R-universe search: directions

cran

circular:Circular Statistics

Circular Statistics, from "Topics in circular Statistics" (2001) S. Rao Jammalamadaka and A. SenGupta, World Scientific.

Maintained by Eduardo García-Portugués. Last updated 7 months ago.

fortran

43.8 match 7 stars 7.76 score 1.1k scripts 40 dependents

jokergoo

circlize:Circular Visualization

Circular layout is an efficient way for the visualization of huge amounts of information. Here this package provides an implementation of circular layout generation in R as well as an enhancement of available software. The flexibility of the package is based on the usage of low-level graphics functions such that self-defined high-level graphics can be easily implemented by users for specific purposes. Together with the seamless connection between the powerful computational and visual environment in R, it gives users more convenience and freedom to design figures for better understanding complex patterns behind multiple dimensional data. The package is described in Gu et al. 2014 <doi:10.1093/bioinformatics/btu393>.

Maintained by Zuguang Gu. Last updated 1 years ago.

21.0 match 983 stars 15.62 score 10k scripts 213 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 13 hours ago.

complex-networks graph-algorithms graph-theory mathematics network-analysis network-graph fortran libxml2 glpk openblas cpp

15.4 match 582 stars 21.11 score 31k scripts 1.9k dependents

tdhock

directlabels:Direct Labels for Multicolor Plots

An extensible framework for automatically placing direct labels onto multicolor 'lattice' or 'ggplot2' plots. Label positions are described using Positioning Methods which can be re-used across several different plots. There are heuristics for examining "trellis" and "ggplot" objects and inferring an appropriate Positioning Method.

Maintained by Toby Dylan Hocking. Last updated 11 months ago.

25.0 match 83 stars 10.62 score 1.8k scripts 16 dependents

cran

Directional:A Collection of Functions for Directional Data Analysis

A collection of functions for directional data (including massive data, with millions of observations) analysis. Hypothesis testing, discriminant and regression analysis, MLE of distributions and more are included. The standard textbook for such data is the "Directional Statistics" by Mardia, K. V. and Jupp, P. E. (2000). Other references include: a) Paine J.P., Preston S.P., Tsagris M. and Wood A.T.A. (2018). "An elliptically symmetric angular Gaussian distribution". Statistics and Computing 28(3): 689-697. <doi:10.1007/s11222-017-9756-4>. b) Tsagris M. and Alenazi A. (2019). "Comparison of discriminant analysis methods on the sphere". Communications in Statistics: Case Studies, Data Analysis and Applications 5(4):467--491. <doi:10.1080/23737484.2019.1684854>. c) Paine J.P., Preston S.P., Tsagris M. and Wood A.T.A. (2020). "Spherical regression models with general covariates and anisotropic errors". Statistics and Computing 30(1): 153--165. <doi:10.1007/s11222-019-09872-2>. d) Tsagris M. and Alenazi A. (2024). "An investigation of hypothesis testing procedures for circular and spherical mean vectors". Communications in Statistics-Simulation and Computation, 53(3): 1387--1408. <doi:10.1080/03610918.2022.2045499>. e) Yu Z. and Huang X. (2024). A new parameterization for elliptically symmetric angular Gaussian distributions of arbitrary dimension. Electronic Journal of Statistics, 18(1): 301--334. <doi:10.1214/23-EJS2210>. f) Tsagris M. and Alzeley O. (2024). "Circular and spherical projected Cauchy distributions: A Novel Framework for Circular and Directional Data Modeling". Australian & New Zealand Journal of Statistics (Accepted for publication). <doi:10.1111/anzs.12434>. g) Tsagris M., Papastamoulis P. and Kato S. (2024). "Directional data analysis: spherical Cauchy or Poisson kernel-based distribution". Statistics and Computing (Accepted for publication). <doi:10.48550/arXiv.2409.03292>.

Maintained by Michail Tsagris. Last updated 1 months ago.

63.7 match 3 stars 4.06 score 3 dependents

rich-iannone

DiagrammeR:Graph/Network Visualization

Build graph/network structures using functions for stepwise addition and deletion of nodes and edges. Work with data available in tables for bulk addition of nodes, edges, and associated metadata. Use graph selections and traversals to apply changes to specific nodes or edges. A wide selection of graph algorithms allow for the analysis of graphs. Visualize the graphs and take advantage of any aesthetic properties assigned to nodes and edges.

Maintained by Richard Iannone. Last updated 2 months ago.

graph graph-functions network-graph property-graph visualization

14.5 match 1.7k stars 15.18 score 3.8k scripts 87 dependents

r-causal

ggdag:Analyze and Create Elegant Directed Acyclic Graphs

Tidy, analyze, and plot directed acyclic graphs (DAGs). 'ggdag' is built on top of 'dagitty', an R package that uses the 'DAGitty' web tool (<https://dagitty.net/>) for creating and analyzing DAGs. 'ggdag' makes it easy to tidy and plot 'dagitty' objects using 'ggplot2' and 'ggraph', as well as common analytic and graphical functions, such as determining adjustment sets and node relationships.

Maintained by Malcolm Barrett. Last updated 8 months ago.

causal-inference dag ggplot-extension

16.1 match 443 stars 11.78 score 1.8k scripts 5 dependents

tobiste

tectonicr:Analyzing the Orientation of Maximum Horizontal Stress

Models the direction of the maximum horizontal stress using relative plate motion parameters. Statistical algorithms to evaluate the modeling results compared with the observed data. Provides plots to visualize the results. Methods described in Stephan et al. (2023) <doi:10.1038/s41598-023-42433-2> and Wdowinski (1998) <doi:10.1016/S0079-1946(98)00091-3>.

Maintained by Tobias Stephan. Last updated 14 days ago.

geology structural-geology tectonics

25.9 match 7 stars 7.26 score 33 scripts

statnet

ergm:Fit, Simulate and Diagnose Exponential-Family Models for Networks

An integrated set of tools to analyze and simulate networks based on exponential-family random graph models (ERGMs). 'ergm' is a part of the Statnet suite of packages for network analysis. See Hunter, Handcock, Butts, Goodreau, and Morris (2008) <doi:10.18637/jss.v024.i03> and Krivitsky, Hunter, Morris, and Klumb (2023) <doi:10.18637/jss.v105.i06>.

Maintained by Pavel N. Krivitsky. Last updated 7 days ago.

10.8 match 100 stars 15.36 score 1.4k scripts 36 dependents

svmiller

peacesciencer:Tools and Data for Quantitative Peace Science Research

These are useful tools and data sets for the study of quantitative peace science. The goal for this package is to include tools and data sets for doing original research that mimics well what a user would have to previously get from a software package that may not be well-sourced or well-supported. Those software bundles were useful the extent to which they encourage replications of long-standing analyses by starting the data-generating process from scratch. However, a lot of the functionality can be done relatively quickly and more transparently in the R programming language.

Maintained by Steve Miller. Last updated 3 days ago.

eugene peace-science

28.5 match 29 stars 5.49 score 211 scripts

audreyqyfu

DIRECT:Bayesian Clustering of Multivariate Data Under the Dirichlet-Process Prior

A Bayesian clustering method for replicated time series or replicated measurements from multiple experimental conditions, e.g., time-course gene expression data. It estimates the number of clusters directly from the data using a Dirichlet-process prior. See Fu, A. Q., Russell, S., Bray, S. and Tavare, S. (2013) Bayesian clustering of replicated time-course gene expression data with weak signals. The Annals of Applied Statistics. 7(3) 1334-1361. <doi:10.1214/13-AOAS650>.

Maintained by Audrey Q. Fu. Last updated 2 years ago.

60.6 match 2.40 score 25 scripts

selesnow

ryandexdirect:Load Data From 'Yandex Direct'

Load data from 'Yandex Direct' API V5 <https://yandex.ru/dev/direct/doc/dg/concepts/about-docpage> into R. Provide function for load lists of campaings, ads, keywords and other objects from 'Yandex Direct' account. Also you can load statistic from API 'Reports Service' <https://yandex.ru/dev/direct/doc/reports/reports-docpage>. And allows keyword bids management.

Maintained by Alexey Seleznev. Last updated 1 months ago.

campaign filterlist wifi

18.7 match 53 stars 7.54 score 44 scripts 1 dependents

urbananalyst

dodgr:Distances on Directed Graphs

Distances on dual-weighted directed graphs using priority-queue shortest paths (Padgham (2019) <doi:10.32866/6945>). Weighted directed graphs have weights from A to B which may differ from those from B to A. Dual-weighted directed graphs have two sets of such weights. A canonical example is a street network to be used for routing in which routes are calculated by weighting distances according to the type of way and mode of transport, yet lengths of routes must be calculated from direct distances.

Maintained by Mark Padgham. Last updated 6 days ago.

distance openstreetmap router shortest-paths street-networks cpp

11.6 match 129 stars 11.53 score 229 scripts 4 dependents

rspatial

geosphere:Spherical Trigonometry

Spherical trigonometry for geographic applications. That is, compute distances and related measures for angular (longitude/latitude) locations.

Maintained by Robert J. Hijmans. Last updated 6 months ago.

cpp

8.6 match 36 stars 13.79 score 5.7k scripts 116 dependents

giscience

openrouteservice:An 'openrouteservice' API Client

The client streamlines access to the services provided by <https://api.openrouteservice.org>. It allows you to painlessly query for directions, isochrones, time-distance matrices, geocoding, elevation, points of interest, and more.

Maintained by Andrzej K. Oleś. Last updated 1 months ago.

api directions gis giscience isochrones openrouteservice openstreetmap pois routing sdk

14.8 match 108 stars 7.89 score 60 scripts

ropensci

spatsoc:Group Animal Relocation Data by Spatial and Temporal Relationship

Detects spatial and temporal groups in GPS relocations (Robitaille et al. (2019) <doi:10.1111/2041-210X.13215>). It can be used to convert GPS relocations to gambit-of-the-group format to build proximity-based social networks In addition, the randomizations function provides data-stream randomization methods suitable for GPS data.

Maintained by Alec L. Robitaille. Last updated 1 months ago.

animal gps network social spatial

11.6 match 24 stars 9.97 score 145 scripts 3 dependents

tbates

umx:Structural Equation Modeling and Twin Modeling in R

Quickly create, run, and report structural equation models, and twin models. See '?umx' for help, and umx_open_CRAN_page("umx") for NEWS. Timothy C. Bates, Michael C. Neale, Hermine H. Maes, (2019). umx: A library for Structural Equation and Twin Modelling in R. Twin Research and Human Genetics, 22, 27-41. <doi:10.1017/thg.2019.2>.

Maintained by Timothy C. Bates. Last updated 2 days ago.

behavior-genetics genetics openmx psychology sem statistics structural-equation-modeling tutorials twin-models umx

12.2 match 44 stars 9.45 score 472 scripts

michaeldorman

mapsapi:'sf'-Compatible Interface to 'Google Maps' APIs

Interface to the 'Google Maps' APIs: (1) routing directions based on the 'Directions' API, returned as 'sf' objects, either as single feature per alternative route, or a single feature per segment per alternative route; (2) travel distance or time matrices based on the 'Distance Matrix' API; (3) geocoded locations based on the 'Geocode' API, returned as 'sf' objects, either points or bounds; (4) map images using the 'Maps Static' API, returned as 'stars' objects.

Maintained by Michael Dorman. Last updated 2 years ago.

16.2 match 51 stars 7.10 score 99 scripts

bioc

AnnotationDbi:Manipulation of SQLite-based annotations in Bioconductor

Implements a user-friendly interface for querying SQLite-based annotation data packages.

Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.

annotation microarray sequencing genomeannotation bioconductor-package core-package

7.6 match 9 stars 15.05 score 3.6k scripts 769 dependents

nredell

forecastML:Time Series Forecasting with Machine Learning Methods

The purpose of 'forecastML' is to simplify the process of multi-step-ahead forecasting with standard machine learning algorithms. 'forecastML' supports lagged, dynamic, static, and grouping features for modeling single and grouped numeric or factor/sequence time series. In addition, simple wrapper functions are used to support model-building with most R packages. This approach to forecasting is inspired by Bergmeir, Hyndman, and Koo's (2018) paper "A note on the validity of cross-validation for evaluating autoregressive time series prediction" <doi:10.1016/j.csda.2017.11.003>.

Maintained by Nickalus Redell. Last updated 5 years ago.

deep-learning direct-forecasting forecast forecasting machine-learning multi-step-ahead-forecasting neural-network python time-series

14.7 match 131 stars 7.64 score 134 scripts

thomasp85

ggraph:An Implementation of Grammar of Graphics for Graphs and Networks

The grammar of graphics as implemented in ggplot2 is a poor fit for graph and network visualizations due to its reliance on tabular data input. ggraph is an extension of the ggplot2 API tailored to graph visualizations and provides the same flexible approach to building up plots layer by layer.

Maintained by Thomas Lin Pedersen. Last updated 1 years ago.

ggplot-extension ggplot2 graph-visualization network-visualization visualization cpp

6.5 match 1.1k stars 16.96 score 9.2k scripts 111 dependents

soerenpannier

emdi:Estimating and Mapping Disaggregated Indicators

Functions that support estimating, assessing and mapping regional disaggregated indicators. So far, estimation methods comprise direct estimation, the model-based unit-level approach Empirical Best Prediction (see "Small area estimation of poverty indicators" by Molina and Rao (2010) <doi:10.1002/cjs.10051>), the area-level model (see "Estimates of income for small places: An application of James-Stein procedures to Census Data" by Fay and Herriot (1979) <doi:10.1080/01621459.1979.10482505>) and various extensions of it (adjusted variance estimation methods, log and arcsin transformation, spatial, robust and measurement error models), as well as their precision estimates. The assessment of the used model is supported by a summary and diagnostic plots. For a suitable presentation of estimates, map plots can be easily created. Furthermore, results can easily be exported to excel. For a detailed description of the package and the methods used see "The R Package emdi for Estimating and Mapping Regionally Disaggregated Indicators" by Kreutzmann et al. (2019) <doi:10.18637/jss.v091.i07> and the second package vignette "A Framework for Producing Small Area Estimates Based on Area-Level Models in R".

Maintained by Soeren Pannier. Last updated 1 years ago.

14.7 match 15 stars 7.26 score 45 scripts 1 dependents

rspatial

terra:Spatial Data Analysis

Methods for spatial data analysis with vector (points, lines, polygons) and raster (grid) data. Methods for vector data include geometric operations such as intersect and buffer. Raster methods include local, focal, global, zonal and geometric operations. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/> to get started. 'terra' replaces the 'raster' package ('terra' can do more, and it is faster and easier to use).

Maintained by Robert J. Hijmans. Last updated 1 days ago.

geospatial raster spatial vector onetbb proj gdal geos cpp

6.0 match 559 stars 17.64 score 17k scripts 851 dependents

cvxgrp

CVXR:Disciplined Convex Optimization

An object-oriented modeling language for disciplined convex programming (DCP) as described in Fu, Narasimhan, and Boyd (2020, <doi:10.18637/jss.v094.i14>). It allows the user to formulate convex optimization problems in a natural way following mathematical convention and DCP rules. The system analyzes the problem, verifies its convexity, converts it into a canonical form, and hands it off to an appropriate solver to obtain the solution. Interfaces to solvers on CRAN and elsewhere are provided, both commercial and open source.

Maintained by Anqi Fu. Last updated 4 months ago.

cpp

8.0 match 207 stars 12.89 score 768 scripts 51 dependents

rspatial

raster:Geographic Data Analysis and Modeling

Reading, writing, manipulating, analyzing and modeling of spatial data. This package has been superseded by the "terra" package <https://CRAN.R-project.org/package=terra>.

Maintained by Robert J. Hijmans. Last updated 2 months ago.

cpp

6.0 match 164 stars 17.05 score 58k scripts 555 dependents

insightsengineering

chevron:Standard TLGs for Clinical Trials Reporting

Provide standard tables, listings, and graphs (TLGs) libraries used in clinical trials. This package implements a structure to reformat the data with 'dunlin', create reporting tables using 'rtables' and 'tern' with standardized input arguments to enable quick generation of standard outputs. In addition, it also provides comprehensive data checks and script generation functionality.

Maintained by Joe Zhu. Last updated 24 days ago.

clinical-trials graphs listings nest reporting tables

12.3 match 12 stars 8.24 score 12 scripts

martin3141

spant:MR Spectroscopy Analysis Tools

Tools for reading, visualising and processing Magnetic Resonance Spectroscopy data. The package includes methods for spectral fitting: Wilson (2021) <DOI:10.1002/mrm.28385> and spectral alignment: Wilson (2018) <DOI:10.1002/mrm.27605>.

Maintained by Martin Wilson. Last updated 30 days ago.

brain mri mrs mrshub spectroscopy fortran

11.7 match 25 stars 8.52 score 81 scripts

jeksterslab

cTMed:Continuous Time Mediation

Calculates standard errors and confidence intervals for effects in continuous-time mediation models. This package extends the work of Deboeck and Preacher (2015) <doi:10.1080/10705511.2014.973960> and Ryan and Hamaker (2021) <doi:10.1007/s11336-021-09767-0> by providing methods to generate standard errors and confidence intervals for the total, direct, and indirect effects in these models.

Maintained by Ivan Jacob Agaloos Pesigan. Last updated 20 days ago.

centrality continuous-time delta-method mediation monte-carlo-method network openblas cpp openmp

21.5 match 4.56 score 24 scripts

hojsgaard

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.

openblas cpp

10.5 match 3 stars 9.24 score 241 scripts 20 dependents

revelle

psych:Procedures for Psychological, Psychometric, and Personality Research

A general purpose toolbox developed originally for personality, psychometric theory and experimental psychology. Functions are primarily for multivariate analysis and scale construction using factor analysis, principal component analysis, cluster analysis and reliability analysis, although others provide basic descriptive statistics. Item Response Theory is done using factor analysis of tetrachoric and polychoric correlations. Functions for analyzing data at multiple levels include within and between group statistics, including correlations and factor analysis. Validation and cross validation of scales developed using basic machine learning algorithms are provided, as are functions for simulating and testing particular item and test structures. Several functions serve as a useful front end for structural equation modeling. Graphical displays of path diagrams, including mediation models, factor analysis and structural equation models are created using basic graphics. Some of the functions are written to support a book on psychometric theory as well as publications in personality research. For more information, see the <https://personality-project.org/r/> web page.

Maintained by William Revelle. Last updated 3 months ago.

6.7 match 52 stars 13.94 score 29k scripts 317 dependents

mrcieu

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 11 days ago.

8.1 match 467 stars 11.23 score 1.7k scripts 1 dependents

ikosmidis

cranly:Package Directives and Collaboration Networks in CRAN

Core visualizations and summaries for the CRAN package database. The package provides comprehensive methods for cleaning up and organizing the information in the CRAN package database, for building package directives networks (depends, imports, suggests, enhances, linking to) and collaboration networks, producing package dependence trees, and for computing useful summaries and producing interactive visualizations from the resulting networks and summaries. The resulting networks can be coerced to 'igraph' <https://CRAN.R-project.org/package=igraph> objects for further analyses and modelling.

Maintained by Ioannis Kosmidis. Last updated 3 years ago.

network-analysis network-visualization

13.2 match 49 stars 6.85 score 32 scripts 1 dependents

yufree

pmd:Paired Mass Distance Analysis for GC/LC-MS Based Non-Targeted Analysis and Reactomics Analysis

Paired mass distance (PMD) analysis proposed in Yu, Olkowicz and Pawliszyn (2018) <doi:10.1016/j.aca.2018.10.062> and PMD based reactomics analysis proposed in Yu and Petrick (2020) <doi:10.1038/s42004-020-00403-z> for gas/liquid chromatography–mass spectrometry (GC/LC-MS) based non-targeted analysis. PMD analysis including GlobalStd algorithm and structure/reaction directed analysis. GlobalStd algorithm could found independent peaks in m/z-retention time profiles based on retention time hierarchical cluster analysis and frequency analysis of paired mass distances within retention time groups. Structure directed analysis could be used to find potential relationship among those independent peaks in different retention time groups based on frequency of paired mass distances. Reactomics analysis could also be performed to build PMD network, assign sources and make biomarker reaction discovery. GUIs for PMD analysis is also included as 'shiny' applications.

Maintained by Miao YU. Last updated 2 months ago.

mass-spectrometry metabolomics non-target

13.5 match 10 stars 6.68 score 40 scripts

finnishcancerregistry

popEpi:Functions for Epidemiological Analysis using Population Data

Enables computation of epidemiological statistics, including those where counts or mortality rates of the reference population are used. Currently supported: excess hazard models (Dickman, Sloggett, Hills, and Hakulinen (2012) <doi:10.1002/sim.1597>), rates, mean survival times, relative/net survival (in particular the Ederer II (Ederer and Heise (1959)) and Pohar Perme (Pohar Perme, Stare, and Esteve (2012) <doi:10.1111/j.1541-0420.2011.01640.x>) estimators), and standardized incidence and mortality ratios, all of which can be easily adjusted for by covariates such as age. Fast splitting and aggregation of 'Lexis' objects (from package 'Epi') and other computations achieved using 'data.table'.

Maintained by Joonas Miettinen. Last updated 2 months ago.

adjust-estimates age-adjusting direct-adjusting epidemiology indirect-adjusting survival

11.1 match 8 stars 8.05 score 117 scripts 1 dependents

r-lib

lintr:A 'Linter' for R Code

Checks adherence to a given style, syntax errors and possible semantic issues. Supports on the fly checking of R code edited with 'RStudio IDE', 'Emacs', 'Vim', 'Sublime Text', 'Atom' and 'Visual Studio Code'.

Maintained by Michael Chirico. Last updated 9 days ago.

linter

5.1 match 1.2k stars 17.00 score 916 scripts 33 dependents

tomkellygenetics

matrixcalc:Collection of Functions for Matrix Calculations

A collection of functions to support matrix calculations for probability, econometric and numerical analysis. There are additional functions that are comparable to APL functions which are useful for actuarial models such as pension mathematics. This package is used for teaching and research purposes at the Department of Finance and Risk Engineering, New York University, Polytechnic Institute, Brooklyn, NY 11201. Horn, R.A. (1990) Matrix Analysis. ISBN 978-0521386326. Lancaster, P. (1969) Theory of Matrices. ISBN 978-0124355507. Lay, D.C. (1995) Linear Algebra: And Its Applications. ISBN 978-0201845563.

Maintained by S. Thomas Kelly. Last updated 4 years ago.

10.1 match 8.32 score 1.7k scripts 149 dependents

mbtyers

riverdist:River Network Distance Computation and Applications

Reads river network shape files and computes network distances. Also included are a variety of computation and graphical tools designed for fisheries telemetry research, such as minimum home range, kernel density estimation, and clustering analysis using empirical k-functions with a bootstrap envelope. Tools are also provided for editing the river networks, meaning there is no reliance on external software.

Maintained by Matt Tyers. Last updated 4 months ago.

11.0 match 26 stars 7.50 score 96 scripts

dmurdoch

plotrix:Various Plotting Functions

Lots of plots, various labeling, axis and color scaling functions. The author/maintainer died in September 2023.

Maintained by Duncan Murdoch. Last updated 1 years ago.

7.3 match 5 stars 11.31 score 9.2k scripts 361 dependents

jimmcl

trajr:Animal Trajectory Analysis

A toolbox to assist with statistical analysis of animal trajectories. It provides simple access to algorithms for calculating and assessing a variety of characteristics such as speed and acceleration, as well as multiple measures of straightness or tortuosity. Some support is provided for 3-dimensional trajectories. McLean & Skowron Volponi (2018) <doi:10.1111/eth.12739>.

Maintained by Jim McLean. Last updated 8 months ago.

10.7 match 27 stars 7.69 score 151 scripts

egarpor

DirStats:Nonparametric Methods for Directional Data

Nonparametric kernel density estimation, bandwidth selection, and other utilities for analyzing directional data. Implements the estimator in Bai, Rao and Zhao (1987) <doi:10.1016/0047-259X(88)90113-3>, the cross-validation bandwidth selectors in Hall, Watson and Cabrera (1987) <doi:10.1093/biomet/74.4.751> and the plug-in bandwidth selectors in García-Portugués (2013) <doi:10.1214/13-ejs821>.

Maintained by Eduardo García-Portugués. Last updated 2 years ago.

directional-statistics nonparametric-statistics statistics fortran

18.4 match 12 stars 4.26 score 7 scripts 1 dependents

robindenz1

adjustedCurves:Confounder-Adjusted Survival Curves and Cumulative Incidence Functions

Estimate and plot confounder-adjusted survival curves using either 'Direct Adjustment', 'Direct Adjustment with Pseudo-Values', various forms of 'Inverse Probability of Treatment Weighting', two forms of 'Augmented Inverse Probability of Treatment Weighting', 'Empirical Likelihood Estimation' or 'Targeted Maximum Likelihood Estimation'. Also includes a significance test for the difference between two adjusted survival curves and the calculation of adjusted restricted mean survival times. Additionally enables the user to estimate and plot cause-specific confounder-adjusted cumulative incidence functions in the competing risks setting using the same methods (with some exceptions). For details, see Denz et. al (2023) <doi:10.1002/sim.9681>.

Maintained by Robin Denz. Last updated 29 days ago.

adjusted confidence-intervals cumulative-incidence survival-curves

9.4 match 38 stars 8.12 score 93 scripts

therneau

survival:Survival Analysis

Contains the core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models.

Maintained by Terry M Therneau. Last updated 3 months ago.

3.5 match 400 stars 20.43 score 29k scripts 3.9k dependents

obrl-soil

h3jsr:Access Uber's H3 Library

Provides access to Uber's H3 library for geospatial indexing via its JavaScript transpile 'h3-js' <https://github.com/uber/h3-js> and 'V8' <https://github.com/jeroen/v8>.

Maintained by Lauren OBrien. Last updated 1 years ago.

discrete-global-grids h3 spatial-indexing

8.5 match 67 stars 8.39 score 205 scripts 4 dependents

richardli

SUMMER:Small-Area-Estimation Unit/Area Models and Methods for Estimation in R

Provides methods for spatial and spatio-temporal smoothing of demographic and health indicators using survey data, with particular focus on estimating and projecting under-five mortality rates, described in Mercer et al. (2015) <doi:10.1214/15-AOAS872>, Li et al. (2019) <doi:10.1371/journal.pone.0210645>, Wu et al. (DHS Spatial Analysis Reports No. 21, 2021), and Li et al. (2023) <doi:10.48550/arXiv.2007.05117>.

Maintained by Zehang R Li. Last updated 2 months ago.

bayesian-inference small-area-estimation space-time

6.8 match 23 stars 10.28 score 134 scripts 2 dependents

teppeiyamamoto

mediation:Causal Mediation Analysis

We implement parametric and non parametric mediation analysis. This package performs the methods and suggestions in Imai, Keele and Yamamoto (2010) <DOI:10.1214/10-STS321>, Imai, Keele and Tingley (2010) <DOI:10.1037/a0020761>, Imai, Tingley and Yamamoto (2013) <DOI:10.1111/j.1467-985X.2012.01032.x>, Imai and Yamamoto (2013) <DOI:10.1093/pan/mps040> and Yamamoto (2013) <http://web.mit.edu/teppei/www/research/IVmediate.pdf>. In addition to the estimation of causal mediation effects, the software also allows researchers to conduct sensitivity analysis for certain parametric models.

Maintained by Teppei Yamamoto. Last updated 6 years ago.

6.7 match 10.48 score 896 scripts 11 dependents

paulhibbing

Observation:Collect and Process Physical Activity Direct Observation Data

Two-part system for first collecting then managing direct observation data, as described by Hibbing PR, Ellingson LD, Dixon PM, & Welk GJ (2018) <doi:10.1249/MSS.0000000000001486>.

Maintained by Paul R. Hibbing. Last updated 3 years ago.

14.9 match 4.70 score 10 scripts

mattblackwell

DirectEffects:Estimating Controlled Direct Effects for Explaining Causal Findings

A set of functions to estimate the controlled direct effect of treatment fixing a potential mediator to a specific value. Implements the sequential g-estimation estimator described in Vansteelandt (2009) <doi:10.1097/EDE.0b013e3181b6f4c9> and Acharya, Blackwell, and Sen (2016) <doi:10.1017/S0003055416000216> and the telescope matching estimator described in Blackwell and Strezhnev (2020) <doi:10.1111/rssa.12759>.

Maintained by Matthew Blackwell. Last updated 20 days ago.

11.5 match 18 stars 6.09 score 17 scripts

r-spatial

sf:Simple Features for R

Support for simple feature access, a standardized way to encode and analyze spatial vector data. Binds to 'GDAL' <doi: 10.5281/zenodo.5884351> for reading and writing data, to 'GEOS' <doi: 10.5281/zenodo.11396894> for geometrical operations, and to 'PROJ' <doi: 10.5281/zenodo.5884394> for projection conversions and datum transformations. Uses by default the 's2' package for geometry operations on geodetic (long/lat degree) coordinates.

Maintained by Edzer Pebesma. Last updated 16 days ago.

gdal geos proj spatial cpp

3.1 match 1.4k stars 22.42 score 117k scripts 1.2k dependents

psychmeta

psychmeta:Psychometric Meta-Analysis Toolkit

Tools for computing bare-bones and psychometric meta-analyses and for generating psychometric data for use in meta-analysis simulations. Supports bare-bones, individual-correction, and artifact-distribution methods for meta-analyzing correlations and d values. Includes tools for converting effect sizes, computing sporadic artifact corrections, reshaping meta-analytic databases, computing multivariate corrections for range variation, and more. Bugs can be reported to <https://github.com/psychmeta/psychmeta/issues> or <issues@psychmeta.com>.

Maintained by Jeffrey A. Dahlke. Last updated 9 months ago.

hacktoberfest meta-analysis psychology psychometric psychometrics

8.2 match 57 stars 8.25 score 151 scripts

easystats

effectsize:Indices of Effect Size

Provide utilities to work with indices of effect size for a wide variety of models and hypothesis tests (see list of supported models using the function 'insight::supported_models()'), allowing computation of and conversion between indices such as Cohen's d, r, odds, etc. References: Ben-Shachar et al. (2020) <doi:10.21105/joss.02815>.

Maintained by Mattan S. Ben-Shachar. Last updated 1 months ago.

anova cohens-d compute conversion correlation effect-size effectsize hacktoberfest hedges-g interpretation standardization standardized statistics

4.1 match 344 stars 16.38 score 1.8k scripts 29 dependents

guido-s

netmeta:Network Meta-Analysis using Frequentist Methods

A comprehensive set of functions providing frequentist methods for network meta-analysis (Balduzzi et al., 2023) <doi:10.18637/jss.v106.i02> and supporting Schwarzer et al. (2015) <doi:10.1007/978-3-319-21416-0>, Chapter 8 "Network Meta-Analysis": - frequentist network meta-analysis following Rücker (2012) <doi:10.1002/jrsm.1058>; - additive network meta-analysis for combinations of treatments (Rücker et al., 2020) <doi:10.1002/bimj.201800167>; - network meta-analysis of binary data using the Mantel-Haenszel or non-central hypergeometric distribution method (Efthimiou et al., 2019) <doi:10.1002/sim.8158>, or penalised logistic regression (Evrenoglou et al., 2022) <doi:10.1002/sim.9562>; - rankograms and ranking of treatments by the Surface under the cumulative ranking curve (SUCRA) (Salanti et al., 2013) <doi:10.1016/j.jclinepi.2010.03.016>; - ranking of treatments using P-scores (frequentist analogue of SUCRAs without resampling) according to Rücker & Schwarzer (2015) <doi:10.1186/s12874-015-0060-8>; - split direct and indirect evidence to check consistency (Dias et al., 2010) <doi:10.1002/sim.3767>, (Efthimiou et al., 2019) <doi:10.1002/sim.8158>; - league table with network meta-analysis results; - 'comparison-adjusted' funnel plot (Chaimani & Salanti, 2012) <doi:10.1002/jrsm.57>; - net heat plot and design-based decomposition of Cochran's Q according to Krahn et al. (2013) <doi:10.1186/1471-2288-13-35>; - measures characterizing the flow of evidence between two treatments by König et al. (2013) <doi:10.1002/sim.6001>; - automated drawing of network graphs described in Rücker & Schwarzer (2016) <doi:10.1002/jrsm.1143>; - partial order of treatment rankings ('poset') and Hasse diagram for 'poset' (Carlsen & Bruggemann, 2014) <doi:10.1002/cem.2569>; (Rücker & Schwarzer, 2017) <doi:10.1002/jrsm.1270>; - contribution matrix as described in Papakonstantinou et al. (2018) <doi:10.12688/f1000research.14770.3> and Davies et al. (2022) <doi:10.1002/sim.9346>; - subgroup network meta-analysis.

Maintained by Guido Schwarzer. Last updated 2 days ago.

meta-analysis network-meta-analysis rstudio

5.7 match 33 stars 11.82 score 199 scripts 10 dependents

kosukeimai

RCT2:Designing and Analyzing Two-Stage Randomized Experiments

Provides various statistical methods for designing and analyzing two-stage randomized controlled trials using the methods developed by Imai, Jiang, and Malani (2021) <doi:10.1080/01621459.2020.1775612> and (2022+) <doi:10.48550/arXiv.2011.07677>. The package enables the estimation of direct and spillover effects, conduct hypotheses tests, and conduct sample size calculation for two-stage randomized controlled trials.

Maintained by Kosuke Imai. Last updated 2 years ago.

14.1 match 5 stars 4.70 score 4 scripts

bioc

metapod:Meta-Analyses on P-Values of Differential Analyses

Implements a variety of methods for combining p-values in differential analyses of genome-scale datasets. Functions can combine p-values across different tests in the same analysis (e.g., genomic windows in ChIP-seq, exons in RNA-seq) or for corresponding tests across separate analyses (e.g., replicated comparisons, effect of different treatment conditions). Support is provided for handling log-transformed input p-values, missing values and weighting where appropriate.

Maintained by Aaron Lun. Last updated 3 months ago.

multiplecomparison differentialpeakcalling cpp

8.8 match 7.44 score 17 scripts 46 dependents

ssa-statistical-team-projects

povmap:Extension to the 'emdi' Package

The R package 'povmap' supports small area estimation of means and poverty headcount rates. It adds several new features to the 'emdi' package (see "The R Package emdi for Estimating and Mapping Regionally Disaggregated Indicators" by Kreutzmann et al. (2019) <doi:10.18637/jss.v091.i07>). These include new options for incorporating survey weights, ex-post benchmarking of estimates, two additional transformations, several new convenient functions to assist with reporting results, and a wrapper function to facilitate access from 'Stata'.

Maintained by Ifeanyi Edochie. Last updated 5 months ago.

14.2 match 1 stars 4.60 score 10 scripts

opengeos

whitebox:'WhiteboxTools' R Frontend

An R frontend for the 'WhiteboxTools' library, which is an advanced geospatial data analysis platform developed by Prof. John Lindsay at the University of Guelph's Geomorphometry and Hydrogeomatics Research Group. 'WhiteboxTools' can be used to perform common geographical information systems (GIS) analysis operations, such as cost-distance analysis, distance buffering, and raster reclassification. Remote sensing and image processing tasks include image enhancement (e.g. panchromatic sharpening, contrast adjustments), image mosaicing, numerous filtering operations, simple classification (k-means), and common image transformations. 'WhiteboxTools' also contains advanced tooling for spatial hydrological analysis (e.g. flow-accumulation, watershed delineation, stream network analysis, sink removal), terrain analysis (e.g. common terrain indices such as slope, curvatures, wetness index, hillshading; hypsometric analysis; multi-scale topographic position analysis), and LiDAR data processing. Suggested citation: Lindsay (2016) <doi:10.1016/j.cageo.2016.07.003>.

Maintained by Andrew Brown. Last updated 5 months ago.

geomorphometry geoprocessing geospatial gis hydrology remote-sensing rstudio

6.7 match 173 stars 9.65 score 203 scripts 2 dependents

bioc

CatsCradle:This package provides methods for analysing spatial transcriptomics data and for discovering gene clusters

This package addresses two broad areas. It allows for in-depth analysis of spatial transcriptomic data by identifying tissue neighbourhoods. These are contiguous regions of tissue surrounding individual cells. 'CatsCradle' allows for the categorisation of neighbourhoods by the cell types contained in them and the genes expressed in them. In particular, it produces Seurat objects whose individual elements are neighbourhoods rather than cells. In addition, it enables the categorisation and annotation of genes by producing Seurat objects whose elements are genes.

Maintained by Michael Shapiro. Last updated 1 months ago.

biologicalquestion statisticalmethod geneexpression singlecell transcriptomics spatial

9.8 match 3 stars 6.50 score

marioangst

motifr:Motif Analysis in Multi-Level Networks

Tools for motif analysis in multi-level networks. Multi-level networks combine multiple networks in one, e.g. social-ecological networks. Motifs are small configurations of nodes and edges (subgraphs) occurring in networks. 'motifr' can visualize multi-level networks, count multi-level network motifs and compare motif occurrences to baseline models. It also identifies contributions of existing or potential edges to motifs to find critical or missing edges. The package is in many parts an R wrapper for the excellent 'SESMotifAnalyser' 'Python' package written by Tim Seppelt.

Maintained by Mario Angst. Last updated 4 years ago.

11.7 match 15 stars 5.43 score 18 scripts

r-lib

remotes:R Package Installation from Remote Repositories, Including 'GitHub'

Download and install R packages stored in 'GitHub', 'GitLab', 'Bitbucket', 'Bioconductor', or plain 'subversion' or 'git' repositories. This package provides the 'install_*' functions in 'devtools'. Indeed most of the code was copied over from 'devtools'.

Maintained by Gábor Csárdi. Last updated 19 days ago.

3.7 match 341 stars 17.30 score 5.8k scripts 248 dependents

easystats

bayestestR:Understand and Describe Bayesian Models and Posterior Distributions

Provides utilities to describe posterior distributions and Bayesian models. It includes point-estimates such as Maximum A Posteriori (MAP), measures of dispersion (Highest Density Interval - HDI; Kruschke, 2015 <doi:10.1016/C2012-0-00477-2>) and indices used for null-hypothesis testing (such as ROPE percentage, pd and Bayes factors). References: Makowski et al. (2021) <doi:10.21105/joss.01541>.

Maintained by Dominique Makowski. Last updated 4 hours ago.

bayes-factors bayesfactor bayesian bayesian-framework credible-interval easystats hacktoberfest hdi map posterior-distributions rope

3.8 match 579 stars 16.83 score 2.2k scripts 82 dependents

r-forge

pcalg:Methods for Graphical Models and Causal Inference

Functions for causal structure learning and causal inference using graphical models. The main algorithms for causal structure learning are PC (for observational data without hidden variables), FCI and RFCI (for observational data with hidden variables), and GIES (for a mix of data from observational studies (i.e. observational data) and data from experiments involving interventions (i.e. interventional data) without hidden variables). For causal inference the IDA algorithm, the Generalized Backdoor Criterion (GBC), the Generalized Adjustment Criterion (GAC) and some related functions are implemented. Functions for incorporating background knowledge are provided.

Maintained by Markus Kalisch. Last updated 6 months ago.

openblas cpp

8.6 match 7.32 score 700 scripts 19 dependents

symbolixau

h3r:Hexagonal Hierarchical Geospatial Indexing System

Provides access to Uber's 'H3' geospatial indexing system via 'h3lib' <https://CRAN.R-project.org/package=h3lib>. 'h3r' is designed to mimic the 'H3' Application Programming Interface (API) <https://h3geo.org/docs/api/indexing/>, so that any function in the API is also available in 'h3r'.

Maintained by David Cooley. Last updated 3 months ago.

13.8 match 5 stars 4.52 score 33 scripts

stathin

ggm:Graphical Markov Models with Mixed Graphs

Provides functions for defining mixed graphs containing three types of edges, directed, undirected and bi-directed, with possibly multiple edges. These graphs are useful because they capture fundamental independence structures in multivariate distributions and in the induced distributions after marginalization and conditioning. The package is especially concerned with Gaussian graphical models for (i) ML estimation for directed acyclic graphs, undirected and bi-directed graphs and ancestral graph models (ii) testing several conditional independencies (iii) checking global identification of DAG Gaussian models with one latent variable (iv) testing Markov equivalences and generating Markov equivalent graphs of specific types.

Maintained by Giovanni M. Marchetti. Last updated 1 years ago.

8.7 match 7.07 score 295 scripts 29 dependents

dmurdoch

rgl:3D Visualization Using OpenGL

Provides medium to high level functions for 3D interactive graphics, including functions modelled on base graphics (plot3d(), etc.) as well as functions for constructing representations of geometric objects (cube3d(), etc.). Output may be on screen using OpenGL, or to various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.

Maintained by Duncan Murdoch. Last updated 2 months ago.

graphics opengl rgl webgl libglu libglvnd libpng libx11 freetype cpp

3.5 match 91 stars 17.49 score 7.3k scripts 300 dependents

ajsims1704

rdecision:Decision Analytic Modelling in Health Economics

Classes and functions for modelling health care interventions using decision trees and semi-Markov models. Mechanisms are provided for associating an uncertainty distribution with each source variable and for ensuring transparency of the mathematical relationships between variables. The package terminology follows Briggs "Decision Modelling for Health Economic Evaluation" (2006, ISBN:978-0-19-852662-9).

Maintained by Andrew Sims. Last updated 1 months ago.

9.3 match 3 stars 6.46 score 22 scripts

ovvo-financial

NNS:Nonlinear Nonparametric Statistics

Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences. NNS offers: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization, Stochastic dominance and Advanced Monte Carlo sampling. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).

Maintained by Fred Viole. Last updated 5 days ago.

clustering econometrics machine-learning nonlinear nonparametric partial-moments statistics time-series cpp

5.4 match 71 stars 10.96 score 66 scripts 3 dependents

symbolixau

googleway:Accesses Google Maps APIs to Retrieve Data and Plot Maps

Provides a mechanism to plot a 'Google Map' from 'R' and overlay it with shapes and markers. Also provides access to 'Google Maps' APIs, including places, directions, roads, distances, geocoding, elevation and timezone.

Maintained by David Cooley. Last updated 6 months ago.

google-map google-maps google-maps-api google-maps-javascript-api spatial spatial-analysis

6.1 match 236 stars 9.67 score 536 scripts 2 dependents

ropensci

stplanr:Sustainable Transport Planning

Tools for transport planning with an emphasis on spatial transport data and non-motorized modes. The package was originally developed to support the 'Propensity to Cycle Tool', a publicly available strategic cycle network planning tool (Lovelace et al. 2017) <doi:10.5198/jtlu.2016.862>, but has since been extended to support public transport routing and accessibility analysis (Moreno-Monroy et al. 2017) <doi:10.1016/j.jtrangeo.2017.08.012> and routing with locally hosted routing engines such as 'OSRM' (Lowans et al. 2023) <doi:10.1016/j.enconman.2023.117337>. The main functions are for creating and manipulating geographic "desire lines" from origin-destination (OD) data (building on the 'od' package); calculating routes on the transport network locally and via interfaces to routing services such as <https://cyclestreets.net/> (Desjardins et al. 2021) <doi:10.1007/s11116-021-10197-1>; and calculating route segment attributes such as bearing. The package implements the 'travel flow aggregration' method described in Morgan and Lovelace (2020) <doi:10.1177/2399808320942779> and the 'OD jittering' method described in Lovelace et al. (2022) <doi:10.32866/001c.33873>. Further information on the package's aim and scope can be found in the vignettes and in a paper in the R Journal (Lovelace and Ellison 2018) <doi:10.32614/RJ-2018-053>, and in a paper outlining the landscape of open source software for geographic methods in transport planning (Lovelace, 2021) <doi:10.1007/s10109-020-00342-2>.

Maintained by Robin Lovelace. Last updated 7 months ago.

cycle cycling desire-lines origin-destination peer-reviewed pubic-transport route-network routes routing spatial transport transport-planning transportation walking

4.8 match 427 stars 12.31 score 684 scripts 3 dependents

dankelley

oce:Analysis of Oceanographic Data

Supports the analysis of Oceanographic data, including 'ADCP' measurements, measurements made with 'argo' floats, 'CTD' measurements, sectional data, sea-level time series, coastline and topographic data, etc. Provides specialized functions for calculating seawater properties such as potential temperature in either the 'UNESCO' or 'TEOS-10' equation of state. Produces graphical displays that conform to the conventions of the Oceanographic literature. This package is discussed extensively by Kelley (2018) "Oceanographic Analysis with R" <doi:10.1007/978-1-4939-8844-0>.

Maintained by Dan Kelley. Last updated 1 days ago.

oceanography fortran cpp

3.8 match 146 stars 15.42 score 4.2k scripts 18 dependents

amices

mice:Multivariate Imputation by Chained Equations

Multiple imputation using Fully Conditional Specification (FCS) implemented by the MICE algorithm as described in Van Buuren and Groothuis-Oudshoorn (2011) <doi:10.18637/jss.v045.i03>. Each variable has its own imputation model. Built-in imputation models are provided for continuous data (predictive mean matching, normal), binary data (logistic regression), unordered categorical data (polytomous logistic regression) and ordered categorical data (proportional odds). MICE can also impute continuous two-level data (normal model, pan, second-level variables). Passive imputation can be used to maintain consistency between variables. Various diagnostic plots are available to inspect the quality of the imputations.

Maintained by Stef van Buuren. Last updated 7 days ago.

chained-equations fcs imputation mice missing-data missing-values multiple-imputation multivariate-data cpp

3.5 match 462 stars 16.50 score 10k scripts 154 dependents

sensitivequestions

list:Statistical Methods for the Item Count Technique and List Experiment

Allows researchers to conduct multivariate statistical analyses of survey data with list experiments. This survey methodology is also known as the item count technique or the unmatched count technique and is an alternative to the commonly used randomized response method. The package implements the methods developed by Imai (2011) <doi:10.1198/jasa.2011.ap10415>, Blair and Imai (2012) <doi:10.1093/pan/mpr048>, Blair, Imai, and Lyall (2013) <doi:10.1111/ajps.12086>, Imai, Park, and Greene (2014) <doi:10.1093/pan/mpu017>, Aronow, Coppock, Crawford, and Green (2015) <doi:10.1093/jssam/smu023>, Chou, Imai, and Rosenfeld (2017) <doi:10.1177/0049124117729711>, and Blair, Chou, and Imai (2018) <https://imai.fas.harvard.edu/research/files/listerror.pdf>. This includes a Bayesian MCMC implementation of regression for the standard and multiple sensitive item list experiment designs and a random effects setup, a Bayesian MCMC hierarchical regression model with up to three hierarchical groups, the combined list experiment and endorsement experiment regression model, a joint model of the list experiment that enables the analysis of the list experiment as a predictor in outcome regression models, a method for combining list experiments with direct questions, and methods for diagnosing and adjusting for response error. In addition, the package implements the statistical test that is designed to detect certain failures of list experiments, and a placebo test for the list experiment using data from direct questions.

Maintained by Graeme Blair. Last updated 1 years ago.

openblas

8.7 match 7 stars 6.60 score 191 scripts

astamm

nloptr:R Interface to NLopt

Solve optimization problems using an R interface to NLopt. NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. See <https://nlopt.readthedocs.io/en/latest/NLopt_Algorithms/> for more information on the available algorithms. Building from included sources requires 'CMake'. On Linux and 'macOS', if a suitable system build of NLopt (2.7.0 or later) is found, it is used; otherwise, it is built from included sources via 'CMake'. On Windows, NLopt is obtained through 'rwinlib' for 'R <= 4.1.x' or grabbed from the appropriate toolchain for 'R >= 4.2.0'.

Maintained by Aymeric Stamm. Last updated 13 hours ago.

cpp

3.3 match 108 stars 17.13 score 1.1k scripts 1.8k dependents

bioc

hmdbQuery:utilities for exploration of human metabolome database

Define utilities for exploration of human metabolome database, including functions to retrieve specific metabolite entries and data snapshots with pairwise associations (metabolite-gene,-protein,-disease).

Maintained by VJ Carey. Last updated 5 months ago.

metabolomics infrastructure

13.3 match 4.11 score 13 scripts

hadley

productplots:Product Plots for R

Framework for visualising tables of counts, proportions and probabilities. The framework is called product plots, alluding to the computation of area as a product of height and width, and the statistical concept of generating a joint distribution from the product of conditional and marginal distributions. The framework, with extensions, is sufficient to encompass over 20 visualisations previously described in fields of statistical graphics and 'infovis', including bar charts, mosaic plots, 'treemaps', equal area plots and fluctuation diagrams.

Maintained by Hadley Wickham. Last updated 6 months ago.

7.5 match 29 stars 7.26 score 74 scripts 5 dependents

robindenz1

simDAG:Simulate Data from a DAG and Associated Node Information

Simulate complex data from a given directed acyclic graph and information about each individual node. Root nodes are simply sampled from the specified distribution. Child Nodes are simulated according to one of many implemented regressions, such as logistic regression, linear regression, poisson regression and more. Also includes a comprehensive framework for discrete-time simulation, which can generate even more complex longitudinal data.

Maintained by Robin Denz. Last updated 21 days ago.

causal-inference directed-acyclic-graph simulation

7.2 match 10 stars 7.55 score 77 scripts

cran

bnlearn:Bayesian Network Structure Learning, Parameter Learning and Inference

Bayesian network structure learning, parameter learning and inference. This package implements constraint-based (PC, GS, IAMB, Inter-IAMB, Fast-IAMB, MMPC, Hiton-PC, HPC), pairwise (ARACNE and Chow-Liu), score-based (Hill-Climbing and Tabu Search) and hybrid (MMHC, RSMAX2, H2PC) structure learning algorithms for discrete, Gaussian and conditional Gaussian networks, along with many score functions and conditional independence tests. The Naive Bayes and the Tree-Augmented Naive Bayes (TAN) classifiers are also implemented. Some utility functions (model comparison and manipulation, random data generation, arc orientation testing, simple and advanced plots) are included, as well as support for parameter estimation (maximum likelihood and Bayesian) and inference, conditional probability queries, cross-validation, bootstrap and model averaging. Development snapshots with the latest bugfixes are available from <https://www.bnlearn.com/>.

Maintained by Marco Scutari. Last updated 2 months ago.

openblas

7.0 match 57 stars 7.72 score 32 dependents

thomasp85

tidygraph:A Tidy API for Graph Manipulation

A graph, while not "tidy" in itself, can be thought of as two tidy data frames describing node and edge data respectively. 'tidygraph' provides an approach to manipulate these two virtual data frames using the API defined in the 'dplyr' package, as well as provides tidy interfaces to a lot of common graph algorithms.

Maintained by Thomas Lin Pedersen. Last updated 1 months ago.

graph-algorithms graph-manipulation igraph network-analysis tidyverse cpp

3.5 match 553 stars 14.74 score 4.6k scripts 136 dependents

luukvdmeer

sfnetworks:Tidy Geospatial Networks

Provides a tidy approach to spatial network analysis, in the form of classes and functions that enable a seamless interaction between the network analysis package 'tidygraph' and the spatial analysis package 'sf'.

Maintained by Lucas van der Meer. Last updated 3 months ago.

geospatial-networks network-analysis rspatial simple-features spatial-analysis spatial-data-science spatial-networks tidygraph tidyverse

5.3 match 372 stars 9.63 score 332 scripts 6 dependents

jagm03

kernstadapt:Adaptive Kernel Estimators for Point Process Intensities on Linear Networks

Adaptive estimation of the first-order intensity function of a spatio-temporal point process using kernels and variable bandwidths. The methodology used for estimation is presented in González and Moraga (2022). <doi:10.48550/arXiv.2208.12026>.

Maintained by Jonatan A González. Last updated 6 months ago.

9.1 match 6 stars 5.51 score 12 scripts

wwiedermann

dda:Direction Dependence Analysis

A collection of tests to analyze the causal direction of dependence in linear models (Wiedermann, W., & von Eye, A., 2025, ISBN: 9781009381390). The package includes functions to perform Direction Dependence Analysis for variable distributions, residual distributions, and independence properties of predictors and residuals in competing causal models. In addition, the package contains functions to test the causal direction of dependence in conditional models (i.e., models with interaction terms) For more information see <https://www.ddaproject.com>.

Maintained by Wolfgang Wiedermann. Last updated 9 days ago.

13.2 match 3.81 score

clugen

clugenr:Multidimensional Cluster Generation Using Support Lines

An implementation of the clugen algorithm for generating multidimensional clusters with arbitrary distributions. Each cluster is supported by a line segment, the position, orientation and length of which guide where the respective points are placed. This package is described in Fachada & de Andrade (2023) <doi:10.1016/j.knosys.2023.110836>.

Maintained by Nuno Fachada. Last updated 7 months ago.

multidimensional-clusters multidimensional-data synthetic-clusters synthetic-data-generator synthetic-dataset-generation

9.2 match 5 stars 5.39 score 14 scripts

dkaschek

dMod:Dynamic Modeling and Parameter Estimation in ODE Models

The framework provides functions to generate ODEs of reaction networks, parameter transformations, observation functions, residual functions, etc. The framework follows the paradigm that derivative information should be used for optimization whenever possible. Therefore, all major functions produce and can handle expressions for symbolic derivatives.

Maintained by Daniel Kaschek. Last updated 10 days ago.

5.9 match 20 stars 8.35 score 251 scripts

haleyjeppson

ggmosaic:Mosaic Plots in the 'ggplot2' Framework

Mosaic plots in the 'ggplot2' framework. Mosaic plot functionality is provided in a single 'ggplot2' layer by calling the geom 'mosaic'.

Maintained by Haley Jeppson. Last updated 6 months ago.

4.2 match 167 stars 11.63 score 1.8k scripts 4 dependents

bioc

LACE:Longitudinal Analysis of Cancer Evolution (LACE)

LACE is an algorithmic framework that processes single-cell somatic mutation profiles from cancer samples collected at different time points and in distinct experimental settings, to produce longitudinal models of cancer evolution. The approach solves a Boolean Matrix Factorization problem with phylogenetic constraints, by maximizing a weighed likelihood function computed on multiple time points.

Maintained by Davide Maspero. Last updated 2 days ago.

biomedicalinformatics singlecell somaticmutation

6.3 match 15 stars 7.75 score 3 scripts

ropenspain

climaemet:Climate AEMET Tools

Tools to download the climatic data of the Spanish Meteorological Agency (AEMET) directly from R using their API and create scientific graphs (climate charts, trend analysis of climate time series, temperature and precipitation anomalies maps, warming stripes graphics, climatograms, etc.).

Maintained by Diego Hernangómez. Last updated 1 months ago.

aemet climate data forecast-api ropenspain science spain weather-api

5.8 match 43 stars 8.32 score 59 scripts

bioc

cellmigRation:Track Cells, Analyze Cell Trajectories and Compute Migration Statistics

Import TIFF images of fluorescently labeled cells, and track cell movements over time. Parallelization is supported for image processing and for fast computation of cell trajectories. In-depth analysis of cell trajectories is enabled by 15 trajectory analysis functions.

Maintained by Waldir Leoncio. Last updated 5 months ago.

cellbiology datarepresentation dataimport bioconductor-package cell-tracking shiny trajectory-analysis

10.5 match 4.60 score 4 scripts

wgunderwood

motifcluster:Motif-Based Spectral Clustering of Weighted Directed Networks

Tools for spectral clustering of weighted directed networks using motif adjacency matrices. Methods perform well on large and sparse networks, and random sampling methods for generating weighted directed networks are also provided. Based on methodology detailed in Underwood, Elliott and Cucuringu (2020) <arXiv:2004.01293>.

Maintained by William George Underwood. Last updated 9 months ago.

8.4 match 26 stars 5.72 score 4 scripts

bioc

rawrr:Direct Access to Orbitrap Data and Beyond

This package wraps the functionality of the Thermo Fisher Scientic RawFileReader .NET 8.0 assembly. Within the R environment, spectra and chromatograms are represented by S3 objects. The package provides basic functions to download and install the required third-party libraries. The package is developed, tested, and used at the Functional Genomics Center Zurich, Switzerland.

Maintained by Christian Panse. Last updated 3 months ago.

massspectrometry proteomics metabolomics infrastructure software fast mass-spectrometry multiplatform orbitrap-ms

5.8 match 56 stars 8.19 score 23 scripts 2 dependents

cran

sae:Small Area Estimation

Functions for small area estimation.

Maintained by Yolanda Marhuenda. Last updated 5 years ago.

8.7 match 6 stars 5.49 score 83 scripts 8 dependents

pyanglab

directPA:Direction Analysis for Pathways and Kinases

Direction analysis is a set of tools designed to identify combinatorial effects of multiple treatments/conditions on pathways and kinases profiled by microarray, RNA-seq, proteomics, or phosphoproteomics data. See Yang P et al (2014) <doi:10.1093/bioinformatics/btt616>; and Yang P et al. (2016) <doi:10.1002/pmic.201600068>.

Maintained by Pengyi Yang. Last updated 1 years ago.

11.3 match 4.14 score 31 scripts 1 dependents

nhejazi

medoutcon:Efficient Natural and Interventional Causal Mediation Analysis

Efficient estimators of interventional (in)direct effects in the presence of mediator-outcome confounding affected by exposure. The effects estimated allow for the impact of the exposure on the outcome through a direct path to be disentangled from that through mediators, even in the presence of intermediate confounders that complicate such a relationship. Currently supported are non-parametric efficient one-step and targeted minimum loss estimators based on the formulation of Díaz, Hejazi, Rudolph, and van der Laan (2020) <doi:10.1093/biomet/asaa085>. Support for efficient estimation of the natural (in)direct effects is also provided, appropriate for settings in which intermediate confounders are absent. The package also supports estimation of these effects when the mediators are measured using outcome-dependent two-phase sampling designs (e.g., case-cohort).

Maintained by Nima Hejazi. Last updated 1 years ago.

causal-inference causal-machine-learning inverse-probability-weights machine-learning mediation-analysis stochastic-interventions targeted-learning treatment-effects

10.4 match 13 stars 4.46 score 22 scripts

nhejazi

medshift:Causal mediation analysis for stochastic interventions

Estimators of a parameter arising in the decomposition of the population intervention (in)direct effect of stochastic interventions in causal mediation analysis, including efficient one-step, targeted minimum loss (TML), re-weighting (IPW), and substitution estimators. The parameter estimated constitutes a part of each of the population intervention (in)direct effects. These estimators may be used in assessing population intervention (in)direct effects under stochastic treatment regimes, including incremental propensity score interventions and modified treatment policies. The methodology was first discussed by I Díaz and NS Hejazi (2020) <doi:10.1111/rssb.12362>.

Maintained by Nima Hejazi. Last updated 3 years ago.

causal-inference inverse-probability-weights machine-learning mediation-analysis stochastic-interventions targeted-learning treatment-effects

12.4 match 9 stars 3.73 score 12 scripts

stan-dev

loo:Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian Models

Efficient approximate leave-one-out cross-validation (LOO) for Bayesian models fit using Markov chain Monte Carlo, as described in Vehtari, Gelman, and Gabry (2017) <doi:10.1007/s11222-016-9696-4>. The approximation uses Pareto smoothed importance sampling (PSIS), a new procedure for regularizing importance weights. As a byproduct of the calculations, we also obtain approximate standard errors for estimated predictive errors and for the comparison of predictive errors between models. The package also provides methods for using stacking and other model weighting techniques to average Bayesian predictive distributions.

Maintained by Jonah Gabry. Last updated 3 days ago.

bayes bayesian bayesian-data-analysis bayesian-inference bayesian-methods bayesian-statistics cross-validation information-criterion model-comparison stan

2.7 match 152 stars 17.30 score 2.6k scripts 297 dependents

bioc

RBGL:An interface to the BOOST graph library

A fairly extensive and comprehensive interface to the graph algorithms contained in the BOOST library.

Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.

graphandnetwork network cpp

5.3 match 8.59 score 320 scripts 132 dependents

egarpor

sphunif:Uniformity Tests on the Circle, Sphere, and Hypersphere

Implementation of uniformity tests on the circle and (hyper)sphere. The main function of the package is unif_test(), which conveniently collects more than 35 tests for assessing uniformity on S^{p-1} = {x in R^p : ||x|| = 1}, p >= 2. The test statistics are implemented in the unif_stat() function, which allows computing several statistics for different samples within a single call, thus facilitating Monte Carlo experiments. Furthermore, the unif_stat_MC() function allows parallelizing them in a simple way. The asymptotic null distributions of the statistics are available through the function unif_stat_distr(). The core of 'sphunif' is coded in C++ by relying on the 'Rcpp' package. The package also provides several novel datasets and gives the replicability for the data applications/simulations in García-Portugués et al. (2021) <doi:10.1007/978-3-030-69944-4_12>, García-Portugués et al. (2023) <doi:10.3150/21-BEJ1454>, García-Portugués et al. (2024) <doi:10.48550/arXiv.2108.09874>, and Fernández-de-Marcos and García-Portugués (2024) <doi:10.48550/arXiv.2405.13531>.

Maintained by Eduardo García-Portugués. Last updated 10 months ago.

circular-statistics directional-statistics uniformity uniformity-tests openblas cpp

7.5 match 8 stars 6.11 score 18 scripts 2 dependents

christophergandrud

networkD3:D3 JavaScript Network Graphs from R

Creates 'D3' 'JavaScript' network, tree, dendrogram, and Sankey graphs from 'R'.

Maintained by Christopher Gandrud. Last updated 6 years ago.

d3js networks

3.4 match 654 stars 13.55 score 3.4k scripts 31 dependents

adeverse

adespatial:Multivariate Multiscale Spatial Analysis

Tools for the multiscale spatial analysis of multivariate data. Several methods are based on the use of a spatial weighting matrix and its eigenvector decomposition (Moran's Eigenvectors Maps, MEM). Several approaches are described in the review Dray et al (2012) <doi:10.1890/11-1183.1>.

Maintained by Aurélie Siberchicot. Last updated 13 days ago.

openblas

4.1 match 36 stars 11.06 score 398 scripts 2 dependents

openair-project

openair:Tools for the Analysis of Air Pollution Data

Tools to analyse, interpret and understand air pollution data. Data are typically regular time series and air quality measurement, meteorological data and dispersion model output can be analysed. The package is described in Carslaw and Ropkins (2012, <doi:10.1016/j.envsoft.2011.09.008>) and subsequent papers.

Maintained by David Carslaw. Last updated 25 days ago.

air-quality air-quality-data meteorology openair cpp

3.5 match 311 stars 12.91 score 1.2k scripts 12 dependents

ropensci

fireexposuR:Compute and Visualize Wildfire Exposure

This package computes and visualizes wildfire exposure using the methods documented in a series of scientific publications.

Maintained by Air Forbes. Last updated 20 days ago.

8.7 match 5 stars 5.23 score 4 scripts

bioc

ChIPpeakAnno:Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data

The package encompasses a range of functions for identifying the closest gene, exon, miRNA, or custom features—such as highly conserved elements and user-supplied transcription factor binding sites. Additionally, users can retrieve sequences around the peaks and obtain enriched Gene Ontology (GO) or Pathway terms. In version 2.0.5 and beyond, new functionalities have been introduced. These include features for identifying peaks associated with bi-directional promoters along with summary statistics (peaksNearBDP), summarizing motif occurrences in peaks (summarizePatternInPeaks), and associating additional identifiers with annotated peaks or enrichedGO (addGeneIDs). The package integrates with various other packages such as biomaRt, IRanges, Biostrings, BSgenome, GO.db, multtest, and stat to enhance its analytical capabilities.

Maintained by Jianhong Ou. Last updated 2 months ago.

annotation chipseq chipchip

5.2 match 8.75 score 584 scripts 6 dependents

steffenmoritz

imputeR:A General Multivariate Imputation Framework

Multivariate Expectation-Maximization (EM) based imputation framework that offers several different algorithms. These include regularisation methods like Lasso and Ridge regression, tree-based models and dimensionality reduction methods like PCA and PLS.

Maintained by Steffen Moritz. Last updated 4 years ago.

missing-data

9.1 match 16 stars 4.94 score 54 scripts

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.

analysis comparative-methods path phylogenetics

5.5 match 13 stars 8.10 score 81 scripts 1 dependents

tidyverse

ggplot2:Create Elegant Data Visualisations Using the Grammar of Graphics

A system for 'declaratively' creating graphics, based on "The Grammar of Graphics". You provide the data, tell 'ggplot2' how to map variables to aesthetics, what graphical primitives to use, and it takes care of the details.

Maintained by Thomas Lin Pedersen. Last updated 9 days ago.

data-visualisation visualisation

1.8 match 6.6k stars 25.10 score 645k scripts 7.5k dependents

bioc

graph:graph: A package to handle graph data structures

A package that implements some simple graph handling capabilities.

Maintained by Bioconductor Package Maintainer. Last updated 11 days ago.

graphandnetwork

3.7 match 11.78 score 764 scripts 342 dependents

sssydysss

TransProR:Analysis and Visualization of Multi-Omics Data

A tool for comprehensive transcriptomic data analysis, with a focus on transcript-level data preprocessing, expression profiling, differential expression analysis, and functional enrichment. It enables researchers to identify key biological processes, disease biomarkers, and gene regulatory mechanisms. 'TransProR' is aimed at researchers and bioinformaticians working with RNA-Seq data, providing an intuitive framework for in-depth analysis and visualization of transcriptomic datasets. The package includes comprehensive documentation and usage examples to guide users through the entire analysis pipeline. The differential expression analysis methods incorporated in the package include 'limma' (Ritchie et al., 2015, <doi:10.1093/nar/gkv007>; Smyth, 2005, <doi:10.1007/0-387-29362-0_23>), 'edgeR' (Robinson et al., 2010, <doi:10.1093/bioinformatics/btp616>), 'DESeq2' (Love et al., 2014, <doi:10.1186/s13059-014-0550-8>), and Wilcoxon tests (Li et al., 2022, <doi:10.1186/s13059-022-02648-4>), providing flexible and robust approaches to RNA-Seq data analysis. For more information, refer to the package vignettes and related publications.

Maintained by Dongyue Yu. Last updated 20 days ago.

5.7 match 174 stars 7.55 score 34 scripts

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 5 days ago.

6.1 match 4 stars 6.99 score 39 scripts

jamiemkass

ENMeval:Automated Tuning and Evaluations of Ecological Niche Models

Runs ecological niche models over all combinations of user-defined settings (i.e., tuning), performs cross validation to evaluate models, and returns data tables to aid in selection of optimal model settings that balance goodness-of-fit and model complexity. Also has functions to partition data spatially (or not) for cross validation, to plot multiple visualizations of results, to run null models to estimate significance and effect sizes of performance metrics, and to calculate range overlap between model predictions, among others. The package was originally built for Maxent models (Phillips et al. 2006, Phillips et al. 2017), but the current version allows possible extensions for any modeling algorithm. The extensive vignette, which guides users through most package functionality but unfortunately has a file size too big for CRAN, can be found here on the package's Github Pages website: <https://jamiemkass.github.io/ENMeval/articles/ENMeval-2.0-vignette.html>.

Maintained by Jamie M. Kass. Last updated 2 months ago.

3.8 match 49 stars 11.25 score 332 scripts 2 dependents

patzaw

BED:Biological Entity Dictionary (BED)

An interface for the 'Neo4j' database providing mapping between different identifiers of biological entities. This Biological Entity Dictionary (BED) has been developed to address three main challenges. The first one is related to the completeness of identifier mappings. Indeed, direct mapping information provided by the different systems are not always complete and can be enriched by mappings provided by other resources. More interestingly, direct mappings not identified by any of these resources can be indirectly inferred by using mappings to a third reference. For example, many human Ensembl gene ID are not directly mapped to any Entrez gene ID but such mappings can be inferred using respective mappings to HGNC ID. The second challenge is related to the mapping of deprecated identifiers. Indeed, entity identifiers can change from one resource release to another. The identifier history is provided by some resources, such as Ensembl or the NCBI, but it is generally not used by mapping tools. The third challenge is related to the automation of the mapping process according to the relationships between the biological entities of interest. Indeed, mapping between gene and protein ID scopes should not be done the same way than between two scopes regarding gene ID. Also, converting identifiers from different organisms should be possible using gene orthologs information. The method has been published by Godard and van Eyll (2018) <doi:10.12688/f1000research.13925.3>.

Maintained by Patrice Godard. Last updated 3 months ago.

6.1 match 8 stars 6.85 score 25 scripts

larsot23

Benchmarking:Benchmark and Frontier Analysis Using DEA and SFA

Methods for frontier analysis, Data Envelopment Analysis (DEA), under different technology assumptions (fdh, vrs, drs, crs, irs, add/frh, and fdh+), and using different efficiency measures (input based, output based, hyperbolic graph, additive, super, and directional efficiency). Peers and slacks are available, partial price information can be included, and optimal cost, revenue and profit can be calculated. Evaluation of mergers is also supported. Methods for graphing the technology sets are also included. There is also support for comparative methods based on Stochastic Frontier Analyses (SFA) and for convex nonparametric least squares of convex functions (STONED). In general, the methods can be used to solve not only standard models, but also many other model variants. It complements the book, Bogetoft and Otto, Benchmarking with DEA, SFA, and R, Springer-Verlag, 2011, but can of course also be used as a stand-alone package.

Maintained by Lars Otto. Last updated 26 days ago.

cpp

6.8 match 7 stars 6.17 score 192 scripts 7 dependents

stocnet

manynet:Many Ways to Make, Modify, Map, Mark, and Measure Myriad Networks

Many tools for making, modifying, mapping, marking, measuring, and motifs and memberships of many different types of networks. All functions operate with matrices, edge lists, and 'igraph', 'network', and 'tidygraph' objects, and on one-mode, two-mode (bipartite), and sometimes three-mode networks. The package includes functions for importing and exporting, creating and generating networks, modifying networks and node and tie attributes, and describing and visualizing networks with sensible defaults.

Maintained by James Hollway. Last updated 3 months ago.

diffusion-models graphs network-analysis

6.5 match 13 stars 6.41 score 35 scripts 1 dependents

bioc

RMassBank:Workflow to process tandem MS files and build MassBank records

Workflow to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records.

Maintained by RMassBank at Eawag. Last updated 5 months ago.

immunooncology bioinformatics massspectrometry metabolomics software openjdk

6.8 match 6.19 score 26 scripts

jamesramsay5

fda:Functional Data Analysis

These functions were developed to support functional data analysis as described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data Analysis. New York: Springer and in Ramsay, J. O., Hooker, Giles, and Graves, Spencer (2009). Functional Data Analysis with R and Matlab (Springer). The package includes data sets and script files working many examples including all but one of the 76 figures in this latter book. Matlab versions are available by ftp from <https://www.psych.mcgill.ca/misc/fda/downloads/FDAfuns/>.

Maintained by James Ramsay. Last updated 4 months ago.

3.4 match 3 stars 12.29 score 2.0k scripts 143 dependents

openanalytics

BIGL:Biochemically Intuitive Generalized Loewe Model

Response surface methods for drug synergy analysis. Available methods include generalized and classical Loewe formulations as well as Highest Single Agent methodology. Response surfaces can be plotted in an interactive 3-D plot and formal statistical tests for presence of synergistic effects are available. Implemented methods and tests are described in the article "BIGL: Biochemically Intuitive Generalized Loewe null model for prediction of the expected combined effect compatible with partial agonism and antagonism" by Koen Van der Borght, Annelies Tourny, Rytis Bagdziunas, Olivier Thas, Maxim Nazarov, Heather Turner, Bie Verbist & Hugo Ceulemans (2017) <doi:10.1038/s41598-017-18068-5>.

Maintained by Maxim Nazarov. Last updated 2 years ago.

6.9 match 7 stars 6.02 score 37 scripts

bioc

Gviz:Plotting data and annotation information along genomic coordinates

Genomic data analyses requires integrated visualization of known genomic information and new experimental data. Gviz uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data.

Maintained by Robert Ivanek. Last updated 5 months ago.

visualization microarray sequencing

3.2 match 79 stars 13.08 score 1.4k scripts 48 dependents

bioc

TrajectoryGeometry:This Package Discovers Directionality in Time and Pseudo-times Series of Gene Expression Patterns

Given a time series or pseudo-times series of gene expression data, we might wish to know: Do the changes in gene expression in these data exhibit directionality? Are there turning points in this directionality. Do different subsets of the data move in different directions? This package uses spherical geometry to probe these sorts of questions. In particular, if we are looking at (say) the first n dimensions of the PCA of gene expression, directionality can be detected as the clustering of points on the (n-1)-dimensional sphere.

Maintained by Michael Shapiro. Last updated 5 months ago.

biologicalquestion statisticalmethod geneexpression singlecell

8.9 match 4.60 score 7 scripts

gagolews

TurtleGraphics:Turtle Graphics

An implementation of turtle graphics <http://en.wikipedia.org/wiki/Turtle_graphics>. Turtle graphics comes from Papert's language Logo and has been used to teach concepts of computer programming.

Maintained by Marek Gagolewski. Last updated 3 years ago.

5.5 match 23 stars 7.21 score 117 scripts 2 dependents

bioc

sSNAPPY:Single Sample directioNAl Pathway Perturbation analYsis

A single sample pathway perturbation testing method for RNA-seq data. The method propagates changes in gene expression down gene-set topologies to compute single-sample directional pathway perturbation scores that reflect potential direction of change. Perturbation scores can be used to test significance of pathway perturbation at both individual-sample and treatment levels.

Maintained by Wenjun Liu. Last updated 5 months ago.

software geneexpression genesetenrichment genesignaling

8.2 match 1 stars 4.83 score 15 scripts

gianpaoloclemente

DirectedClustering:Directed Weighted Clustering Coefficient

Allows the computation of clustering coefficients for directed and weighted networks by using different approaches. It allows to compute clustering coefficients that are not present in 'igraph' package. A description of clustering coefficients can be found in "Directed clustering in weighted networks: a new perspective", Clemente, G.P., Grassi, R. (2017), <doi:10.1016/j.chaos.2017.12.007>.

Maintained by Gian Paolo Clemente. Last updated 6 months ago.

9.1 match 5 stars 4.35 score 8 scripts 1 dependents

rominsal

pspatreg:Spatial and Spatio-Temporal Semiparametric Regression Models with Spatial Lags

Estimation and inference of spatial and spatio-temporal semiparametric models including spatial or spatio-temporal non-parametric trends, parametric and non-parametric covariates and, possibly, a spatial lag for the dependent variable and temporal correlation in the noise. The spatio-temporal trend can be decomposed in ANOVA way including main and interaction functional terms. Use of SAP algorithm to estimate the spatial or spatio-temporal trend and non-parametric covariates. The methodology of these models can be found in next references Basile, R. et al. (2014), <doi:10.1016/j.jedc.2014.06.011>; Rodriguez-Alvarez, M.X. et al. (2015) <doi:10.1007/s11222-014-9464-2> and, particularly referred to the focus of the package, Minguez, R., Basile, R. and Durban, M. (2020) <doi:10.1007/s10260-019-00492-8>.

Maintained by Roman Minguez. Last updated 3 years ago.

6.1 match 12 stars 6.44 score 77 scripts

dfsp-spirit

freesurferformats:Read and Write 'FreeSurfer' Neuroimaging File Formats

Provides functions to read and write neuroimaging data in various file formats, with a focus on 'FreeSurfer' <http://freesurfer.net/> formats. This includes, but is not limited to, the following file formats: 1) MGH/MGZ format files, which can contain multi-dimensional images or other data. Typically they contain time-series of three-dimensional brain scans acquired by magnetic resonance imaging (MRI). They can also contain vertex-wise measures of surface morphometry data. The MGH format is named after the Massachusetts General Hospital, and the MGZ format is a compressed version of the same format. 2) 'FreeSurfer' morphometry data files in binary 'curv' format. These contain vertex-wise surface measures, i.e., one scalar value for each vertex of a brain surface mesh. These are typically values like the cortical thickness or brain surface area at each vertex. 3) Annotation file format. This contains a brain surface parcellation derived from a cortical atlas. 4) Surface file format. Contains a brain surface mesh, given by a list of vertices and a list of faces.

Maintained by Tim Schäfer. Last updated 6 months ago.

brain brain-atlas brain-surfaces curv dti fileformats freesurfer label mesh mgh mri neuroimaging parcellation research surface voxel

4.8 match 23 stars 8.07 score 25 scripts 8 dependents

ropensci

grainchanger:Moving-Window and Direct Data Aggregation

Data aggregation via moving window or direct methods. Aggregate a fine-resolution raster to a grid. The moving window method smooths the surface using a specified function within a moving window of a specified size and shape prior to aggregation. The direct method simply aggregates to the grid using the specified function.

Maintained by Laura Graham. Last updated 2 years ago.

7.1 match 52 stars 5.46 score 28 scripts

frbcesab

chessboard:Create Network Connections Based on Chess Moves

Provides functions to work with directed (asymmetric) and undirected (symmetric) spatial networks. It makes the creation of connectivity matrices easier, i.e. a binary matrix of dimension n x n, where n is the number of nodes (sampling units) indicating the presence (1) or the absence (0) of an edge (link) between pairs of nodes. Different network objects can be produced by 'chessboard': node list, neighbor list, edge list, connectivity matrix. It can also produce objects that will be used later in Moran's Eigenvector Maps (Dray et al. (2006) <doi:10.1016/j.ecolmodel.2006.02.015>) and Asymetric Eigenvector Maps (Blanchet et al. (2008) <doi:10.1016/j.ecolmodel.2008.04.001>), methods available in the package 'adespatial' (Dray et al. (2023) <https://CRAN.R-project.org/package=adespatial>). This work is part of the FRB-CESAB working group Bridge <https://www.fondationbiodiversite.fr/en/the-frb-in-action/programs-and-projects/le-cesab/bridge/>.

Maintained by Nicolas Casajus. Last updated 1 years ago.

connectivity-matrix directed-networks neighborhood network one-dimensional-networks spatial-networks two-dimensional-networks undirected-networks

8.0 match 4 stars 4.78 score

bioc

wiggleplotr:Make read coverage plots from BigWig files

Tools to visualise read coverage from sequencing experiments together with genomic annotations (genes, transcripts, peaks). Introns of long transcripts can be rescaled to a fixed length for better visualisation of exonic read coverage.

Maintained by Kaur Alasoo. Last updated 5 months ago.

immunooncology coverage rnaseq chipseq sequencing visualization geneexpression transcription alternativesplicing

7.0 match 5.49 score 26 scripts 1 dependents

santikka

dosearch:Causal Effect Identification from Multiple Incomplete Data Sources

Identification of causal effects from arbitrary observational and experimental probability distributions via do-calculus and standard probability manipulations using a search-based algorithm by Tikka, Hyttinen and Karvanen (2021) <doi:10.18637/jss.v099.i05>. Allows for the presence of mechanisms related to selection bias (Bareinboim and Tian, 2015) <doi:10.1609/aaai.v29i1.9679>, transportability (Bareinboim and Pearl, 2014) <http://ftp.cs.ucla.edu/pub/stat_ser/r443.pdf>, missing data (Mohan, Pearl, and Tian, 2013) <http://ftp.cs.ucla.edu/pub/stat_ser/r410.pdf>) and arbitrary combinations of these. Also supports identification in the presence of context-specific independence (CSI) relations through labeled directed acyclic graphs (LDAG). For details on CSIs see (Corander et al., 2019) <doi:10.1016/j.apal.2019.04.004>.

Maintained by Santtu Tikka. Last updated 8 months ago.

c-plus-plus causal-inference causal-models causality causality-algorithms directed-acyclic-graph graphs labeled-graphs cpp

7.2 match 7 stars 5.32 score 8 scripts 1 dependents

astrazeneca

maraca:The Maraca Plot: Visualization of Hierarchical Composite Endpoints in Clinical Trials

Library that supports visual interpretation of hierarchical composite endpoints (HCEs). HCEs are complex constructs used as primary endpoints in clinical trials, combining outcomes of different types into ordinal endpoints, in which each patient contributes the most clinically important event (one and only one) to the analysis. See Karpefors M et al. (2022) <doi:10.1177/17407745221134949>.

Maintained by Monika Huhn. Last updated 4 months ago.

6.2 match 3 stars 6.11 score 16 scripts

trenchproject

TrenchR:Tools for Microclimate and Biophysical Ecology

Tools for translating environmental change into organismal response. Microclimate models to vertically scale weather station data to organismal heights. The biophysical modeling tools include both general models for heat flows and specific models to predict body temperatures for a variety of ectothermic taxa. Additional functions model and temporally partition air and soil temperatures and solar radiation. Utility functions estimate the organismal and environmental parameters needed for biophysical ecology. 'TrenchR' focuses on relatively simple and modular functions so users can create transparent and flexible biophysical models. Many functions are derived from Gates (1980) <doi:10.1007/978-1-4612-6024-0> and Campbell and Norman (1988) <isbn:9780387949376>.

Maintained by Lauren Buckley. Last updated 1 years ago.

5.5 match 13 stars 6.89 score 43 scripts

robinhankin

elliptic:Weierstrass and Jacobi Elliptic Functions

A suite of elliptic and related functions including Weierstrass and Jacobi forms. Also includes various tools for manipulating and visualizing complex functions.

Maintained by Robin K. S. Hankin. Last updated 12 days ago.

4.0 match 3 stars 9.31 score 54 scripts 79 dependents

reimandlab

ActivePathways:Integrative Pathway Enrichment Analysis of Multivariate Omics Data

Framework for analysing multiple omics datasets in the context of molecular pathways, biological processes and other types of gene sets. The package uses p-value merging to combine gene- or protein-level signals, followed by ranked hypergeometric tests to determine enriched pathways and processes. Genes can be integrated using directional constraints that reflect how the input datasets are expected interact with one another. This approach allows researchers to interpret a series of omics datasets in the context of known biology and gene function, and discover associations that are only apparent when several datasets are combined. The recent version of the package is part of the following publication: Directional integration and pathway enrichment analysis for multi-omics data. Slobodyanyuk M^, Bahcheli AT^, Klein ZP, Bayati M, Strug LJ, Reimand J. Nature Communications (2024) <doi:10.1038/s41467-024-49986-4>.

Maintained by Juri Reimand. Last updated 8 months ago.

4.3 match 107 stars 8.61 score 35 scripts 2 dependents

cran

Spillover:Spillover/Connectedness Index Based on VAR Modelling

A user-friendly tool for estimating both total and directional connectedness spillovers based on Diebold and Yilmaz (2009, 2012). It also provides the user with rolling estimation for total and net indices. User can find both orthogonalized and generalized versions for each kind of measures. See Diebold and Yilmaz (2009, 2012) find them at <doi:10.1111/j.1468-0297.2008.02208.x> and <doi:10.1016/j.ijforecast.2011.02.006>.

Maintained by Jilber Urbina. Last updated 1 years ago.

9.5 match 8 stars 3.86 score

r-lib

gargle:Utilities for Working with Google APIs

Provides utilities for working with Google APIs <https://developers.google.com/apis-explorer>. This includes functions and classes for handling common credential types and for preparing, executing, and processing HTTP requests.

Maintained by Jennifer Bryan. Last updated 2 years ago.

authentication google

2.5 match 113 stars 14.88 score 266 scripts 192 dependents

vegandevs

vegan:Community Ecology Package

Ordination methods, diversity analysis and other functions for community and vegetation ecologists.

Maintained by Jari Oksanen. Last updated 16 days ago.

ecological-modelling ecology ordination fortran openblas

1.9 match 472 stars 19.41 score 15k scripts 440 dependents

bioc

OmnipathR:OmniPath web service client and more

A client for the OmniPath web service (https://www.omnipathdb.org) and many other resources. It also includes functions to transform and pretty print some of the downloaded data, functions to access a number of other resources such as BioPlex, ConsensusPathDB, EVEX, Gene Ontology, Guide to Pharmacology (IUPHAR/BPS), Harmonizome, HTRIdb, Human Phenotype Ontology, InWeb InBioMap, KEGG Pathway, Pathway Commons, Ramilowski et al. 2015, RegNetwork, ReMap, TF census, TRRUST and Vinayagam et al. 2011. Furthermore, OmnipathR features a close integration with the NicheNet method for ligand activity prediction from transcriptomics data, and its R implementation `nichenetr` (available only on github).

Maintained by Denes Turei. Last updated 19 days ago.

graphandnetwork network pathways software thirdpartyclient dataimport datarepresentation genesignaling generegulation systemsbiology transcriptomics singlecell annotation kegg complexes enzyme-ptm networks networks-biology omnipath proteins quarto

3.7 match 126 stars 9.90 score 226 scripts 2 dependents

jslefche

piecewiseSEM:Piecewise Structural Equation Modeling

Implements piecewise structural equation modeling from a single list of structural equations, with new methods for non-linear, latent, and composite variables, standardized coefficients, query-based prediction and indirect effects. See <http://jslefche.github.io/piecewiseSEM/> for more.

Maintained by Jon Lefcheck. Last updated 9 months ago.

sem

3.7 match 163 stars 9.85 score 452 scripts

dcomtois

summarytools:Tools to Quickly and Neatly Summarize Data

Data frame summaries, cross-tabulations, weight-enabled frequency tables and common descriptive (univariate) statistics in concise tables available in a variety of formats (plain ASCII, Markdown and HTML). A good point-of-entry for exploring data, both for experienced and new R users.

Maintained by Dominic Comtois. Last updated 1 days ago.

descriptive-statistics frequency-table html-report markdown pander pandoc pandoc-markdown rmarkdown rstudio

2.5 match 526 stars 14.52 score 2.9k scripts 6 dependents

cran

network:Classes for Relational Data

Tools to create and modify network objects. The network class can represent a range of relational data types, and supports arbitrary vertex/edge/graph attributes.

Maintained by Carter T. Butts. Last updated 3 months ago.

4.7 match 3 stars 7.65 score 146 dependents

geoffjentry

twitteR:R Based Twitter Client

Provides an interface to the Twitter web API.

Maintained by Jeff Gentry. Last updated 9 years ago.

3.5 match 254 stars 10.18 score 2.0k scripts 1 dependents

santikka

causaleffect:Deriving Expressions of Joint Interventional Distributions and Transport Formulas in Causal Models

Functions for identification and transportation of causal effects. Provides a conditional causal effect identification algorithm (IDC) by Shpitser, I. and Pearl, J. (2006) <http://ftp.cs.ucla.edu/pub/stat_ser/r329-uai.pdf>, an algorithm for transportability from multiple domains with limited experiments by Bareinboim, E. and Pearl, J. (2014) <http://ftp.cs.ucla.edu/pub/stat_ser/r443.pdf>, and a selection bias recovery algorithm by Bareinboim, E. and Tian, J. (2015) <http://ftp.cs.ucla.edu/pub/stat_ser/r445.pdf>. All of the previously mentioned algorithms are based on a causal effect identification algorithm by Tian , J. (2002) <http://ftp.cs.ucla.edu/pub/stat_ser/r309.pdf>.

Maintained by Santtu Tikka. Last updated 2 years ago.

causal-inference causal-models causality-algorithms directed-acyclic-graph graphs identifiability identification igraph

6.7 match 29 stars 5.28 score 44 scripts 1 dependents

strevisani

SurfRough:Calculate Surface/Image Texture Indexes

Methods for the computation of surface/image texture indices using a geostatistical based approach (Trevisani et al. (2023) <doi:10.1016/j.geomorph.2023.108838>). It provides various functions for the computation of surface texture indices (e.g., omnidirectional roughness and roughness anisotropy), including the ones based on the robust MAD estimator. The kernels included in the software permit also to calculate the surface/image texture indices directly from the input surface (i.e., without de-trending) using increments of order 2. It also provides the new radial roughness index (RRI), representing the improvement of the popular topographic roughness index (TRI). The framework can be easily extended with ad-hoc surface/image texture indices.

Maintained by Sebastiano Trevisani. Last updated 2 days ago.

cpp

9.6 match 1 stars 3.65 score

egarpor

rotasym:Tests for Rotational Symmetry on the Hypersphere

Implementation of the tests for rotational symmetry on the hypersphere proposed in García-Portugués, Paindaveine and Verdebout (2020) <doi:10.1080/01621459.2019.1665527>. The package also implements the proposed distributions on the hypersphere, based on the tangent-normal decomposition, and allows for the replication of the data application considered in the paper.

Maintained by Eduardo García-Portugués. Last updated 4 days ago.

circular-statistics directional-statistics goodness-of-fit semiparametric statistics cpp

7.5 match 2 stars 4.68 score 32 scripts 5 dependents

santikka

cfid:Identification of Counterfactual Queries in Causal Models

Facilitates the identification of counterfactual queries in structural causal models via the ID* and IDC* algorithms by Shpitser, I. and Pearl, J. (2007, 2008) <arXiv:1206.5294>, <https://jmlr.org/papers/v9/shpitser08a.html>. Provides a simple interface for defining causal diagrams and counterfactual conjunctions. Construction of parallel worlds graphs and counterfactual graphs is carried out automatically based on the counterfactual query and the causal diagram. See Tikka, S. (2023) <doi:10.32614/RJ-2023-053> for a tutorial of the package.

Maintained by Santtu Tikka. Last updated 8 months ago.

causal-inference causal-models causality-algorithms counterfactual counterfactuals directed-acyclic-graph identifiability

8.7 match 7 stars 4.02 score 2 scripts 1 dependents

pbreheny

biglasso:Extending Lasso Model Fitting to Big Data

Extend lasso and elastic-net model fitting for large data sets that cannot be loaded into memory. Designed to be more memory- and computation-efficient than existing lasso-fitting packages like 'glmnet' and 'ncvreg', thus allowing the user to analyze big data with limited RAM <doi:10.32614/RJ-2021-001>.

Maintained by Patrick Breheny. Last updated 11 days ago.

bigdata lasso out-of-core parallel-computing cpp openmp

3.5 match 113 stars 9.84 score 74 scripts 1 dependents

micbtz

equateIRT:IRT Equating Methods

Computation of direct, chain and average (bisector) equating coefficients with standard errors using Item Response Theory (IRT) methods for dichotomous items (Battauz (2013) <doi:10.1007/s11336-012-9316-y>, Battauz (2015) <doi:10.18637/jss.v068.i07>). Test scoring can be performed by true score equating and observed score equating methods. DIF detection can be performed using a Wald-type test (Battauz (2019) <doi:10.1007/s10260-018-00442-w>). The package includes tests to assess the stability of the equating transformations (Battauz(2022) <doi:10.1111/stan.12277>).

Maintained by Michela Battauz. Last updated 5 months ago.

7.3 match 4.70 score 35 scripts 2 dependents

tlverse

tmle3mediate:Targeted Learning for Causal Mediation Analysis

Targeted maximum likelihood (TML) estimation of population-level causal effects in mediation analysis. The causal effects are defined by joint static or stochastic interventions applied to the exposure and the mediator. Targeted doubly robust estimators are provided for the classical natural direct and indirect effects, as well as the more recently developed population intervention direct and indirect effects.

Maintained by Nima Hejazi. Last updated 4 years ago.

causal-inference causal-mediation-analysis machine-learning mediation-analysis stochastic-interventions targeted-learning treatment-effects

11.6 match 6 stars 2.98 score 16 scripts

bluefoxr

COINr:Composite Indicator Construction and Analysis

A comprehensive high-level package, for composite indicator construction and analysis. It is a "development environment" for composite indicators and scoreboards, which includes utilities for construction (indicator selection, denomination, imputation, data treatment, normalisation, weighting and aggregation) and analysis (multivariate analysis, correlation plotting, short cuts for principal component analysis, global sensitivity analysis, and more). A composite indicator is completely encapsulated inside a single hierarchical list called a "coin". This allows a fast and efficient work flow, as well as making quick copies, testing methodological variations and making comparisons. It also includes many plotting options, both statistical (scatter plots, distribution plots) as well as for presenting results.

Maintained by William Becker. Last updated 2 months ago.

3.8 match 26 stars 9.07 score 73 scripts 1 dependents

zarquon42b

Morpho:Calculations and Visualisations Related to Geometric Morphometrics

A toolset for Geometric Morphometrics and mesh processing. This includes (among other stuff) mesh deformations based on reference points, permutation tests, detection of outliers, processing of sliding semi-landmarks and semi-automated surface landmark placement.

Maintained by Stefan Schlager. Last updated 5 months ago.

openblas cpp openmp

3.4 match 51 stars 10.00 score 218 scripts 13 dependents

r-forge

mlogit:Multinomial Logit Models

Maximum Likelihood estimation of random utility discrete choice models, as described in Kenneth Train (2009) Discrete Choice Methods with Simulations <doi:10.1017/CBO9780511805271>.

Maintained by Yves Croissant. Last updated 5 years ago.

3.5 match 9.81 score 1.2k scripts 14 dependents

tanaylab

tgstat:Amos Tanay's Group High Performance Statistical Utilities

A collection of high performance utilities to compute distance, correlation, auto correlation, clustering and other tasks. Contains graph clustering algorithm described in "MetaCell: analysis of single-cell RNA-seq data using K-nn graph partitions" (Yael Baran, Akhiad Bercovich, Arnau Sebe-Pedros, Yaniv Lubling, Amir Giladi, Elad Chomsky, Zohar Meir, Michael Hoichman, Aviezer Lifshitz & Amos Tanay, 2019 <doi:10.1186/s13059-019-1812-2>).

Maintained by Aviezer Lifshitz. Last updated 6 months ago.

algorithms-implemented correlation knn statistics openblas cpp

5.6 match 8 stars 6.06 score 24 scripts 1 dependents

drwolf85

spMC:Continuous-Lag Spatial Markov Chains

A set of functions is provided for 1) the stratum lengths analysis along a chosen direction, 2) fast estimation of continuous lag spatial Markov chains model parameters and probability computing (also for large data sets), 3) transition probability maps and transiograms drawing, 4) simulation methods for categorical random fields. More details on the methodology are discussed in Sartore (2013) <doi:10.32614/RJ-2013-022> and Sartore et al. (2016) <doi:10.1016/j.cageo.2016.06.001>.

Maintained by Luca Sartore. Last updated 2 years ago.

openblas openmp

11.5 match 3 stars 2.92 score 55 scripts

mittelmark

snha:Creating Correlation Networks using St. Nicolas House Analysis

Create correlation networks using St. Nicolas House Analysis ('SNHA'). The package can be used for visualizing multivariate data similar to Principal Component Analysis or Multidimensional Scaling using a ranking approach. In contrast to 'MDS' and 'PCA', 'SNHA' uses a network approach to explore interacting variables. For details see 'Hermanussen et. al. 2021', <doi:10.3390/ijerph18041741>.

Maintained by Detlef Groth. Last updated 8 months ago.

correlation-analysis network network-analysis network-reconstruction

7.0 match 6 stars 4.78 score 7 scripts

kjhealy

gssrdoc:Document General Social Survey Variable

The General Social Survey (GSS) is a long-running, mostly annual survey of US households. It is administered by the National Opinion Research Center (NORC). This package contains the a tibble with information on the survey variables, together with every variable documented as an R help page. For more information on the GSS see \url{http://gss.norc.org}.

Maintained by Kieran Healy. Last updated 11 months ago.

14.7 match 2.28 score 38 scripts

cran

cqrReg:Quantile, Composite Quantile Regression and Regularized Versions

Estimate quantile regression(QR) and composite quantile regression (cqr) and with adaptive lasso penalty using interior point (IP), majorize and minimize(MM), coordinate descent (CD), and alternating direction method of multipliers algorithms(ADMM).

Maintained by Jueyu Gao. Last updated 3 years ago.

openblas cpp

13.4 match 5 stars 2.48 score 20 scripts 1 dependents

tidyverse

purrr:Functional Programming Tools

A complete and consistent functional programming toolkit for R.

Maintained by Hadley Wickham. Last updated 1 months ago.

functional-programming

1.5 match 1.3k stars 22.12 score 59k scripts 6.9k dependents

sanfordweisberg

dr:Methods for Dimension Reduction for Regression

Functions, methods, and datasets for fitting dimension reduction regression, using slicing (methods SAVE and SIR), Principal Hessian Directions (phd, using residuals and the response), and an iterative IRE. Partial methods, that condition on categorical predictors are also available. A variety of tests, and stepwise deletion of predictors, is also included. Also included is code for computing permutation tests of dimension. Adding additional methods of estimating dimension is straightforward. For documentation, see the vignette in the package. With version 3.0.4, the arguments for dr.step have been modified.

Maintained by Sanford Weisberg. Last updated 10 years ago.

6.8 match 4.87 score 122 scripts 10 dependents

christophergandrud

d3Network:The Old Package for Creating D3 JavaScript Network, Tree, Dendrogram, and Sankey Graphs

!!! NOTE: Active development has moved to the networkD3 package. !!!

Maintained by Christopher Gandrud. Last updated 10 years ago.

5.0 match 172 stars 6.63 score 82 scripts

mdneuzerling

ptvapi:Access the 'Public Transport Victoria' Timetable API

Access the 'Public Transport Victoria' Timetable API <https://www.ptv.vic.gov.au/footer/data-and-reporting/datasets/ptv-timetable-api/>, with results returned as familiar R data structures. Retrieve information on stops, routes, disruptions, departures, and more.

Maintained by David Neuzerling. Last updated 1 years ago.

8.4 match 18 stars 3.95 score 2 scripts

bioc

sevenbridges:Seven Bridges Platform API Client and Common Workflow Language Tool Builder in R

R client and utilities for Seven Bridges platform API, from Cancer Genomics Cloud to other Seven Bridges supported platforms.

Maintained by Phil Webster. Last updated 5 months ago.

software dataimport thirdpartyclient api-client bioconductor bioinformatics cloud common-workflow-language sevenbridges

4.4 match 35 stars 7.40 score 24 scripts

jepusto

ARPobservation:Tools for Simulating Direct Behavioral Observation Recording Procedures Based on Alternating Renewal Processes

Tools for simulating data generated by direct observation recording. Behavior streams are simulated based on an alternating renewal process, given specified distributions of event durations and interim times. Different procedures for recording data can then be applied to the simulated behavior streams. Functions are provided for the following recording methods: continuous duration recording, event counting, momentary time sampling, partial interval recording, whole interval recording, and augmented interval recording.

Maintained by James E. Pustejovsky. Last updated 2 years ago.

7.4 match 4.41 score 52 scripts

easystats

insight:Easy Access to Model Information for Various Model Objects

A tool to provide an easy, intuitive and consistent access to information contained in various R models, like model formulas, model terms, information about random effects, data that was used to fit the model or data from response variables. 'insight' mainly revolves around two types of functions: Functions that find (the names of) information, starting with 'find_', and functions that get the underlying data, starting with 'get_'. The package has a consistent syntax and works with many different model objects, where otherwise functions to access these information are missing.

Maintained by Daniel Lüdecke. Last updated 5 days ago.

easystats hacktoberfest insight models names predictors random

1.9 match 412 stars 17.24 score 568 scripts 210 dependents

coolbutuseless

yyjsonr:Fast 'JSON', 'NDJSON' and 'GeoJSON' Parser and Generator

A fast 'JSON' parser, generator and validator which converts 'JSON', 'NDJSON' (Newline Delimited 'JSON') and 'GeoJSON' (Geographic 'JSON') data to/from R objects. The standard R data types are supported (e.g. logical, numeric, integer) with configurable handling of NULL and NA values. Data frames, atomic vectors and lists are all supported as data containers translated to/from 'JSON'. 'GeoJSON' data is read in as 'simple features' objects. This implementation wraps the 'yyjson' 'C' library which is available from <https://github.com/ibireme/yyjson>.

Maintained by Mike Cheng. Last updated 4 months ago.

zlib

3.4 match 147 stars 9.56 score 22 scripts 9 dependents

egarpor

ridgetorus:PCA on the Torus via Density Ridges

Implementation of a Principal Component Analysis (PCA) in the torus via density ridge estimation. The main function, ridge_pca(), obtains the relevant density ridge for bivariate sine von Mises and bivariate wrapped Cauchy distribution models and provides the associated scores and variance decomposition. Auxiliary functions for evaluating, fitting, and sampling these models are also provided. The package provides replicability to García-Portugués and Prieto-Tirado (2023) <doi:10.1007/s11222-023-10273-9>.

Maintained by Eduardo García-Portugués. Last updated 2 years ago.

circular-statistics dimensionality-reduction directional-statistics openblas cpp

7.5 match 4 stars 4.30 score 9 scripts

tkhdyanagi

latenetwork:Inference on LATEs under Network Interference of Unknown Form

Estimating causal parameters in the presence of treatment spillover is of great interest in statistics. This package provides tools for instrumental variables estimation of average causal effects under network interference of unknown form. The target parameters are the local average direct effect, the local average indirect effect, the local average overall effect, and the local average spillover effect. The methods are developed by Hoshino and Yanagi (2023) <doi:10.48550/arXiv.2108.07455>.

Maintained by Takahide Yanagi. Last updated 2 years ago.

econometrics

8.1 match 4.00 score 5 scripts

weiliang

clusterGeneration:Random Cluster Generation (with Specified Degree of Separation)

We developed the clusterGeneration package to provide functions for generating random clusters, generating random covariance/correlation matrices, calculating a separation index (data and population version) for pairs of clusters or cluster distributions, and 1-D and 2-D projection plots to visualize clusters. The package also contains a function to generate random clusters based on factorial designs with factors such as degree of separation, number of clusters, number of variables, number of noisy variables.

Maintained by Weiliang Qiu. Last updated 2 years ago.

4.9 match 1 stars 6.45 score 225 scripts 94 dependents

alanarnholt

BSDA:Basic Statistics and Data Analysis

Data sets for book "Basic Statistics and Data Analysis" by Larry J. Kitchens.

Maintained by Alan T. Arnholt. Last updated 2 years ago.

3.5 match 7 stars 9.11 score 1.3k scripts 6 dependents

ewenharrison

finalfit:Quickly Create Elegant Regression Results Tables and Plots when Modelling

Generate regression results tables and plots in final format for publication. Explore models and export directly to PDF and 'Word' using 'RMarkdown'.

Maintained by Ewen Harrison. Last updated 7 months ago.

2.8 match 270 stars 11.43 score 1.0k scripts

bioc

multiMiR:Integration of multiple microRNA-target databases with their disease and drug associations

A collection of microRNAs/targets from external resources, including validated microRNA-target databases (miRecords, miRTarBase and TarBase), predicted microRNA-target databases (DIANA-microT, ElMMo, MicroCosm, miRanda, miRDB, PicTar, PITA and TargetScan) and microRNA-disease/drug databases (miR2Disease, Pharmaco-miR VerSe and PhenomiR).

Maintained by Spencer Mahaffey. Last updated 5 months ago.

mirnadata homo_sapiens_data mus_musculus_data rattus_norvegicus_data organismdata microrna-sequence sql

3.8 match 20 stars 8.45 score 141 scripts

rohelab

fastRG:Sample Generalized Random Dot Product Graphs in Linear Time

Samples generalized random product graphs, a generalization of a broad class of network models. Given matrices X, S, and Y with with non-negative entries, samples a matrix with expectation X S Y^T and independent Poisson or Bernoulli entries using the fastRG algorithm of Rohe et al. (2017) <https://www.jmlr.org/papers/v19/17-128.html>. The algorithm first samples the number of edges and then puts them down one-by-one. As a result it is O(m) where m is the number of edges, a dramatic improvement over element-wise algorithms that which require O(n^2) operations to sample a random graph, where n is the number of nodes.

Maintained by Alex Hayes. Last updated 7 months ago.

adjacency-matrix graph-sampling latent-factors

7.0 match 5 stars 4.52 score 22 scripts

kisungyou

ADMM:Algorithms using Alternating Direction Method of Multipliers

Provides algorithms to solve popular optimization problems in statistics such as regression or denoising based on Alternating Direction Method of Multipliers (ADMM). See Boyd et al (2010) <doi:10.1561/2200000016> for complete introduction to the method.

Maintained by Kisung You. Last updated 4 years ago.

openblas cpp openmp

5.1 match 6 stars 6.08 score 15 scripts 9 dependents

andrisignorell

DescTools:Tools for Descriptive Statistics

A collection of miscellaneous basic statistic functions and convenience wrappers for efficiently describing data. The author's intention was to create a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. The package contains furthermore functions to produce documents using MS Word (or PowerPoint) and functions to import data from Excel. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in absence of convincing alternatives). The 'BigCamelCase' style was consequently applied to functions borrowed from contributed R packages as well.

Maintained by Andri Signorell. Last updated 9 hours ago.

fortran cpp

1.9 match 87 stars 16.70 score 7.7k scripts 99 dependents

bioc

BiRewire:High-performing routines for the randomization of a bipartite graph (or a binary event matrix), undirected and directed signed graph preserving degree distribution (or marginal totals)

Fast functions for bipartite network rewiring through N consecutive switching steps (See References) and for the computation of the minimal number of switching steps to be performed in order to maximise the dissimilarity with respect to the original network. Includes functions for the analysis of the introduced randomness across the switching steps and several other routines to analyse the resulting networks and their natural projections. Extension to undirected networks and directed signed networks is also provided. Starting from version 1.9.7 a more precise bound (especially for small network) has been implemented. Starting from version 2.2.0 the analysis routine is more complete and a visual montioring of the underlying Markov Chain has been implemented. Starting from 3.6.0 the library can handle also matrices with NA (not for the directed signed graphs). Since version 3.27.1 it is possible to add a constraint for dsg generation: usually positive and negative arc between two nodes could be not accepted.

Maintained by Andrea Gobbi. Last updated 5 months ago.

network

6.9 match 4.54 score 35 scripts

easystats

parameters:Processing of Model Parameters

Utilities for processing the parameters of various statistical models. Beyond computing p values, CIs, and other indices for a wide variety of models (see list of supported models using the function 'insight::supported_models()'), this package implements features like bootstrapping or simulating of parameters and models, feature reduction (feature extraction and variable selection) as well as functions to describe data and variable characteristics (e.g. skewness, kurtosis, smoothness or distribution).

Maintained by Daniel Lüdecke. Last updated 2 days ago.

beta bootstrap ci confidence-intervals data-reduction easystats fa feature-extraction feature-reduction hacktoberfest parameters pca pvalues regression-models robust-statistics standardize standardized-estimates statistical-models

2.0 match 453 stars 15.65 score 1.8k scripts 56 dependents

sfeuerriegel

SentimentAnalysis:Dictionary-Based Sentiment Analysis

Performs a sentiment analysis of textual contents in R. This implementation utilizes various existing dictionaries, such as Harvard IV, or finance-specific dictionaries. Furthermore, it can also create customized dictionaries. The latter uses LASSO regularization as a statistical approach to select relevant terms based on an exogenous response variable.

Maintained by Nicolas Proellochs. Last updated 2 years ago.

3.8 match 149 stars 8.34 score 242 scripts 1 dependents

jtextor

celltrackR:Motion Trajectory Analysis

Methods for analyzing (cell) motion in two or three dimensions. Available measures include displacement, confinement ratio, autocorrelation, straightness, turning angle, and fractal dimension. Measures can be applied to entire tracks, steps, or subtracks with varying length. While the methodology has been developed for cell trajectory analysis, it is applicable to anything that moves including animals, people, or vehicles. Some of the methodology implemented in this packages was described by: Beauchemin, Dixit, and Perelson (2007) <doi:10.4049/jimmunol.178.9.5505>, Beltman, Maree, and de Boer (2009) <doi:10.1038/nri2638>, Gneiting and Schlather (2004) <doi:10.1137/S0036144501394387>, Mokhtari, Mech, Zitzmann, Hasenberg, Gunzer, and Figge (2013) <doi:10.1371/journal.pone.0080808>, Moreau, Lemaitre, Terriac, Azar, Piel, Lennon-Dumenil, and Bousso (2012) <doi:10.1016/j.immuni.2012.05.014>, Textor, Peixoto, Henrickson, Sinn, von Andrian, and Westermann (2011) <doi:10.1073/pnas.1102288108>, Textor, Sinn, and de Boer (2013) <doi:10.1186/1471-2105-14-S6-S10>, Textor, Henrickson, Mandl, von Andrian, Westermann, de Boer, and Beltman (2014) <doi:10.1371/journal.pcbi.1003752>.

Maintained by Johannes Textor. Last updated 7 months ago.

10.1 match 3.08 score 6 scripts

ropensci

phruta:Phylogenetic Reconstruction and Time-dating

The phruta R package is designed to simplify the basic phylogenetic pipeline. Specifically, all code is run within the same program and data from intermediate steps are saved in independent folders. Furthermore, all code is run within the same environment which increases the reproducibility of your analysis. phruta retrieves gene sequences, combines newly downloaded and local gene sequences, and performs sequence alignments.

Maintained by Cristian Roman Palacios. Last updated 8 months ago.

6.5 match 9 stars 4.75 score 14 scripts

briencj

dae:Functions Useful in the Design and ANOVA of Experiments

The content falls into the following groupings: (i) Data, (ii) Factor manipulation functions, (iii) Design functions, (iv) ANOVA functions, (v) Matrix functions, (vi) Projector and canonical efficiency functions, and (vii) Miscellaneous functions. There is a vignette describing how to use the design functions for randomizing and assessing designs available as a vignette called 'DesignNotes'. The ANOVA functions facilitate the extraction of information when the 'Error' function has been used in the call to 'aov'. The package 'dae' can also be installed from <http://chris.brien.name/rpackages/>.

Maintained by Chris Brien. Last updated 4 months ago.

3.6 match 1 stars 8.62 score 356 scripts 7 dependents

michelnivard

gptstudio:Use Large Language Models Directly in your Development Environment

Large language models are readily accessible via API. This package lowers the barrier to use the API inside of your development environment. For more on the API, see <https://platform.openai.com/docs/introduction>.

Maintained by James Wade. Last updated 6 days ago.

chatgpt gpt-3 rstudio rstudio-addin

2.9 match 924 stars 10.83 score 43 scripts 1 dependents

bioc

Rsamtools:Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.

Maintained by Bioconductor Package Maintainer. Last updated 4 months ago.

dataimport sequencing coverage alignment qualitycontrol bioconductor-package core-package curl bzip2 xz-utils zlib cpp

2.0 match 28 stars 15.42 score 3.2k scripts 566 dependents

jeremygelb

spNetwork:Spatial Analysis on Network

Perform spatial analysis on network. Implement several methods for spatial analysis on network: Network Kernel Density estimation, building of spatial matrices based on network distance ('listw' objects from 'spdep' package), K functions estimation for point pattern analysis on network, k nearest neighbours on network, reachable area calculation, and graph generation References: Okabe et al (2019) <doi:10.1080/13658810802475491>; Okabe et al (2012, ISBN:978-0470770818);Baddeley et al (2015, ISBN:9781482210200).

Maintained by Jeremy Gelb. Last updated 2 days ago.

kernel kernel-density-estimation network network-analysis spatial spatial-analysis spatial-data-analysis cpp

4.0 match 38 stars 7.69 score 52 scripts

gentrywhite

DSSP:Implementation of the Direct Sampling Spatial Prior

Draw samples from the direct sampling spatial prior model as described in G. White, D. Sun, P. Speckman (2019) <arXiv:1906.05575>. The basic model assumes a Gaussian likelihood and derives a spatial prior based on thin-plate splines.

Maintained by Gentry White. Last updated 3 years ago.

openblas cpp openmp

8.3 match 1 stars 3.70 score 6 scripts

walkerke

mapboxapi:R Interface to 'Mapbox' Web Services

Includes support for 'Mapbox' Navigation APIs, including directions, isochrones, and route optimization; the Search API for forward and reverse geocoding; the Maps API for interacting with 'Mapbox' vector tilesets and visualizing 'Mapbox' maps in R; and 'Mapbox Tiling Service' and 'tippecanoe' for generating map tiles. See <https://docs.mapbox.com/api/> for more information about the 'Mapbox' APIs.

Maintained by Kyle Walker. Last updated 2 months ago.

4.0 match 112 stars 7.61 score 304 scripts

andrewhooker

PopED:Population (and Individual) Optimal Experimental Design

Optimal experimental designs for both population and individual studies based on nonlinear mixed-effect models. Often this is based on a computation of the Fisher Information Matrix. This package was developed for pharmacometric problems, and examples and predefined models are available for these types of systems. The methods are described in Nyberg et al. (2012) <doi:10.1016/j.cmpb.2012.05.005>, and Foracchia et al. (2004) <doi:10.1016/S0169-2607(03)00073-7>.

Maintained by Andrew C. Hooker. Last updated 5 months ago.

nlme optimal-design pharmacodynamics pharmacokinetics pharmacometrics pkpd population population-model

3.2 match 33 stars 9.58 score 300 scripts 1 dependents

bioc

MOSClip:Multi Omics Survival Clip

Topological pathway analysis tool able to integrate multi-omics data. It finds survival-associated modules or significant modules for two-class analysis. This tool have two main methods: pathway tests and module tests. The latter method allows the user to dig inside the pathways itself.

Maintained by Paolo Martini. Last updated 5 months ago.

software statisticalmethod graphandnetwork survival regression dimensionreduction pathways reactome

5.7 match 5.34 score 5 scripts

joshuaulrich

quantmod:Quantitative Financial Modelling Framework

Specify, build, trade, and analyse quantitative financial trading strategies.

Maintained by Joshua M. Ulrich. Last updated 14 days ago.

algorithmic-trading charting data-import finance time-series

1.9 match 839 stars 16.17 score 8.1k scripts 343 dependents

paulojus

geoR:Analysis of Geostatistical Data

Geostatistical analysis including variogram-based, likelihood-based and Bayesian methods. Software companion for Diggle and Ribeiro (2007) <doi:10.1007/978-0-387-48536-2>.

Maintained by Paulo Justiniano Ribeiro Jr. Last updated 1 years ago.

4.0 match 10 stars 7.57 score 1.8k scripts 12 dependents

hugo-marques

ORFID:Manage and Summarize Data from Oregon RFID ORMR and ORSR Antenna Readers

Automates and standardizes the import of raw data from Oregon RFID (radio-frequency identification) ORMR (Oregon RFID Multi-Reader) and ORSR (Oregon RFID Single Reader) antenna readers. Compiled data can then be combined within multi-reader arrays for further analysis, including summarizing tag and reader detections, determining tag direction, and calculating antenna efficiency.

Maintained by Annika Putt. Last updated 2 years ago.

7.0 match 4 stars 4.30 score 6 scripts

american-institutes-for-research

EdSurvey:Analysis of NCES Education Survey and Assessment Data

Read in and analyze functions for education survey and assessment data from the National Center for Education Statistics (NCES) <https://nces.ed.gov/>, including National Assessment of Educational Progress (NAEP) data <https://nces.ed.gov/nationsreportcard/> and data from the International Assessment Database: Organisation for Economic Co-operation and Development (OECD) <https://www.oecd.org/en/about/directorates/directorate-for-education-and-skills.html>, including Programme for International Student Assessment (PISA), Teaching and Learning International Survey (TALIS), Programme for the International Assessment of Adult Competencies (PIAAC), and International Association for the Evaluation of Educational Achievement (IEA) <https://www.iea.nl/>, including Trends in International Mathematics and Science Study (TIMSS), TIMSS Advanced, Progress in International Reading Literacy Study (PIRLS), International Civic and Citizenship Study (ICCS), International Computer and Information Literacy Study (ICILS), and Civic Education Study (CivEd).

Maintained by Paul Bailey. Last updated 16 days ago.

3.8 match 10 stars 7.86 score 139 scripts 1 dependents

winvector

rqdatatable:'rquery' for 'data.table'

Implements the 'rquery' piped Codd-style query algebra using 'data.table'. This allows for a high-speed in memory implementation of Codd-style data manipulation tools.

Maintained by John Mount. Last updated 2 years ago.

3.7 match 38 stars 8.10 score 142 scripts 2 dependents

thomasp85

ggforce:Accelerating 'ggplot2'

The aim of 'ggplot2' is to aid in visual data investigations. This focus has led to a lack of facilities for composing specialised plots. 'ggforce' aims to be a collection of mainly new stats and geoms that fills this gap. All additional functionality is aimed to come through the official extension system so using 'ggforce' should be a stable experience.

Maintained by Thomas Lin Pedersen. Last updated 1 years ago.

ggplot-extension ggplot2 visualization cpp

1.9 match 920 stars 15.83 score 9.3k scripts 293 dependents

pcruniversum

MBmca:Nucleic Acid Melting Curve Analysis

Lightweight utilities for nucleic acid melting curve analysis are important in life sciences and diagnostics. This software can be used for the analysis and presentation of melting curve data from microbead-based assays (surface melting curve analysis) and reactions in solution (e.g., quantitative PCR (qPCR), real-time isothermal Amplification). Further information are described in detail in two publications in The R Journal [ <https://journal.r-project.org/archive/2013-2/roediger-bohm-schimke.pdf>; <https://journal.r-project.org/archive/2015-1/RJ-2015-1.pdf>].

Maintained by Stefan Roediger. Last updated 4 years ago.

6.5 match 4 stars 4.53 score 17 scripts

thermostats

ssdGSA:Single Sample Directional Gene Set Analysis

A method that inherits the standard gene set variation analysis (GSVA) method and also provides the option to use summary statistics from any analysis (disease vs healthy, lesional side vs nonlesional side, etc..) input to define the direction of gene sets used for directional gene set score calculation for a given disease. Note to use this package, GSVA(>= 1.52.1) is needed to pre-installed. Hanzelmann, S., Castelo, R., and Guinney, J. (2013) <doi:10.1186/1471-2105-14-7>.

Maintained by Xingpeng Li. Last updated 8 months ago.

14.8 match 2.00 score 3 scripts

um-kevinhe

pprof:Modeling, Standardization and Testing for Provider Profiling

Implements linear and generalized linear models for provider profiling, incorporating both fixed and random effects. For large-scale providers, the linear profiled-based method and the SerBIN method for binary data reduce the computational burden. Provides post-modeling features, such as indirect and direct standardization measures, hypothesis testing, confidence intervals, and post-estimation visualization. For more information, see Wu et al. (2022) <doi:10.1002/sim.9387>.

Maintained by Xiaohan Liu. Last updated 5 days ago.

openblas cpp openmp

7.2 match 4.08 score 3 scripts

jsjuni

rollupTree:Perform Recursive Computations

Mass rollup for a Bill of Materials is an example of a class of computations in which elements are arranged in a tree structure and some property of each element is a computed function of the corresponding values of its child elements. Leaf elements, i.e., those with no children, have values assigned. In many cases, the combining function is simple arithmetic sum; in other cases (e.g., mass properties), the combiner may involve other information such as the geometric relationship between parent and child, or statistical relations such as root-sum-of-squares (RSS). This package implements a general function for such problems. It is adapted to specific recursive computations by functional programming techniques; the caller passes a function as the update parameter to rollup() (or, at a lower level, passes functions as the get, set, combine, and override parameters to update_prop()) at runtime to specify the desired operations. The implementation relies on graph-theoretic algorithms from the 'igraph' package of Csárdi, et al. (2006 <doi:10.5281/zenodo.7682609>).

Maintained by James Steven Jenkins. Last updated 10 days ago.

5.5 match 2 stars 5.32 score 1 dependents

bioc

monocle:Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq

Monocle performs differential expression and time-series analysis for single-cell expression experiments. It orders individual cells according to progress through a biological process, without knowing ahead of time which genes define progress through that process. Monocle also performs differential expression analysis, clustering, visualization, and other useful tasks on single cell expression data. It is designed to work with RNA-Seq and qPCR data, but could be used with other types as well.

Maintained by Cole Trapnell. Last updated 5 months ago.

immunooncology sequencing rnaseq geneexpression differentialexpression infrastructure dataimport datarepresentation visualization clustering multiplecomparison qualitycontrol cpp

3.2 match 8.89 score 1.6k scripts 2 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.

4.1 match 38 stars 6.94 score 19 scripts

r-lib

covr:Test Coverage for Packages

Track and report code coverage for your package and (optionally) upload the results to a coverage service like 'Codecov' <https://about.codecov.io> or 'Coveralls' <https://coveralls.io>. Code coverage is a measure of the amount of code being exercised by a set of tests. It is an indirect measure of test quality and completeness. This package is compatible with any testing methodology or framework and tracks coverage of both R code and compiled C/C++/FORTRAN code.

Maintained by Jim Hester. Last updated 1 months ago.

codecov coverage coverage-report travis-ci

1.9 match 337 stars 15.25 score 2.3k scripts 9 dependents

whipson

maestro:Orchestration of Data Pipelines

Framework for creating and orchestrating data pipelines. Organize, orchestrate, and monitor multiple pipelines in a single project. Use tags to decorate functions with scheduling parameters and configuration.

Maintained by Will Hipson. Last updated 2 days ago.

3.1 match 117 stars 9.11 score 150 scripts

marconotaro

HEMDAG:Hierarchical Ensemble Methods for Directed Acyclic Graphs

An implementation of several Hierarchical Ensemble Methods (HEMs) for Directed Acyclic Graphs (DAGs). 'HEMDAG' package: 1) reconciles flat predictions with the topology of the ontology; 2) can enhance the predictions of virtually any flat learning methods by taking into account the hierarchical relationships between ontology classes; 3) provides biologically meaningful predictions that always obey the true-path-rule, the biological and logical rule that governs the internal coherence of biomedical ontologies; 4) is specifically designed for exploiting the hierarchical relationships of DAG-structured taxonomies, such as the Human Phenotype Ontology (HPO) or the Gene Ontology (GO), but can be safely applied to tree-structured taxonomies as well (as FunCat), since trees are DAGs; 5) scales nicely both in terms of the complexity of the taxonomy and in the cardinality of the examples; 6) provides several utility functions to process and analyze graphs; 7) provides several performance metrics to evaluate HEMs algorithms. (Marco Notaro, Max Schubach, Peter N. Robinson and Giorgio Valentini (2017) <doi:10.1186/s12859-017-1854-y>).

Maintained by Marco Notaro. Last updated 4 months ago.

cpp

8.9 match 3.20 score 32 scripts

alexchristensen

NetworkToolbox:Methods and Measures for Brain, Cognitive, and Psychometric Network Analysis

Implements network analysis and graph theory measures used in neuroscience, cognitive science, and psychology. Methods include various filtering methods and approaches such as threshold, dependency (Kenett, Tumminello, Madi, Gur-Gershgoren, Mantegna, & Ben-Jacob, 2010 <doi:10.1371/journal.pone.0015032>), Information Filtering Networks (Barfuss, Massara, Di Matteo, & Aste, 2016 <doi:10.1103/PhysRevE.94.062306>), and Efficiency-Cost Optimization (Fallani, Latora, & Chavez, 2017 <doi:10.1371/journal.pcbi.1005305>). Brain methods include the recently developed Connectome Predictive Modeling (see references in package). Also implements several network measures including local network characteristics (e.g., centrality), community-level network characteristics (e.g., community centrality), global network characteristics (e.g., clustering coefficient), and various other measures associated with the reliability and reproducibility of network analysis.

Maintained by Alexander Christensen. Last updated 2 years ago.

network-analysis

4.0 match 23 stars 6.99 score 101 scripts 4 dependents

rdatatable

data.table:Extension of `data.frame`

Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.

Maintained by Tyson Barrett. Last updated 4 hours ago.

1.2 match 3.7k stars 23.52 score 230k scripts 4.6k dependents

mountainmath

cancensus:Access, Retrieve, and Work with Canadian Census Data and Geography

Integrated, convenient, and uniform access to Canadian Census data and geography retrieved using the 'CensusMapper' API. This package produces analysis-ready tidy data frames and spatial data in multiple formats, as well as convenience functions for working with Census variables, variable hierarchies, and region selection. API keys are freely available with free registration at <https://censusmapper.ca/api>. Census data and boundary geometries are reproduced and distributed on an "as is" basis with the permission of Statistics Canada (Statistics Canada 2001; 2006; 2011; 2016; 2021).

Maintained by Dmitry Shkolnik. Last updated 1 years ago.

3.2 match 82 stars 8.80 score 414 scripts

thomasp85

gganimate:A Grammar of Animated Graphics

The grammar of graphics as implemented in the 'ggplot2' package has been successful in providing a powerful API for creating static visualisation. In order to extend the API for animated graphics this package provides a completely new set of grammar, fully compatible with 'ggplot2' for specifying transitions and animations in a flexible and extensible way.

Maintained by Thomas Lin Pedersen. Last updated 1 years ago.

animation data-visualization ggplot-extension ggplot2 transition

1.8 match 2.0k stars 15.87 score 13k scripts 25 dependents

netcoupler

NetCoupler:Inference of Causal Links Between a Network and an External Variable

The 'NetCoupler' algorithm identifies potential direct effects of correlated, high-dimensional variables formed as a network with an external variable. The external variable may act as the dependent/response variable or as an independent/predictor variable to the network.

Maintained by Luke Johnston. Last updated 1 years ago.

5.7 match 6 stars 4.78 score 7 scripts