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
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
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
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
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
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
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