Ecosyste.ms: Repos

An open API service providing repository metadata for many open source software ecosystems.

Package Usage: cran: phytools

Phylogenetic Tools for Comparative Biology (and Other Things)
49 versions
Latest release: 5 months ago
63 dependent packages
7,867 downloads last month

View more package details: https://packages.ecosyste.ms/registries/cran.r-project.org/packages/phytools

View more repository details: https://repos.ecosyste.ms/hosts/GitHub/repositories/liamrevell%2Fphytools

Dependent Repos 156

GabrielNakamura/Herodotools
Herodotools: R package for analysis of historical biogeography
  • * DESCRIPTION

Size: 178 MB - Last synced: 4 months ago - Pushed: 4 months ago

ericgoolsby/Rphylopars
Phylogenetic Comparative Tools for Missing Data and Within-Species Variation
  • * DESCRIPTION

Size: 893 KB - Last synced: 11 days ago - Pushed: over 1 year ago

cran/avotrex
:exclamation: This is a read-only mirror of the CRAN R package repository. avotrex — A Global Dataset of Anthropogenic Extinct Birds and their Traits: Phylogeny Builder
  • * DESCRIPTION

Size: 1.64 MB - Last synced: 1 day ago - Pushed: 1 day ago

ruffleymr/CAMI
Community Assembly Model Inference
  • * DESCRIPTION

Size: 191 MB - Last synced: 8 months ago - Pushed: almost 5 years ago

trollius/jive-package
jive-package
  • * DESCRIPTION

Size: 992 KB - Last synced: 3 months ago - Pushed: almost 10 years ago

eliotmiller/R2phylowood
Convert species centroids to phylowood input
  • * DESCRIPTION

Size: 141 KB - Last synced: 10 months ago - Pushed: almost 10 years ago

r-forge/bmhyd
Read-only mirror of "bmhyd" from r-forge SVN.
  • * pkg/DESCRIPTION

Size: 185 KB - Last synced: 10 months ago - Pushed: over 2 years ago

YosefLab/VISION
Signature Analysis and Visualization for Single-Cell RNA-seq
  • * DESCRIPTION

Size: 94.6 MB - Last synced: 20 days ago - Pushed: 4 months ago

rseng/rsepedia-analysis
Exploring clustering of research software encyclopedia entries
  • * _repos/github/GabrielNakamura/FishPhyloMaker/DESCRIPTION
  • >= 0.3.93 _repos/github/ropensci/RNeXML/DESCRIPTION
  • * _repos/github/ropensci/brranching/DESCRIPTION

Size: 435 MB - Last synced: 18 days ago - Pushed: 19 days ago

leondap/recluster
  • * DESCRIPTION

Size: 256 KB - Last synced: 7 months ago - Pushed: 8 months ago

dpasqualin/sfreemap
A Simulation Free approach for Stochastic Mapping
  • >= 0.6 DESCRIPTION

Size: 4.37 MB - Last synced: 8 months ago - Pushed: 11 months ago

jsigao/prioritree
  • * DESCRIPTION

Size: 49 MB - Last synced: 20 days ago - Pushed: over 1 year ago

wanyuac/GeneMates
An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences
  • >= 0.6 DESCRIPTION

Size: 2.4 MB - Last synced: 8 months ago - Pushed: almost 2 years ago

bimberlabinternal/CellMembrane
An R package with wrappers and pipelines for single cell RNA-seq analysis
  • * DESCRIPTION

Size: 140 MB - Last synced: 1 day ago - Pushed: 2 days ago

cran/phylocurve
:exclamation: This is a read-only mirror of the CRAN R package repository. phylocurve — Phylogenetic Comparative Methods for High-Dimensional Traits. Homepage: http://www.phylocurve.org
  • * DESCRIPTION

Size: 132 KB - Last synced: 7 months ago - Pushed: about 4 years ago

csoneson/compcodeR
  • * DESCRIPTION

Size: 4.2 MB - Last synced: 14 days ago - Pushed: 15 days ago

caitiecollins/treeWAS
treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes
  • * DESCRIPTION

Size: 90.1 MB - Last synced: 3 months ago - Pushed: 3 months ago

RafaelSdeSouza/AMADA
  • * DESCRIPTION

Size: 2.23 MB - Last synced: 2 months ago - Pushed: almost 9 years ago

dpasqualin/sfreemapr
Alternative implementation of Sfreemap - Simulation Free approach for Stochastic Mapping
  • >= 0.3 DESCRIPTION

Size: 31.3 KB - Last synced: about 1 year ago - Pushed: over 8 years ago

phylotastic/datelife
R package containing datelife's core functionality
  • * DESCRIPTION

Size: 237 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

joelewis101/blantyreESBL
Data and code repository for study aiming to understand ESBL carriage in Blantyre, Malawi
  • * DESCRIPTION

Size: 243 MB - Last synced: 7 months ago - Pushed: 7 months ago

iramosgutierrez/randtip
  • * DESCRIPTION

Size: 25.4 MB - Last synced: 3 months ago - Pushed: 3 months ago

GabrielNakamura/mcfly
mcfly package
  • * DESCRIPTION

Size: 844 KB - Last synced: 11 months ago - Pushed: 11 months ago

gtonkinhill/rhierbaps
rhierbaps: R implementation of hierBAPS
  • * DESCRIPTION

Size: 1.63 MB - Last synced: 7 months ago - Pushed: about 3 years ago

JanEngelstaedter/cophy
Generating, analysing and plotting cophylogenies
  • >= 0.6 DESCRIPTION

Size: 2.18 MB - Last synced: 7 months ago - Pushed: 7 months ago

jennahamlin/tinselR
An Amazing Shiny App
  • * DESCRIPTION

Size: 24.9 MB - Last synced: 3 months ago - Pushed: over 2 years ago

AlsammanAlsamman/alignstatplot
  • * DESCRIPTION

Size: 18 MB - Last synced: 3 months ago - Pushed: 3 months ago

alexpiper/taxreturn
An R package for creating taxonomic reference databases for metabarcoding studies
  • * DESCRIPTION

Size: 2.32 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

EvolEcolGroup/mtDNAcombine
  • * DESCRIPTION

Size: 590 KB - Last synced: 8 months ago - Pushed: almost 3 years ago

cran/RAM
:exclamation: This is a read-only mirror of the CRAN R package repository. RAM — R for Amplicon-Sequencing-Based Microbial-Ecology. Homepage: https://cran.r-project.org/package=RAM, https://bitbucket.org/Wen_Chen/ram_releases/src/ Report bugs for this package: https://bitbucket.org/Wen_Chen/ram_releases/issues/
  • * DESCRIPTION

Size: 5.43 MB - Last synced: 8 months ago - Pushed: about 6 years ago

cran/TKF
:exclamation: This is a read-only mirror of the CRAN R package repository. TKF — Pairwise Distance Estimation with TKF91 and TKF92 Model
  • >= 0.4 DESCRIPTION

Size: 167 KB - Last synced: 10 months ago - Pushed: about 9 years ago

cedatorma/recpd
Evolutionary Reconstruction and Phylogenetic Diversity of Traits in Recombining Bacterial Populations
  • * DESCRIPTION

Size: 7.96 MB - Last synced: about 1 year ago - Pushed: about 2 years ago

JClavel/mvMORPH
mvMORPH: an R package for fitting multivariate evolutionary models to morphometric data
  • * DESCRIPTION

Size: 10.8 MB - Last synced: 24 days ago - Pushed: about 2 months ago

VEuPathDB/microbiomeComputations
  • * DESCRIPTION

Size: 1.59 MB - Last synced: 3 months ago - Pushed: 3 months ago

r-pkg-team/r-cran-treespace
r-cran-treespace packaging
  • * DESCRIPTION

Last synced: over 1 year ago

r-pkg-team/r-cran-rnexml
r-cran-rnexml packaging
  • >= 0.3.93 DESCRIPTION

Last synced: over 1 year ago

pbastide/PhylogeneticEM
Implementation of the EM algorithm for the detection of shifts in a phylogeny.
  • >= 0.5.38 DESCRIPTION

Size: 5.49 MB - Last synced: 20 days ago - Pushed: 3 months ago

cran/mvMORPH
:exclamation: This is a read-only mirror of the CRAN R package repository. mvMORPH — Multivariate Comparative Tools for Fitting Evolutionary Models to Morphometric Data. Homepage: https://github.com/JClavel/mvMORPH
  • * DESCRIPTION

Size: 3.93 MB - Last synced: 6 months ago - Pushed: 6 months ago

graemetlloyd/Claddis
R package for cladistic disparity
  • * DESCRIPTION

Size: 3.25 MB - Last synced: 28 days ago - Pushed: 28 days ago

willpearse/pez
Phylogenetics for the Environmental Sciences
  • >= 0.6 DESCRIPTION

Size: 3.48 MB - Last synced: 10 months ago - Pushed: almost 5 years ago

willgearty/deeptime
Plotting Tools for Anyone Working in Deep Time
  • * DESCRIPTION

Size: 55.2 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

NoonanM/ctpm
  • * DESCRIPTION

Size: 225 KB - Last synced: 13 days ago - Pushed: over 2 years ago

biometry/tapnet
Predict interaction frequencies of bipartite networks
  • * tapnet/DESCRIPTION

Size: 6.5 MB - Last synced: 22 days ago - Pushed: 6 months ago

Caetanods/ratematrix
Bayesian estimation of the evolutionary rate matrix.
  • * DESCRIPTION

Size: 8.89 MB - Last synced: 12 days ago - Pushed: over 1 year ago

uyedaj/treeplyr
An R package for using dplyr on matched tree and data objects
  • * DESCRIPTION

Size: 1.85 MB - Last synced: 6 months ago - Pushed: over 1 year ago

marlonecobos/nichevol
Tools for ecological niche evolution assessment considering uncertainty
  • >= 0.6 DESCRIPTION

Size: 1.34 MB - Last synced: 7 months ago - Pushed: about 1 year ago

ropensci/treestartr
An R package for making starting trees from combined molecular, morphological and stratigraphic data
  • >= 0.6 DESCRIPTION

Size: 2.77 MB - Last synced: 13 days ago - Pushed: over 4 years ago

cran/pez
:exclamation: This is a read-only mirror of the CRAN R package repository. pez — Phylogenetics for the Environmental Sciences
  • >= 0.6 DESCRIPTION

Size: 1.26 MB - Last synced: 8 months ago - Pushed: almost 2 years ago

JeroenSmaers/evomap
R package for evolutionary mapping of continuous traits
  • * DESCRIPTION

Size: 115 KB - Last synced: 8 months ago - Pushed: about 6 years ago

cran/RPANDA
:exclamation: This is a read-only mirror of the CRAN R package repository. RPANDA — Phylogenetic ANalyses of DiversificAtion. Homepage: https://github.com/hmorlon/PANDA
  • * DESCRIPTION

Size: 2.07 MB - Last synced: 3 months ago - Pushed: 3 months ago

jonchang/fishtree
The R interface to the Fish Tree of Life
  • * DESCRIPTION

Size: 11 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

eliotmiller/addTaxa
An R package to add missing taxa to molecular phylogenies
  • * DESCRIPTION

Size: 129 KB - Last synced: 5 months ago - Pushed: 5 months ago

ferroao/idiogramFISH
  • * DESCRIPTION
  • * inst/shinyApps/iBoard/www/DESCRIPTION

Last synced: about 1 year ago

cran/Rphylopars
:exclamation: This is a read-only mirror of the CRAN R package repository. Rphylopars — Phylogenetic Comparative Tools for Missing Data and Within-Species Variation. Homepage: https://github.com/ericgoolsby/Rphylopars/wiki
  • * DESCRIPTION

Size: 582 KB - Last synced: 5 months ago - Pushed: 5 months ago

rsetienne/DAISIE
DAISIE
  • * DESCRIPTION

Size: 37.5 MB - Last synced: 18 days ago - Pushed: 18 days ago

NickWilliamsSanger/rsimpop
  • * DESCRIPTION

Size: 2.53 MB - Last synced: 4 months ago - Pushed: almost 3 years ago

TheoreticalEcology/ecodata
A collection of ecological datasets for teaching
  • * DESCRIPTION

Size: 18.5 MB - Last synced: 10 months ago - Pushed: 12 months ago

cran/Claddis
:exclamation: This is a read-only mirror of the CRAN R package repository. Claddis — Measuring Morphological Diversity and Evolutionary Tempo
  • * DESCRIPTION

Size: 427 KB - Last synced: 10 months ago - Pushed: over 3 years ago

thej022214/OUwie
Estimates and compares rate differences of continuous character evolution under Brownian motion and a new set of Ornstein-Uhlenbeck (OU) models that allow the strength of selection and drift to vary across selective regimes.
  • * DESCRIPTION

Size: 5.98 MB - Last synced: 3 days ago - Pushed: about 1 month ago

cboettig/codemeta
:package: A smaller codemetar
  • >= 0.3.93 tests/testthat/test_examples/RNeXML/DESCRIPTION

Size: 1.48 MB - Last synced: about 2 months ago - Pushed: 7 months ago

vanderleidebastiani/daee
daee - Data Analysis for Ecology and Evolution
  • * DESCRIPTION

Size: 304 KB - Last synced: 10 months ago - Pushed: over 3 years ago

rsetienne/DDD
Diversity-Dependent Diversification
  • * DESCRIPTION

Size: 813 KB - Last synced: about 1 month ago - Pushed: about 1 month ago

katiesaund/hogwash
Three bacterial GWAS methods all rolled into one easy-to-use R package
  • * DESCRIPTION

Size: 11.8 MB - Last synced: 8 months ago - Pushed: over 2 years ago

cran/DDD
:exclamation: This is a read-only mirror of the CRAN R package repository. DDD — Diversity-Dependent Diversification
  • * DESCRIPTION

Size: 465 KB - Last synced: 10 months ago - Pushed: 11 months ago

cran/corHMM
:exclamation: This is a read-only mirror of the CRAN R package repository. corHMM — Hidden Markov Models of Character Evolution
  • * DESCRIPTION

Size: 2.53 MB - Last synced: 8 months ago - Pushed: almost 2 years ago

cran/evobiR
:exclamation: This is a read-only mirror of the CRAN R package repository. evobiR — Comparative and Population Genetic Analyses. Homepage: http://www.uta.edu/karyodb/evobiR/
  • * DESCRIPTION

Size: 179 KB - Last synced: 8 months ago - Pushed: over 8 years ago

uyedaj/bayou
  • * DESCRIPTION

Size: 8.9 MB - Last synced: 5 months ago - Pushed: 5 months ago

cran/geiger
:exclamation: This is a read-only mirror of the CRAN R package repository. geiger — Analysis of Evolutionary Diversification
  • >= 0.7.31 DESCRIPTION

Size: 2.26 MB - Last synced: 7 months ago - Pushed: about 1 year ago

cran/paleotree
:exclamation: This is a read-only mirror of the CRAN R package repository. paleotree — Paleontological and Phylogenetic Analyses of Evolution. Homepage: https://github.com/dwbapst/paleotree Report bugs for this package: https://github.com/dwbapst/paleotree/issues
  • >= 0.6 DESCRIPTION

Size: 2.15 MB - Last synced: 8 months ago - Pushed: almost 2 years ago

AtlasOfLivingAustralia/ALA4R
Access data and resources hosted by the Atlas of Living Australia (ALA)
  • * DESCRIPTION

Size: 23 MB - Last synced: 14 days ago - Pushed: over 2 years ago

Wen_Chen/ram_releases
Releases of R packages and scripts
  • * RAM/DESCRIPTION
  • * RAM.Rcheck/RAM/DESCRIPTION

Size: 79.2 MB - Last synced: almost 2 years ago

andrew-hipp/morton
Tools (in R) for manipulation of phylogenetic, genetic, and other biodiversity data
  • * DESCRIPTION

Size: 138 KB - Last synced: about 2 months ago - Pushed: about 2 months ago

cran/monogeneaGM
:exclamation: This is a read-only mirror of the CRAN R package repository. monogeneaGM — Geometric Morphometric Analysis of Monogenean Anchors
  • * DESCRIPTION

Size: 1.28 MB - Last synced: 8 months ago - Pushed: about 8 years ago

ropensci/brranching
I can haz all the phylogenies
  • * DESCRIPTION

Size: 3.17 MB - Last synced: 21 days ago - Pushed: over 1 year ago

hmorlon/PANDA
Phylogenetic ANalyses of DiversificAtion
  • * DESCRIPTION

Size: 111 MB - Last synced: 10 days ago - Pushed: about 1 month ago

nclark-lab/RERconverge
Analysis of convergence between organismal traits and DNA/protein sequences
  • * DESCRIPTION

Size: 179 MB - Last synced: 3 months ago - Pushed: 3 months ago

bomeara/selac
Model by O'Meara, Chai, and Gilchrist for SELection on Amino acids and/or Codons
  • * DESCRIPTION

Size: 3.6 MB - Last synced: 10 months ago - Pushed: over 2 years ago

millacarmona/morphospace
A package for people who can’t visualize morphospaces good and who wanna learn to do other geometric morphometrics stuff good too.
  • * DESCRIPTION

Size: 179 MB - Last synced: about 2 months ago - Pushed: about 2 months ago

rsetienne/PBD
Protracted Birth-Death model in R
  • * PBD/DESCRIPTION

Size: 2 MB - Last synced: 6 months ago - Pushed: 6 months ago

cran/hisse
:exclamation: This is a read-only mirror of the CRAN R package repository. hisse — Hidden State Speciation and Extinction
  • * DESCRIPTION

Size: 15.9 MB - Last synced: 8 months ago - Pushed: over 1 year ago

PoonLab/clustuneR
Implementing clustering algorithms on genetic data and finding optimal parameters through the performance of predictive growth models.
  • >= 1.0 DESCRIPTION

Size: 85.1 MB - Last synced: 5 months ago - Pushed: 5 months ago

neurogenomics/orthogene
🧬 o r t h o g e n e 🧬✨✨✨✨✨✨✨ Interspecies gene mapping✨✨✨✨✨ 🦠 🔁 🌱 🔁 🌳 🔁 🍎 🔁 🍊 🔁 🪱 🔁 🪰 🔁 🐟 🔁 🦎 🔁 🐓 🔁 🦇 🔁 🐄 🔁 🐖 🔁 🐐 🔁 🐎 🔁 🐈 🔁 🐕 🔁 🐁 🔁 🐒 🔁 🦧 🔁 🦍 🔁 🏃‍♀️
  • * DESCRIPTION

Size: 7.21 MB - Last synced: 24 days ago - Pushed: 5 months ago

revbayes/RevGadgets
Postprocessing gadgets for output generated by RevBayes
  • >= 0.7 DESCRIPTION

Size: 115 MB - Last synced: about 16 hours ago - Pushed: 1 day ago

bomeara/omearatenure
Brian O'Meara tenure packet (in progress)
  • * Software/OUwie/DESCRIPTION

Size: 42 MB - Last synced: about 1 year ago - Pushed: over 9 years ago

cran/PBD
:exclamation: This is a read-only mirror of the CRAN R package repository. PBD — Protracted Birth-Death Model of Diversification
  • * DESCRIPTION

Size: 70.3 KB - Last synced: 10 months ago - Pushed: about 7 years ago

TGuillerme/SpatioTemporal_Disparity
  • * Functions/disparity/DESCRIPTION

Size: 3.3 GB - Last synced: 10 months ago - Pushed: over 6 years ago

oschwery/MonoPhy
R package to explore monophyly
  • * DESCRIPTION

Size: 1.51 MB - Last synced: 28 days ago - Pushed: 29 days ago

YuLab-SMU/ggtreeSpace
🕸️Exploring phylomorphospace using 'ggtree'
  • * DESCRIPTION

Size: 394 KB - Last synced: 18 days ago - Pushed: 19 days ago

leonelhalsina/lemad
R package LEMAD: Lineage Extinction Model of Ancestral Distribution
  • * DESCRIPTION

Size: 6.38 MB - Last synced: 7 months ago - Pushed: 7 months ago

thej022214/corHMM
Fits a generalized form of the covarion model that allows different transition rate classes on different portions of a phylogeny by treating rate classes as “hidden” states in a Markov process.
  • * DESCRIPTION

Size: 4.08 MB - Last synced: about 3 hours ago - Pushed: about 4 hours ago

sckott/sacbox
Library of R functions from me and others
  • * DESCRIPTION

Size: 79.1 KB - Last synced: about 2 months ago - Pushed: over 3 years ago

GabrielNakamura/FishPhyloMaker
Making phylogenies for a list of fish species
  • * DESCRIPTION

Size: 3.43 MB - Last synced: 3 months ago - Pushed: 3 months ago

gtonkinhill/fastbaps
A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data
  • * DESCRIPTION

Size: 2.27 MB - Last synced: 8 months ago - Pushed: over 1 year ago

ropensci/RNeXML
Implementing semantically rich NeXML I/O in R
  • >= 0.3.93 DESCRIPTION

Size: 8.54 MB - Last synced: 21 days ago - Pushed: 27 days ago

cran/convevol
:exclamation: This is a read-only mirror of the CRAN R package repository. convevol — Analysis of Convergent Evolution
  • * DESCRIPTION

Size: 61.5 KB - Last synced: 8 months ago - Pushed: 11 months ago

cran/recluster
:exclamation: This is a read-only mirror of the CRAN R package repository. recluster — Ordination Methods for the Analysis of Beta-Diversity Indices. Homepage: https://github.com/leondap/recluster
  • * DESCRIPTION

Size: 79.1 KB - Last synced: 8 months ago - Pushed: almost 4 years ago