Referenced by ⇅
Year
ACDC : Analysis of Congruent Diversification Classes (Version 1.0.0)
2022
apTreeshape : Analyses of Phylogenetic Treeshape (Version 1.5-0.1)
2005
BayesSPsurv : Bayesian Spatial Split Population Survival Model (Version 0.1.4)
2020
brranching : Fetch "Phylogenies" from Many Sources (Version 0.7.0)
2015
dcGOR : Analysis of Ontologies and Protein Domain Annotations (Version 1.0.6)
2014
ggmotif : Extract and Visualize Motif Information from MEME Software (Version 0.2.1)
2021
HierDpart : Partitioning Hierarchical Diversity and Differentiation Across
Metrics and Scales, from Genes to Ecosystems (Version 1.5.0)
2018
liayson : Linking Singe-Cell Transcriptomes Atween Contemporary
Subpopulation Genomes (Version 1.0.5)
2018
perfectphyloR : Reconstruct Perfect Phylogenies from DNA Sequence Data (Version 0.2.1)
2019
PIGShift : Polygenic Inverse Gamma Shifts (Version 1.0.1)
2014
pirouette : Create a Bayesian Posterior from a Phylogeny (Version 1.6.9)
2022
prewas : Data Pre-Processing for Bacterial Genome-Wide Association
Studies (Version 1.1.1)
2020
Rarefy : Rarefaction Methods (Version 1.1.1)
2020
safedata : Interface to Data from the SAFE Project (Version 1.1.3)
2020
treeducken : Nested Phylogenetic Tree Simulator (Version 1.1.0)
2020
treeplyr : "dplyr" Functionality for Matched Tree and Data Objects (Version 0.1.10)
2016
sandwichr : Spatial Interpolation Based on Spatial Stratified Heterogeneity (Version 1.0.4)
2022
PhyInsight : DNA Sequence Analysis & Generation Tree Creation (Version 0.1.0)
2023
StructFDR : False Discovery Control Procedure Integrating the Prior Structure Information (Version 1.4)
2016
changeRangeR : Change Metrics for Species Geographic Ranges (Version 1.1.0)
2022
bite : Bayesian Integrative Models of Trait Evolution (Version 0.3)
2020
datelife : Scientific Data on Time of Lineage Divergence for Your Taxa (Version 0.6.8)
2022
OpenTreeChronograms : Open Tree of Life Chronograms (Version 2022.1.28)
2022
GaMaBioMD : Diversity Analysis for Sequence Data (Version 0.2.0)
2024
HTSSIP : High Throughput Sequencing of Stable Isotope Probing Data Analysis (Version 1.4.1)
2016
phyloclim : Integrating Phylogenetics and Climatic Niche Modeling (Version 0.9.5)
2009
dartR : Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis (Version 2.9.9.5)
2017
coil : Contextualization and Evaluation of COI-5P Barcode Data (Version 1.2.4)
2019
Anaconda : Targeted Differential and Global Enrichment Analysis of Taxonomic Rank by Shared Asvs (Version 0.1.5)
2022
Apoderoides : Prioritize and Delete Erroneous Taxa in a Large Phylogenetic Tree (Version 3.0.1)
2024
BAMMtools : Analysis and Visualization of Macroevolutionary Dynamics on Phylogenetic Trees (Version 2.1.12)
2014
BIEN : Tools for Accessing the Botanical Information and Ecology Network Database (Version 1.2.7)
2017
Canopy : Accessing Intra-Tumor Heterogeneity and Tracking Longitudinal and Spatial Clonal Evolutionary History by Next-Generation Sequencing (Version 1.3.0)
2015
DAISIEprep : Extracts Phylogenetic Island Community Data from Phylogenetic Trees (Version 1.0.1)
2023
DAISIE : Dynamical Assembly of Islands by Speciation, Immigration and Extinction (Version 4.6.0)
2015
DAMOCLES : Dynamic Assembly Model of Colonization, Local Extinction and Speciation (Version 2.3)
2014
DHARMa : Residual Diagnostics for Hierarchical (Multi-Level / Mixed) Regression Models (Version 0.4.7)
2016
EvoPhylo : Pre- And Postprocessing of Morphological Data from Relaxed Clock Bayesian Phylogenetics (Version 0.3.5)
2022
FAVA : Quantify Compositional Variability Across Relative Abundance Vectors (Version 1.0.9)
2024
FD : Measuring Functional Diversity (FD) from Multiple Traits, and Other Tools for Functional Ecology (Version 1.0-12.3)
2009
GUniFrac : Generalized UniFrac Distances, Distance-Based Multivariate Methods and Feature-Based Univariate Methods for Microbiome Data Analysis (Version 1.9)
2012
HACSim : Iterative Extrapolation of Species' Haplotype Accumulation Curves for Genetic Diversity Assessment (Version 1.0.7-1)
2019
HMPTrees : Statistical Object Oriented Data Analysis of RDP-Based Taxonomic Trees from Human Microbiome Data (Version 1.4)
2011
MCMCtreeR : Prepare MCMCtree Analyses and Plot Bayesian Divergence Time Analyses Estimates on Trees (Version 1.1)
2019
MLVSBM : A Stochastic Block Model for Multilevel Networks (Version 0.2.4)
2021
OptCirClust : Circular, Periodic, or Framed Data Clustering: Fast, Optimal, and Reproducible (Version 0.0.4)
2020
PCMBase : Simulation and Likelihood Calculation of Phylogenetic Comparative Models (Version 1.2.15)
2018
POSTm : Phylogeny-Guided OTU-Specific Association Test for Microbiome Data (Version 1.4)
2021
PVR : Phylogenetic Eigenvectors Regression and Phylogentic Signal-Representation Curve (Version 0.3)
2012
Quartet : Comparison of Phylogenetic Trees Using Quartet and Split Measures (Version 1.2.7)
2019
RRPP : Linear Model Evaluation with Randomized Residuals in a Permutation Procedure (Version 2.1.2)
2018
Rphylopars : Phylogenetic Comparative Tools for Missing Data and Within-Species Variation (Version 0.3.10)
2015
Rtropical : Data Analysis Tools over Space of Phylogenetic Trees Using Tropical Geometry (Version 1.2.1)
2021
SPARTAAS : Statistical Pattern Recognition and daTing using Archaeological Artefacts assemblageS (Version 1.2.4)
2021
STraTUS : Enumeration and Uniform Sampling of Transmission Trees for a Known Phylogeny (Version 1.1.2)
2019
SigTree : Identify and Visualize Significantly Responsive Branches in a Phylogenetic Tree (Version 1.10.6)
2013
SoilTaxonomy : A System of Soil Classification for Making and Interpreting Soil Surveys (Version 0.2.8)
2021
TESS : Diversification Rate Estimation and Fast Simulation of Reconstructed Phylogenetic Trees under Tree-Wide Time-Heterogeneous Birth-Death Processes Including Mass-Extinction Events (Version 2.1.2)
2012
TreeSimGM : Simulating Phylogenetic Trees under General Bellman Harris and Lineage Shift Model (Version 2.5)
2013
ade4 : Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences (Version 1.7-23)
2002
aphylo : Statistical Inference and Prediction of Annotations in Phylogenetic Trees (Version 0.3-6)
2022
autoGO : Auto-GO: Reproducible, Robust and High Quality Ontology Enrichment Visualizations (Version 1.0.3)
2023
avotrex : A Global Dataset of Anthropogenic Extinct Birds and their Traits: Phylogeny Builder (Version 1.3.0)
2024
betapart : Partitioning Beta Diversity into Turnover and Nestedness Components (Version 1.6.1)
2012
ctpm : Continuous-Time Phylogenetic Modeling (Version 1.0.1)
2021
ddtlcm : Latent Class Analysis with Dirichlet Diffusion Tree Process Prior (Version 0.2.1)
2023
dynamicSDM : Species Distribution and Abundance Modelling at High Spatio-Temporal Resolution (Version 1.3.4)
2023
evolved : Open Software for Teaching Evolutionary Biology at Multiple Scales Through Virtual Inquiries (Version 1.0.0)
2024
geneHapR : Gene Haplotype Statistics, Phenotype Association and Visualization (Version 1.2.4)
2022
ggrasp : Gaussian-Based Genome Representative Selector with Prioritization (Version 1.2)
2018
hagis : Analysis of Plant Pathogen Pathotype Complexities, Distributions and Diversity (Version 4.0.0)
2019
haplotypes : Manipulating DNA Sequences and Estimating Unambiguous Haplotype Network with Statistical Parsimony (Version 1.1.3.2)
2015
harmonicmeanp : Harmonic Mean p-Values and Model Averaging by Mean Maximum Likelihood (Version 3.0.1)
2017
hilldiv : Integral Analysis of Diversity Based on Hill Numbers (Version 1.5.1)
2019
iCAMP : Infer Community Assembly Mechanisms by Phylogenetic-Bin-Based Null Model Analysis (Version 1.5.12)
2020
iNEXT.3D : Interpolation and Extrapolation for Three Dimensions of Biodiversity (Version 1.0.12)
2024
iNEXT.beta3D : Interpolation and Extrapolation with Beta Diversity for Three Dimensions of Biodiversity (Version 1.0.2)
2024
immunarch : Multi-Modal Immune Repertoire Analytics for Immunotherapy and Vaccine Design in R (Version 0.10.3)
2020
indelmiss : Insertion Deletion Analysis While Accounting for Possible Missing Data (Version 1.0.10)
2016
jackalope : A Swift, Versatile Phylogenomic and High-Throughput Sequencing Simulator (Version 1.1.6)
2019
jrich : Jack-Knife Support for Evolutionary Distinctiveness Indices I and W (Version 0.60-35)
2016
kmer : Fast K-Mer Counting and Clustering for Biological Sequence Analysis (Version 1.1.2)
2018
mFD : Compute and Illustrate the Multiple Facets of Functional Diversity (Version 1.0.7)
2021
meconetcomp : Compare Microbial Networks of 'trans_network' Class of 'microeco' Package (Version 0.7.0)
2022
metacoder : Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data (Version 0.3.8)
2016
metagear : Comprehensive Research Synthesis Tools for Systematic Reviews and Meta-Analysis (Version 0.7)
2015
mmodely : Modeling Multivariate Origins Determinants - Evolutionary Lineages in Ecology (Version 0.2.5)
2022
mvMORPH : Multivariate Comparative Tools for Fitting Evolutionary Models to Morphometric Data (Version 1.2.1)
2013
mvSLOUCH : Multivariate Stochastic Linear Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses (Version 2.7.7)
2013
nichevol : Tools for Ecological Niche Evolution Assessment Considering Uncertainty (Version 0.1.20)
2020
orthGS : Orthology vs Paralogy Relationships among Glutamine Synthetase from Plants (Version 0.1.8)
2024
ouch : Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses (Version 2.20)
2004
outbreaker2 : Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data (Version 1.1.4)
2017
pcmabc : Approximate Bayesian Computations for Phylogenetic Comparative Methods (Version 1.1.3)
2018
phyext2 : An Extension (for Package 'SigTree') of Some of the Classes in Package 'phylobase' (Version 0.0.4)
2015
phylocanvas : Interactive Phylogenetic Trees Using the 'Phylocanvas' JavaScript Library (Version 0.1.3)
2017
phylotools : Phylogenetic Tools for Eco-Phylogenetics (Version 0.2.2)
2010
poolfstat : Computing f-Statistics and Building Admixture Graphs Based on Allele Count or Pool-Seq Read Count Data (Version 3.0.0)
2018
ppgm : PaleoPhyloGeographic Modeling of Climate Niches and Species Distributions (Version 1.1)
2024
primerTree : Visually Assessing the Specificity and Informativeness of Primer Pairs (Version 1.1.0)
2013
rapidphylo : Rapidly Estimates Phylogeny from Large Allele Frequency Data Using Root Distances Method (Version 0.1.2)
2022
rdiversity : Measurement and Partitioning of Similarity-Sensitive Biodiversity (Version 2.2.0)
2017
rehh : Searching for Footprints of Selection using 'Extended Haplotype Homozygosity' Based Tests (Version 3.2.2)
2012
secsse : Several Examined and Concealed States-Dependent Speciation and Extinction (Version 3.5.0)
2019
sidier : Substitution and Indel Distances to Infer Evolutionary Relationships (Version 4.1.1)
2013
symmoments : Symbolic Central and Noncentral Moments of the Multivariate Normal Distribution (Version 1.2.1.1)
2010
treedater : Fast Molecular Clock Dating of Phylogenetic Trees with Rate Variation (Version 1.0.2)
2018
treenomial : Comparison of Trees using a Tree Defining Polynomial (Version 1.1.4)
2019
treesliceR : To Slice Phylogenetic Trees and Infer Evolutionary Patterns Over Time (Version 1.1.0)
2023
treestartr : Generate Starting Trees for Combined Molecular, Morphological and Stratigraphic Data (Version 0.1.0)
2019
geneHapR
Visualization : (Version )
0
RPANDA : Phylogenetic ANalyses of DiversificAtion (Version 2.5)
2014
ips : Interfaces to Phylogenetic Software in R (Version 0.0.13)
2014
shipunov : Miscellaneous Functions from Alexey Shipunov (Version 1.17.1)
2019
TransPhylo : Inference of Transmission Tree from a Dated Phylogeny (Version 1.4.5)
2020
motmot : Models of Trait Macroevolution on Trees (Version 2.1.3)
2012
nodiv : Compares the Distribution of Sister Clades Through a Phylogeny (Version 1.4.3)
2014
phyloraster : Evolutionary Diversity Metrics for Raster Data (Version 2.3.0)
2023
Claddis : Measuring Morphological Diversity and Evolutionary Tempo (Version 0.7.0)
2015
CommEcol : Community Ecology Analyses (Version 1.8.1)
2016
CongreveLamsdell2016 : Distance Metrics for Trees Generated by Congreve and Lamsdell (Version 1.0.3)
2019
DAISIE
Extinction : (Version )
0
DAISIEprep
Trees : (Version )
0
DAMOCLES
Speciation : (Version )
0
DCLEAR : Distance Based Cell Lineage Reconstruction (Version 1.0.13)
2021
DDD : Diversity-Dependent Diversification (Version 5.2.4)
2012
EnvNJ : Whole Genome Phylogenies Using Sequence Environments (Version 0.1.3)
2021
EpiModel : Mathematical Modeling of Infectious Disease Dynamics (Version 2.5.0)
2013
NicheBarcoding : Niche-model-Based Species Identification (Version 1.0)
2021
AnnotationBustR : Extract Subsequences from GenBank Annotations (Version 1.3.0)
2017
AntibodyForests : Delineating Inter- And Intra-Antibody Repertoire Evolution (Version 1.1.0)
2025
Apoderoides
Tree : (Version )
0
BAT : Biodiversity Assessment Tools (Version 2.11.0)
2014
BOLDconnectR
Data : (Version )
0
BSTZINB : Association Among Disease Counts and Socio-Environmental Factors (Version 2.0.1)
2024
BarcodingR : Species Identification using DNA Barcodes (Version 1.0-3)
2016
BoSSA : A Bunch of Structure and Sequence Analysis (Version 3.7)
2009
CALANGO : Comparative Analysis with Annotation-Based Genomic Components (Version 1.0.20)
2021
CRABS : Congruent Rate Analyses in Birth-Death Scenarios (Version 1.2.0)
2022
CTNote : CTN Outcomes, Treatments, and Endpoints (Version 0.1.0)
2022
ENMTools : Analysis of Niche Evolution using Niche and Distribution Models (Version 1.1.5)
2020
FAVA
Vectors : (Version )
0
FinePop : Fine-Scale Population Analysis (Version 1.5.2)
2016
FishPhyloMaker : Phylogenies for a List of Finned-Ray Fishes (Version 0.2.0)
2021
FossilSim : Simulation and Plots for Fossil and Taxonomy Data (Version 2.4.3)
2018
FuncDiv : Compute Contributional Diversity Metrics (Version 1.0.0)
2023
GIFT : Access to the Global Inventory of Floras and Traits (GIFT) (Version 1.3.3)
2023
GLSME : Generalized Least Squares with Measurement Error (Version 1.0.5)
2014
GOCompare : Comprehensive GO Terms Comparison Between Species (Version 1.0.2.2)
2021
GeometricMorphometricsMix : Heterogeneous Methods for Shape and Other Multidimensional Data (Version 0.6.0.1)
2026
HSAUR : A Handbook of Statistical Analyses Using R (1st Edition) (Version 1.3-11)
2006
HSAUR2 : A Handbook of Statistical Analyses Using R (2nd Edition) (Version 1.1-21)
2009
HSAUR3 : A Handbook of Statistical Analyses Using R (3rd Edition) (Version 1.0-15)
2014
Hmsc : Hierarchical Model of Species Communities (Version 3.3-7)
2019
HybridMicrobiomes : Analysis of Host-Associated Microbiomes from Hybrid Organisms (Version 0.1.1)
2023
JNplots : Visualize Outputs from the 'Johnson-Neyman' Technique (Version 0.1.2)
2023
LorMe : Lightweight One-Line Resolving Microbial Ecology Program (Version 2.0.2)
2024
MACER : Molecular Acquisition, Cleaning, and Evaluation in R 'MACER' (Version 0.2.1)
2021
MAGNAMWAR : A Pipeline for Meta-Genome Wide Association (Version 2.0.4)
2017
MCMCglmm : MCMC Generalised Linear Mixed Models (Version 2.36)
2009
ML.MSBD : Maximum Likelihood Inference on Multi-State Trees (Version 1.2.1)
2017
MPSEM : Modelling Phylogenetic Signals using Eigenvector Maps (Version 0.6-1)
2013
MSCquartets : Analyzing Gene Tree Quartets under the Multi-Species Coalescent (Version 3.2)
2019
MSCsimtester : Tests of Multispecies Coalescent Gene Tree Simulator Output (Version 1.1)
2021
MVA : An Introduction to Applied Multivariate Analysis with R (Version 1.0-9)
2011
MiSPU : Microbiome Based Sum of Powered Score (MiSPU) Tests (Version 1.0)
2016
MiscMetabar : Miscellaneous Functions for Metabarcoding Analysis (Version 0.14.4)
2024
MonoPhy : Explore Monophyly of Taxonomic Groups in a Phylogeny (Version 1.3.2)
2015
MorphSim : Simulate Discrete Character Data along Phylogenetic Trees (Version 0.1.0)
2026
MultiTraits : Analyzing and Visualizing Multidimensional Plant Traits (Version 0.6.0)
2024
NST : Normalized Stochasticity Ratio (Version 3.1.10)
2019
OUwie : Analysis of Evolutionary Rates in an OU Framework (Version 2.10)
2011
OmicFlow : Fast and Efficient (Automated) Analysis of Sparse Omics Data (Version 1.4.2)
2025
PBD : Protracted Birth-Death Model of Diversification (Version 1.4)
2014
PCPS : Principal Coordinates of Phylogenetic Structure (Version 1.0.8)
2014
PNC
Communities : (Version )
0
POMS : Phylogenetic Organization of Metagenomic Signals (Version 1.0.1)
2022
POSTm
Data : (Version )
0
POUMM : The Phylogenetic Ornstein-Uhlenbeck Mixed Model (Version 2.1.8)
2017
PhySortR : A Fast, Flexible Tool for Sorting Phylogenetic Trees (Version 1.0.9)
2015
PhylogeneticEM : Automatic Shift Detection using a Phylogenetic EM (Version 1.8.1)
2017
Plasmidprofiler : Visualization of Plasmid Profile Results (Version 0.1.6)
2017
Platypus : Single-Cell Immune Repertoire and Gene Expression Analysis (Version 3.6.0)
2021
Quartet
Measures : (Version )
0
RAINBOWR : Genome-Wide Association Study with SNP-Set Methods (Version 0.1.38)
2019
RNeXML : Semantically Rich I/O for the 'NeXML' Format (Version 2.4.11)
2014
RPesto : Phylogenetic Estimation of Shifts in the Tempo of Origination (Version 0.1.4)
2025
RPointCloud : Visualizing Topological Loops and Voids (Version 0.8.0)
2024
RRgeo : Species Distribution Modelling for Rare Species (Version 0.0.6)
2025
RRmorph : 3D Morphological Analyses with 'RRphylo' (Version 0.0.2)
2025
RRphylo : Phylogenetic Ridge Regression Methods for Comparative Studies (Version 3.0.2)
2018
RVAideMemoire : Testing and Plotting Procedures for Biostatistics (Version 0.9-83-12)
2011
RevGadgets : Visualization and Post-Processing of 'RevBayes' Analyses (Version 1.2.1)
2021
Revticulate : Interaction with "RevBayes" in R (Version 1.0.0)
2021
Rogue : Identify Rogue Taxa in Sets of Phylogenetic Trees (Version 2.1.7)
2021
Rsearch : Processing and Analyzing Amplicon Sequence Data (Version 1.0.0)
2025
Rtapas : Random Tanglegram Partitions (Version 1.2)
2022
STEPCAM : ABC-SMC Inference of STEPCAM (Version 1.2.3)
2014
SVAlignR
Data : (Version )
0
SemanticDistance : Compute Semantic Distance Between Text Constituents (Version 0.1.1)
2025
SeqFeatR : A Tool to Associate FASTA Sequences and Features (Version 0.3.1)
2014
Seurat : Tools for Single Cell Genomics (Version 5.4.0)
2017
ShiVa
Variance : (Version )
0
SiPhyNetwork : A Phylogenetic Simulator for Reticulate Evolution (Version 1.1.0)
2022
SoilTaxonomy
Surveys : (Version )
0
StratPal : Stratigraphic Paleobiology Modeling Pipelines (Version 0.7.1)
2024
Sysrecon : Systematical Metabolic Reconstruction (Version 0.1.3)
2022
TBRDist : Rearrangement Distances Between Unrooted Phylogenetic Trees (Version 1.0.3)
2020
TML : Tropical Geometry Tools for Machine Learning (Version 2.3.0)
2023
TSLA : Tree-Guided Rare Feature Selection and Logic Aggregation (Version 0.1.2)
2025
TextMiningGUI : Text Mining GUI Interface (Version 0.3)
2020
TiPS : Trajectories and Phylogenies Simulator (Version 1.3.0)
2021
TotalCopheneticIndex : Quantify the Balance of Phylogenetic Trees (Version 2.0.1)
2016
TreeDiagram : Tree Diagram (Version 0.1.1)
2020
TreeDist : Calculate and Map Distances Between Phylogenetic Trees (Version 2.11.1)
2020
TreeSearch : Phylogenetic Analysis with Discrete Character Data (Version 1.7.0)
2017
TreeSim : Simulating Phylogenetic Trees (Version 2.4)
2010
TreeTools : Create, Modify and Analyse Phylogenetic Trees (Version 2.0.0)
2019
VDJgermlines : Variable, Diversity and Joining Sequences from Various Species (Version 0.1)
2018
VIProDesign : A Comprehensive Tool for Protein Design (Version 0.1.0)
2025
Xplortext : Statistical Analysis of Textual Data (Version 1.5.5)
2017
aPCoA : Covariate Adjusted PCoA Plot (Version 1.3)
2020
abdiv : Alpha and Beta Diversity Measures (Version 0.2.0)
2020
adaptiveGPCA : Adaptive Generalized PCA (Version 0.1.3)
2017
adegenet : Exploratory Analysis of Genetic and Genomic Data (Version 2.1.11)
2007
adephylo : Exploratory Analyses for the Phylogenetic Comparative Method (Version 1.1-17)
2009
adespatial : Multivariate Multiscale Spatial Analysis (Version 0.3-28)
2016
adiv : Analysis of Diversity (Version 2.2.1)
2017
admtools : Estimate and Manipulate Age-Depth Models (Version 0.6.0)
2023
alakazam : Immunoglobulin Clonal Lineage and Diversity Analysis (Version 1.4.2)
2016
apex : Phylogenetic Methods for Multiple Gene Data (Version 1.0.7)
2015
aphid : Analysis with Profile Hidden Markov Models (Version 1.3.5)
2017
aqp : Algorithms for Quantitative Pedology (Version 2.3)
2010
arakno : ARAchnid KNowledge Online (Version 1.3.1)
2021
asnipe : Animal Social Network Inference and Permutations for Ecologists (Version 1.1.17)
2016
avotrex
Traits : (Version )
0
babette : Control 'BEAST2' (Version 2.3.4)
2020
beastier : Call 'BEAST2' (Version 2.5.2)
2019
beautier : 'BEAUti' from R (Version 2.6.12)
2018
betapart
Components : (Version )
0
bioregion : Comparison of Bioregionalisation Methods (Version 1.2.0)
2023
bioseq : A Toolbox for Manipulating Biological Sequences (Version 0.1.5)
2020
bivariatemaps : Creates Bivariate Maps (Version 1.7)
2022
blastar : BLAST and Sequence Analysis Tools (Version 0.1.1)
2026
bnpsd : Simulate Genotypes from the BN-PSD Admixture Model (Version 1.3.13)
2018
brms : Bayesian Regression Models using 'Stan' (Version 2.23.0)
2015
canaper : Categorical Analysis of Neo- And Paleo-Endemism (Version 1.0.1)
2022
caper : Comparative Analyses of Phylogenetics and Evolution in R (Version 1.0.4)
2011
castor : Efficient Phylogenetics on Large Trees (Version 1.8.5)
2017
cati : Community Assembly by Traits: Individuals and Beyond (Version 0.99.4)
2014
cauphy : Trait Evolution on Phylogenies Using the Cauchy Process (Version 1.0.3)
2023
chemodiv : Analysing Chemodiversity of Phytochemical Data (Version 0.3.1)
2022
circlizePlus
Visualization : (Version )
0
cloneRate : Estimate Growth Rates from Phylogenetic Trees (Version 0.2.3)
2023
clue : Cluster Ensembles (Version 0.3-66)
2004
coalescentMCMC : MCMC Algorithms for the Coalescent (Version 0.4-4)
2012
colordistance : Distance Metrics for Image Color Similarity (Version 1.1.2)
2017
concatipede : Easy Concatenation of Fasta Sequences (Version 1.0.1)
2021
convevol : Analysis of Convergent Evolution (Version 2.2.1)
2013
copyseparator : Assembling Long Gene Copies from Short Read Data (Version 1.2.0)
2022
corHMM : Hidden Markov Models of Character Evolution (Version 2.8)
2013
covid19.analytics : Load and Analyze Live Data from the COVID-19 Pandemic (Version 2.1.3.3)
2020
dartR.base : Analysing 'SNP' and 'Silicodart' Data - Basic Functions (Version 1.0.7)
2023
data.tree : General Purpose Hierarchical Data Structure (Version 1.2.0)
2015
ddtlcm
Prior : (Version )
0
debar : A Post-Clustering Denoiser for COI-5P Barcode Data (Version 0.1.1)
2019
deepSTRAPP : Test for Differences in Diversification Rates over Time (Version 1.0.0)
2026
deeptime : Plotting Tools for Anyone Working in Deep Time (Version 2.3.1)
2021
delimtools : Helper Functions for Species Delimitation Analysis (Version 0.2.1)
2025
dendextend : Extending 'dendrogram' Functionality in R (Version 1.19.1)
2014
dispRity : Measuring Disparity (Version 1.9)
2018
distory : Distance Between Phylogenetic Histories (Version 1.4.5)
2012
divent : Entropy Partitioning to Measure Diversity (Version 0.5-3)
2024
diversitree : Comparative 'Phylogenetic' Analyses of Diversification (Version 0.10-1)
2010
divraster : Diversity Metrics Calculations for Rasterized Data (Version 1.2.3)
2023
do3PCA : Probabilistic Phylogenetic Principal Component Analysis (Version 1.0.0)
2024
dowser : B Cell Receptor Phylogenetics Toolkit (Version 2.4.0)
2021
e2tree : Explainable Ensemble Trees (Version 0.2.0)
2025
ecolottery : Coalescent-Based Simulation of Ecological Communities (Version 1.0.2)
2017
ecoregime : Analysis of Ecological Dynamic Regimes (Version 0.3.0)
2023
ecospat : Spatial Ecology Miscellaneous Methods (Version 4.1.2)
2014
ecotraj : Ecological Trajectory Analysis (Version 1.2.0)
2021
entropart : Entropy Partitioning to Measure Diversity (Version 1.6-16)
2013
enveomics.R : Various Utilities for Microbial Genomics and Metagenomics (Version 1.10.0)
2016
epm : EcoPhyloMapper (Version 1.1.6)
2022
evobiR : Comparative and Population Genetic Analyses (Version 1.1)
2013
evolqg : Evolutionary Quantitative Genetics (Version 0.3-6)
2015
evolvability : Calculation of Evolvability Parameters (Version 2.0.1)
2014
fido : Bayesian Multinomial Logistic Normal Regression (Version 1.1.2)
2022
file2meco : Transform Files to 'microtable' Object with 'microeco' Package (Version 0.9.1)
2021
fishtree : Interface to the Fish Tree of Life API (Version 0.3.4)
2018
funspace : Creating and Representing Functional Trait Spaces (Version 0.2.2)
2023
geiger : Analysis of Evolutionary Diversification (Version 2.0.11)
2007
genBaRcode : Analysis and Visualization Tools for Genetic Barcode Data (Version 1.2.8)
2017
geomorph : Geometric Morphometric Analyses of 2D and 3D Landmark Data (Version 4.0.10)
2012
ggimage : Use Image in 'ggplot2' (Version 0.3.5)
2017
ggmuller : Create Muller Plots of Evolutionary Dynamics (Version 0.7.0)
2017
ggrasp
Prioritization : (Version )
0
glinvci : Phylogenetic Comparative Methods with Uncertainty Estimates (Version 1.2.4)
2021
gllvm : Generalized Linear Latent Variable Models (Version 2.0.5)
2017
glmmTMB : Generalized Linear Mixed Models using Template Model Builder (Version 1.1.14)
2017
gpyramid : Identify Efficient Crossing Schemes for Gene Pyramiding (Version 0.0.1)
2025
gquad : Prediction of G Quadruplexes and Other Non-B DNA Motifs (Version 2.1-2)
2015
gromovlab : Gromov-Hausdorff Type Distances for Labeled Metric Spaces (Version 0.8-3)
2015
harmonicmeanp
Likelihood : (Version )
0
harrietr : Wrangle Phylogenetic Distance Matrices and Other Utilities (Version 0.2.3)
2017
hierfstat : Estimation and Tests of Hierarchical F-Statistics (Version 0.5-11)
2004
hillR : Diversity Through Hill Numbers (Version 0.5.2)
2018
hisse : Hidden State Speciation and Extinction (Version 2.1.11)
2015
holobiont : Microbiome Analysis Tools (Version 0.1.3)
2024
homals : Gifi Methods for Optimal Scaling (Version 1.0-11)
2003
iCellR : Analyzing High-Throughput Single Cell Sequencing Data (Version 1.7.0)
2019
iNEXT.3D
Biodiversity : (Version )
0
idar : Individual Diversity-Area Relationships (Version 1.6)
2017
igraph : Network Analysis and Visualization (Version 2.2.1)
2006
inecolr : Modeling and Plotting for Ecologist (Version 0.1.0)
2025
insect : Informatic Sequence Classification Trees (Version 1.4.4)
2018
insight : Easy Access to Model Information for Various Model Objects (Version 1.4.4)
2019
ipADMIXTURE : Iterative Pruning Population Admixture Inference Framework (Version 0.1.2)
2020
itol.toolkit : Helper Functions for 'Interactive Tree Of Life' (Version 1.1.12)
2023
jSDM : Joint Species Distribution Models (Version 0.2.7)
2019
jackalope
Simulator : (Version )
0
kmer
Analysis : (Version )
0
lingtypology : Linguistic Typology and Mapping (Version 1.1.24)
2016
longreadvqs : Viral Quasispecies Comparison from Long-Read Sequencing Data (Version 0.1.4)
2024
mFD
Diversity : (Version )
0
markophylo : Markov Chain Models for Phylogenetic Trees (Version 1.0.9)
2015
mcbette : Model Comparison Using 'babette' (Version 1.15.3)
2020
mdendro : Extended Agglomerative Hierarchical Clustering (Version 2.2.3)
2018
mecoturn : Decipher Microbial Turnover along a Gradient (Version 0.3.1)
2023
metadat : Meta-Analysis Datasets (Version 1.4-0)
2021
metafor : Meta-Analysis Package for R (Version 4.8-0)
2009
microeco : Microbial Community Ecology Data Analysis (Version 1.16.0)
2020
mrIML : Multi-Response (Multivariate) Interpretable Machine Learning (Version 2.2.0)
2025
msaR : Multiple Sequence Alignment for R Shiny (Version 0.6.0)
2016
multilaterals : Transitive Index Numbers for Cross-Sections and Panel Data (Version 2.0)
2017
mycolorsTB : Color Palettes for Mycobacterium Tuberculosis Data Visualization (Version 0.1.1)
2025
nLTT : Calculate the NLTT Statistic (Version 1.4.10)
2015
netdiffuseR : Analysis of Diffusion and Contagion Processes on Networks (Version 1.24.0)
2016
nichevol
Uncertainty : (Version )
0
nodeSub : Simulate DNA Alignments Using Node Substitutions (Version 1.2.9)
2021
nosoi : A Forward Agent-Based Transmission Chain Simulator (Version 1.1.2)
2020
numbat : Haplotype-Aware CNV Analysis from scRNA-Seq (Version 1.5.1)
2022
occCite : Querying and Managing Large Biodiversity Occurrence Datasets (Version 0.6.1)
2020
ontophylo : Ontology-Informed Phylogenetic Comparative Analyses (Version 1.1.3)
2023
oppr : Optimal Project Prioritization (Version 1.0.5)
2019
ouch
Hypotheses : (Version )
0
outbreaks : A Collection of Disease Outbreak Data (Version 1.9.0)
2016
paco : Procrustes Application to Cophylogenetic Analysis (Version 0.4.2)
2015
palaeoverse : Prepare and Explore Data for Palaeobiological Analyses (Version 1.4.0)
2022
paleoDiv : Extracting and Visualizing Paleobiodiversity (Version 0.4.6)
2024
paleobuddy : Simulating Diversification Dynamics (Version 1.1.0)
2021
paleotree : Paleontological and Phylogenetic Analyses of Evolution (Version 3.4.7)
2012
pcmabc
Methods : (Version )
0
pctax : Professional Comprehensive Omics Data Analysis (Version 0.1.3)
2024
pegas : Population and Evolutionary Genetics Analysis System (Version 1.4)
2009
perspectev : Permutation of Species During Turnover Events (Version 1.1)
2015
pez : Phylogenetics for the Environmental Sciences (Version 1.2-5)
2014
phangorn : Phylogenetic Reconstruction and Analysis (Version 2.12.1)
2008
phyclust : Phylogenetic Clustering (Phyloclustering) (Version 0.1-34)
2010
phylepic : Combined Visualisation of Phylogenetic and Epidemiological Data (Version 0.3.0)
2024
phyloTop : Calculating Topological Properties of Phylogenies (Version 2.1.3)
2013
phylobase : Base Package for Phylogenetic Structures and Comparative Data (Version 0.8.12)
2009
phylocomr : Interface to 'Phylocom' (Version 0.3.4)
2018
phylogram : Dendrograms for Evolutionary Analysis (Version 2.1.0)
2017
phylolm : Phylogenetic Linear Regression (Version 2.6.5)
2013
phylopairs : Comparative Analyses of Lineage-Pair Traits (Version 0.1.1)
2024
phylopath : Perform Phylogenetic Path Analysis (Version 1.3.1)
2016
phyloregion : Biogeographic Regionalization and Macroecology (Version 1.0.9)
2020
phylosem : Phylogenetic Structural Equation Model (Version 1.1.4)
2023
phylosignal : Exploring the Phylogenetic Signal in Continuous Traits (Version 1.3.1)
2015
phylosignalDB : Explore Phylogenetic Signals Using Distance-Based Methods (Version 0.2.2)
2025
phylospatial : Spatial Phylogenetic Analysis (Version 1.2.1)
2025
phylotate : Phylogenies with Annotations (Version 1.3)
2017
phylter : Detect and Remove Outliers in Phylogenomics Datasets (Version 0.9.12)
2023
phyr : Model Based Phylogenetic Analysis (Version 1.1.3)
2019
phytools : Phylogenetic Tools for Comparative Biology (and Other Things) (Version 2.5-2)
2011
picante : Integrating Phylogenies and Ecology (Version 1.8.2)
2008
plotbb : Grammar of Graphics for 'base' Plot (Version 0.1.0)
2021
polysat : Tools for Polyploid Microsatellite Analysis (Version 1.7-7)
2010
pooledpeaks : Genetic Analysis of Pooled Samples (Version 1.2.2)
2024
popkin : Estimate Kinship and FST under Arbitrary Population Structure (Version 1.3.23)
2018
poppr : Genetic Analysis of Populations with Mixed Reproduction (Version 2.9.8)
2013
poweRbal : Phylogenetic Tree Models and the Power of Tree Shape Statistics (Version 0.0.1.1)
2024
ppgm
Distributions : (Version )
0
primerTree
Pairs : (Version )
0
prioritizr : Systematic Conservation Prioritization in R (Version 8.1.0)
2016
qlcData : Processing Data for Quantitative Language Comparison (Version 0.3)
2015
quiddich : QUick IDentification of DIagnostic CHaracters (Version 1.0.0)
2019
rKOMICS : Minicircle Sequence Classes (MSC) Analyses (Version 1.3)
2021
ratematrix : Bayesian Estimation of the Evolutionary Rate Matrix (Version 1.2.5)
2018
rbiom : Read/Write, Analyze, and Visualize 'BIOM' Data (Version 2.2.1)
2020
rdiversity
Biodiversity : (Version )
0
readyomics
Pipeline : (Version )
0
recluster : Ordination Methods for the Analysis of Beta-Diversity Indices (Version 2.9)
2013
refdb : A DNA Reference Library Manager (Version 0.1.2)
2022
restez : Create and Query a Local Copy of 'GenBank' in R (Version 2.1.5)
2018
rhierbaps : Clustering Genetic Sequence Data Using the HierBAPS Algorithm (Version 1.1.4)
2018
rncl : An Interface to the Nexus Class Library (Version 0.8.9)
2014
rotl : Interface to the 'Open Tree of Life' API (Version 3.1.1)
2015
rphylopic : Get Silhouettes of Organisms from PhyloPic (Version 1.6.0)
2018
rr2 : R2s for Regression Models (Version 1.1.1)
2018
rrnni : Manipulate with RNNI Tree Space (Version 0.1.1)
2022
rwty : R We There Yet? Visualizing MCMC Convergence in Phylogenetics (Version 1.0.3)
2016
sand : Statistical Analysis of Network Data with R, 2nd Edition (Version 2.0.0)
2014
scistreer : Maximum-Likelihood Perfect Phylogeny Inference at Scale (Version 1.2.0)
2022
scrm : Simulating the Evolution of Biological Sequences (Version 1.7.5)
2014
secsse
Extinction : (Version )
0
sensiPhy : Sensitivity Analysis for Comparative Methods (Version 0.8.5)
2016
sharpshootR : A Soil Survey Toolkit (Version 2.4)
2014
shazam : Immunoglobulin Somatic Hypermutation Analysis (Version 1.3.1)
2016
shinyTempSignal : Explore Temporal and Other Phylogenetic Signals (Version 0.0.8)
2022
shinyWGD : 'Shiny' Application for Whole Genome Duplication Analysis (Version 1.0.0)
2024
sidier
Relationships : (Version )
0
slendr : A Simulation Framework for Spatiotemporal Population Genetics (Version 1.4.0)
2022
slouch : Stochastic Linear Ornstein-Uhlenbeck Comparative Hypotheses (Version 2.1.5)
2018
spANOVA : Analysis of Field Trials with Geostatistics & Spatial AR Models (Version 0.99.4)
2019
spider : Species Identity and Evolution in R (Version 1.5.1)
2011
spiralize : Visualize Data on Spirals (Version 1.1.0)
2021
strap : Stratigraphic Tree Analysis for Palaeontology (Version 1.6-1)
2014
structSSI
Structure : (Version )
0
stylo : Stylometric Multivariate Analyses (Version 0.7.5)
2013
subniche : Within Outlying Mean Indexes: Refining the 'OMI' Analysis (Version 1.6)
2016
supportR : Support Functions for Wrangling and Visualization (Version 1.6.0)
2023
surface : Fitting Hansen Models to Investigate Convergent Evolution (Version 0.6)
2013
tabs : Temporal Altitudinal Biogeographic Shifts (Version 0.1.1)
2025
tapnet : Trait Matching and Abundance for Predicting Bipartite Networks (Version 0.6)
2021
taxize : Taxonomic Information from Around the Web (Version 0.10.0)
2012
taxlist : Handling Taxonomic Lists (Version 0.3.5)
2017
tbea : Pre- And Post-Processing in Bayesian Evolutionary Analyses (Version 1.7.0)
2024
tidygraph : A Tidy API for Graph Manipulation (Version 1.3.1)
2017
tidysq : Tidy Processing and Analysis of Biological Sequences (Version 1.2.3)
2021
tidytree : A Tidy Tool for Phylogenetic Tree Data Manipulation (Version 0.4.7)
2017
topolow : Force-Directed Euclidean Embedding of Dissimilarity Data (Version 2.0.1)
2025
tracerer : Tracer from R (Version 2.2.3)
2018
treats : Trees and Traits Simulations (Version 1.1.6)
2023
treeDA : Tree-Based Discriminant Analysis (Version 0.0.5)
2017
treebalance : Computation of Tree (Im)Balance Indices (Version 1.2.0)
2021
treebase : Discovery, Access and Manipulation of 'TreeBASE' Phylogenies (Version 0.1.5)
2011
treedata.table : Manipulation of Matched Phylogenies and Data using 'data.table' (Version 0.1.1)
2020
treedater
Variation : (Version )
0
treesliceR
Time : (Version )
0
treespace : Statistical Exploration of Landscapes of Phylogenetic Trees (Version 1.1.4.4)
2017
treestats : Phylogenetic Tree Statistics (Version 1.70.8)
2024
treestructure : Detect Population Structure Within Phylogenetic Trees (Version 0.7.0)
2020
vcfR : Manipulate and Visualize VCF Data (Version 1.15.0)
2016
vhica : Vertical and Horizontal Inheritance Consistence Analysis (Version 0.2.9)
2016
warbleR : Streamline Bioacoustic Analysis (Version 1.1.37)
2015
windex : Analysing Convergent Evolution using the Wheatsheaf Index (Version 2.1.0)
2014
yatah : Yet Another TAxonomy Handler (Version 1.0.0)
2019
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RPKG Scholar presents a tabulation of an author's contribution in the development of R packages stored in the Comprehensive R Archive Network (CRAN).
Within this site, we consider package dependencies (suggests,imports,depends,enhances) as citations because we believe that using one's package to develop another is tantamount to citing the author of the package being imported, suggested or enhanced.
