobiology
23 stars 3.61 score 95 dependencies 1 dependentstreedater - Fast Molecular Clock Dating of Phylogenetic Trees with Rate Variation
Functions for estimating times of common ancestry and molecular clock rates of evolution using a variety of evolutionary models, parametric and nonparametric bootstrap confidence intervals, methods for detecting outlier lineages, root-to-tip regression, and a statistical test for selecting molecular clock models. The methods are described in Volz, E.M. and S.D.W. Frost (2017) <doi:10.1093/ve/vex025>.
Last updated 2 years ago
23 stars 3.56 score 9 dependencieshillR - Diversity Through Hill Numbers
Calculate taxonomic, functional and phylogenetic diversity measures through Hill Numbers proposed by Chao, Chiu and Jost (2014) <doi:10.1146/annurev-ecolsys-120213-091540>.
Last updated 3 months ago
biodiversityhill-numbers
30 stars 3.53 score 73 dependencies 3 dependents![](https://github.com/EricMarcon/entropart/raw/HEAD/man/figures/logo.png)
entropart - Entropy Partitioning to Measure Diversity
Measurement and partitioning of diversity, based on Tsallis entropy, following Marcon and Herault (2015) <doi:10.18637/jss.v067.i08>. 'entropart' provides functions to calculate alpha, beta and gamma diversity of communities, including phylogenetic and functional diversity. Estimation-bias corrections are available.
Last updated 5 months ago
biodiversitydiversityentropy-partitioningestimatormeasurespecies
8 stars 3.44 score 75 dependencies 1 dependentsTreeTools - Create, Modify and Analyse Phylogenetic Trees
Efficient implementations of functions for the creation, modification and analysis of phylogenetic trees. Applications include: generation of trees with specified shapes; tree rearrangement; analysis of tree shape; rooting of trees and extraction of subtrees; calculation and depiction of split support; plotting the position of rogue taxa (Klopfstein & Spasojevic 2019) <doi:10.1371/journal.pone.0212942>; calculation of ancestor-descendant relationships, of 'stemwardness' (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>, and of tree balance (Mir et al. 2013, Lemant et al. 2022) <doi:10.1016/j.mbs.2012.10.005>, <doi:10.1093/sysbio/syac027>; artificial extinction (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>; import and export of trees from Newick, Nexus (Maddison et al. 1997) <doi:10.1093/sysbio/46.4.590>, and TNT <https://www.lillo.org.ar/phylogeny/tnt/> formats; and analysis of splits and cladistic information.
Last updated 2 days ago
evolutionary-biologyphylogenetic-treesphylogenetics
15 stars 3.42 score 22 dependencies 9 dependentsRphylopars - Phylogenetic Comparative Tools for Missing Data and Within-Species Variation
Tools for performing phylogenetic comparative methods for datasets with with multiple observations per species (intraspecific variation or measurement error) and/or missing data (Goolsby et al. 2017). Performs ancestral state reconstruction and missing data imputation on the estimated evolutionary model, which can be specified as Brownian Motion, Ornstein-Uhlenbeck, Early-Burst, Pagel's lambda, kappa, or delta, or a star phylogeny.
Last updated 2 years ago
28 stars 3.39 score 74 dependenciesQuartet - Comparison of Phylogenetic Trees Using Quartet and Split Measures
Calculates the number of four-taxon subtrees consistent with a pair of cladograms, calculating the symmetric quartet distance of Bandelt & Dress (1986), Reconstructing the shape of a tree from observed dissimilarity data, Advances in Applied Mathematics, 7, 309-343 <doi:10.1016/0196-8858(86)90038-2>, and using the tqDist algorithm of Sand et al. (2014), tqDist: a library for computing the quartet and triplet distances between binary or general trees, Bioinformatics, 30, 2079–2080 <doi:10.1093/bioinformatics/btu157> for pairs of binary trees.
Last updated 2 months ago
bioinformaticscomparisonphylogenetic-treesphylogeneticsquartetquartet-distanceresearch-tooltree
9 stars 3.35 score 51 dependenciesMCMCglmm - MCMC Generalised Linear Mixed Models
Fits Multivariate Generalised Linear Mixed Models (and related models) using Markov chain Monte Carlo techniques (Hadfield 2010 J. Stat. Soft.).
Last updated 2 months ago
2 stars 3.07 score 10 dependencies 11 dependentstreespace - Statistical Exploration of Landscapes of Phylogenetic Trees
Tools for the exploration of distributions of phylogenetic trees. This package includes a 'shiny' interface which can be started from R using treespaceServer(). For further details see Jombart et al. (2017) <DOI:10.1111/1755-0998.12676>.
Last updated 11 months ago
27 stars 3.06 score 148 dependenciesbeautier - 'BEAUti' from R
'BEAST2' (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'BEAUti 2' (which is part of 'BEAST2') is a GUI tool that allows users to specify the many possible setups and generates the XML file 'BEAST2' needs to run. This package provides a way to create 'BEAST2' input files without active user input, but using R function calls instead.
Last updated 19 days ago
bayesianbeastbeast2beautiphylogenetic-inferencephylogenetics
13 stars 2.96 score 22 dependencies 5 dependentsdiversitree - Comparative 'Phylogenetic' Analyses of Diversification
Contains a number of comparative 'phylogenetic' methods, mostly focusing on analysing diversification and character evolution. Contains implementations of 'BiSSE' (Binary State 'Speciation' and Extinction) and its unresolved tree extensions, 'MuSSE' (Multiple State 'Speciation' and Extinction), 'QuaSSE', 'GeoSSE', and 'BiSSE-ness' Other included methods include Markov models of discrete and continuous trait evolution and constant rate 'speciation' and extinction.
Last updated 10 months ago
30 stars 2.82 score 7 dependencies 2 dependentsphylotools - Phylogenetic Tools for Eco-Phylogenetics
A collection of tools for building RAxML supermatrix using PHYLIP or aligned FASTA files. These functions will be useful for building large phylogenies using multiple markers.
Last updated 3 years ago
11 stars 2.81 score 5 dependenciesouch - Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses
Fit and compare Ornstein-Uhlenbeck models for evolution along a phylogenetic tree.
Last updated 23 days ago
adaptive-regimebrownian-motionornstein-uhlenbeckornstein-uhlenbeck-modelsouchphylogenetic-comparative-hypothesesphylogenetic-comparative-methodsphylogenetic-datareact
15 stars 2.72 score 1 dependencies 4 dependentscorHMM - Hidden Markov Models of Character Evolution
Fits hidden Markov models of discrete character evolution which allow different transition rate classes on different portions of a phylogeny. Beaulieu et al (2013) <doi:10.1093/sysbio/syt034>.
Last updated 29 days ago
11 stars 2.66 score 62 dependencies 2 dependentsbeastier - Call 'BEAST2'
'BEAST2' (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'BEAST2' is a command-line tool. This package provides a way to call 'BEAST2' from an 'R' function call.
Last updated 19 days ago
bayesianbeastbeast2phylogenetic-inferencephylogenetics
10 stars 2.63 score 63 dependencies 4 dependentsevobiR - Evolutionary Biology in R
Comparative analysis of continuous traits influencing discrete states, and utility tools to facilitate comparative analyses. Implementations of ABBA/BABA type statistics to test for introgression in genomic data.
Last updated 3 months ago
14 stars 2.50 score 71 dependenciestreeplyr - 'dplyr' Functionality for Matched Tree and Data Objects
Matches phylogenetic trees and trait data, and allows simultaneous manipulation of the tree and data using 'dplyr'.
Last updated 1 years ago
33 stars 2.50 score 61 dependenciesphylocomr - Interface to 'Phylocom'
Interface to 'Phylocom' (<https://phylodiversity.net/phylocom/>), a library for analysis of 'phylogenetic' community structure and character evolution. Includes low level methods for interacting with the three executables, as well as higher level interfaces for methods like 'aot', 'ecovolve', 'bladj', 'phylomatic', and more.
Last updated 1 years ago
phylogenyphylocomphylodiversitycommunity structurecharacter evolutionspeciescommunity-ecologyecologyevolution
14 stars 2.47 score 12 dependencies 4 dependentsphylogram - Dendrograms for Evolutionary Analysis
Contains functions for developing phylogenetic trees as deeply-nested lists ("dendrogram" objects). Enables bi-directional conversion between dendrogram and "phylo" objects (see Paradis et al (2004) <doi:10.1093/bioinformatics/btg412>), and features several tools for command-line tree manipulation and import/export via Newick parenthetic text.
Last updated 5 years ago
peer-reviewed
11 stars 2.42 score 5 dependencies 8 dependentsRevGadgets - Visualization and Post-Processing of 'RevBayes' Analyses
Processes and visualizes the output of complex phylogenetic analyses from the 'RevBayes' phylogenetic graphical modeling software.
Last updated 8 months ago
13 stars 2.36 score 105 dependenciestreebase - Discovery, Access and Manipulation of 'TreeBASE' Phylogenies
Interface to the API for 'TreeBASE' <http://treebase.org> from 'R.' 'TreeBASE' is a repository of user-submitted phylogenetic trees (of species, population, or genes) and the data used to create them.
Last updated 5 months ago
10 stars 2.36 score 16 dependencies 2 dependentsadephylo - Exploratory Analyses for the Phylogenetic Comparative Method
Multivariate tools to analyze comparative data, i.e. a phylogeny and some traits measured for each taxa. The package contains functions to represent comparative data, compute phylogenetic proximities, perform multivariate analysis with phylogenetic constraints and test for the presence of phylogenetic autocorrelation. The package is described in Jombart et al (2010) <doi:10.1093/bioinformatics/btq292>.
Last updated 8 days ago
9 stars 2.18 score 88 dependencies 4 dependentshisse - Hidden State Speciation and Extinction
Sets up and executes a HiSSE model (Hidden State Speciation and Extinction) on a phylogeny and character sets to test for hidden shifts in trait dependent rates of diversification. Beaulieu and O'Meara (2016) <doi:10.1093/sysbio/syw022>.
Last updated 9 days ago
6 stars 2.17 score 77 dependencies![](https://github.com/ropensci/phylotaR/raw/HEAD/logo.png)
phylotaR - Automated Phylogenetic Sequence Cluster Identification from 'GenBank'
A pipeline for the identification, within taxonomic groups, of orthologous sequence clusters from 'GenBank' <https://www.ncbi.nlm.nih.gov/genbank/> as the first step in a phylogenetic analysis. The pipeline depends on a local alignment search tool and is, therefore, not dependent on differences in gene naming conventions and naming errors.
Last updated 8 days ago
blastngenbankpeer-reviewedphylogeneticssequence-alignment
23 stars 2.14 score 69 dependenciesepm - EcoPhyloMapper
Facilitates the aggregation of species' geographic ranges from vector or raster spatial data, and that enables the calculation of various morphological and phylogenetic community metrics across geography. Citation: Title, PO, DL Swiderski and ML Zelditch (2022) <doi:10.1111/2041-210X.13914>.
Last updated 9 days ago
12 stars 2.11 score 21 dependenciesbayou - Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies
Tools for fitting and simulating multi-optima Ornstein-Uhlenbeck models to phylogenetic comparative data using Bayesian reversible-jump methods.
Last updated 29 days ago
21 stars 2.09 score 63 dependenciestracerer - Tracer from R
'BEAST2' (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'Tracer' (<https://github.com/beast-dev/tracer/>) is a GUI tool to parse and analyze the files generated by 'BEAST2'. This package provides a way to parse and analyze 'BEAST2' input files without active user input, but using R function calls instead.
Last updated 10 months ago
8 stars 2.06 score 3 dependencies 3 dependentsbrranching - Fetch 'Phylogenies' from Many Sources
Includes methods for fetching 'phylogenies' from a variety of sources, including the 'Phylomatic' web service (<http://phylodiversity.net/phylomatic/>), and 'Phylocom' (<https://github.com/phylocom/phylocom/>).
Last updated 2 years ago
phylogenytreephylomaticmolecularplantsphylogenies
18 stars 2.05 score 137 dependencies 1 dependentsTreeSearch - Phylogenetic Analysis with Discrete Character Data
Reconstruct phylogenetic trees from discrete data. Inapplicable character states are handled using the algorithm of Brazeau, Guillerme and Smith (2019) <doi:10.1093/sysbio/syy083> with the "Morphy" library, under equal or implied step weights. Contains a "shiny" user interface for interactive tree search and exploration of results, including character visualization, rogue taxon detection, tree space mapping, and cluster consensus trees (Smith 2022a, b) <doi:10.1093/sysbio/syab099>, <doi:10.1093/sysbio/syab100>. Profile Parsimony (Faith and Trueman, 2001) <doi:10.1080/10635150118627>, Successive Approximations (Farris, 1969) <doi:10.2307/2412182> and custom optimality criteria are implemented.
Last updated 2 months ago
bioinformaticsmorphological-analysisphylogeneticsresearch-tooltree-search
5 stars 1.89 score 87 dependenciesFossilSim - Simulation of Fossil and Taxonomy Data
Simulating taxonomy and fossil data on phylogenetic trees under mechanistic models of speciation, preservation and sampling.
Last updated 19 days ago
8 stars 1.85 score 5 dependencies 1 dependentssensiPhy - Sensitivity Analysis for Comparative Methods
An implementation of sensitivity analysis for phylogenetic comparative methods. The package is an umbrella of statistical and graphical methods that estimate and report different types of uncertainty in PCM: (i) Species Sampling uncertainty (sample size; influential species and clades). (ii) Phylogenetic uncertainty (different topologies and/or branch lengths). (iii) Data uncertainty (intraspecific variation and measurement error).
Last updated 4 years ago
comparative-methodsecologyevolutionphylogeneticssensitivity-analysis
12 stars 1.71 score 65 dependenciesips - Interfaces to Phylogenetic Software in R
Functions that wrap popular phylogenetic software for sequence alignment, masking of sequence alignments, and estimation of phylogenies and ancestral character states.
Last updated 3 months ago
10 stars 1.69 score 41 dependencies 2 dependentssecsse - Several Examined and Concealed States-Dependent Speciation and Extinction
Simultaneously infers state-dependent diversification across two or more states of a single or multiple traits while accounting for the role of a possible concealed trait. See Herrera-Alsina et al. (2019) <doi:10.1093/sysbio/syy057>.
Last updated 3 months ago
1 stars 1.68 score 66 dependenciesapex - Phylogenetic Methods for Multiple Gene Data
Toolkit for the analysis of multiple gene data (Jombart et al. 2017) <doi:10.1111/1755-0998.12567>. 'apex' implements the new S4 classes 'multidna', 'multiphyDat' and associated methods to handle aligned DNA sequences from multiple genes.
Last updated 6 months ago
5 stars 1.66 score 76 dependenciesRogue - Identify Rogue Taxa in Sets of Phylogenetic Trees
Rogue ("wildcard") taxa are leaves with uncertain phylogenetic position. Their position may vary from tree to tree under inference methods that yield a tree set (e.g. bootstrapping, Bayesian tree searches, maximum parsimony). The presence of rogue taxa in a tree set can potentially remove all information from a consensus tree. The information content of a consensus tree - a function of its resolution and branch support values - can often be increased by removing rogue taxa. 'Rogue' provides an explicitly information-theoretic approach to rogue detection (Smith 2022) <doi:10.1093/sysbio/syab099>, and an interface to 'RogueNaRok' (Aberer et al. 2013) <doi:10.1093/sysbio/sys078>.
Last updated 5 months ago
consensus-treephylogenetic-treesphylogenetics
2 stars 1.60 score 55 dependencies 2 dependentsaphylo - Statistical Inference and Prediction of Annotations in Phylogenetic Trees
Implements a parsimonious evolutionary model to analyze and predict gene-functional annotations in phylogenetic trees as described in Vega Yon et al. (2021) <doi:10.1371/journal.pcbi.1007948>. Focusing on computational efficiency, 'aphylo' makes it possible to estimate pooled phylogenetic models, including thousands (hundreds) of annotations (trees) in the same run. The package also provides the tools for visualization of annotated phylogenies, calculation of posterior probabilities (prediction) and goodness-of-fit assessment featured in Vega Yon et al. (2021).
Last updated 9 months ago
annotationsinferencephylogeneticsrcpparmadillo
6 stars 1.59 score 12 dependenciesPHYLOGR - Functions for Phylogenetically Based Statistical Analyses
Manipulation and analysis of phylogenetically simulated data sets and phylogenetically based analyses using GLS.
Last updated 4 years ago
1.59 score 0 dependenciesphylocanvas - Interactive Phylogenetic Trees Using the 'Phylocanvas' JavaScript Library
Create and customize interactive phylogenetic trees using the 'phylocanvas' JavaScript library and the 'htmlwidgets' package. These trees can be used directly from the R console, from 'RStudio', in Shiny apps, and in R Markdown documents. See <http://phylocanvas.org/> for more information on the 'phylocanvas' library.
Last updated 7 years ago
htmlwidgetsphylogeny
9 stars 1.58 score 69 dependencies![](https://github.com/oschwery/MonoPhy/raw/HEAD/man/figures/logo.png)
MonoPhy - Explore Monophyly of Taxonomic Groups in a Phylogeny
Requires rooted phylogeny as input and creates a table of genera, their monophyly-status, which taxa cause problems in monophyly etc. Different information can be extracted from the output and a plot function allows visualization of the results in a number of ways. "MonoPhy: a simple R package to find and visualize monophyly issues." Schwery, O. & O'Meara, B.C. (2016) <doi:10.7717/peerj-cs.56>.
Last updated 3 months ago
5 stars 1.49 score 134 dependenciesAnnotationBustR - Extract Subsequences from GenBank Annotations
Extraction of subsequences into FASTA files from GenBank annotations where gene names may vary among accessions. Borstein & O'Meara (2018) <doi:10.7717/peerj.5179>.
Last updated 5 months ago
5 stars 1.47 score 12 dependencies![](https://github.com/ropensci/treedata.table/raw/HEAD/man/figures/logo.png)
treedata.table - Manipulation of Matched Phylogenies and Data using 'data.table'
An implementation that combines trait data and a phylogenetic tree (or trees) into a single object of class treedata.table. The resulting object can be easily manipulated to simultaneously change the trait- and tree-level sampling. Currently implemented functions allow users to use a 'data.table' syntax when performing operations on the trait dataset within the treedata.table object.
Last updated 3 years ago
7 stars 1.46 score 60 dependenciesdietr - Diet Estimated Trophic Levels
Estimates fractional trophic level from quantitative and qualitative diet data and calculates electivity indices in R. Borstein (2020) <doi:10.1007/s10750-020-04417-5>.
Last updated 5 months ago
dietelectivitytrophic
5 stars 1.40 score 49 dependenciesFishPhyloMaker - Phylogenies for a List of Finned-Ray Fishes
Provides an alternative to facilitate the construction of a phylogeny for fish species from a list of species or a community matrix using as a backbone the phylogenetic tree proposed by Rabosky et al. (2018) <doi:10.1038/s41586-018-0273-1>.
Last updated 7 months ago
6 stars 1.40 score 107 dependenciesphyloTop - Calculating Topological Properties of Phylogenies
Tools for calculating and viewing topological properties of phylogenetic trees.
Last updated 2 years ago
1 stars 1.27 score 86 dependenciesEvoPhylo - Pre- And Postprocessing of Morphological Data from Relaxed Clock Bayesian Phylogenetics
Performs automated morphological character partitioning for phylogenetic analyses and analyze macroevolutionary parameter outputs from clock (time-calibrated) Bayesian inference analyses, following concepts introduced by Simões and Pierce (2021) <doi:10.1038/s41559-021-01532-x>.
Last updated 1 years ago
4 stars 1.26 score 163 dependenciespaleobuddy - Simulating Diversification Dynamics
Simulation of species diversification, fossil records, and phylogenies. While the literature on species birth-death simulators is extensive, including important software like 'paleotree' and 'APE', we concluded there were interesting gaps to be filled regarding possible diversification scenarios. Here we strove for flexibility over focus, implementing a large array of regimens for users to experiment with and combine. In this way, 'paleobuddy' can be used in complement to other simulators as a flexible jack of all trades, or, in the case of scenarios implemented only here, can allow for robust and easy simulations for novel situations. Environmental data modified from that in 'RPANDA': Morlon H. et al (2016) <doi:10.1111/2041-210X.12526>.
Last updated 1 years ago
evolutionmacroevolutionpaleobiologypaleontologyphylogenetics
5 stars 1.25 score 0 dependenciesRevticulate - Interaction with "RevBayes" in R
Interaction with "RevBayes" via R. Objects created in "RevBayes" can be passed into the R environment, and many types can be converted into similar R objects. To download "RevBayes", go to <https://revbayes.github.io/download>.
Last updated 2 years ago
8 stars 1.08 score 43 dependenciespmc - Phylogenetic Monte Carlo
Monte Carlo based model choice for applied phylogenetics of continuous traits. Method described in Carl Boettiger, Graham Coop, Peter Ralph (2012) Is your phylogeny informative? Measuring the power of comparative methods, Evolution 66 (7) 2240-51. <doi:10.1111/j.1558-5646.2011.01574.x>.
Last updated 10 months ago
2 stars 1.03 score 65 dependenciesmcmc3r - Tools to work with MCMCtree
Tools to work with MCMCtree, a program for Bayesian inference of species divergence times.
Last updated 11 days ago
2 stars 0.91 score 7 dependenciesdentist - Dents the Likelihood Surface to Estimate Parameter Uncertainty
This will sample points around a specified distance from the maximum likelihood estimates. This should be a better way to estimate uncertainty than using the Hessian of the likelihood equation. It works by "denting" the likelihood surface to make a ridge at the desired difference in log likelihood and then "walks" around this dented surface, sampling points.
Last updated 4 months ago
3 stars 0.91 score 0 dependenciesidendr0 - Interactive Dendrograms
Interactive dendrogram that enables the user to select and color clusters, to zoom and pan the dendrogram, and to visualize the clustered data not only in a built-in heat map, but also in 'GGobi' interactive plots and user-supplied plots. This is a backport of Qt-based 'idendro' (<https://github.com/tsieger/idendro>) to base R graphics and Tcl/Tk GUI.
Last updated 3 years ago
7 stars 0.82 score 1 dependenciesTreEvo - Using ABC to Understand Trait Evolution
Various functions for estimating parameters of trait evolution in comparative analyses using Approximate Bayesian Computation.
Last updated 1 years ago
1 stars 0.71 score 102 dependenciesbppr - An R package for BPP
Functions to work with the multi-species coalescent program BPP, for example, functions to calibrate BPP trees to geological time.
Last updated 1 years ago
6 stars 0.71 score 0 dependenciesTBRDist - Rearrangement Distances Between Unrooted Phylogenetic Trees
Fast calculation of the Subtree Prune and Regraft (SPR), Tree Bisection and Reconnection (TBR) and Replug distances between unrooted trees, using the algorithms of Whidden and Matsen (2017) <arxiv:1511.07529>.
Last updated 3 years ago
phylogeneticstree-distancedistance-calculationphylogenetic-trees
0.64 score 50 dependenciesselac - Selection Models for Amino Acid and/or Codon Evolution
Sets up and executes a SelAC model (Selection on Amino acids and codons) for testing the presence of selection in amino acid or codon among a set of genes on a fixed phylogeny. Beaulieu et al (2019) <doi:10.1093/molbev/msy222>.
Last updated 3 years ago
0.61 score 52 dependenciespaleoTS - Analyze Paleontological Time-Series
Facilitates analysis of paleontological sequences of trait values. Functions are provided to fit, using maximum likelihood, simple evolutionary models (including unbiased random walks, directional evolution,stasis, Ornstein-Uhlenbeck, covariate-tracking) and complex models (punctuation, mode shifts).
Last updated 2 months ago
1 stars 0.49 score 5 dependencies 1 dependentsphyloclim - Integrating Phylogenetics and Climatic Niche Modeling
Implements some methods in phyloclimatic modeling: estimation of ancestral climatic niches, age-range-correlation, niche equivalency test and background-similarity test.
Last updated 3 months ago
2 stars 0.36 score 10 dependenciesrphylotastic - An R Interface to 'Phylotastic' Web Services
This wraps the 'Phylotastic' services APIs described on Web Services at <www.phylotastic.org>. The main use case is to return a phylogenetic tree for a set of species, but the services also include ways to extract species names from web pages, perform taxonomic name resolution, retrieve a list of all descendant species of a taxon, find images of a species, and more.
Last updated 12 months ago
0.36 score 147 dependencieslaser - Likelihood Analysis of Speciation/Extinction Rates from Phylogenies
laser implements maximum likelihood methods based on the birth-death process to test whether diversification rates have changed over time and whether rates vary among lineages.
Last updated 11 years ago
2 stars 0.09 score 58 dependenciesBMhyb - Comparative Methods for Phylogenetic Networks
Analyze the phenotypic evolution of species of hybrid origin on a phylogenetic network. This can detect a burst of variation at the formation of a hybrid as well as an increase or decrease in trait value at a hybridization event. Parameters are estimated by maximum likelihood, and model averaging can be done automatically. Users need to enter a comparative data set and a phylogenetic network.
Last updated 3 years ago
0.00 score 90 dependenciesclosesamples - Gets feasible taxon samples on a tree
Often you want to pick species at random, but don't have access to all the possible species, and your group might be a nonrandom set. However, you might have a taxonomy, perhaps a bad one, for all the species. This will let you pick species at random on that full taxonomy and then pick a species out of the possible set closest to this. You could still have a biased sample, but way less biased.
Last updated 3 years ago
0.00 score 129 dependenciesflipped - Applies various odd models for coin flipping
Everyone uses the binomial as the distribution for coin flipping: this assumes for a given coin, the probability of landing heads is constant for all time. It is likely a very sound assumption. However, even for this simple example other models may be possible. This package contains such models.
Last updated 3 years ago
0.00 score 1 dependenciespopularitree - Subsamples a tree to get popular taxa
Often you want to show a reduced summary tree. Taxa chosen should span all the tree (for example, a tree of mammals should not have just primates) but also be recognizable groups to your audience. This lets you select a final tree size you want, criteria you want to use, and finds the tree that maximizes the criteria.
Last updated 7 years ago
0.00 score 128 dependenciesRateViz - Visualizations for instantaneous rate matrices
This package uses an instantaneous rate matrix (such as is used for models of DNA evolution, morphological character change over evolutionary history, and other areas) and summarizes it in various ways. These could include bubble plots, a network showing transitions, or calculations to figure out likely paths between two states.
Last updated 7 years ago
0.00 score 14 dependencies