Showing 200 of total 452 results (show query)
adeverse
ade4:Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences
Tools for multivariate data analysis. Several methods are provided for the analysis (i.e., ordination) of one-table (e.g., principal component analysis, correspondence analysis), two-table (e.g., coinertia analysis, redundancy analysis), three-table (e.g., RLQ analysis) and K-table (e.g., STATIS, multiple coinertia analysis). The philosophy of the package is described in Dray and Dufour (2007) <doi:10.18637/jss.v022.i04>.
Maintained by Aurélie Siberchicot. Last updated 12 days ago.
63.4 match 39 stars 14.96 score 2.2k scripts 256 dependents
ropensci
traits:Species Trait Data from Around the Web
Species trait data from many different sources, including sequence data from 'NCBI' (<https://www.ncbi.nlm.nih.gov/>), plant trait data from 'BETYdb', data from 'EOL' 'Traitbank', 'Birdlife' International, and more.
Maintained by David LeBauer. Last updated 2 months ago.
traitsapiweb-servicesspeciestaxonomyapi-client
88.7 match 41 stars 8.65 score 82 scripts 11 dependents
frbcesab
funbiogeo:Functional Biogeography Analyses
Helps users with analyses in functional biogeogeography by loading and combining data, computing trait coverage, as well as computing functional diversity indices, drawing maps, correlating them with the environment, and upscaling assemblages.
Maintained by Nicolas Casajus. Last updated 4 days ago.
functional-biogeographyfunctional-diversityfunctional-trait
73.1 match 11 stars 5.60 score 8 scripts
funecology
fundiversity:Easy Computation of Functional Diversity Indices
Computes six functional diversity indices. These are namely, Functional Divergence (FDiv), Function Evenness (FEve), Functional Richness (FRic), Functional Richness intersections (FRic_intersect), Functional Dispersion (FDis), and Rao's entropy (Q) (reviewed in Villéger et al. 2008 <doi:10.1890/07-1206.1>). Provides efficient, modular, and parallel functions to compute functional diversity indices (Grenié & Gruson 2023 <doi:10.1111/ecog.06585>).
Maintained by Matthias Grenié. Last updated 8 months ago.
biodiversitybiodiversity-indicatorsbiodiversity-informaticsfunctional-diversityfunctional-ecologyfunctional-traitfunctional-traitstraittrait-basedtraits
55.6 match 38 stars 7.34 score 38 scriptsadeverse
adephylo: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>.
Maintained by Aurélie Siberchicot. Last updated 2 days ago.
37.5 match 9 stars 10.05 score 312 scripts 4 dependents
pecanproject
PEcAn.DB:PEcAn Functions Used for Ecological Forecasts and Reanalysis
The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PECAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation.
Maintained by David LeBauer. Last updated 2 days ago.
bayesiancyberinfrastructuredata-assimilationdata-scienceecosystem-modelecosystem-scienceforecastingmeta-analysisnational-science-foundationpecanplants
30.3 match 216 stars 11.88 score 127 scripts 27 dependents
traitecoevo
austraits:Helpful functions to access the AusTraits database and wrangle data from other traits.build databases
`austraits` allow users to **access, explore and wrangle data** from traits.build relational databases. It is also an R interface to AusTraits, the Australian plant trait database. This package contains functions for joining data from various tables, filtering to specific records, combining multiple databases and visualising the distribution of the data. We expect this package will assist users in working with `traits.build` databases.
Maintained by Fonti Kar. Last updated 2 months ago.
58.1 match 22 stars 5.93 score 43 scripts 1 dependents
ramiromagno
gwasrapidd:'REST' 'API' Client for the 'NHGRI'-'EBI' 'GWAS' Catalog
'GWAS' R 'API' Data Download. This package provides easy access to the 'NHGRI'-'EBI' 'GWAS' Catalog data by accessing the 'REST' 'API' <https://www.ebi.ac.uk/gwas/rest/docs/api/>.
Maintained by Ramiro Magno. Last updated 1 years ago.
thirdpartyclientbiomedicalinformaticsgenomewideassociationsnpassociation-studiesgwas-cataloghumanrest-clienttraittrait-ontology
38.4 match 95 stars 8.10 score 49 scripts 1 dependents
cmlmagneville
mFD:Compute and Illustrate the Multiple Facets of Functional Diversity
Computing functional traits-based distances between pairs of species for species gathered in assemblages allowing to build several functional spaces. The package allows to compute functional diversity indices assessing the distribution of species (and of their dominance) in a given functional space for each assemblage and the overlap between assemblages in a given functional space, see: Chao et al. (2018) <doi:10.1002/ecm.1343>, Maire et al. (2015) <doi:10.1111/geb.12299>, Mouillot et al. (2013) <doi:10.1016/j.tree.2012.10.004>, Mouillot et al. (2014) <doi:10.1073/pnas.1317625111>, Ricotta and Szeidl (2009) <doi:10.1016/j.tpb.2009.10.001>. Graphical outputs are included. Visit the 'mFD' website for more information, documentation and examples.
Maintained by Camille Magneville. Last updated 3 months ago.
39.3 match 26 stars 7.35 score 61 scripts
plant-functional-trait-course
traitstrap:Bootstrap Trait Values to Calculate Moments
Calculates trait moments from trait and community data using the methods developed in Maitner et al (2021) <doi:10.22541/au.162196147.76797968/v1>.
Maintained by Richard James Telford. Last updated 9 months ago.
41.0 match 12 stars 5.83 score 28 scripts
gaynorr
AlphaSimR:Breeding Program Simulations
The successor to the 'AlphaSim' software for breeding program simulation [Faux et al. (2016) <doi:10.3835/plantgenome2016.02.0013>]. Used for stochastic simulations of breeding programs to the level of DNA sequence for every individual. Contained is a wide range of functions for modeling common tasks in a breeding program, such as selection and crossing. These functions allow for constructing simulations of highly complex plant and animal breeding programs via scripting in the R software environment. Such simulations can be used to evaluate overall breeding program performance and conduct research into breeding program design, such as implementation of genomic selection. Included is the 'Markovian Coalescent Simulator' ('MaCS') for fast simulation of biallelic sequences according to a population demographic history [Chen et al. (2009) <doi:10.1101/gr.083634.108>].
Maintained by Chris Gaynor. Last updated 4 months ago.
breedinggenomicssimulationopenblascppopenmp
23.1 match 47 stars 10.22 score 534 scripts 2 dependents
puttickmacroevolution
motmot:Models of Trait Macroevolution on Trees
Functions for fitting models of trait evolution on phylogenies for continuous traits. The majority of functions described in Thomas and Freckleton (2012) <doi:10.1111/j.2041-210X.2011.00132.x> and include functions that allow for tests of variation in the rates of trait evolution.
Maintained by Mark Puttick. Last updated 5 years ago.
34.1 match 4 stars 6.05 score 35 scriptstraitecoevo
traits.build:A workflow for harmonising trait data from diverse sources into a documented standard structure
The `traits.build` package provides a workflow to harmonise trait data from diverse sources. The code was originally built to support AusTraits (see Falster et al 2021, <doi:10.1038/s41597-021-01006-6>, <https://github.com/traitecoevo/autraits.build>) and has been generalised here to support construction of other trait databases. For detailed instructions and examples see <https://traitecoevo.github.io/traits.build-book/>.
Maintained by Daniel Falster. Last updated 3 months ago.
56.0 match 10 stars 3.40 score 25 scripts
jclavel
mvMORPH: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>.
Maintained by Julien Clavel. Last updated 1 months ago.
19.5 match 17 stars 9.46 score 189 scripts 3 dependents
tguillerme
treats:Trees and Traits Simulations
A modular package for simulating phylogenetic trees and species traits jointly. Trees can be simulated using modular birth-death parameters (e.g. changing starting parameters or algorithm rules). Traits can be simulated in any way designed by the user. The growth of the tree and the traits can influence each other through modifiers objects providing rules for affecting each other. Finally, events can be created to modify both the tree and the traits under specific conditions ( Guillerme, 2024 <DOI:10.1111/2041-210X.14306>).
Maintained by Thomas Guillerme. Last updated 2 months ago.
37.3 match 3 stars 4.63 score 19 scripts
giobo
TR8:A Tool for Downloading Functional Traits Data for Plant Species
Plant ecologists often need to collect "traits" data about plant species which are often scattered among various databases: TR8 contains a set of tools which take care of automatically retrieving some of those functional traits data for plant species from publicly available databases (The Ecological Flora of the British Isles, LEDA traitbase, Ellenberg values for Italian Flora, Mycorrhizal intensity databases, BROT, PLANTS, Jepson Flora Project). The TR8 name, inspired by "car plates" jokes, was chosen since it both reminds of the main object of the package and is extremely short to type.
Maintained by Gionata Bocci. Last updated 6 months ago.
27.4 match 20 stars 6.16 score 16 scripts
rekyt
funrar:Functional Rarity Indices Computation
Computes functional rarity indices as proposed by Violle et al. (2017) <doi:10.1016/j.tree.2017.02.002>. Various indices can be computed using both regional and local information. Functional Rarity combines both the functional aspect of rarity as well as the extent aspect of rarity. 'funrar' is presented in Grenié et al. (2017) <doi:10.1111/ddi.12629>.
Maintained by Matthias Grenié. Last updated 11 months ago.
ecological-modelsecologyraritytraits
20.6 match 17 stars 7.85 score 233 scripts 1 dependents
skembel
picante: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>.
Maintained by Steven W. Kembel. Last updated 2 years ago.
13.8 match 34 stars 11.42 score 1.1k scripts 16 dependents
bmaitner
BIEN:Tools for Accessing the Botanical Information and Ecology Network Database
Provides Tools for Accessing the Botanical Information and Ecology Network Database. The BIEN database contains cleaned and standardized botanical data including occurrence, trait, plot and taxonomic data (See <https://bien.nceas.ucsb.edu/bien/> for more Information). This package provides functions that query the BIEN database by constructing and executing optimized SQL queries.
Maintained by Brian Maitner. Last updated 1 months ago.
24.9 match 6.04 score 205 scripts 5 dependents
kbroman
qtl:Tools for Analyzing QTL Experiments
Analysis of experimental crosses to identify genes (called quantitative trait loci, QTLs) contributing to variation in quantitative traits. Broman et al. (2003) <doi:10.1093/bioinformatics/btg112>.
Maintained by Karl W Broman. Last updated 7 months ago.
11.5 match 80 stars 12.79 score 2.4k scripts 29 dependents
igraph
igraph:Network Analysis and Visualization
Routines for simple graphs and network analysis. It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.
Maintained by Kirill Müller. Last updated 2 days ago.
complex-networksgraph-algorithmsgraph-theorymathematicsnetwork-analysisnetwork-graphfortranlibxml2glpkopenblascpp
6.9 match 581 stars 21.10 score 31k scripts 1.9k dependents
ochoalab
simtrait:Simulate Complex Traits from Genotypes
Simulate complex traits given a SNP genotype matrix and model parameters (the desired heritability, optional environment group effects, number of causal loci, and either the true ancestral allele frequencies used to generate the genotypes or the mean kinship for a real dataset). Emphasis is on avoiding common biases due to the use of estimated allele frequencies. The code selects random loci to be causal, constructs coefficients for these loci and random independent non-genetic effects, and can optionally generate random group effects. Traits can follow three models: random coefficients, fixed effect sizes, and infinitesimal (multivariate normal). GWAS method benchmarking functions are also provided. Described in Yao and Ochoa (2023) <doi:10.7554/eLife.79238>.
Maintained by Alejandro Ochoa. Last updated 4 months ago.
27.2 match 5 stars 5.32 score 21 scripts
squidlobster
castor:Efficient Phylogenetics on Large Trees
Efficient phylogenetic analyses on massive phylogenies comprising up to millions of tips. Functions include pruning, rerooting, calculation of most-recent common ancestors, calculating distances from the tree root and calculating pairwise distances. Calculation of phylogenetic signal and mean trait depth (trait conservatism), ancestral state reconstruction and hidden character prediction of discrete characters, simulating and fitting models of trait evolution, fitting and simulating diversification models, dating trees, comparing trees, and reading/writing trees in Newick format. Citation: Louca, Stilianos and Doebeli, Michael (2017) <doi:10.1093/bioinformatics/btx701>.
Maintained by Stilianos Louca. Last updated 4 months ago.
25.1 match 2 stars 5.75 score 450 scripts 9 dependents
lcrawlab
mvMAPIT:Multivariate Genome Wide Marginal Epistasis Test
Epistasis, commonly defined as the interaction between genetic loci, is known to play an important role in the phenotypic variation of complex traits. As a result, many statistical methods have been developed to identify genetic variants that are involved in epistasis, and nearly all of these approaches carry out this task by focusing on analyzing one trait at a time. Previous studies have shown that jointly modeling multiple phenotypes can often dramatically increase statistical power for association mapping. In this package, we present the 'multivariate MArginal ePIstasis Test' ('mvMAPIT') – a multi-outcome generalization of a recently proposed epistatic detection method which seeks to detect marginal epistasis or the combined pairwise interaction effects between a given variant and all other variants. By searching for marginal epistatic effects, one can identify genetic variants that are involved in epistasis without the need to identify the exact partners with which the variants interact – thus, potentially alleviating much of the statistical and computational burden associated with conventional explicit search based methods. Our proposed 'mvMAPIT' builds upon this strategy by taking advantage of correlation structure between traits to improve the identification of variants involved in epistasis. We formulate 'mvMAPIT' as a multivariate linear mixed model and develop a multi-trait variance component estimation algorithm for efficient parameter inference and P-value computation. Together with reasonable model approximations, our proposed approach is scalable to moderately sized genome-wide association studies. Crawford et al. (2017) <doi:10.1371/journal.pgen.1006869>. Stamp et al. (2023) <doi:10.1093/g3journal/jkad118>.
Maintained by Julian Stamp. Last updated 5 months ago.
cppepistasisepistasis-analysisgwasgwas-toolslinear-mixed-modelsmapitmvmapitvariance-componentsopenblascppopenmp
20.7 match 11 stars 6.90 score 17 scripts 1 dependents
danforthcenter
pcvr:Plant Phenotyping and Bayesian Statistics
Analyse common types of plant phenotyping data, provide a simplified interface to longitudinal growth modeling and select Bayesian statistics, and streamline use of 'PlantCV' output. Several Bayesian methods and reporting guidelines for Bayesian methods are described in Kruschke (2018) <doi:10.1177/2515245918771304>, Kruschke (2013) <doi:10.1037/a0029146>, and Kruschke (2021) <doi:10.1038/s41562-021-01177-7>.
Maintained by Josh Sumner. Last updated 4 days ago.
19.1 match 4 stars 6.99 score 39 scripts
pavel-fibich
gawdis:Multi-Trait Dissimilarity with more Uniform Contributions
R function gawdis() produces multi-trait dissimilarity with more uniform contributions of different traits. de Bello et al. (2021) <doi:10.1111/2041-210X.13537> presented the approach based on minimizing the differences in the correlation between the dissimilarity of each trait, or groups of traits, and the multi-trait dissimilarity. This is done using either an analytic or a numerical solution, both available in the function.
Maintained by Pavel Fibich. Last updated 2 years ago.
dissimilarityfdgowdismulti-trait-dissimilaritytrait
25.2 match 5 stars 5.20 score 21 scripts 1 dependents
bioc
gwascat:representing and modeling data in the EMBL-EBI GWAS catalog
Represent and model data in the EMBL-EBI GWAS catalog.
Maintained by VJ Carey. Last updated 5 months ago.
21.7 match 6.05 score 110 scripts 2 dependentsbioc
ASSET:An R package for subset-based association analysis of heterogeneous traits and subtypes
An R package for subset-based analysis of heterogeneous traits and disease subtypes. The package allows the user to search through all possible subsets of z-scores to identify the subset of traits giving the best meta-analyzed z-score. Further, it returns a p-value adjusting for the multiple-testing involved in the search. It also allows for searching for the best combination of disease subtypes associated with each variant.
Maintained by Samsiddhi Bhattacharjee. Last updated 5 months ago.
statisticalmethodsnpgenomewideassociationmultiplecomparison
20.8 match 5.71 score 85 scripts 1 dependents
paternogbc
sensiPhy: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).
Maintained by Gustavo Paterno. Last updated 5 years ago.
comparative-methodsecologyevolutionphylogeneticssensitivity-analysis
18.2 match 13 stars 6.38 score 61 scriptsropensci
rredlist:'IUCN' Red List Client
'IUCN' Red List (<https://api.iucnredlist.org/>) client. The 'IUCN' Red List is a global list of threatened and endangered species. Functions cover all of the Red List 'API' routes. An 'API' key is required.
Maintained by William Gearty. Last updated 1 months ago.
iucnbiodiversityapiweb-servicestraitshabitatspeciesconservationapi-wrapperiucn-red-listtaxize
10.0 match 53 stars 11.49 score 195 scripts 24 dependents
fkeck
phylosignal: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.
Maintained by Francois Keck. Last updated 1 years ago.
15.6 match 16 stars 7.22 score 104 scripts
chiliubio
microeco:Microbial Community Ecology Data Analysis
A series of statistical and plotting approaches in microbial community ecology based on the R6 class. The classes are designed for data preprocessing, taxa abundance plotting, alpha diversity analysis, beta diversity analysis, differential abundance test, null model analysis, network analysis, machine learning, environmental data analysis and functional analysis.
Maintained by Chi Liu. Last updated 4 days ago.
10.9 match 219 stars 10.11 score 211 scripts 3 dependentstraitecoevo
plant:A Package for Modelling Forest Trait Ecology and Evolution
Solves trait, size and patch structured model from (Falster et al. 2016) using either method of characteristics or as stochastic, finite-sized population.
Maintained by Daniel Falster. Last updated 7 days ago.
c-plus-plusdemographydynamicecologyevolutionforestsplant-physiologyscience-researchsimulationtraitcpp
18.0 match 53 stars 5.87 score
biogeomacro
GIFT:Access to the Global Inventory of Floras and Traits (GIFT)
Retrieving regional plant checklists, species traits and distributions, and environmental data from the Global Inventory of Floras and Traits (GIFT). More information about the GIFT database can be found at <https://gift.uni-goettingen.de/about> and the map of available floras can be visualized at <https://gift.uni-goettingen.de/map>. The API and associated queries can be accessed according the following scheme: <https://gift.uni-goettingen.de/api/extended/index2.0.php?query=env_raster>.
Maintained by Pierre Denelle. Last updated 6 days ago.
biodiversitybiodiversity-informaticsplants-databaseplants-distribution
16.0 match 18 stars 6.51 score 24 scripts
biometris
douconca:Double Constrained Correspondence Analysis for Trait-Environment Analysis in Ecology
Double constrained correspondence analysis (dc-CA) analyzes (multi-)trait (multi-)environment ecological data by using the 'vegan' package and native R code. Throughout the two step algorithm of ter Braak et al. (2018) is used. This algorithm combines and extends community- (sample-) and species-level analyses, i.e. the usual community weighted means (CWM)-based regression analysis and the species-level analysis of species-niche centroids (SNC)-based regression analysis. The two steps use canonical correspondence analysis to regress the abundance data on to the traits and (weighted) redundancy analysis to regress the CWM of the orthonormalized traits on to the environmental predictors. The function dc_CA() has an option to divide the abundance data of a site by the site total, giving equal site weights. This division has the advantage that the multivariate analysis corresponds with an unweighted (multi-trait) community-level analysis, instead of being weighted. The first step of the algorithm uses vegan::cca(). The second step uses wrda() but vegan::rda() if the site weights are equal. This version has a predict() function. For details see ter Braak et al. 2018 <doi:10.1007/s10651-017-0395-x>.
Maintained by Bart-Jan van Rossum. Last updated 3 months ago.
correspondence-analysisecologyecology-modelingmulti-environmentmulti-trait
20.6 match 5.02 score 6 scripts
chr1swallace
coloc:Colocalisation Tests of Two Genetic Traits
Performs the colocalisation tests described in Giambartolomei et al (2013) <doi:10.1371/journal.pgen.1004383>, Wallace (2020) <doi:10.1371/journal.pgen.1008720>, Wallace (2021) <doi:10.1371/journal.pgen.1009440>.
Maintained by Chris Wallace. Last updated 4 months ago.
8.4 match 162 stars 12.23 score 916 scripts 3 dependents
leelabsg
SKAT:SNP-Set (Sequence) Kernel Association Test
Functions for kernel-regression-based association tests including Burden test, SKAT and SKAT-O. These methods aggregate individual SNP score statistics in a SNP set and efficiently compute SNP-set level p-values.
Maintained by Seunggeun (Shawn) Lee. Last updated 1 months ago.
10.4 match 45 stars 9.70 score 268 scripts 16 dependents
kwstat
agridat:Agricultural Datasets
Datasets from books, papers, and websites related to agriculture. Example graphics and analyses are included. Data come from small-plot trials, multi-environment trials, uniformity trials, yield monitors, and more.
Maintained by Kevin Wright. Last updated 27 days ago.
8.7 match 125 stars 11.02 score 1.7k scripts 2 dependents
plangfelder
WGCNA:Weighted Correlation Network Analysis
Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data as originally described in Horvath and Zhang (2005) <doi:10.2202/1544-6115.1128> and Langfelder and Horvath (2008) <doi:10.1186/1471-2105-9-559>. Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits. Also includes a number of utility functions for data manipulation and visualization.
Maintained by Peter Langfelder. Last updated 6 months ago.
9.5 match 54 stars 9.65 score 5.3k scripts 32 dependents
emmanuelparadis
ape:Analyses of Phylogenetics and Evolution
Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.
Maintained by Emmanuel Paradis. Last updated 1 months ago.
5.3 match 64 stars 17.18 score 13k scripts 601 dependents
ax3man
phylopath:Perform Phylogenetic Path Analysis
A comprehensive and easy to use R implementation of confirmatory phylogenetic path analysis as described by Von Hardenberg and Gonzalez-Voyer (2012) <doi:10.1111/j.1558-5646.2012.01790.x>.
Maintained by Wouter van der Bijl. Last updated 6 months ago.
analysiscomparative-methodspathphylogenetics
11.0 match 13 stars 8.10 score 81 scripts 1 dependents
dannyarends
ctl:Correlated Trait Locus Mapping
Identification and network inference of genetic loci associated with correlation changes in quantitative traits (called correlated trait loci, CTLs). Arends et al. (2016) <doi:10.21105/joss.00087>.
Maintained by Danny Arends. Last updated 1 years ago.
25.6 match 3.31 score 103 scripts
cran
paleoTS: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).
Maintained by Gene Hunt. Last updated 6 months ago.
18.1 match 1 stars 4.48 score 2 dependents
giopogg
jtdm:Joint Modelling of Functional Traits
Fitting and analyzing a Joint Trait Distribution Model. The Joint Trait Distribution Model is implemented in the Bayesian framework using conjugate priors and posteriors, thus guaranteeing fast inference. In particular the package computes joint probabilities and multivariate confidence intervals, and enables the investigation of how they depend on the environment through partial response curves. The method implemented by the package is described in Poggiato et al. (2023) <doi:10.1111/geb.13706>.
Maintained by Giovanni Poggiato. Last updated 6 months ago.
16.2 match 9 stars 4.95 score 7 scripts
jonesor
Rage:Life History Metrics from Matrix Population Models
Functions for calculating life history metrics using matrix population models ('MPMs'). Described in Jones et al. (2021) <doi:10.1101/2021.04.26.441330>.
Maintained by Owen Jones. Last updated 3 months ago.
9.8 match 11 stars 8.17 score 62 scripts 1 dependents
project-gen3sis
gen3sis:General Engine for Eco-Evolutionary Simulations
Contains an engine for spatially-explicit eco-evolutionary mechanistic models with a modular implementation and several support functions. It allows exploring the consequences of ecological and macroevolutionary processes across realistic or theoretical spatio-temporal landscapes on biodiversity patterns as a general term. Reference: Oskar Hagen, Benjamin Flueck, Fabian Fopp, Juliano S. Cabral, Florian Hartig, Mikael Pontarp, Thiago F. Rangel, Loic Pellissier (2021) "gen3sis: A general engine for eco-evolutionary simulations of the processes that shape Earth's biodiversity" <doi:10.1371/journal.pbio.3001340>.
Maintained by Oskar Hagen. Last updated 1 years ago.
biodiversityecologyevolutionmechanisticmodelmodelingsimulationcpp
10.5 match 29 stars 7.56 score 69 scripts
mrcieu
epigraphdb:Interface Package for the 'EpiGraphDB' Platform
The interface package to access data from the 'EpiGraphDB' <https://epigraphdb.org> platform. It provides easy access to the 'EpiGraphDB' platform with functions that query the corresponding REST endpoints on the API <https://api.epigraphdb.org> and return the response data in the 'tibble' data frame format.
Maintained by Yi Liu. Last updated 3 years ago.
api-clientbioinformaticsepidemiologygraph-databasemendelian-randomizationphenotypes
13.2 match 27 stars 6.02 score 13 scripts
temp20250212
MultiTraits:Analyzing and Visualizing Multidimensional Plant Traits
Implements analytical methods for multidimensional plant traits, including Competitors-Stress tolerators-Ruderals strategy analysis using leaf traits, Leaf-Height-Seed strategy analysis, Niche Periodicity Table analysis, and Trait Network analysis. Provides functions for data analysis, visualization, and network metrics calculation. Methods are based on Grime (1974) <doi:10.1038/250026a0>, Pierce et al. (2017) <doi:10.1111/1365-2435.12882>, Westoby (1998) <doi:10.1023/A:1004327224729>, Yang et al. (2022) <doi:10.1016/j.foreco.2022.120540>, Winemiller et al. (2015) <doi:10.1111/ele.12462>, He et al. (2020) <doi:10.1016/j.tree.2020.06.003>.
Maintained by Anonymous Author. Last updated 23 days ago.
19.6 match 3.90 score 16 scripts
melff
RKernel:Yet another R kernel for Jupyter
Provides a kernel for Jupyter.
Maintained by Martin Elff. Last updated 14 days ago.
jupyterjupyter-kerneljupyter-kernelsjupyter-notebook
16.5 match 38 stars 4.60 score
mrcieu
gwasglue2:GWAS summary data sources connected to analytical tools
Description: Many tools exist that use GWAS summary data for colocalisation, fine mapping, Mendelian randomization, visualisation, etc. This package is a conduit that connects R packages that can retrieve GWAS summary data to various tools for analysing those data.
Maintained by Rita Rasteiro. Last updated 1 years ago.
13.1 match 21 stars 5.69 score 11 scripts 2 dependents
ichcha-m
cophescan:Adaptation of the Coloc Method for PheWAS
A Bayesian method for Phenome-wide association studies (PheWAS) that identifies causal associations between genetic variants and traits, while simultaneously addressing confounding due to linkage disequilibrium. For details see Manipur et al (2023) <doi:10.1101/2023.06.29.546856>.
Maintained by Ichcha Manipur. Last updated 9 months ago.
12.7 match 6 stars 5.76 score 24 scripts
dwarton
mvabund:Statistical Methods for Analysing Multivariate Abundance Data
A set of tools for displaying, modeling and analysing multivariate abundance data in community ecology. See 'mvabund-package.Rd' for details of overall package organization. The package is implemented with the Gnu Scientific Library (<http://www.gnu.org/software/gsl/>) and 'Rcpp' (<http://dirk.eddelbuettel.com/code/rcpp.html>) 'R' / 'C++' classes.
Maintained by David Warton. Last updated 1 years ago.
7.1 match 10 stars 10.13 score 680 scripts 5 dependentsplant-functional-trait-course
fluxible:Ecosystem Gas Fluxes Calculations for Closed Loop Chamber Setup
Processes the raw data from closed loop flux chamber (or tent) setups into ecosystem gas fluxes usable for analysis. It goes from a data frame of gas concentration over time (which can contain several measurements) and a meta data file indicating which measurement was done when, to a data frame of ecosystem gas fluxes including quality diagnostics. Functions provided include different models (exponential as described in Zhao et al (2018) <doi:10.1016/j.agrformet.2018.08.022>, quadratic and linear) to estimate the fluxes from the raw data, quality assessment, plotting for visual check and calculation of fluxes based on the setup specific parameters (chamber size, plot area, ...).
Maintained by Joseph Gaudard. Last updated 13 hours ago.
12.5 match 5.69 score 12 scripts
rsetienne
secsse: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>.
Maintained by Rampal S. Etienne. Last updated 11 months ago.
12.2 match 1 stars 5.83 score 34 scripts
kbhoehn
dowser:B Cell Receptor Phylogenetics Toolkit
Provides a set of functions for inferring, visualizing, and analyzing B cell phylogenetic trees. Provides methods to 1) reconstruct unmutated ancestral sequences, 2) build B cell phylogenetic trees using multiple methods, 3) visualize trees with metadata at the tips, 4) reconstruct intermediate sequences, 5) detect biased ancestor-descendant relationships among metadata types Workflow examples available at documentation site (see URL). Citations: Hoehn et al (2022) <doi:10.1371/journal.pcbi.1009885>, Hoehn et al (2021) <doi:10.1101/2021.01.06.425648>.
Maintained by Kenneth Hoehn. Last updated 2 months ago.
10.4 match 6.81 score 84 scripts
sinnweja
haplo.stats:Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous
Routines for the analysis of indirectly measured haplotypes. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers). The main functions are: haplo.em(), haplo.glm(), haplo.score(), and haplo.power(); all of which have detailed examples in the vignette.
Maintained by Jason P. Sinnwell. Last updated 6 months ago.
11.5 match 2 stars 5.98 score 96 scripts 12 dependents
drizopoulos
ltm:Latent Trait Models under IRT
Analysis of multivariate dichotomous and polytomous data using latent trait models under the Item Response Theory approach. It includes the Rasch, the Two-Parameter Logistic, the Birnbaum's Three-Parameter, the Graded Response, and the Generalized Partial Credit Models.
Maintained by Dimitris Rizopoulos. Last updated 3 years ago.
7.0 match 30 stars 9.59 score 1.0k scripts 27 dependents
hojsgaard
doBy:Groupwise Statistics, LSmeans, Linear Estimates, Utilities
Utility package containing: 1) Facilities for working with grouped data: 'do' something to data stratified 'by' some variables. 2) LSmeans (least-squares means), general linear estimates. 3) Restrict functions to a smaller domain. 4) Miscellaneous other utilities.
Maintained by Søren Højsgaard. Last updated 4 days ago.
4.5 match 1 stars 14.94 score 3.2k scripts 939 dependentsbioc
traseR:GWAS trait-associated SNP enrichment analyses in genomic intervals
traseR performs GWAS trait-associated SNP enrichment analyses in genomic intervals using different hypothesis testing approaches, also provides various functionalities to explore and visualize the results.
Maintained by li chen. Last updated 5 months ago.
geneticssequencingcoveragealignmentqualitycontroldataimport
19.9 match 3.30 score 3 scripts
aplantin
MiRKAT:Microbiome Regression-Based Kernel Association Tests
Test for overall association between microbiome composition data and phenotypes via phylogenetic kernels. The phenotype can be univariate continuous or binary (Zhao et al. (2015) <doi:10.1016/j.ajhg.2015.04.003>), survival outcomes (Plantinga et al. (2017) <doi:10.1186/s40168-017-0239-9>), multivariate (Zhan et al. (2017) <doi:10.1002/gepi.22030>) and structured phenotypes (Zhan et al. (2017) <doi:10.1111/biom.12684>). The package can also use robust regression (unpublished work) and integrated quantile regression (Wang et al. (2021) <doi:10.1093/bioinformatics/btab668>). In each case, the microbiome community effect is modeled nonparametrically through a kernel function, which can incorporate phylogenetic tree information.
Maintained by Anna Plantinga. Last updated 2 years ago.
13.1 match 3 stars 4.74 score 183 scriptspecanproject
PEcAn.utils:PEcAn Functions Used for Ecological Forecasts and Reanalysis
The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PEcAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation.
Maintained by Rob Kooper. Last updated 2 days ago.
bayesiancyberinfrastructuredata-assimilationdata-scienceecosystem-modelecosystem-scienceforecastingmeta-analysisnational-science-foundationpecanplants
5.7 match 216 stars 10.92 score 218 scripts 35 dependentsrsetienne
DAISIE:Dynamical Assembly of Islands by Speciation, Immigration and Extinction
Simulates and computes the (maximum) likelihood of a dynamical model of island biota assembly through speciation, immigration and extinction. See Valente et al. (2015) <doi:10.1111/ele.12461>.
Maintained by Rampal S. Etienne. Last updated 1 months ago.
7.0 match 9 stars 8.59 score 55 scripts 1 dependentsrekyt
fdcoexist:Multi-Species Trait-Based Coexistence Model in Discrete time
A modified Beverton-Holt model used in the Denelle, Grenié et al. manuscript that expresses environmental filtering, limiting similarity and hierarchical competition explicitely in function of species traits. This package provides all the code necessary to rerun the analyses of the manuscript.
Maintained by Matthias Grenié. Last updated 2 years ago.
22.2 match 2.70 score 1 scriptspecanproject
PEcAn.MA:PEcAn Functions Used for Meta-Analysis
The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PECAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation. The PEcAn.MA package contains the functions used in the Bayesian meta-analysis of trait data.
Maintained by David LeBauer. Last updated 2 days ago.
bayesiancyberinfrastructuredata-assimilationdata-scienceecosystem-modelecosystem-scienceforecastingmeta-analysisnational-science-foundationpecanplantsjagscpp
6.0 match 216 stars 9.88 score 7 scripts 7 dependents
elaliberte
FD:Measuring Functional Diversity (FD) from Multiple Traits, and Other Tools for Functional Ecology
Computes different multidimensional FD indices. Implements a distance-based framework to measure FD that allows any number and type of functional traits, and can also consider species relative abundances. Also contains other useful tools for functional ecology.
Maintained by Etienne Laliberté. Last updated 1 years ago.
8.7 match 4 stars 6.54 score 586 scripts 15 dependents
adrientaudiere
cati:Community Assembly by Traits: Individuals and Beyond
Detect and quantify community assembly processes using trait values of individuals or populations, the T-statistics and other metrics, and dedicated null models.
Maintained by Adrien Taudiere. Last updated 4 months ago.
10.6 match 12 stars 5.33 score 15 scriptsbioc
metaCCA:Summary Statistics-Based Multivariate Meta-Analysis of Genome-Wide Association Studies Using Canonical Correlation Analysis
metaCCA performs multivariate analysis of a single or multiple GWAS based on univariate regression coefficients. It allows multivariate representation of both phenotype and genotype. metaCCA extends the statistical technique of canonical correlation analysis to the setting where original individual-level records are not available, and employs a covariance shrinkage algorithm to achieve robustness.
Maintained by Anna Cichonska. Last updated 5 months ago.
genomewideassociationsnpgeneticsregressionstatisticalmethodsoftware
13.2 match 4.26 score 5 scripts
danheck
TreeBUGS:Hierarchical Multinomial Processing Tree Modeling
User-friendly analysis of hierarchical multinomial processing tree (MPT) models that are often used in cognitive psychology. Implements the latent-trait MPT approach (Klauer, 2010) <DOI:10.1007/s11336-009-9141-0> and the beta-MPT approach (Smith & Batchelder, 2010) <DOI:10.1016/j.jmp.2009.06.007> to model heterogeneity of participants. MPT models are conveniently specified by an .eqn-file as used by other MPT software and data are provided by a .csv-file or directly in R. Models are either fitted by calling JAGS or by an MPT-tailored Gibbs sampler in C++ (only for nonhierarchical and beta MPT models). Provides tests of heterogeneity and MPT-tailored summaries and plotting functions. A detailed documentation is available in Heck, Arnold, & Arnold (2018) <DOI:10.3758/s13428-017-0869-7> and a tutorial on MPT modeling can be found in Schmidt, Erdfelder, & Heck (2023) <DOI:10.1037/met0000561>.
Maintained by Daniel W. Heck. Last updated 3 days ago.
6.8 match 12 stars 8.01 score 53 scripts 1 dependents
richfitz
diversitree: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.
Maintained by Richard G. FitzJohn. Last updated 6 months ago.
6.4 match 33 stars 8.51 score 524 scripts 4 dependents
carlosp-carmona
TPD:Methods for Measuring Functional Diversity Based on Trait Probability Density
Tools to calculate trait probability density functions (TPD) at any scale (e.g. populations, species, communities). TPD functions are used to compute several indices of functional diversity, as well as its partition across scales. These indices constitute a unified framework that incorporates the underlying probabilistic nature of trait distributions into uni- or multidimensional functional trait-based studies. See Carmona et al. (2016) <doi:10.1016/j.tree.2016.02.003> for further information.
Maintained by Carlos P. Carmona. Last updated 6 years ago.
15.9 match 2 stars 3.42 score 33 scripts
mpio-be
rangeMapper:A Platform for the Study of Macro-Ecology of Life History Traits
Tools for generation of (life-history) traits and diversity maps on hexagonal or square grids. Valcu et al.(2012) <doi:10.1111/j.1466-8238.2011.00739.x>.
Maintained by Mihai Valcu. Last updated 2 years ago.
assemblage-levelecologygloballife-history-traitsraster-cellspecies
10.0 match 8 stars 5.38 score 30 scripts
predictiveecology
LandR:Landscape Ecosystem Modelling in R
Utilities for 'LandR' suite of landscape simulation models. These models simulate forest vegetation dynamics based on LANDIS-II, and incorporate fire and insect disturbance, as well as other important ecological processes. Models are implemented as 'SpaDES' modules.
Maintained by Eliot J B McIntire. Last updated 3 days ago.
ecological-modellinglandscape-ecosystem-modellingspades
8.8 match 17 stars 6.07 score 12 scripts 4 dependents
kenaho1
asbio:A Collection of Statistical Tools for Biologists
Contains functions from: Aho, K. (2014) Foundational and Applied Statistics for Biologists using R. CRC/Taylor and Francis, Boca Raton, FL, ISBN: 978-1-4398-7338-0.
Maintained by Ken Aho. Last updated 2 months ago.
7.3 match 5 stars 7.32 score 310 scripts 3 dependents
smwindecker
mixchar:Mixture Model for the Deconvolution of Thermal Decay Curves
Deconvolution of thermal decay curves allows you to quantify proportions of biomass components in plant litter. Thermal decay curves derived from thermogravimetric analysis (TGA) are imported, modified, and then modelled in a three- or four- part mixture model using the Fraser-Suzuki function. The output is estimates for weights of pseudo-components corresponding to hemicellulose, cellulose, and lignin. For more information see: Müller-Hagedorn, M. and Bockhorn, H. (2007) <doi:10.1016/j.jaap.2006.12.008>, Órfão, J. J. M. and Figueiredo, J. L. (2001) <doi:10.1016/S0040-6031(01)00634-7>, and Yang, H. and Yan, R. and Chen, H. and Zheng, C. and Lee, D. H. and Liang, D. T. (2006) <doi:10.1021/ef0580117>.
Maintained by Saras Windecker. Last updated 2 years ago.
10.0 match 10 stars 5.26 score 18 scriptssinnweja
pleio:Pleiotropy Test for Multiple Traits on a Genetic Marker
Perform tests for pleiotropy of multiple traits of various variable types on genotypes for a genetic marker.
Maintained by Jason Sinnwell. Last updated 1 years ago.
17.1 match 3.00 score 7 scripts
akeyel
multirich:Calculate Multivariate Richness via UTC and sUTC
Functions to calculate Unique Trait Combinations (UTC) and scaled Unique Trait Combinations (sUTC) as measures of multivariate richness. The package can also calculate beta-diversity for trait richness and can partition this into nestedness-related and turnover components. The code will also calculate several measures of overlap. See Keyel and Wiegand (2016) <doi:10.1111/2041-210X.12558> for more details.
Maintained by Alexander Keyel. Last updated 4 years ago.
13.8 match 3.70 score 6 scripts
sizespectrum
mizer:Dynamic Multi-Species Size Spectrum Modelling
A set of classes and methods to set up and run multi-species, trait based and community size spectrum ecological models, focused on the marine environment.
Maintained by Gustav Delius. Last updated 2 months ago.
ecosystem-modelfish-population-dynamicsfisheriesfisheries-managementmarine-ecosystempopulation-dynamicssimulationsize-structurespecies-interactionstransport-equationcpp
5.3 match 38 stars 9.43 score 207 scripts
philchalmers
mirt:Multidimensional Item Response Theory
Analysis of discrete response data using unidimensional and multidimensional item analysis models under the Item Response Theory paradigm (Chalmers (2012) <doi:10.18637/jss.v048.i06>). Exploratory and confirmatory item factor analysis models are estimated with quadrature (EM) or stochastic (MHRM) methods. Confirmatory bi-factor and two-tier models are available for modeling item testlets using dimension reduction EM algorithms, while multiple group analyses and mixed effects designs are included for detecting differential item, bundle, and test functioning, and for modeling item and person covariates. Finally, latent class models such as the DINA, DINO, multidimensional latent class, mixture IRT models, and zero-inflated response models are supported, as well as a wide family of probabilistic unfolding models.
Maintained by Phil Chalmers. Last updated 10 days ago.
3.4 match 210 stars 14.98 score 2.5k scripts 40 dependents
brpetrucci
paleobuddy: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>.
Maintained by Bruno do Rosario Petrucci. Last updated 1 months ago.
evolutionmacroevolutionpaleobiologypaleontologyphylogenetics
10.1 match 6 stars 4.95 score 4 scripts
lamho86
phylolm: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.
Maintained by Lam Si Tung Ho. Last updated 4 months ago.
4.5 match 33 stars 10.79 score 318 scripts 14 dependents
flaviomoc
divraster:Diversity Metrics Calculations for Rasterized Data
Alpha and beta diversity for taxonomic (TD), functional (FD), and phylogenetic (PD) dimensions based on rasters. Spatial and temporal beta diversity can be partitioned into replacement and richness difference components. It also calculates standardized effect size for FD and PD alpha diversity and the average individual traits across multilayer rasters. The layers of the raster represent species, while the cells represent communities. Methods details can be found at Cardoso et al. 2022 <https://CRAN.R-project.org/package=BAT> and Heming et al. 2023 <https://CRAN.R-project.org/package=SESraster>.
Maintained by Flávio M. M. Mota. Last updated 7 months ago.
9.0 match 10 stars 5.30 score 7 scripts
thej022214
corHMM: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>.
Maintained by Jeremy Beaulieu. Last updated 27 days ago.
5.0 match 12 stars 9.48 score 422 scripts 2 dependentsbioc
PCAN:Phenotype Consensus ANalysis (PCAN)
Phenotypes comparison based on a pathway consensus approach. Assess the relationship between candidate genes and a set of phenotypes based on additional genes related to the candidate (e.g. Pathways or network neighbors).
Maintained by Matthew Page. Last updated 5 months ago.
annotationsequencinggeneticsfunctionalpredictionvariantannotationpathwaysnetwork
10.8 match 4.15 score 7 scripts
mmaechler
cluster:"Finding Groups in Data": Cluster Analysis Extended Rousseeuw et al.
Methods for Cluster analysis. Much extended the original from Peter Rousseeuw, Anja Struyf and Mia Hubert, based on Kaufman and Rousseeuw (1990) "Finding Groups in Data".
Maintained by Martin Maechler. Last updated 4 days ago.
3.8 match 3 stars 11.98 score 14k scripts 2.2k dependents
samuelbfernandes
simplePHENOTYPES:Simulation of Pleiotropic, Linked and Epistatic Phenotypes
The number of studies involving correlated traits and the availability of tools to handle this type of data has increased considerably in the last decade. With such a demand, we need tools for testing hypotheses related to single and multi-trait (correlated) phenotypes based on many genetic settings. Thus, we implemented various options for simulation of pleiotropy and Linkage Disequilibrium under additive, dominance and epistatic models. The simulation currently takes a marker data set as an input and then uses it for simulating multiple traits as described in Fernandes and Lipka (2020) <doi:10.1186/s12859-020-03804-y>.
Maintained by Samuel Fernandes. Last updated 3 years ago.
8.9 match 12 stars 4.95 score 15 scripts
fboehm
qtl2pleio:Testing Pleiotropy in Multiparental Populations
We implement an adaptation of Jiang & Zeng's (1995) <https://www.genetics.org/content/140/3/1111> likelihood ratio test for testing the null hypothesis of pleiotropy against the alternative hypothesis, two separate quantitative trait loci. The test differs from that in Jiang & Zeng (1995) <https://www.genetics.org/content/140/3/1111> and that in Tian et al. (2016) <doi:10.1534/genetics.115.183624> in that our test accommodates multiparental populations.
Maintained by Frederick J Boehm. Last updated 4 years ago.
multiparental-populationsquantitative-geneticsquantitative-traitcpp
9.9 match 5 stars 4.41 score 26 scripts
leef-uzh
LEEF.analysis:Access Functions, Tests and Basic Analysis of the RRD Data from the LEEF Project
Provides simple access functions to read data out of the sqlite RRD database. SQL queries can be configured in a yaml config file and used.
Maintained by Rainer M. Krug. Last updated 1 months ago.
17.8 match 2.44 score 23 scripts
geomorphr
geomorph: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.
Maintained by Dean Adams. Last updated 1 months ago.
3.6 match 76 stars 12.05 score 700 scripts 6 dependents
friendly
heplots:Visualizing Hypothesis Tests in Multivariate Linear Models
Provides HE plot and other functions for visualizing hypothesis tests in multivariate linear models. HE plots represent sums-of-squares-and-products matrices for linear hypotheses and for error using ellipses (in two dimensions) and ellipsoids (in three dimensions). The related 'candisc' package provides visualizations in a reduced-rank canonical discriminant space when there are more than a few response variables.
Maintained by Michael Friendly. Last updated 8 days ago.
linear-hypothesesmatricesmultivariate-linear-modelsplotrepeated-measure-designsvisualizing-hypothesis-tests
3.8 match 9 stars 11.49 score 1.1k scripts 7 dependents
jinghuazhao
gap:Genetic Analysis Package
As first reported [Zhao, J. H. 2007. "gap: Genetic Analysis Package". J Stat Soft 23(8):1-18. <doi:10.18637/jss.v023.i08>], it is designed as an integrated package for genetic data analysis of both population and family data. Currently, it contains functions for sample size calculations of both population-based and family-based designs, probability of familial disease aggregation, kinship calculation, statistics in linkage analysis, and association analysis involving genetic markers including haplotype analysis with or without environmental covariates. Over years, the package has been developed in-between many projects hence also in line with the name (gap).
Maintained by Jing Hua Zhao. Last updated 16 days ago.
3.5 match 12 stars 11.88 score 448 scripts 16 dependentshojsgaard
gRbase:A Package for Graphical Modelling in R
The 'gRbase' package provides graphical modelling features used by e.g. the packages 'gRain', 'gRim' and 'gRc'. 'gRbase' implements graph algorithms including (i) maximum cardinality search (for marked and unmarked graphs). (ii) moralization, (iii) triangulation, (iv) creation of junction tree. 'gRbase' facilitates array operations, 'gRbase' implements functions for testing for conditional independence. 'gRbase' illustrates how hierarchical log-linear models may be implemented and describes concept of graphical meta data. The facilities of the package are documented in the book by Højsgaard, Edwards and Lauritzen (2012, <doi:10.1007/978-1-4614-2299-0>) and in the paper by Dethlefsen and Højsgaard, (2005, <doi:10.18637/jss.v014.i17>). Please see 'citation("gRbase")' for citation details.
Maintained by Søren Højsgaard. Last updated 4 months ago.
4.5 match 3 stars 9.24 score 241 scripts 20 dependents
cristiancastiglione
sgdGMF:Estimation of Generalized Matrix Factorization Models via Stochastic Gradient Descent
Efficient framework to estimate high-dimensional generalized matrix factorization models using penalized maximum likelihood under a dispersion exponential family specification. Either deterministic and stochastic methods are implemented for the numerical maximization. In particular, the package implements the stochastic gradient descent algorithm with a block-wise mini-batch strategy to speed up the computations and an efficient adaptive learning rate schedule to stabilize the convergence. All the theoretical details can be found in Castiglione, Segers, Clement, Risso (2024, <https://arxiv.org/abs/2412.20509>). Other methods considered for the optimization are the alternated iterative re-weighted least squares and the quasi-Newton method with diagonal approximation of the Fisher information matrix discussed in Kidzinski, Hui, Warton, Hastie (2022, <http://jmlr.org/papers/v23/20-1104.html>).
Maintained by Cristian Castiglione. Last updated 11 days ago.
5.3 match 10 stars 7.75 score 108 scripts
kkholst
mets:Analysis of Multivariate Event Times
Implementation of various statistical models for multivariate event history data <doi:10.1007/s10985-013-9244-x>. Including multivariate cumulative incidence models <doi:10.1002/sim.6016>, and bivariate random effects probit models (Liability models) <doi:10.1016/j.csda.2015.01.014>. Modern methods for survival analysis, including regression modelling (Cox, Fine-Gray, Ghosh-Lin, Binomial regression) with fast computation of influence functions.
Maintained by Klaus K. Holst. Last updated 2 days ago.
multivariate-time-to-eventsurvival-analysistime-to-eventfortranopenblascpp
3.0 match 14 stars 13.47 score 236 scripts 42 dependents
frmunoz
ecolottery:Coalescent-Based Simulation of Ecological Communities
Coalescent-Based Simulation of Ecological Communities as proposed by Munoz et al. (2018) <doi:10.1111/2041-210X.12918>. The package includes a tool for estimating parameters of community assembly by using Approximate Bayesian Computation.
Maintained by François Munoz. Last updated 2 years ago.
6.4 match 15 stars 6.18 score 17 scripts 1 dependents
lukejharmon
geiger:Analysis of Evolutionary Diversification
Methods for fitting macroevolutionary models to phylogenetic trees Pennell (2014) <doi:10.1093/bioinformatics/btu181>.
Maintained by Luke Harmon. Last updated 2 years ago.
5.0 match 1 stars 7.84 score 2.3k scripts 28 dependents
covaruber
sommer:Solving Mixed Model Equations in R
Structural multivariate-univariate linear mixed model solver for estimation of multiple random effects with unknown variance-covariance structures (e.g., heterogeneous and unstructured) and known covariance among levels of random effects (e.g., pedigree and genomic relationship matrices) (Covarrubias-Pazaran, 2016 <doi:10.1371/journal.pone.0156744>; Maier et al., 2015 <doi:10.1016/j.ajhg.2014.12.006>; Jensen et al., 1997). REML estimates can be obtained using the Direct-Inversion Newton-Raphson and Direct-Inversion Average Information algorithms for the problems r x r (r being the number of records) or using the Henderson-based average information algorithm for the problem c x c (c being the number of coefficients to estimate). Spatial models can also be fitted using the two-dimensional spline functionality available.
Maintained by Giovanny Covarrubias-Pazaran. Last updated 21 days ago.
average-informationmixed-modelsrcpparmadilloopenblascppopenmp
3.1 match 43 stars 12.70 score 300 scripts 9 dependentsbioc
BioNERO:Biological Network Reconstruction Omnibus
BioNERO aims to integrate all aspects of biological network inference in a single package, including data preprocessing, exploratory analyses, network inference, and analyses for biological interpretations. BioNERO can be used to infer gene coexpression networks (GCNs) and gene regulatory networks (GRNs) from gene expression data. Additionally, it can be used to explore topological properties of protein-protein interaction (PPI) networks. GCN inference relies on the popular WGCNA algorithm. GRN inference is based on the "wisdom of the crowds" principle, which consists in inferring GRNs with multiple algorithms (here, CLR, GENIE3 and ARACNE) and calculating the average rank for each interaction pair. As all steps of network analyses are included in this package, BioNERO makes users avoid having to learn the syntaxes of several packages and how to communicate between them. Finally, users can also identify consensus modules across independent expression sets and calculate intra and interspecies module preservation statistics between different networks.
Maintained by Fabricio Almeida-Silva. Last updated 5 months ago.
softwaregeneexpressiongeneregulationsystemsbiologygraphandnetworkpreprocessingnetworknetworkinference
5.0 match 27 stars 7.78 score 50 scripts 1 dependentsbioc
GWENA:Pipeline for augmented co-expression analysis
The development of high-throughput sequencing led to increased use of co-expression analysis to go beyong single feature (i.e. gene) focus. We propose GWENA (Gene Whole co-Expression Network Analysis) , a tool designed to perform gene co-expression network analysis and explore the results in a single pipeline. It includes functional enrichment of modules of co-expressed genes, phenotypcal association, topological analysis and comparison of networks configuration between conditions.
Maintained by Gwenaëlle Lemoine. Last updated 5 months ago.
softwaregeneexpressionnetworkclusteringgraphandnetworkgenesetenrichmentpathwaysvisualizationrnaseqtranscriptomicsmrnamicroarraymicroarraynetworkenrichmentsequencinggoco-expressionenrichment-analysisgenenetwork-analysispipeline
6.7 match 24 stars 5.76 score 12 scripts
yulab-smu
TDbook:Companion Package for the Book "Data Integration, Manipulation and Visualization of Phylogenetic Trees" by Guangchuang Yu (2022, ISBN:9781032233574, doi:10.1201/9781003279242)
The companion package that provides all the datasets used in the book "Data Integration, Manipulation and Visualization of Phylogenetic Trees" by Guangchuang Yu (2022, ISBN:9781032233574, doi:10.1201/9781003279242).
Maintained by Guangchuang Yu. Last updated 3 years ago.
7.9 match 13 stars 4.88 score 59 scripts
darunabas
phyloregion:Biogeographic Regionalization and Macroecology
Computational infrastructure for biogeography, community ecology, and biodiversity conservation (Daru et al. 2020) <doi:10.1111/2041-210X.13478>. It is based on the methods described in Daru et al. (2020) <doi:10.1038/s41467-020-15921-6>. The original conceptual work is described in Daru et al. (2017) <doi:10.1016/j.tree.2017.08.013> on patterns and processes of biogeographical regionalization. Additionally, the package contains fast and efficient functions to compute more standard conservation measures such as phylogenetic diversity, phylogenetic endemism, evolutionary distinctiveness and global endangerment, as well as compositional turnover (e.g., beta diversity).
Maintained by Barnabas H. Daru. Last updated 5 months ago.
5.3 match 18 stars 7.21 score 50 scripts 1 dependentscran
BGLR:Bayesian Generalized Linear Regression
Bayesian Generalized Linear Regression.
Maintained by Paulino Perez Rodriguez. Last updated 5 months ago.
7.4 match 2 stars 5.18 score 5 dependentsmrcieu
TwoSampleMR:Two Sample MR Functions and Interface to MRC Integrative Epidemiology Unit OpenGWAS Database
A package for performing Mendelian randomization using GWAS summary data. It uses the IEU OpenGWAS database <https://gwas.mrcieu.ac.uk/> to automatically obtain data, and a wide range of methods to run the analysis.
Maintained by Gibran Hemani. Last updated 10 days ago.
3.3 match 467 stars 11.23 score 1.7k scripts 1 dependents
daijiang
phyr:Model Based Phylogenetic Analysis
A collection of functions to do model-based phylogenetic analysis. It includes functions to calculate community phylogenetic diversity, to estimate correlations among functional traits while accounting for phylogenetic relationships, and to fit phylogenetic generalized linear mixed models. The Bayesian phylogenetic generalized linear mixed models are fitted with the 'INLA' package (<https://www.r-inla.org>).
Maintained by Daijiang Li. Last updated 1 years ago.
bayesianglmminlaphylogenyspecies-distribution-modelingopenblascpp
4.3 match 31 stars 8.67 score 107 scripts 2 dependentsbioc
FamAgg:Pedigree Analysis and Familial Aggregation
Framework providing basic pedigree analysis and plotting utilities as well as a variety of methods to evaluate familial aggregation of traits in large pedigrees.
Maintained by Johannes Rainer. Last updated 5 months ago.
6.8 match 1 stars 5.26 score 5 scriptslcrawlab
smer:Sparse Marginal Epistasis Test
The Sparse Marginal Epistasis Test is a computationally efficient genetics method which detects statistical epistasis in complex traits; see Stamp et al. (2025, <doi:10.1101/2025.01.11.632557>) for details.
Maintained by Julian Stamp. Last updated 2 months ago.
genomewideassociationepistasisgeneticssnplinearmixedmodelcppepistasis-analysisepistatisgwasgwas-toolsmapitzlibcppopenmp
7.2 match 1 stars 4.95 score 8 scripts
willgearty
deeptime:Plotting Tools for Anyone Working in Deep Time
Extends the functionality of other plotting packages (notably 'ggplot2') to help facilitate the plotting of data over long time intervals, including, but not limited to, geological, evolutionary, and ecological data. The primary goal of 'deeptime' is to enable users to add highly customizable timescales to their visualizations. Other functions are also included to assist with other areas of deep time visualization.
Maintained by William Gearty. Last updated 3 months ago.
geologyggplot2paleontologyvisualization
3.3 match 92 stars 10.61 score 207 scripts 3 dependents
bartjanvanrossum
statgenQTLxT:Multi-Trait and Multi-Trial Genome Wide Association Studies
Fast multi-trait and multi-trail Genome Wide Association Studies (GWAS) following the method described in Zhou and Stephens. (2014), <doi:10.1038/nmeth.2848>. One of a series of statistical genetic packages for streamlining the analysis of typical plant breeding experiments developed by Biometris.
Maintained by Bart-Jan van Rossum. Last updated 1 years ago.
13.1 match 2.70 score 2 scripts
bwiernik
configural:Multivariate Profile Analysis
R functions for criterion profile analysis, Davison and Davenport (2002) <doi:10.1037/1082-989X.7.4.468> and meta-analytic criterion profile analysis, Wiernik, Wilmot, Davison, and Ones (2020) <doi:10.1037/met0000305>. Sensitivity analyses to aid in interpreting criterion profile analysis results are also included.
Maintained by Brenton M. Wiernik. Last updated 12 months ago.
8.7 match 4 stars 3.96 score 23 scripts
neonscience
neonOS:Basic Data Wrangling for NEON Observational Data
NEON observational data are provided via the NEON Data Portal <https://www.neonscience.org> and NEON API, and can be downloaded and reformatted by the 'neonUtilities' package. NEON observational data (human-observed measurements, and analyses derived from human-collected samples, such as tree diameters and algal chemistry) are published in a format consisting of one or more tabular data files. This package provides tools for performing common operations on NEON observational data, including checking for duplicates and joining tables.
Maintained by Claire Lunch. Last updated 9 months ago.
6.6 match 2 stars 5.02 score 70 scripts 1 dependents
tpook92
MoBPS:Modular Breeding Program Simulator
Framework for the simulation framework for the simulation of complex breeding programs and compare their economic and genetic impact. The package is also used as the background simulator for our a web-based interface <http:www.mobps.de>. Associated publication: Pook et al. (2020) <doi:10.1534/g3.120.401193>.
Maintained by Torsten Pook. Last updated 3 years ago.
13.9 match 2.35 score 45 scripts
rqtl
qtl2:Quantitative Trait Locus Mapping in Experimental Crosses
Provides a set of tools to perform quantitative trait locus (QTL) analysis in experimental crosses. It is a reimplementation of the 'R/qtl' package to better handle high-dimensional data and complex cross designs. Broman et al. (2019) <doi:10.1534/genetics.118.301595>.
Maintained by Karl W Broman. Last updated 8 days ago.
3.4 match 34 stars 9.48 score 1.1k scripts 5 dependents
caetanods
ratematrix:Bayesian Estimation of the Evolutionary Rate Matrix
The Evolutionary Rate Matrix is a variance-covariance matrix which describes both the rates of trait evolution and the evolutionary correlation among multiple traits. This package has functions to estimate these parameters using Bayesian MCMC. It is possible to test if the pattern of evolutionary correlations among traits has changed between predictive regimes painted along the branches of the phylogenetic tree. Regimes can be created a priori or estimated as part of the MCMC under a joint estimation approach. The package has functions to run MCMC chains, plot results, evaluate convergence, and summarize posterior distributions.
Maintained by Daniel Caetano. Last updated 2 years ago.
5.5 match 10 stars 5.91 score 18 scripts 1 dependentspecanproject
PEcAn.workflow:PEcAn Functions Used for Ecological Forecasts and Reanalysis
The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PEcAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation. This package provides workhorse functions that can be used to run the major steps of a PEcAn analysis.
Maintained by David LeBauer. Last updated 2 days ago.
bayesiancyberinfrastructuredata-assimilationdata-scienceecosystem-modelecosystem-scienceforecastingmeta-analysisnational-science-foundationpecanplantsjagscpp
3.6 match 216 stars 8.82 score 15 scripts 4 dependentsbioc
BUS:Gene network reconstruction
This package can be used to compute associations among genes (gene-networks) or between genes and some external traits (i.e. clinical).
Maintained by Yuanhua Liu. Last updated 5 months ago.
8.1 match 3.90 score 6 scripts
jakobraymaekers
cellWise:Analyzing Data with Cellwise Outliers
Tools for detecting cellwise outliers and robust methods to analyze data which may contain them. Contains the implementation of the algorithms described in Rousseeuw and Van den Bossche (2018) <doi:10.1080/00401706.2017.1340909> (open access) Hubert et al. (2019) <doi:10.1080/00401706.2018.1562989> (open access), Raymaekers and Rousseeuw (2021) <doi:10.1080/00401706.2019.1677270> (open access), Raymaekers and Rousseeuw (2021) <doi:10.1007/s10994-021-05960-5> (open access), Raymaekers and Rousseeuw (2021) <doi:10.52933/jdssv.v1i3.18> (open access), Raymaekers and Rousseeuw (2022) <arXiv:2207.13493> (open access) Rousseeuw (2022) <doi:10.1016/j.ecosta.2023.01.007> (open access). Examples can be found in the vignettes: "DDC_examples", "MacroPCA_examples", "wrap_examples", "transfo_examples", "DI_examples", "cellMCD_examples" , "Correspondence_analysis_examples", and "cellwise_weights_examples".
Maintained by Jakob Raymaekers. Last updated 1 years ago.
5.2 match 2 stars 6.06 score 54 scripts 16 dependents
grealesm
RapidoPGS:A Fast and Light Package to Compute Polygenic Risk Scores
Quickly computes polygenic scores from GWAS summary statistics of either case-control or quantitative traits without parameter tuning. Reales,G., Vigorito, E., Kelemen,M., Wallace,C. (2021) <doi:10.1101/2020.07.24.220392> "RápidoPGS: A rapid polygenic score calculator for summary GWAS data without a test dataset".
Maintained by Guillermo Reales. Last updated 25 days ago.
5.6 match 13 stars 5.59 score 9 scripts
mpi-bgc-functional-biogeography
rtry:Preprocessing Plant Trait Data
Designed to support the application of plant trait data providing easy applicable functions for the basic steps of data preprocessing, e.g. data import, data exploration, selection of columns and rows, excluding trait data according to different attributes, geocoding, long- to wide-table transformation, and data export. 'rtry' was initially developed as part of the TRY R project to preprocess trait data received via the TRY database.
Maintained by Olee Hoi Ying Lam. Last updated 2 years ago.
5.3 match 24 stars 5.94 score 24 scriptsbiometris
statgenGWAS:Genome Wide Association Studies
Fast single trait Genome Wide Association Studies (GWAS) following the method described in Kang et al. (2010), <doi:10.1038/ng.548>. One of a series of statistical genetic packages for streamlining the analysis of typical plant breeding experiments developed by Biometris.
Maintained by Bart-Jan van Rossum. Last updated 4 months ago.
5.1 match 14 stars 6.14 score 15 scripts 3 dependents
geco-bern
rsofun:The P-Model and BiomeE Modelling Framework
Implements the Simulating Optimal FUNctioning framework for site-scale simulations of ecosystem processes, including model calibration. It contains 'Fortran 90' modules for the P-model (Stocker et al. (2020) <doi:10.5194/gmd-13-1545-2020>), SPLASH (Davis et al. (2017) <doi:10.5194/gmd-10-689-2017>) and BiomeE (Weng et al. (2015) <doi:10.5194/bg-12-2655-2015>).
Maintained by Benjamin Stocker. Last updated 13 days ago.
dgvmgrowthmodelingp-modelsimulationvegetation-dynamicsfortran
3.4 match 26 stars 8.77 score 119 scripts
pbastide
PhylogeneticEM:Automatic Shift Detection using a Phylogenetic EM
Implementation of the automatic shift detection method for Brownian Motion (BM) or Ornstein–Uhlenbeck (OU) models of trait evolution on phylogenies. Some tools to handle equivalent shifts configurations are also available. See Bastide et al. (2017) <doi:10.1111/rssb.12206> and Bastide et al. (2018) <doi:10.1093/sysbio/syy005>.
Maintained by Paul Bastide. Last updated 30 days ago.
4.3 match 16 stars 6.96 score 47 scripts
bio-services
LinkageMapView:Plot Linkage Group Maps with Quantitative Trait Loci
Produces high resolution, publication ready linkage maps and quantitative trait loci maps. Input can be output from 'R/qtl', simple text or comma delimited files. Output is currently a portable document file.
Maintained by Steven Blanchard. Last updated 5 years ago.
4.6 match 9 stars 6.55 score 79 scripts
emitanaka
edibble:Encapsulating Elements of Experimental Design
A system to facilitate designing comparative (and non-comparative) experiments using the grammar of experimental designs <https://emitanaka.org/edibble-book/>. An experimental design is treated as an intermediate, mutable object that is built progressively by fundamental experimental components like units, treatments, and their relation. The system aids in experimental planning, management and workflow.
Maintained by Emi Tanaka. Last updated 4 months ago.
4.0 match 217 stars 7.43 score 62 scripts
markustjansen
ThurMod:Thurstonian CFA and Thurstonian IRT Modeling
Fit Thurstonian forced-choice models (CFA (simple and factor) and IRT) in R. This package allows for the analysis of item response modeling (IRT) as well as confirmatory factor analysis (CFA) in the Thurstonian framework. Currently, estimation can be performed by 'Mplus' and 'lavaan'. References: Brown & Maydeu-Olivares (2011) <doi:10.1177/0013164410375112>; Jansen, M. T., & Schulze, R. (in review). The Thurstonian linked block design: Improving Thurstonian modeling for paired comparison and ranking data.; Maydeu-Olivares & Böckenholt (2005) <doi:10.1037/1082-989X.10.3.285>.
Maintained by Markus Thomas Jansen. Last updated 1 years ago.
9.9 match 3.00 score 2 scripts
jarrodhadfield
MCMCglmm: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.).
Maintained by Jarrod Hadfield. Last updated 3 months ago.
3.3 match 2 stars 8.83 score 1.2k scripts 13 dependents
jjustison
SiPhyNetwork:A Phylogenetic Simulator for Reticulate Evolution
A simulator for reticulate evolution under a birth-death-hybridization process. Here the birth-death process is extended to consider reticulate Evolution by allowing hybridization events to occur. The general purpose simulator allows the modeling of three different reticulate patterns: lineage generative hybridization, lineage neutral hybridization, and lineage degenerative hybridization. Users can also specify hybridization events to be dependent on a trait value or genetic distance. We also extend some phylogenetic tree utility and plotting functions for networks. We allow two different stopping conditions: simulated to a fixed time or number of taxa. When simulating to a fixed number of taxa, the user can simulate under the Generalized Sampling Approach that properly simulates phylogenies when assuming a uniform prior on the root age.
Maintained by Joshua Justison. Last updated 6 months ago.
5.5 match 11 stars 5.25 score 16 scripts
cajoterbraak
TraitEnvMLMWA:Weighted Averaging (WA) and Multi-Level Methods (MLM) for Trait-Environment Association in Functional and Community Ecology
This package grew out of the paper New robust weighted averaging- and model-based methods for assessing trait-environment relationships (Methods in Ecology and Evolution). The model-based methods are GLMMs, here called multi-level models (MLM), of which the novel MLM3 outperforms all existing methods. MLM3 has up to 30% more power, but the WA-methods are 500 times faster than MLM3. The main function for WA-methods is CWMSNC_regressions. The main functions for MLM3 are make_obj_for_traitenv, expand4glmm and MLM3_p_max.
Maintained by Cajo ter Braak. Last updated 2 years ago.
16.4 match 1.70 score
hckiang
glinvci:Phylogenetic Comparative Methods with Uncertainty Estimates
A framework for analytically computing the asymptotic confidence intervals and maximum-likelihood estimates of a class of continuous-time Gaussian branching processes defined by Mitov V, Bartoszek K, Asimomitis G, Stadler T (2019) <doi:10.1016/j.tpb.2019.11.005>. The class of model includes the widely used Ornstein-Uhlenbeck and Brownian motion branching processes. The framework is designed to be flexible enough so that the users can easily specify their own sub-models, or re-parameterizations, and obtain the maximum-likelihood estimates and confidence intervals of their own custom models.
Maintained by Woodrow Kiang. Last updated 11 months ago.
7.0 match 4.00 score 5 scriptscovaruber
evola:Evolutionary Algorithm
Runs a genetic algorithm using the 'AlphaSimR' machinery <doi:10.1093/g3journal/jkaa017> and the coalescent simulator 'MaCS' <doi:10.1101/gr.083634.108>.
Maintained by Giovanny Covarrubias-Pazaran. Last updated 5 days ago.
6.5 match 1 stars 4.23 score 3 scripts
hturner
BradleyTerry2:Bradley-Terry Models
Specify and fit the Bradley-Terry model, including structured versions in which the parameters are related to explanatory variables through a linear predictor and versions with contest-specific effects, such as a home advantage.
Maintained by Heather Turner. Last updated 6 years ago.
bradley-terry-modelspaired-comparisonsstatistical-models
3.4 match 20 stars 7.97 score 172 scripts 1 dependentsbioc
ASGSCA:Association Studies for multiple SNPs and multiple traits using Generalized Structured Equation Models
The package provides tools to model and test the association between multiple genotypes and multiple traits, taking into account the prior biological knowledge. Genes, and clinical pathways are incorporated in the model as latent variables. The method is based on Generalized Structured Component Analysis (GSCA).
Maintained by Hela Romdhani. Last updated 5 months ago.
8.1 match 3.30 score 3 scripts
nandp1
gpbStat:Comprehensive Statistical Analysis of Plant Breeding Experiments
Performs statistical data analysis of various Plant Breeding experiments. Contains functions for Line by Tester analysis as per Arunachalam, V.(1974) <http://repository.ias.ac.in/89299/> and Diallel analysis as per Griffing, B. (1956) <https://www.publish.csiro.au/bi/pdf/BI9560463>.
Maintained by Nandan Patil. Last updated 4 months ago.
biometricsgeneticsplantbreeding
4.4 match 3 stars 6.08 score 27 scripts
lan
MTAR:Multi-Trait Analysis of Rare-Variant Association Study
Perform multi-trait rare-variant association tests using the summary statistics and adjust for possible sample overlap. Package is based on "Multi-Trait Analysis of Rare-Variant Association Summary Statistics using MTAR" by Luo, L., Shen, J., Zhang, H., Chhibber, A. Mehrotra, D.V., Tang, Z., 2019 (submitted).
Maintained by Lan Luo. Last updated 5 years ago.
13.2 match 2.00 score 7 scripts
biometry
tapnet:Trait Matching and Abundance for Predicting Bipartite Networks
Functions to produce, fit and predict from bipartite networks with abundance, trait and phylogenetic information. Its methods are described in detail in Benadi, G., Dormann, C.F., Fruend, J., Stephan, R. & Vazquez, D.P. (2021) Quantitative prediction of interactions in bipartite networks based on traits, abundances, and phylogeny. The American Naturalist, in press.
Maintained by Carsten Dormann. Last updated 6 months ago.
7.1 match 1 stars 3.70 score 2 scripts
gilles-didier
cauphy:Trait Evolution on Phylogenies Using the Cauchy Process
The Cauchy Process can model pulsed continuous trait evolution on phylogenies. The likelihood is tractable, and is used for parameter inference and ancestral trait reconstruction. See Bastide and Didier (2023) <doi:10.1093/sysbio/syad053>.
Maintained by Paul Bastide. Last updated 6 months ago.
7.1 match 1 stars 3.70 score 4 scripts
macroecology
letsR:Data Handling and Analysis in Macroecology
Handling, processing, and analyzing geographic data on species' distributions and environmental variables. Read Vilela & Villalobos (2015) <doi:10.1111/2041-210X.12401> for details.
Maintained by Bruno Vilela. Last updated 2 months ago.
2.9 match 29 stars 8.87 score 104 scripts
leahfeuerstahler
flexmet:Flexible Latent Trait Metrics using the Filtered Monotonic Polynomial Item Response Model
Application of the filtered monotonic polynomial (FMP) item response model to flexibly fit item response models. The package includes tools that allow the item response model to be build on any monotonic transformation of the latent trait metric, as described by Feuerstahler (2019) <doi:10.1007/s11336-018-9642-9>.
Maintained by Leah Feuerstahler. Last updated 4 years ago.
8.1 match 1 stars 3.18 score 15 scriptsbioc
MICSQTL:MICSQTL (Multi-omic deconvolution, Integration and Cell-type-specific Quantitative Trait Loci)
Our pipeline, MICSQTL, utilizes scRNA-seq reference and bulk transcriptomes to estimate cellular composition in the matched bulk proteomes. The expression of genes and proteins at either bulk level or cell type level can be integrated by Angle-based Joint and Individual Variation Explained (AJIVE) framework. Meanwhile, MICSQTL can perform cell-type-specic quantitative trait loci (QTL) mapping to proteins or transcripts based on the input of bulk expression data and the estimated cellular composition per molecule type, without the need for single cell sequencing. We use matched transcriptome-proteome from human brain frontal cortex tissue samples to demonstrate the input and output of our tool.
Maintained by Qian Li. Last updated 5 months ago.
geneexpressiongeneticsproteomicsrnaseqsequencingsinglecellsoftwarevisualizationcellbasedassayscoverage
6.0 match 4.30 score 3 scripts
kmburkett
hapassoc:Inference of Trait Associations with SNP Haplotypes and Other Attributes using the EM Algorithm
The following R functions are used for inference of trait associations with haplotypes and other covariates in generalized linear models. The functions are developed primarily for data collected in cohort or cross-sectional studies. They can accommodate uncertain haplotype phase and handle missing genotypes at some SNPs.
Maintained by K. Burkett. Last updated 3 years ago.
8.5 match 2.98 score 16 scripts
helenkettle
microPop:Process-Based Modelling of Microbial Populations
Modelling interacting microbial populations - example applications include human gut microbiota, rumen microbiota and phytoplankton. Solves a system of ordinary differential equations to simulate microbial growth and resource uptake over time. This version contains network visualisation functions.
Maintained by Helen Kettle. Last updated 3 years ago.
9.6 match 2.64 score 11 scriptsropensci
taxlist:Handling Taxonomic Lists
Handling taxonomic lists through objects of class 'taxlist'. This package provides functions to import species lists from 'Turboveg' (<https://www.synbiosys.alterra.nl/turboveg/>) and the possibility to create backups from resulting R-objects. Also quick displays are implemented as summary-methods.
Maintained by Miguel Alvarez. Last updated 6 months ago.
3.6 match 12 stars 7.07 score 81 scripts 2 dependents
rdinnager
phyf:Phylogenetic Flow Objects for Easy Manipulation and Modelling of Data on Phylogenetic Trees and Graphs
The {phyf} package implements a tibble and vctrs based object for storing phylogenetic trees along with data. It is fast and flexible and directly produces data structures useful for phylogenetic modelling in the {fibre} package.
Maintained by Russell Dinnage. Last updated 7 months ago.
6.0 match 1 stars 4.20 score 53 scripts 1 dependents
kingaa
ouch:Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses
Fit and compare Ornstein-Uhlenbeck models for evolution along a phylogenetic tree.
Maintained by Aaron A. King. Last updated 4 months ago.
adaptive-regimebrownian-motionornstein-uhlenbeckornstein-uhlenbeck-modelsouchphylogenetic-comparative-hypothesesphylogenetic-comparative-methodsphylogenetic-datareact
3.7 match 15 stars 6.87 score 68 scripts 4 dependentsropensci
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.
Maintained by Cristian Roman-Palacios. Last updated 4 years ago.
4.9 match 7 stars 5.12 score 25 scripts
psoerensen
qgg:Statistical Tools for Quantitative Genetic Analyses
Provides an infrastructure for efficient processing of large-scale genetic and phenotypic data including core functions for: 1) fitting linear mixed models, 2) constructing marker-based genomic relationship matrices, 3) estimating genetic parameters (heritability and correlation), 4) performing genomic prediction and genetic risk profiling, and 5) single or multi-marker association analyses. Rohde et al. (2019) <doi:10.1101/503631>.
Maintained by Peter Soerensen. Last updated 18 hours ago.
3.5 match 36 stars 6.98 score 47 scripts
aravind-j
augmentedRCBD:Analysis of Augmented Randomised Complete Block Designs
Functions for analysis of data generated from experiments in augmented randomised complete block design according to Federer, W.T. (1961) <doi:10.2307/2527837>. Computes analysis of variance, adjusted means, descriptive statistics, genetic variability statistics etc. Further includes data visualization and report generation functions.
Maintained by J. Aravind. Last updated 5 months ago.
augmented-blockaugmented-designaugmented-rcbd
4.1 match 7 stars 5.94 score 21 scripts
agrdatasci
gosset:Tools for Data Analysis in Experimental Agriculture
Methods to analyse experimental agriculture data, from data synthesis to model selection and visualisation. The package is named after W.S. Gosset aka ‘Student’, a pioneer of modern statistics in small sample experimental design and analysis.
Maintained by Kauê de Sousa. Last updated 3 months ago.
experimental-designrankings-data
3.8 match 6 stars 6.44 score 23 scripts
sammo3182
drhutools:Political Science Academic Research Gears
Using these tools to simplify the research process of political science and other social sciences. The current version can create folder system for academic project in political science, calculate psychological trait scores, visualize experimental and spatial data, and set up color-blind palette, functions used in academic research of political psychology or political science in general.
Maintained by Yue Hu. Last updated 3 months ago.
5.4 match 2 stars 4.45 score 3 scripts
matthewwolak
nadiv:(Non)Additive Genetic Relatedness Matrices
Constructs (non)additive genetic relationship matrices, and their inverses, from a pedigree to be used in linear mixed effect models (A.K.A. the 'animal model'). Also includes other functions to facilitate the use of animal models. Some functions have been created to be used in conjunction with the R package 'asreml' for the 'ASReml' software, which can be obtained upon purchase from 'VSN' international (<https://vsni.co.uk/software/asreml>).
Maintained by Matthew Wolak. Last updated 10 months ago.
3.3 match 20 stars 7.13 score 151 scripts 3 dependentscran
IDmeasurer:Assessment of Individual Identity in Animal Signals
Provides tools for assessment and quantification of individual identity information in animal signals. This package accompanies a research article by Linhart et al. (2019) <doi:10.1101/546143>: "Measuring individual identity information in animal signals: Overview and performance of available identity metrics".
Maintained by Pavel Linhart. Last updated 6 years ago.
8.8 match 2.70 score 4 scripts
rmgpanw
gtexr:Query the GTEx Portal API
A convenient R interface to the Genotype-Tissue Expression (GTEx) Portal API. For more information on the API, see <https://gtexportal.org/api/v2/redoc>.
Maintained by Alasdair Warwick. Last updated 6 months ago.
api-wrapperbioinformaticseqtlgtexsqtl
3.6 match 5 stars 6.41 score 5 scripts
pnovack-gottshall
ecospace:Simulating Community Assembly and Ecological Diversification Using Ecospace Frameworks
Implements stochastic simulations of community assembly (ecological diversification) using customizable ecospace frameworks (functional trait spaces). Provides a wrapper to calculate common ecological disparity and functional ecology statistical dynamics as a function of species richness. Functions are written so they will work in a parallel-computing environment.
Maintained by Phil Novack-Gottshall. Last updated 5 years ago.
5.1 match 5 stars 4.51 score 13 scripts
blasbenito
virtualPollen:Simulating Pollen Curves from Virtual Taxa with Different Life and Niche Traits
Tools to generate virtual environmental drivers with a given temporal autocorrelation, and to simulate pollen curves at annual resolution over millennial time-scales based on these drivers and virtual taxa with different life traits and niche features. It also provides the means to simulate quasi-realistic pollen-data conditions by applying simulated accumulation rates and given depth intervals between consecutive samples.
Maintained by Blas M. Benito. Last updated 3 years ago.
5.0 match 5 stars 4.40 score 5 scriptsramiromagno
quincunx:REST API Client for the 'PGS' Catalog
Programmatic access to the 'PGS' Catalog. This package provides easy access to 'PGS' Catalog data by accessing the REST API <https://www.pgscatalog.org/rest/>.
Maintained by Ramiro Magno. Last updated 3 years ago.
ebigwaspolygenic-risk-scorespolygenic-scores
7.1 match 14 stars 3.10 score 18 scripts
azizka
conserveR:Identifying Conservation Prioritization Methods Based on Data Availability
Helping biologists to choose the most suitable approach to link their research to conservation. After answering few questions on the data available, geographic and taxonomic scope, 'conserveR' ranks existing methods for conservation prioritization and systematic conservation planning by suitability. The methods data base of 'conserveR' contains 133 methods for conservation prioritization based on a systematic review of > 12,000 scientific publications from the fields of spatial conservation prioritization, systematic conservation planning, biogeography and ecology.
Maintained by Alexander Zizka. Last updated 4 years ago.
6.0 match 8 stars 3.60 score
kopperud
slouch:Stochastic Linear Ornstein-Uhlenbeck Comparative Hypotheses
An implementation of a phylogenetic comparative method. It can fit univariate among-species Ornstein-Uhlenbeck models of phenotypic trait evolution, where the trait evolves towards a primary optimum. The optimum can be modelled as a single parameter, as multiple discrete regimes on the phylogenetic tree, and/or with continuous covariates. See also Hansen (1997) <doi:10.2307/2411186>, Butler & King (2004) <doi:10.1086/426002>, Hansen et al. (2008) <doi:10.1111/j.1558-5646.2008.00412.x>.
Maintained by Bjørn Tore Kopperud. Last updated 1 years ago.
4.2 match 2 stars 5.12 score 44 scripts 1 dependents
florianjansen
vegdata:Access Vegetation Databases and Treat Taxonomy
Handling of vegetation data from different sources ( Turboveg 2.0 <https://www.synbiosys.alterra.nl/turboveg/>; the German national repository <https://www.vegetweb.de> and others. Taxonomic harmonization (given appropriate taxonomic lists, e.g. the German taxonomic standard list "GermanSL", <https://germansl.infinitenature.org>).
Maintained by Florian Jansen. Last updated 1 years ago.
5.6 match 2 stars 3.84 score 38 scripts 3 dependentscran
comsimitv:Flexible Framework for Simulating Community Assembly
Flexible framework for trait-based simulation of community assembly, where components could be replaced by user-defined function and that allows variation of traits within species.
Maintained by Zoltan Botta-Dukat. Last updated 4 years ago.
10.7 match 2.00 score 3 scripts
biologicalrecordscentre
rYoutheria:Access to the YouTheria Mammal Trait Database
A programmatic interface to web-services of YouTheria. YouTheria is an online database of mammalian trait data <http://www.utheria.org.uk/>.
Maintained by Tom August. Last updated 6 years ago.
5.3 match 2 stars 4.00 score 10 scripts
joe-wayman
avotrex:A Global Dataset of Anthropogenic Extinct Birds and their Traits: Phylogeny Builder
Grafts the extinct bird species from the 'Avotrex' database (Sayol et al., in review) on to the 'BirdTree' phylogenies <https://birdtree.org>, using a set of different commands.
Maintained by Joseph Wayman. Last updated 7 months ago.
4.4 match 4.74 score 8 scripts
frederic-santos
AnthropMMD:An R Package for the Mean Measure of Divergence (MMD)
Offers a graphical user interface for the calculation of the mean measure of divergence, with facilities for trait selection and graphical representations <doi:10.1002/ajpa.23336>.
Maintained by Frédéric Santos. Last updated 1 years ago.
5.4 match 3.90 score 16 scripts
klvoje
evoTS:Analyses of Evolutionary Time-Series
Facilitates univariate and multivariate analysis of evolutionary sequences of phenotypic change. The package extends the modeling framework available in the 'paleoTS' package. Please see <https://klvoje.github.io/evoTS/index.html> for information about the package and the implemented models.
Maintained by Kjetil Lysne Voje. Last updated 9 months ago.
4.9 match 1 stars 4.26 score 184 scripts
zankrut20
selection.index:Analysis of Selection Index in Plant Breeding
The aim of most plant breeding programmes is simultaneous improvement of several characters. An objective method involving simultaneous selection for several attributes then becomes necessary. It has been recognised that most rapid improvements in the economic value is expected from selection applied simultaneously to all the characters which determine the economic value of a plant, and appropriate assigned weights to each character according to their economic importance, heritability and correlations between characters. So the selection for economic value is a complex matter. If the component characters are combined together into an index in such a way that when selection is applied to the index, as if index is the character to be improved, most rapid improvement of economic value is expected. Such an index was first proposed by Smith (1937 <doi:10.1111/j.1469-1809.1936.tb02143.x>) based on the Fisher's (1936 <doi:10.1111/j.1469-1809.1936.tb02137.x>) "discriminant function" Dabholkar (1999 <https://books.google.co.in/books?id=mlFtumAXQ0oC&lpg=PA4&ots=Xgxp1qLuxS&dq=elements%20of%20biometrical%20genetics&lr&pg=PP1#v=onepage&q&f=false>). In this package selection index is calculated based on the Smith (1937) selection index method.
Maintained by Zankrut Goyani. Last updated 5 months ago.
agricultureanimal-scienceplant-breedingrstudioselection-indexselection-indicessmith-selection-index
5.1 match 2 stars 4.00 score 5 scripts
jimclarkatduke
gjam:Generalized Joint Attribute Modeling
Analyzes joint attribute data (e.g., species abundance) that are combinations of continuous and discrete data with Gibbs sampling. Full model and computation details are described in Clark et al. (2018) <doi:10.1002/ecm.1241>.
Maintained by James S. Clark. Last updated 3 years ago.
6.4 match 3.18 score 150 scriptscarlosp-carmona
funspace:Creating and Representing Functional Trait Spaces
Estimation of functional spaces based on traits of organisms. The package includes functions to impute missing trait values (with or without considering phylogenetic information), and to create, represent and analyse two dimensional functional spaces based on principal components analysis, other ordination methods, or raw traits. It also allows for mapping a third variable onto the functional space. See 'Carmona et al. (2021)' <doi:10.1038/s41586-021-03871-y>, 'Puglielli et al. (2021)' <doi:10.1111/nph.16952>, 'Carmona et al. (2021)' <doi:10.1126/sciadv.abf2675>, 'Carmona et al. (2019)' <doi:10.1002/ecy.2876> for more information.
Maintained by Carlos P. Carmona. Last updated 9 months ago.
14.6 match 2 stars 1.38 score 12 scripts
raydanner
SongEvo:An Individual-Based Model of Bird Song Evolution
Simulates the cultural evolution of quantitative traits of bird song. 'SongEvo' is an individual- (agent-) based model. 'SongEvo' is spatially-explicit and can be parameterized with, and tested against, measured song data. Functions are available for model implementation, sensitivity analyses, parameter optimization, model validation, and hypothesis testing.
Maintained by Raymond Danner. Last updated 5 years ago.
4.4 match 2 stars 4.51 score 16 scripts
crwerner
FieldSimR:Simulation of Plot Errors and Phenotypes in Plant Breeding Field Trials
Simulates plot data in multi-environment field trials with one or more traits. Its core function generates plot errors that capture spatial trend, random error (noise), and extraneous variation, which are combined at a user-defined ratio. Phenotypes can be generated by combining the plot errors with simulated genetic values that capture genotype-by-environment (GxE) interaction using wrapper functions for the R package `AlphaSimR`.
Maintained by Christian Werner. Last updated 2 days ago.
2.8 match 9 stars 7.13 score 62 scripts
mbant
BayesSUR:Bayesian Seemingly Unrelated Regression Models in High-Dimensional Settings
Bayesian seemingly unrelated regression with general variable selection and dense/sparse covariance matrix. The sparse seemingly unrelated regression is described in Bottolo et al. (2021) <doi:10.1111/rssc.12490>, the software paper is in Zhao et al. (2021) <doi:10.18637/jss.v100.i11>, and the model with random effects is described in Zhao et al. (2024) <doi:10.1093/jrsssc/qlad102>.
Maintained by Zhi Zhao. Last updated 7 months ago.
3.3 match 8 stars 6.05 score 3 scripts
bjoelle
FossilSim:Simulation and Plots for Fossil and Taxonomy Data
Simulating and plotting taxonomy and fossil data on phylogenetic trees under mechanistic models of speciation, preservation and sampling.
Maintained by Joelle Barido-Sottani. Last updated 5 months ago.
3.8 match 1 stars 5.24 score 65 scripts 1 dependentstguillerme
dispRity: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.
Maintained by Thomas Guillerme. Last updated 2 days ago.
disparityecologymultidimensionalitypalaeobiology
2.3 match 26 stars 8.69 score 220 scripts 1 dependentsbioc
ggtreeSpace:Visualizing Phylomorphospaces using 'ggtree'
This package is a comprehensive visualization tool specifically designed for exploring phylomorphospace. It not only simplifies the process of generating phylomorphospace, but also enhances it with the capability to add graphic layers to the plot with grammar of graphics to create fully annotated phylomorphospaces. It also provide some utilities to help interpret evolutionary patterns.
Maintained by Guangchuang Yu. Last updated 5 months ago.
annotationvisualizationphylogeneticssoftware
3.3 match 5 stars 5.86 score 12 scripts
frareb
devRate:Quantify the Relationship Between Development Rate and Temperature in Ectotherms
A set of functions to quantify the relationship between development rate and temperature and to build phenological models. The package comprises a set of models and estimated parameters borrowed from a literature review in ectotherms. The methods and literature review are described in Rebaudo et al. (2018) <doi:10.1111/2041-210X.12935>, Rebaudo and Rabhi (2018) <doi:10.1111/eea.12693>, and Regnier et al. (2021) <doi:10.1093/ee/nvab115>. An example can be found in Rebaudo et al. (2017) <doi:10.1007/s13355-017-0480-5>.
Maintained by Francois Rebaudo. Last updated 2 years ago.
3.7 match 3 stars 5.31 score 15 scripts
fmichonneau
phylobase:Base Package for Phylogenetic Structures and Comparative Data
Provides a base S4 class for comparative methods, incorporating one or more trees and trait data.
Maintained by Francois Michonneau. Last updated 1 years ago.
1.7 match 18 stars 11.14 score 394 scripts 18 dependents
tgouhier
synchrony:Methods for Computing Spatial, Temporal, and Spatiotemporal Statistics
Methods for computing spatial, temporal, and spatiotemporal statistics as described in Gouhier and Guichard (2014) [https://doi.org/10.1111/2041-210X.12188]. These methods include empirical univariate, bivariate and multivariate variograms; fitting variogram models; phase locking and synchrony analysis; generating autocorrelated and cross-correlated matrices.
Maintained by Tarik C. Gouhier. Last updated 5 years ago.
4.0 match 10 stars 4.84 score 46 scripts
famuvie
breedR:Statistical Methods for Forest Genetic Resources Analysts
Statistical tools to build predictive models for the breeders community. It aims to assess the genetic value of individuals under a number of situations, including spatial autocorrelation, genetic/environment interaction and competition. It is under active development as part of the Trees4Future project, particularly developed having forest genetic trials in mind. But can be used for animals or other situations as well.
Maintained by Facundo Muñoz. Last updated 8 months ago.
3.5 match 33 stars 5.44 score 24 scriptspecanproject
PEcAn.priors:PEcAn Functions Used to Estimate Priors from Data
Functions to estimate priors from data.
Maintained by David LeBauer. Last updated 2 days ago.
bayesiancyberinfrastructuredata-assimilationdata-scienceecosystem-modelecosystem-scienceforecastingmeta-analysisnational-science-foundationpecanplantsjagscpp
1.9 match 216 stars 9.93 score 13 scripts 6 dependentsbiometris
statgenHTP:High Throughput Phenotyping (HTP) Data Analysis
Phenotypic analysis of data coming from high throughput phenotyping (HTP) platforms, including different types of outlier detection, spatial analysis, and parameter estimation. The package is being developed within the EPPN2020 project (<https://eppn2020.plant-phenotyping.eu/>). Some functions have been created to be used in conjunction with the R package 'asreml' for the 'ASReml' software, which can be obtained upon purchase from 'VSN' international (<https://vsni.co.uk/software/asreml-r/>).
Maintained by Bart-Jan van Rossum. Last updated 3 months ago.
geneticshigh-troughput-phenotyping
3.4 match 4 stars 5.43 score 17 scriptsthej022214
hisse: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>.
Maintained by Jeremy Beaulieu. Last updated 1 months ago.
2.2 match 6 stars 8.45 score 152 scriptsfrederic-santos
PELVIS:Probabilistic Sex Estimate using Logistic Regression, Based on VISual Traits of the Human Os Coxae
An R-Shiny application implementing a method of sexing the human os coxae based on logistic regressions and Bruzek's nonmetric traits <doi:10.1002/ajpa.23855>.
Maintained by Frédéric Santos. Last updated 2 years ago.
6.5 match 2.81 score 13 scripts
flujoo
personr:Test Your Personality
An R-package-version of an open online science-based personality test from <https://openpsychometrics.org/tests/IPIP-BFFM/>, providing a better-designed interface and a more detailed report. The core command launch_test() opens a personality test in your browser, and generates a report after you click "Submit". In this report, your results are compared with other people's, to show what these results mean. Other people's data is from <https://openpsychometrics.org/_rawdata/BIG5.zip>.
Maintained by Renfei Mao. Last updated 4 years ago.
big-five-traitspersonality-testshiny-apps
6.7 match 2.70 score 2 scripts