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yrosseel

lavaan:Latent Variable Analysis

Fit a variety of latent variable models, including confirmatory factor analysis, structural equation modeling and latent growth curve models.

Maintained by Yves Rosseel. Last updated 2 days ago.

factor-analysisgrowth-curve-modelslatent-variablesmissing-datamultilevel-modelsmultivariate-analysispath-analysispsychometricsstatistical-modelingstructural-equation-modeling

454 stars 16.82 score 8.4k scripts 218 dependents

mhahsler

arules:Mining Association Rules and Frequent Itemsets

Provides the infrastructure for representing, manipulating and analyzing transaction data and patterns (frequent itemsets and association rules). Also provides C implementations of the association mining algorithms Apriori and Eclat. Hahsler, Gruen and Hornik (2005) <doi:10.18637/jss.v014.i15>.

Maintained by Michael Hahsler. Last updated 2 months ago.

arulesassociation-rulesfrequent-itemsets

194 stars 13.99 score 3.3k scripts 28 dependents

projectmosaic

mosaic:Project MOSAIC Statistics and Mathematics Teaching Utilities

Data sets and utilities from Project MOSAIC (<http://www.mosaic-web.org>) used to teach mathematics, statistics, computation and modeling. Funded by the NSF, Project MOSAIC is a community of educators working to tie together aspects of quantitative work that students in science, technology, engineering and mathematics will need in their professional lives, but which are usually taught in isolation, if at all.

Maintained by Randall Pruim. Last updated 1 years ago.

93 stars 13.32 score 7.2k scripts 7 dependents

r-forge

tm:Text Mining Package

A framework for text mining applications within R.

Maintained by Kurt Hornik. Last updated 1 months ago.

cpp

13.00 score 14k scripts 100 dependents

ropensci

rotl:Interface to the 'Open Tree of Life' API

An interface to the 'Open Tree of Life' API to retrieve phylogenetic trees, information about studies used to assemble the synthetic tree, and utilities to match taxonomic names to 'Open Tree identifiers'. The 'Open Tree of Life' aims at assembling a comprehensive phylogenetic tree for all named species.

Maintained by Francois Michonneau. Last updated 2 years ago.

metadataropensciphylogeneticsindependant-contrastsbiodiversitypeer-reviewedphylogenytaxonomy

40 stars 12.05 score 356 scripts 29 dependents

hadley

pryr:Tools for Computing on the Language

Useful tools to pry back the covers of R and understand the language at a deeper level.

Maintained by Hadley Wickham. Last updated 1 years ago.

cpp

204 stars 11.93 score 1.9k scripts 57 dependents

jmsigner

amt:Animal Movement Tools

Manage and analyze animal movement data. The functionality of 'amt' includes methods to calculate home ranges, track statistics (e.g. step lengths, speed, or turning angles), prepare data for fitting habitat selection analyses, and simulation of space-use from fitted step-selection functions.

Maintained by Johannes Signer. Last updated 5 months ago.

41 stars 10.54 score 418 scripts

romanzenka

RUnit:R Unit Test Framework

R functions implementing a standard Unit Testing framework, with additional code inspection and report generation tools.

Maintained by Roman Zenka. Last updated 1 years ago.

2 stars 10.49 score 1.7k scripts 58 dependents

ropensci

spocc:Interface to Species Occurrence Data Sources

A programmatic interface to many species occurrence data sources, including Global Biodiversity Information Facility ('GBIF'), 'iNaturalist', 'eBird', Integrated Digitized 'Biocollections' ('iDigBio'), 'VertNet', Ocean 'Biogeographic' Information System ('OBIS'), and Atlas of Living Australia ('ALA'). Includes functionality for retrieving species occurrence data, and combining those data.

Maintained by Hannah Owens. Last updated 2 months ago.

specimensapiweb-servicesoccurrencesspeciestaxonomygbifinatvertnetebirdidigbioobisalaantwebbisondataecoengineinaturalistoccurrencespecies-occurrencespocc

118 stars 10.09 score 552 scripts 5 dependents

nepem-ufsc

metan:Multi Environment Trials Analysis

Performs stability analysis of multi-environment trial data using parametric and non-parametric methods. Parametric methods includes Additive Main Effects and Multiplicative Interaction (AMMI) analysis by Gauch (2013) <doi:10.2135/cropsci2013.04.0241>, Ecovalence by Wricke (1965), Genotype plus Genotype-Environment (GGE) biplot analysis by Yan & Kang (2003) <doi:10.1201/9781420040371>, geometric adaptability index by Mohammadi & Amri (2008) <doi:10.1007/s10681-007-9600-6>, joint regression analysis by Eberhart & Russel (1966) <doi:10.2135/cropsci1966.0011183X000600010011x>, genotypic confidence index by Annicchiarico (1992), Murakami & Cruz's (2004) method, power law residuals (POLAR) statistics by Doring et al. (2015) <doi:10.1016/j.fcr.2015.08.005>, scale-adjusted coefficient of variation by Doring & Reckling (2018) <doi:10.1016/j.eja.2018.06.007>, stability variance by Shukla (1972) <doi:10.1038/hdy.1972.87>, weighted average of absolute scores by Olivoto et al. (2019a) <doi:10.2134/agronj2019.03.0220>, and multi-trait stability index by Olivoto et al. (2019b) <doi:10.2134/agronj2019.03.0221>. Non-parametric methods includes superiority index by Lin & Binns (1988) <doi:10.4141/cjps88-018>, nonparametric measures of phenotypic stability by Huehn (1990) <doi:10.1007/BF00024241>, TOP third statistic by Fox et al. (1990) <doi:10.1007/BF00040364>. Functions for computing biometrical analysis such as path analysis, canonical correlation, partial correlation, clustering analysis, and tools for inspecting, manipulating, summarizing and plotting typical multi-environment trial data are also provided.

Maintained by Tiago Olivoto. Last updated 21 days ago.

2 stars 9.48 score 1.3k scripts 2 dependents

integrated-inferences

CausalQueries:Make, Update, and Query Binary Causal Models

Users can declare causal models over binary nodes, update beliefs about causal types given data, and calculate arbitrary queries. Updating is implemented in 'stan'. See Humphreys and Jacobs, 2023, Integrated Inferences (<DOI: 10.1017/9781316718636>) and Pearl, 2009 Causality (<DOI:10.1017/CBO9780511803161>).

Maintained by Till Tietz. Last updated 1 months ago.

bayescausaldagsmixedmethodsstancpp

28 stars 9.02 score 54 scripts

openvolley

datavolley:Reading and Analyzing DataVolley Scout Files

Provides functions for parsing and working with volleyball match files in DataVolley format.

Maintained by Ben Raymond. Last updated 2 months ago.

openvolleysports-analyticsvolleyball

31 stars 8.24 score 94 scripts 11 dependents

momx

Momocs:Morphometrics using R

The goal of 'Momocs' is to provide a complete, convenient, reproducible and open-source toolkit for 2D morphometrics. It includes most common 2D morphometrics approaches on outlines, open outlines, configurations of landmarks, traditional morphometrics, and facilities for data preparation, manipulation and visualization with a consistent grammar throughout. It allows reproducible, complex morphometrics analyses and other morphometrics approaches should be easy to plug in, or develop from, on top of this canvas.

Maintained by Vincent Bonhomme. Last updated 1 years ago.

morphometrics

51 stars 7.42 score 346 scripts

projectmosaic

mosaicCore:Common Utilities for Other MOSAIC-Family Packages

Common utilities used in other MOSAIC-family packages are collected here.

Maintained by Randall Pruim. Last updated 1 years ago.

1 stars 7.07 score 113 scripts 26 dependents

predictiveecology

NetLogoR:Build and Run Spatially Explicit Agent-Based Models

Build and run spatially explicit agent-based models using only the R platform. 'NetLogoR' follows the same framework as the 'NetLogo' software (Wilensky (1999) <http://ccl.northwestern.edu/netlogo/>) and is a translation in R of the structure and functions of 'NetLogo'. 'NetLogoR' provides new R classes to define model agents and functions to implement spatially explicit agent-based models in the R environment. This package allows benefiting of the fast and easy coding phase from the highly developed 'NetLogo' framework, coupled with the versatility, power and massive resources of the R software. Examples of two models from the NetLogo software repository (Ants <http://ccl.northwestern.edu/netlogo/models/Ants>) and Wolf-Sheep-Predation (<http://ccl.northwestern.edu/netlogo/models/WolfSheepPredation>), and a third, Butterfly, from Railsback and Grimm (2012) <https://www.railsback-grimm-abm-book.com/>, all written using 'NetLogoR' are available. The 'NetLogo' code of the original version of these models is provided alongside. A programming guide inspired from the 'NetLogo' Programming Guide (<https://ccl.northwestern.edu/netlogo/docs/programming.html>) and a dictionary of 'NetLogo' primitives (<https://ccl.northwestern.edu/netlogo/docs/dictionary.html>) equivalences are also available. NOTE: To increment 'time', these functions can use a for loop or can be integrated with a discrete event simulator, such as 'SpaDES' (<https://cran.r-project.org/package=SpaDES>). The suggested package 'fastshp' can be installed with 'install.packages("fastshp", repos = ("<https://rforge.net>"), type = "source")'.

Maintained by Eliot J B McIntire. Last updated 4 months ago.

40 stars 6.96 score 19 scripts

januarharianto

respR:Import, Process, Analyse, and Calculate Rates from Respirometry Data

Provides a structural, reproducible workflow for the processing and analysis of respirometry data. It contains analytical functions and utilities for working with oxygen time-series to determine respiration or oxygen production rates, and to make it easier to report and share analyses. See Harianto et al. 2019 <doi:10.1111/2041-210X.13162>.

Maintained by Nicholas Carey. Last updated 11 months ago.

respirometryrstudio

12 stars 5.64 score 90 scripts

llrs

experDesign:Design Experiments for Batches

Distributes samples in batches while making batches homogeneous according to their description. Allows for an arbitrary number of variables, both numeric and categorical. For quality control it provides functions to subset a representative sample.

Maintained by Lluís Revilla Sancho. Last updated 3 months ago.

batchexperiment-design

10 stars 5.48 score 1 scripts

prdm0

AcceptReject:Acceptance-Rejection Method for Generating Pseudo-Random Observations

Provides a function that implements the acceptance-rejection method in an optimized manner to generate pseudo-random observations for discrete or continuous random variables. Proposed by von Neumann J. (1951), <https://mcnp.lanl.gov/pdf_files/>, the function is optimized to work in parallel on Unix-based operating systems and performs well on Windows systems. The acceptance-rejection method implemented optimizes the probability of generating observations from the desired random variable, by simply providing the probability function or probability density function, in the discrete and continuous cases, respectively. Implementation is based on references CASELLA, George at al. (2004) <https://www.jstor.org/stable/4356322>, NEAL, Radford M. (2003) <https://www.jstor.org/stable/3448413> and Bishop, Christopher M. (2006, ISBN: 978-0387310732).

Maintained by Pedro Rafael D. Marinho. Last updated 10 months ago.

monte-carlomonte-carlo-simulationrejection-samplingstatistics-librarycpp

1 stars 5.00 score 7 scripts

r-forge

sse:Sample Size Estimation

Provides functions to evaluate user-defined power functions for a parameter range, and draws a sensitivity plot. It also provides a resampling procedure for semi-parametric sample size estimation and methods for adding information to a Sweave report.

Maintained by Thomas Fabbro. Last updated 4 years ago.

4.41 score 16 scripts

rogiersbart

rui:A simple set of UI functions

This package provides a wrapper around different cli and usethis functions, aiming at providing a small but consistent set of verbs to construct a simple R package UI.

Maintained by Bart Rogiers. Last updated 9 months ago.

3.48 score 2 dependents

tdjorgensen

simsem:SIMulated Structural Equation Modeling

Provides an easy framework for Monte Carlo simulation in structural equation modeling, which can be used for various purposes, such as such as model fit evaluation, power analysis, or missing data handling and planning.

Maintained by Terrence D. Jorgensen. Last updated 4 years ago.

3.40 score 276 scripts

cran

flux:Flux Rate Calculation from Dynamic Closed Chamber Measurements

Functions for the calculation of greenhouse gas flux rates from closed chamber concentration measurements. The package follows a modular concept: Fluxes can be calculated in just two simple steps or in several steps if more control in details is wanted. Additionally plot and preparation functions as well as functions for modelling gpp and reco are provided.

Maintained by Gerald Jurasinski. Last updated 3 years ago.

2 stars 3.21 score 3 dependents

openvolley

peranavolley:Perana Sports Volleyball Files

Basic functions for reading and working with Perana Sports volleyball scouting files.

Maintained by Ben Raymond. Last updated 10 months ago.

2.95 score 1 scripts 6 dependents

cran

hiphop:Parentage Assignment using Bi-Allelic Genetic Markers

Can be used for paternity and maternity assignment and outperforms conventional methods where closely related individuals occur in the pool of possible parents. The method compares the genotypes of offspring with any combination of potentials parents and scores the number of mismatches of these individuals at bi-allelic genetic markers (e.g. Single Nucleotide Polymorphisms). It elaborates on a prior exclusion method based on the Homozygous Opposite Test (HOT; Huisman 2017 <doi:10.1111/1755-0998.12665>) by introducing the additional exclusion criterion HIPHOP (Homozygous Identical Parents, Heterozygous Offspring are Precluded; Cockburn et al., in revision). Potential parents are excluded if they have more mismatches than can be expected due to genotyping error and mutation, and thereby one can identify the true genetic parents and detect situations where one (or both) of the true parents is not sampled. Package 'hiphop' can deal with (a) the case where there is contextual information about parentage of the mother (i.e. a female has been seen to be involved in reproductive tasks such as nest building), but paternity is unknown (e.g. due to promiscuity), (b) where both parents need to be assigned, because there is no contextual information on which female laid eggs and which male fertilized them (e.g. polygynandrous mating system where multiple females and males deposit young in a common nest, or organisms with external fertilisation that breed in aggregations). For details: Cockburn, A., Penalba, J.V.,Jaccoud, D.,Kilian, A., Brouwer, L., Double, M.C., Margraf, N., Osmond, H.L., van de Pol, M. and Kruuk, L.E.B. (in revision). HIPHOP: improved paternity assignment among close relatives using a simple exclusion method for bi-allelic markers. Molecular Ecology Resources, DOI to be added upon acceptance.

Maintained by Martijn van de Pol. Last updated 5 years ago.

1 stars 2.70 score

cran

arulesSequences:Mining Frequent Sequences

Add-on for arules to handle and mine frequent sequences. Provides interfaces to the C++ implementation of cSPADE by Mohammed J. Zaki.

Maintained by Christian Buchta. Last updated 7 months ago.

12 stars 2.63 score

jcc9

cata:Analysis of Check-All-that-Apply (CATA) Data

Package contains functions for analyzing check-all-that-apply (CATA) data from consumer and sensory tests. Cochran's Q test, McNemar's test, and Penalty-Lift analysis are provided; for details, see Meyners, Castura & Carr (2013) <doi:10.1016/j.foodqual.2013.06.010>. Cluster analysis can be performed using b-cluster analysis, then evaluated using various measures; for details, see Castura, Meyners, Varela & Næs (2022) <doi:10.1016/j.foodqual.2022.104564>. Methods are adapted to cluster consumers based on their product-related hedonic responses; for details, see Castura, Meyners, Pohjanheimo, Varela & Næs (2023) <doi:10.1111/joss.12860>. Permutation tests based on the L1-norm methods are provided; for details, see Chaya, Castura & Greenacre (2025) <doi:10.48550/arXiv.2502.15945>.

Maintained by J.C. Castura. Last updated 1 months ago.

1.60 score

kurthornik

W3CMarkupValidator:R Interface to W3C Markup Validation Services

R interface to a W3C Markup Validation service. See <https://validator.w3.org/> for more information.

Maintained by Kurt Hornik. Last updated 2 years ago.

1.00 score 2 scripts

cran

InspectChangepoint:High-Dimensional Changepoint Estimation via Sparse Projection

Provides a data-driven projection-based method for estimating changepoints in high-dimensional time series. Multiple changepoints are estimated using a (wild) binary segmentation scheme.

Maintained by Tengyao Wang. Last updated 3 years ago.

1 stars 1.00 score

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