Showing 200 of total 988 results (show query)
tidyverse
purrr:Functional Programming Tools
A complete and consistent functional programming toolkit for R.
Maintained by Hadley Wickham. Last updated 1 months ago.
14.8 match 1.3k stars 22.12 score 59k scripts 6.9k dependents
dbosak01
sassy:Makes 'R' Easier for Everyone
A meta-package that aims to make 'R' easier for everyone, especially programmers who have a background in 'SAS®' software. This set of packages brings many useful concepts to 'R', including data libraries, data dictionaries, formats and format catalogs, a data step, and a traceable log. The 'flagship' package is a reporting package that can output in text, rich text, 'PDF', 'HTML', and 'DOCX' file formats.
Maintained by David Bosak. Last updated 6 months ago.
35.2 match 21 stars 7.74 score 92 scripts
relund
gMOIP:Tools for 2D and 3D Plots of Single and Multi-Objective Linear/Integer Programming Models
Make 2D and 3D plots of linear programming (LP), integer linear programming (ILP), or mixed integer linear programming (MILP) models with up to three objectives. Plots of both the solution and criterion space are possible. For instance the non-dominated (Pareto) set for bi-objective LP/ILP/MILP programming models (see vignettes for an overview). The package also contains an function for checking if a point is inside the convex hull.
Maintained by Lars Relund Nielsen. Last updated 5 months ago.
2d-plot3d-plotbi-objectiveconvex-hullinteger-programminglinear-programmingmathmilpmixed-integer-programmingmulti-objectivepolytopetri-objectivevisualization
32.1 match 5 stars 7.83 score 79 scripts 3 dependents
pharmaverse
admiral:ADaM in R Asset Library
A toolbox for programming Clinical Data Interchange Standards Consortium (CDISC) compliant Analysis Data Model (ADaM) datasets in R. ADaM datasets are a mandatory part of any New Drug or Biologics License Application submitted to the United States Food and Drug Administration (FDA). Analysis derivations are implemented in accordance with the "Analysis Data Model Implementation Guide" (CDISC Analysis Data Model Team, 2021, <https://www.cdisc.org/standards/foundational/adam>).
Maintained by Ben Straub. Last updated 3 days ago.
cdiscclinical-trialsopen-source
17.8 match 236 stars 13.89 score 486 scripts 4 dependents
biodiverse
unmarked:Models for Data from Unmarked Animals
Fits hierarchical models of animal abundance and occurrence to data collected using survey methods such as point counts, site occupancy sampling, distance sampling, removal sampling, and double observer sampling. Parameters governing the state and observation processes can be modeled as functions of covariates. References: Kellner et al. (2023) <doi:10.1111/2041-210X.14123>, Fiske and Chandler (2011) <doi:10.18637/jss.v043.i10>.
Maintained by Ken Kellner. Last updated 1 months ago.
15.2 match 4 stars 13.02 score 652 scripts 12 dependents
yihui
knitr:A General-Purpose Package for Dynamic Report Generation in R
Provides a general-purpose tool for dynamic report generation in R using Literate Programming techniques.
Maintained by Yihui Xie. Last updated 12 hours ago.
dynamic-documentsknitrliterate-programmingrmarkdownsweave
8.0 match 2.4k stars 23.62 score 116k scripts 4.2k dependents
rstudio
rmarkdown:Dynamic Documents for R
Convert R Markdown documents into a variety of formats.
Maintained by Yihui Xie. Last updated 4 months ago.
literate-programmingmarkdownpandocrmarkdown
7.5 match 2.9k stars 21.79 score 14k scripts 3.7k dependentsrstudio
promises:Abstractions for Promise-Based Asynchronous Programming
Provides fundamental abstractions for doing asynchronous programming in R using promises. Asynchronous programming is useful for allowing a single R process to orchestrate multiple tasks in the background while also attending to something else. Semantics are similar to 'JavaScript' promises, but with a syntax that is idiomatic R.
Maintained by Joe Cheng. Last updated 1 months ago.
9.5 match 204 stars 17.10 score 688 scripts 2.6k dependents
dirkschumacher
ompr:Model and Solve Mixed Integer Linear Programs
Model mixed integer linear programs in an algebraic way directly in R. The model is solver-independent and thus offers the possibility to solve a model with different solvers. It currently only supports linear constraints and objective functions. See the 'ompr' website <https://dirkschumacher.github.io/ompr/> for more information, documentation and examples.
Maintained by Dirk Schumacher. Last updated 2 years ago.
integer-programminglinear-programmingmilpmipoptimization
18.4 match 268 stars 8.33 score 321 scripts 6 dependents
ropensci
karel:Learning programming with Karel the robot
This is the R implementation of Karel the robot, a programming language created by Dr. R. E. Pattis at Stanford University in 1981. Karel is an useful tool to teach introductory concepts about general programming, such as algorithmic decomposition, conditional statements, loops, etc., in an interactive and fun way, by writing programs to make Karel the robot achieve certain tasks in the world she lives in. Originally based on Pascal, Karel was implemented in many languages through these decades, including 'Java', 'C++', 'Ruby' and 'Python'. This is the first package implementing Karel in R.
Maintained by Marcos Prunello. Last updated 8 months ago.
21.4 match 10 stars 6.87 score 31 scripts
gaborcsardi
lpSolve:Interface to 'Lp_solve' v. 5.5 to Solve Linear/Integer Programs
Lp_solve is freely available (under LGPL 2) software for solving linear, integer and mixed integer programs. In this implementation we supply a "wrapper" function in C and some R functions that solve general linear/integer problems, assignment problems, and transportation problems. This version calls lp_solve version 5.5.
Maintained by Gábor Csárdi. Last updated 3 months ago.
10.9 match 21 stars 12.62 score 1.2k scripts 453 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 17 hours ago.
5.8 match 3.7k stars 23.53 score 230k scripts 4.6k dependents
rapporter
pander:An R 'Pandoc' Writer
Contains some functions catching all messages, 'stdout' and other useful information while evaluating R code and other helpers to return user specified text elements (like: header, paragraph, table, image, lists etc.) in 'pandoc' markdown or several type of R objects similarly automatically transformed to markdown format. Also capable of exporting/converting (the resulting) complex 'pandoc' documents to e.g. HTML, 'PDF', 'docx' or 'odt'. This latter reporting feature is supported in brew syntax or with a custom reference class with a smarty caching 'backend'.
Maintained by Gergely Daróczi. Last updated 14 days ago.
literate-programmingmarkdownpandocpandoc-markdownreproducible-researchrmarkdowncpp
7.5 match 297 stars 16.60 score 7.6k scripts 108 dependents
stan-dev
cmdstanr:R Interface to 'CmdStan'
A lightweight interface to 'Stan' <https://mc-stan.org>. The 'CmdStanR' interface is an alternative to 'RStan' that calls the command line interface for compilation and running algorithms instead of interfacing with C++ via 'Rcpp'. This has many benefits including always being compatible with the latest version of Stan, fewer installation errors, fewer unexpected crashes in RStudio, and a more permissive license.
Maintained by Andrew Johnson. Last updated 9 months ago.
bayesbayesianmarkov-chain-monte-carlomaximum-likelihoodmcmcstanvariational-inference
10.0 match 145 stars 12.27 score 5.2k scripts 9 dependents
nimble-dev
nimble:MCMC, Particle Filtering, and Programmable Hierarchical Modeling
A system for writing hierarchical statistical models largely compatible with 'BUGS' and 'JAGS', writing nimbleFunctions to operate models and do basic R-style math, and compiling both models and nimbleFunctions via custom-generated C++. 'NIMBLE' includes default methods for MCMC, Laplace Approximation, Monte Carlo Expectation Maximization, and some other tools. The nimbleFunction system makes it easy to do things like implement new MCMC samplers from R, customize the assignment of samplers to different parts of a model from R, and compile the new samplers automatically via C++ alongside the samplers 'NIMBLE' provides. 'NIMBLE' extends the 'BUGS'/'JAGS' language by making it extensible: New distributions and functions can be added, including as calls to external compiled code. Although most people think of MCMC as the main goal of the 'BUGS'/'JAGS' language for writing models, one can use 'NIMBLE' for writing arbitrary other kinds of model-generic algorithms as well. A full User Manual is available at <https://r-nimble.org>.
Maintained by Christopher Paciorek. Last updated 3 days ago.
bayesian-inferencebayesian-methodshierarchical-modelsmcmcprobabilistic-programmingopenblascpp
9.3 match 169 stars 12.97 score 2.6k scripts 19 dependents
midfieldr
midfieldr:Tools and Methods for Working with MIDFIELD Data in 'R'
Provides tools and demonstrates methods for working with individual undergraduate student-level records (registrar's data) in 'R'. Tools include filters for program codes, data sufficiency, and timely completion. Methods include gathering blocs of records, computing quantitative metrics such as graduation rate, and creating charts to visualize comparisons. 'midfieldr' interacts with practice data provided in 'midfielddata', an R data package available at <https://midfieldr.github.io/midfielddata/>. 'midfieldr' also interacts with the full MIDFIELD database for users who have access. This work is supported by the US National Science Foundation through grant numbers 1545667 and 2142087.
Maintained by Richard Layton. Last updated 2 months ago.
21.2 match 2 stars 5.56 score 26 scripts
hadley
proto:Prototype Object-Based Programming
An object oriented system using object-based, also called prototype-based, rather than class-based object oriented ideas.
Maintained by Hadley Wickham. Last updated 8 years ago.
9.8 match 12 stars 11.65 score 366 scripts 110 dependents
arecibo
nonparaeff:Nonparametric Methods for Measuring Efficiency and Productivity
Efficiency and productivity indices are measured using this package. This package contains functions for measuring efficiency and productivity of decision making units (DMUs) under the framework of Data Envelopment Analysis (DEA) and its variations.
Maintained by Dong-hyun Oh. Last updated 3 years ago.
25.1 match 4.47 score 18 scripts 11 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.
12.1 match 7 stars 9.11 score 1.3k scripts 6 dependentspharmaverse
admiralonco:Oncology Extension Package for ADaM in 'R' Asset Library
Programming oncology specific Clinical Data Interchange Standards Consortium (CDISC) compliant Analysis Data Model (ADaM) datasets in 'R'. ADaM datasets are a mandatory part of any New Drug or Biologics License Application submitted to the United States Food and Drug Administration (FDA). Analysis derivations are implemented in accordance with the "Analysis Data Model Implementation Guide" (CDISC Analysis Data Model Team (2021), <https://www.cdisc.org/standards/foundational/adam>). The package is an extension package of the 'admiral' package.
Maintained by Stefan Bundfuss. Last updated 2 months ago.
12.5 match 32 stars 8.66 score 30 scripts
osqp
osqp:Quadratic Programming Solver using the 'OSQP' Library
Provides bindings to the 'OSQP' solver. The 'OSQP' solver is a numerical optimization package or solving convex quadratic programs written in 'C' and based on the alternating direction method of multipliers. See <doi:10.48550/arXiv.1711.08013> for details.
Maintained by Balasubramanian Narasimhan. Last updated 9 months ago.
admmconvex-optimizationlassomachine-learningoperator-splittingquadratic-programmingcpp
12.8 match 12 stars 8.21 score 47 scripts 65 dependentsropensci
assertr:Assertive Programming for R Analysis Pipelines
Provides functionality to assert conditions that have to be met so that errors in data used in analysis pipelines can fail quickly. Similar to 'stopifnot()' but more powerful, friendly, and easier for use in pipelines.
Maintained by Tony Fischetti. Last updated 11 months ago.
analysis-pipelineassertion-libraryassertion-methodsassertionspeer-reviewedpredicate-functions
9.1 match 478 stars 11.39 score 452 scripts 12 dependents
sterniii3
drugdevelopR:Utility-Based Optimal Phase II/III Drug Development Planning
Plan optimal sample size allocation and go/no-go decision rules for phase II/III drug development programs with time-to-event, binary or normally distributed endpoints when assuming fixed treatment effects or a prior distribution for the treatment effect, using methods from Kirchner et al. (2016) <doi:10.1002/sim.6624> and Preussler (2020). Optimal is in the sense of maximal expected utility, where the utility is a function taking into account the expected cost and benefit of the program. It is possible to extend to more complex settings with bias correction (Preussler S et al. (2020) <doi:10.1186/s12874-020-01093-w>), multiple phase III trials (Preussler et al. (2019) <doi:10.1002/bimj.201700241>), multi-arm trials (Preussler et al. (2019) <doi:10.1080/19466315.2019.1702092>), and multiple endpoints (Kieser et al. (2018) <doi:10.1002/pst.1861>).
Maintained by Lukas D. Sauer. Last updated 2 months ago.
15.9 match 3 stars 6.39 score 15 scripts
mlr-org
mlr3pipelines:Preprocessing Operators and Pipelines for 'mlr3'
Dataflow programming toolkit that enriches 'mlr3' with a diverse set of pipelining operators ('PipeOps') that can be composed into graphs. Operations exist for data preprocessing, model fitting, and ensemble learning. Graphs can themselves be treated as 'mlr3' 'Learners' and can therefore be resampled, benchmarked, and tuned.
Maintained by Martin Binder. Last updated 7 days ago.
baggingdata-sciencedataflow-programmingensemble-learningmachine-learningmlr3pipelinespreprocessingstacking
8.0 match 141 stars 12.36 score 448 scripts 7 dependentsstan-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 1 days ago.
bayesbayesianbayesian-data-analysisbayesian-inferencebayesian-methodsbayesian-statisticscross-validationinformation-criterionmodel-comparisonstan
5.7 match 152 stars 17.30 score 2.6k scripts 297 dependents
olbapjose
FuzzyLP:Fuzzy Linear Programming
Provides methods to solve Fuzzy Linear Programming Problems with fuzzy constraints (following different approaches proposed by Verdegay, Zimmermann, Werners and Tanaka), fuzzy costs, and fuzzy technological matrix.
Maintained by Pablo J. Villacorta. Last updated 2 years ago.
26.5 match 3.70 score 8 scripts
spedygiorgio
markovchain:Easy Handling Discrete Time Markov Chains
Functions and S4 methods to create and manage discrete time Markov chains more easily. In addition functions to perform statistical (fitting and drawing random variates) and probabilistic (analysis of their structural proprieties) analysis are provided. See Spedicato (2017) <doi:10.32614/RJ-2017-036>. Some functions for continuous times Markov chains depend on the suggested ctmcd package.
Maintained by Giorgio Alfredo Spedicato. Last updated 4 months ago.
ctmcdtmcmarkov-chainmarkov-modelr-programmingrcppopenblascpp
7.5 match 104 stars 12.78 score 712 scripts 4 dependents
program--
fipio:Lightweight Federal Information Processing System (FIPS) Code Information Retrieval
Provides a lightweight suite of functions for retrieving information about 5-digit or 2-digit US FIPS codes.
Maintained by Justin Singh-Mohudpur. Last updated 1 years ago.
information-retrievalspatialus-data
20.0 match 14 stars 4.77 score 14 scripts 2 dependents
aggregate-genius
periscope2:Enterprise Streamlined 'shiny' Application Framework Using 'bs4Dash'
A framework for building enterprise, scalable and UI-standardized 'shiny' applications. It brings enhanced features such as 'bootstrap' v4 <https://getbootstrap.com/docs/4.0/getting-started/introduction/>, additional and enhanced 'shiny' modules, customizable UI features, as well as an enhanced application file organization paradigm. This update allows developers to harness the ability to build powerful applications and enriches the 'shiny' developers' experience when building and maintaining applications.
Maintained by Mohammed Ali. Last updated 1 months ago.
14.7 match 9 stars 6.49 score 34 scripts
atahk
pscl:Political Science Computational Laboratory
Bayesian analysis of item-response theory (IRT) models, roll call analysis; computing highest density regions; maximum likelihood estimation of zero-inflated and hurdle models for count data; goodness-of-fit measures for GLMs; data sets used in writing and teaching; seats-votes curves.
Maintained by Simon Jackman. Last updated 1 years ago.
7.0 match 67 stars 13.28 score 2.7k scripts 54 dependentstidyverse
dplyr:A Grammar of Data Manipulation
A fast, consistent tool for working with data frame like objects, both in memory and out of memory.
Maintained by Hadley Wickham. Last updated 12 days ago.
3.8 match 4.8k stars 24.68 score 659k scripts 7.8k dependentsprogram--
hilbert:Coordinate Indexing on Hilbert Curves
Provides utilities for encoding and decoding coordinates to/from Hilbert curves based on the iterative encoding implementation described in Chen et al. (2006) <doi:10.1002/spe.793>.
Maintained by Justin Singh-Mohudpur. Last updated 3 years ago.
20.0 match 5 stars 4.40 score 5 scriptstidyverse
tidyr:Tidy Messy Data
Tools to help to create tidy data, where each column is a variable, each row is an observation, and each cell contains a single value. 'tidyr' contains tools for changing the shape (pivoting) and hierarchy (nesting and 'unnesting') of a dataset, turning deeply nested lists into rectangular data frames ('rectangling'), and extracting values out of string columns. It also includes tools for working with missing values (both implicit and explicit).
Maintained by Hadley Wickham. Last updated 12 days ago.
3.8 match 1.4k stars 22.88 score 168k scripts 5.5k dependents
bioc
CARNIVAL:A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming
An upgraded causal reasoning tool from Melas et al in R with updated assignments of TFs' weights from PROGENy scores. Optimization parameters can be freely adjusted and multiple solutions can be obtained and aggregated.
Maintained by Attila Gabor. Last updated 5 months ago.
transcriptomicsgeneexpressionnetworkcausal-modelsfootprintsinteger-linear-programmingpathway-enrichment-analysis
9.4 match 57 stars 9.03 score 90 scripts 1 dependents
scmethods
scregclust:Reconstructing the Regulatory Programs of Target Genes in scRNA-Seq Data
Implementation of the scregclust algorithm described in Larsson, Held, et al. (2024) <doi:10.1038/s41467-024-53954-3> which reconstructs regulatory programs of target genes in scRNA-seq data. Target genes are clustered into modules and each module is associated with a linear model describing the regulatory program.
Maintained by Felix Held. Last updated 2 months ago.
clusteringregulatory-programsscrna-seq-analysiscppopenmp
12.8 match 9 stars 6.45 score 21 scripts
rcppcore
RcppParallel:Parallel Programming Tools for 'Rcpp'
High level functions for parallel programming with 'Rcpp'. For example, the 'parallelFor()' function can be used to convert the work of a standard serial "for" loop into a parallel one and the 'parallelReduce()' function can be used for accumulating aggregate or other values.
Maintained by Kevin Ushey. Last updated 2 months ago.
5.5 match 173 stars 14.89 score 215 scripts 790 dependents
sebkrantz
collapse:Advanced and Fast Data Transformation
A C/C++ based package for advanced data transformation and statistical computing in R that is extremely fast, class-agnostic, robust and programmer friendly. Core functionality includes a rich set of S3 generic grouped and weighted statistical functions for vectors, matrices and data frames, which provide efficient low-level vectorizations, OpenMP multithreading, and skip missing values by default. These are integrated with fast grouping and ordering algorithms (also callable from C), and efficient data manipulation functions. The package also provides a flexible and rigorous approach to time series and panel data in R. It further includes fast functions for common statistical procedures, detailed (grouped, weighted) summary statistics, powerful tools to work with nested data, fast data object conversions, functions for memory efficient R programming, and helpers to effectively deal with variable labels, attributes, and missing data. It is well integrated with base R classes, 'dplyr'/'tibble', 'data.table', 'sf', 'units', 'plm' (panel-series and data frames), and 'xts'/'zoo'.
Maintained by Sebastian Krantz. Last updated 4 days ago.
data-aggregationdata-analysisdata-manipulationdata-processingdata-sciencedata-transformationeconometricshigh-performancepanel-datascientific-computingstatisticstime-seriesweightedweightscppopenmp
4.7 match 672 stars 16.63 score 708 scripts 97 dependents
nickch-k
causaldata:Example Data Sets for Causal Inference Textbooks
Example data sets to run the example problems from causal inference textbooks. Currently, contains data sets for Huntington-Klein, Nick (2021) "The Effect" <https://theeffectbook.net>, first and second edition, Cunningham, Scott (2021, ISBN-13: 978-0-300-25168-5) "Causal Inference: The Mixtape", and Hernán, Miguel and James Robins (2020) "Causal Inference: What If" <https://www.hsph.harvard.edu/miguel-hernan/causal-inference-book/>.
Maintained by Nick Huntington-Klein. Last updated 4 months ago.
10.3 match 136 stars 7.43 score 144 scripts 1 dependents
hwborchers
pracma:Practical Numerical Math Functions
Provides a large number of functions from numerical analysis and linear algebra, numerical optimization, differential equations, time series, plus some well-known special mathematical functions. Uses 'MATLAB' function names where appropriate to simplify porting.
Maintained by Hans W. Borchers. Last updated 1 years ago.
6.1 match 29 stars 12.34 score 6.6k scripts 931 dependents
berwinturlach
quadprog:Functions to Solve Quadratic Programming Problems
This package contains routines and documentation for solving quadratic programming problems.
Maintained by Berwin A. Turlach. Last updated 5 years ago.
7.3 match 3 stars 10.27 score 972 scripts 1.2k dependents
cb4ds
periscope:Enterprise Streamlined 'Shiny' Application Framework
An enterprise-targeted scalable and UI-standardized 'shiny' framework including a variety of developer convenience functions with the goal of both streamlining robust application development while assisting with creating a consistent user experience regardless of application or developer.
Maintained by Constance Brett. Last updated 1 months ago.
10.7 match 18 stars 7.02 score 73 scripts
stevenmmortimer
salesforcer:An Implementation of 'Salesforce' APIs Using Tidy Principles
Functions connecting to the 'Salesforce' Platform APIs (REST, SOAP, Bulk 1.0, Bulk 2.0, Metadata, Reports and Dashboards) <https://trailhead.salesforce.com/content/learn/modules/api_basics/api_basics_overview>. "API" is an acronym for "application programming interface". Most all calls from these APIs are supported as they use CSV, XML or JSON data that can be parsed into R data structures. For more details please see the 'Salesforce' API documentation and this package's website <https://stevenmmortimer.github.io/salesforcer/> for more information, documentation, and examples.
Maintained by Steven M. Mortimer. Last updated 4 months ago.
api-wrappersr-languager-programmingsalesforcesalesforce-apis
8.0 match 82 stars 9.27 score 191 scripts
gaynorr
AlphaSimR:Breeding Program Simulations
The successor to the 'AlphaSim' software for breeding program simulation [Faux et al. (2016) <doi:10.3835/plantgenome2016.02.0013>]. Used for stochastic simulations of breeding programs to the level of DNA sequence for every individual. Contained is a wide range of functions for modeling common tasks in a breeding program, such as selection and crossing. These functions allow for constructing simulations of highly complex plant and animal breeding programs via scripting in the R software environment. Such simulations can be used to evaluate overall breeding program performance and conduct research into breeding program design, such as implementation of genomic selection. Included is the 'Markovian Coalescent Simulator' ('MaCS') for fast simulation of biallelic sequences according to a population demographic history [Chen et al. (2009) <doi:10.1101/gr.083634.108>].
Maintained by Chris Gaynor. Last updated 4 months ago.
breedinggenomicssimulationopenblascppopenmp
7.0 match 47 stars 10.22 score 534 scripts 2 dependents
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 29 days ago.
brainmrimrsmrshubspectroscopyfortran
8.4 match 24 stars 8.55 score 81 scripts
iqis
mod:Lightweight and Self-Contained Modules for Code Organization
Creates modules inline or from a file. Modules can contain any R object and be nested. Each module have their own scope and package "search path" that does not interfere with one another or the user's working environment.
Maintained by Siqi Zhang. Last updated 5 years ago.
datatypemodulemodulesprogramming
10.0 match 4 stars 7.08 score 1.2k scripts
r-gregmisc
gdata:Various R Programming Tools for Data Manipulation
Various R programming tools for data manipulation, including medical unit conversions, combining objects, character vector operations, factor manipulation, obtaining information about R objects, generating fixed-width format files, extracting components of date & time objects, operations on columns of data frames, matrix operations, operations on vectors, operations on data frames, value of last evaluated expression, and a resample() wrapper for sample() that ensures consistent behavior for both scalar and vector arguments.
Maintained by Arni Magnusson. Last updated 2 months ago.
5.2 match 9 stars 13.62 score 4.5k scripts 124 dependents
wahani
modules:Self Contained Units of Source Code
Provides modules as an organizational unit for source code. Modules enforce to be more rigorous when defining dependencies and have a local search path. They can be used as a sub unit within packages or in scripts.
Maintained by Sebastian Warnholz. Last updated 1 years ago.
7.5 match 83 stars 9.39 score 192 scripts 7 dependents
icarda-git
QBMS:Query the Breeding Management System(s)
This R package assists breeders in linking data systems with their analytic pipelines, a crucial step in digitizing breeding processes. It supports querying and retrieving phenotypic and genotypic data from systems like 'EBS' <https://ebs.excellenceinbreeding.org/>, 'BMS' <https://bmspro.io>, 'BreedBase' <https://breedbase.org>, and 'GIGWA' <https://github.com/SouthGreenPlatform/Gigwa2> (using 'BrAPI' <https://brapi.org> calls). Extra helper functions support environmental data sources, including 'TerraClimate' <https://www.climatologylab.org/terraclimate.html> and 'FAO' 'HWSDv2' <https://gaez.fao.org/pages/hwsd> soil database.
Maintained by Khaled Al-Shamaa. Last updated 6 months ago.
8.8 match 8 stars 7.85 score 33 scripts 1 dependentsstan-dev
rstan:R Interface to Stan
User-facing R functions are provided to parse, compile, test, estimate, and analyze Stan models by accessing the header-only Stan library provided by the 'StanHeaders' package. The Stan project develops a probabilistic programming language that implements full Bayesian statistical inference via Markov Chain Monte Carlo, rough Bayesian inference via 'variational' approximation, and (optionally penalized) maximum likelihood estimation via optimization. In all three cases, automatic differentiation is used to quickly and accurately evaluate gradients without burdening the user with the need to derive the partial derivatives.
Maintained by Ben Goodrich. Last updated 1 days ago.
bayesian-data-analysisbayesian-inferencebayesian-statisticsmcmcstancpp
3.6 match 1.1k stars 18.67 score 14k scripts 279 dependents
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.
28.8 match 2.28 score 38 scripts
carmonalab
GeneNMF:Non-Negative Matrix Factorization for Single-Cell Omics
A collection of methods to extract gene programs from single-cell gene expression data using non-negative matrix factorization (NMF). 'GeneNMF' contains functions to directly interact with the 'Seurat' toolkit and derive interpretable gene program signatures.
Maintained by Massimo Andreatta. Last updated 9 days ago.
9.6 match 102 stars 6.63 score 12 scripts
jgx65
hierfstat:Estimation and Tests of Hierarchical F-Statistics
Estimates hierarchical F-statistics from haploid or diploid genetic data with any numbers of levels in the hierarchy, following the algorithm of Yang (Evolution(1998), 52:950). Tests via randomisations the significance of each F and variance components, using the likelihood-ratio statistics G (Goudet et al. (1996) <https://academic.oup.com/genetics/article/144/4/1933/6017091>). Estimates genetic diversity statistics for haploid and diploid genetic datasets in various formats, including inbreeding and coancestry coefficients, and population specific F-statistics following Weir and Goudet (2017) <https://academic.oup.com/genetics/article/206/4/2085/6072590>.
Maintained by Jerome Goudet. Last updated 4 months ago.
devtoolsfstatisticsgwashierfstatkinshippopulation-geneticspopulation-genomicsquantitative-geneticssimulations
5.8 match 25 stars 10.94 score 560 scripts 4 dependents
leonawicz
tabr:Music Notation Syntax, Manipulation, Analysis and Transcription in R
Provides a music notation syntax and a collection of music programming functions for generating, manipulating, organizing, and analyzing musical information in R. Music syntax can be entered directly in character strings, for example to quickly transcribe short pieces of music. The package contains functions for directly performing various mathematical, logical and organizational operations and musical transformations on special object classes that facilitate working with music data and notation. The same music data can be organized in tidy data frames for a familiar and powerful approach to the analysis of large amounts of structured music data. Functions are available for mapping seamlessly between these formats and their representations of musical information. The package also provides an API to 'LilyPond' (<https://lilypond.org/>) for transcribing musical representations in R into tablature ("tabs") and sheet music. 'LilyPond' is open source music engraving software for generating high quality sheet music based on markup syntax. The package generates 'LilyPond' files from R code and can pass them to the 'LilyPond' command line interface to be rendered into sheet music PDF files or inserted into R markdown documents. The package offers nominal MIDI file output support in conjunction with rendering sheet music. The package can read MIDI files and attempts to structure the MIDI data to integrate as best as possible with the data structures and functionality found throughout the package.
Maintained by Matthew Leonawicz. Last updated 6 months ago.
guitar-tablaturelilypondlilypond-apimusic-analysismusic-datamusic-notationmusic-programmingmusic-syntaxmusic-transcriptionsheet-music
8.0 match 132 stars 7.87 score 94 scripts
uofuepibio
epiworldR:Fast Agent-Based Epi Models
A flexible framework for Agent-Based Models (ABM), the 'epiworldR' package provides methods for prototyping disease outbreaks and transmission models using a 'C++' backend, making it very fast. It supports multiple epidemiological models, including the Susceptible-Infected-Susceptible (SIS), Susceptible-Infected-Removed (SIR), Susceptible-Exposed-Infected-Removed (SEIR), and others, involving arbitrary mitigation policies and multiple-disease models. Users can specify infectiousness/susceptibility rates as a function of agents' features, providing great complexity for the model dynamics. Furthermore, 'epiworldR' is ideal for simulation studies featuring large populations.
Maintained by Andrew Pulsipher. Last updated 10 days ago.
abmagent-based-modelingcovid-19epidemicsepidemiologyr-programmingrpackrpkgseirseir-modelsimulationsirsir-modelcppopenmp
7.5 match 9 stars 8.33 score 58 scripts 1 dependents
luomus
finbif:Interface for the 'Finnish Biodiversity Information Facility' API
A programmatic interface to the 'Finnish Biodiversity Information Facility' ('FinBIF') API (<https://api.laji.fi>). 'FinBIF' aggregates Finnish biodiversity data from multiple sources in a single open access portal for researchers, citizen scientists, industry and government. 'FinBIF' allows users of biodiversity information to find, access, combine and visualise data on Finnish plants, animals and microorganisms. The 'finbif' package makes the publicly available data in 'FinBIF' easily accessible to programmers. Biodiversity information is available on taxonomy and taxon occurrence. Occurrence data can be filtered by taxon, time, location and other variables. The data accessed are conveniently preformatted for subsequent analyses.
Maintained by William K. Morris. Last updated 5 days ago.
apibiodiversitybiodiversity-informaticsbiodiversity-informationfinbiffinbif-accessoccurrencesr-programmingspeciesspecimenstaxontaxonomyweb-services
7.5 match 5 stars 8.15 score 42 scripts 3 dependents
flujoo
gm:Create Music with Ease
Provides a simple and intuitive high-level language for music representation. Generates and embeds music scores and audio files in 'RStudio', 'R Markdown' documents, and R 'Jupyter Notebooks'. Internally, uses 'MusicXML' <https://github.com/w3c/musicxml> to represent music, and 'MuseScore' <https://musescore.org/> to convert 'MusicXML'.
Maintained by Renfei Mao. Last updated 8 months ago.
algorithmic-compositionmusic-programmingmusicxml
7.5 match 207 stars 8.06 score 35 scripts
opendendro
dplR:Dendrochronology Program Library in R
Perform tree-ring analyses such as detrending, chronology building, and cross dating. Read and write standard file formats used in dendrochronology.
Maintained by Andy Bunn. Last updated 18 days ago.
5.0 match 39 stars 11.71 score 546 scripts 26 dependents
critical-infrastructure-systems-lab
reservoir:Tools for Analysis, Design, and Operation of Water Supply Storages
Measure single-storage water supply system performance using resilience, reliability, and vulnerability metrics; assess storage-yield- reliability relationships; determine no-fail storage with sequent peak analysis; optimize release decisions for water supply, hydropower, and multi-objective reservoirs using deterministic and stochastic dynamic programming; generate inflow replicates using parametric and non-parametric models; evaluate inflow persistence using the Hurst coefficient.
Maintained by Sean Turner. Last updated 4 years ago.
hydrologyreservoirsimulationwater-resources
14.5 match 28 stars 4.00 score 18 scriptsropensci
rix:Reproducible Data Science Environments with 'Nix'
Simplifies the creation of reproducible data science environments using the 'Nix' package manager, as described in Dolstra (2006) <ISBN 90-393-4130-3>. The included `rix()` function generates a complete description of the environment as a `default.nix` file, which can then be built using 'Nix'. This results in project specific software environments with pinned versions of R, packages, linked system dependencies, and other tools. Additional helpers make it easy to run R code in 'Nix' software environments for testing and production.
Maintained by Bruno Rodrigues. Last updated 3 days ago.
nixpeer-reviewedreproducibilityreproducible-research
5.4 match 235 stars 10.54 score 67 scripts
fchamroukhi
samurais:Statistical Models for the Unsupervised Segmentation of Time-Series ('SaMUraiS')
Provides a variety of original and flexible user-friendly statistical latent variable models and unsupervised learning algorithms to segment and represent time-series data (univariate or multivariate), and more generally, longitudinal data, which include regime changes. 'samurais' is built upon the following packages, each of them is an autonomous time-series segmentation approach: Regression with Hidden Logistic Process ('RHLP'), Hidden Markov Model Regression ('HMMR'), Multivariate 'RHLP' ('MRHLP'), Multivariate 'HMMR' ('MHMMR'), Piece-Wise regression ('PWR'). For the advantages/differences of each of them, the user is referred to our mentioned paper references. These models are originally introduced and written in 'Matlab' by Faicel Chamroukhi <https://github.com/fchamroukhi?&tab=repositories&q=time-series&type=public&language=matlab>.
Maintained by Florian Lecocq. Last updated 5 years ago.
artificial-intelligencechange-point-detectiondata-sciencedynamic-programmingem-algorithmhidden-markov-modelshidden-process-regressionhuman-activity-recognitionlatent-variable-modelsmodel-selectionmultivariate-timeseriesnewton-raphsonpiecewise-regressionstatistical-inferencestatistical-learningtime-series-analysistime-series-clusteringopenblascpp
9.2 match 12 stars 6.18 score 28 scripts
stevecondylios
priceR:Economics and Pricing Tools
Functions to aid in micro and macro economic analysis and handling of price and currency data. Includes extraction of relevant inflation and exchange rate data from World Bank API, data cleaning/parsing, and standardisation. Inflation adjustment calculations as found in Principles of Macroeconomics by Gregory Mankiw et al (2014). Current and historical end of day exchange rates for 171 currencies from the European Central Bank Statistical Data Warehouse (2020) <https://sdw.ecb.europa.eu/curConverter.do>.
Maintained by Steve Condylios. Last updated 7 months ago.
data-scienceeconometricseconomicsfinancemodelingr-programmingstatistics
7.5 match 59 stars 7.37 score 102 scripts
ocean-tracking-network
glatos:A package for the Great Lakes Acoustic Telemetry Observation System
Functions useful to members of the Great Lakes Acoustic Telemetry Observation System https://glatos.glos.us; many more broadly relevant to simulating, processing, analysing, and visualizing acoustic telemetry data.
Maintained by Christopher Holbrook. Last updated 6 months ago.
8.6 match 10 stars 6.38 score 112 scripts
henrikbengtsson
R.utils:Various Programming Utilities
Utility functions useful when programming and developing R packages.
Maintained by Henrik Bengtsson. Last updated 1 years ago.
3.9 match 63 stars 13.74 score 5.7k scripts 814 dependents
flyaflya
causact:Fast, Easy, and Visual Bayesian Inference
Accelerate Bayesian analytics workflows in 'R' through interactive modelling, visualization, and inference. Define probabilistic graphical models using directed acyclic graphs (DAGs) as a unifying language for business stakeholders, statisticians, and programmers. This package relies on interfacing with the 'numpyro' python package.
Maintained by Adam Fleischhacker. Last updated 2 months ago.
bayesian-inferencedagsposterior-probabilityprobabilistic-graphical-modelsprobabilistic-programming
7.5 match 45 stars 7.15 score 52 scripts
snoweye
pbdZMQ:Programming with Big Data -- Interface to 'ZeroMQ'
'ZeroMQ' is a well-known library for high-performance asynchronous messaging in scalable, distributed applications. This package provides high level R wrapper functions to easily utilize 'ZeroMQ'. We mainly focus on interactive client/server programming frameworks. For convenience, a minimal 'ZeroMQ' library (4.2.2) is shipped with 'pbdZMQ', which can be used if no system installation of 'ZeroMQ' is available. A few wrapper functions compatible with 'rzmq' are also provided.
Maintained by Wei-Chen Chen. Last updated 6 months ago.
5.3 match 17 stars 9.92 score 46 scripts 26 dependents
talgalili
gplots:Various R Programming Tools for Plotting Data
Various R programming tools for plotting data, including: - calculating and plotting locally smoothed summary function as ('bandplot', 'wapply'), - enhanced versions of standard plots ('barplot2', 'boxplot2', 'heatmap.2', 'smartlegend'), - manipulating colors ('col2hex', 'colorpanel', 'redgreen', 'greenred', 'bluered', 'redblue', 'rich.colors'), - calculating and plotting two-dimensional data summaries ('ci2d', 'hist2d'), - enhanced regression diagnostic plots ('lmplot2', 'residplot'), - formula-enabled interface to 'stats::lowess' function ('lowess'), - displaying textual data in plots ('textplot', 'sinkplot'), - plotting dots whose size reflects the relative magnitude of the elements ('balloonplot', 'bubbleplot'), - plotting "Venn" diagrams ('venn'), - displaying Open-Office style plots ('ooplot'), - plotting multiple data on same region, with separate axes ('overplot'), - plotting means and confidence intervals ('plotCI', 'plotmeans'), - spacing points in an x-y plot so they don't overlap ('space').
Maintained by Tal Galili. Last updated 5 months ago.
3.4 match 13 stars 15.11 score 13k scripts 482 dependents
spsanderson
tidyAML:Automatic Machine Learning with 'tidymodels'
The goal of this package will be to provide a simple interface for automatic machine learning that fits the 'tidymodels' framework. The intention is to work for regression and classification problems with a simple verb framework.
Maintained by Steven Sanderson. Last updated 11 months ago.
automatic-machine-learningautomlclassificationmachine-learningparsnipr-languager-programmingregressiontidytidymodelstidyverse
7.5 match 68 stars 6.87 score 36 scripts 1 dependents
winvector
wrapr:Wrap R Tools for Debugging and Parametric Programming
Tools for writing and debugging R code. Provides: '%.>%' dot-pipe (an 'S3' configurable pipe), unpack/to (R style multiple assignment/return), 'build_frame()'/'draw_frame()' ('data.frame' example tools), 'qc()' (quoting concatenate), ':=' (named map builder), 'let()' (converts non-standard evaluation interfaces to parametric standard evaluation interfaces, inspired by 'gtools::strmacro()' and 'base::bquote()'), and more.
Maintained by John Mount. Last updated 2 years ago.
4.6 match 137 stars 11.11 score 390 scripts 12 dependents
rte-antares-rpackage
antaresViz:Antares Visualizations
Visualize results generated by Antares, a powerful open source software developed by RTE to simulate and study electric power systems (more information about 'Antares' here: <https://github.com/AntaresSimulatorTeam/Antares_Simulator>). This package provides functions that create interactive charts to help 'Antares' users visually explore the results of their simulations.
Maintained by Tatiana Vargas. Last updated 2 months ago.
adequacybilandygraphselectricenergyleafletlinear-programmingmanipulatewidgemonte-carlo-simulationoptimizationplotlyprevisionnelrenewable-energyrteshinyshiny-appssimulationstochastic-simulation-algorithmtyndp
7.5 match 21 stars 6.83 score 32 scripts
r-forge
fPortfolio:Rmetrics - Portfolio Selection and Optimization
A collection of functions to optimize portfolios and to analyze them from different points of view.
Maintained by Stefan Theussl. Last updated 3 months ago.
7.7 match 1 stars 6.66 score 179 scripts 2 dependents
cran
lambda.r:Modeling Data with Functional Programming
A language extension to efficiently write functional programs in R. Syntax extensions include multi-part function definitions, pattern matching, guard statements, built-in (optional) type safety.
Maintained by Brian Lee Yung Rowe. Last updated 5 years ago.
7.4 match 1 stars 6.89 score 33 scripts 1.2k dependentsbioc
snpStats:SnpMatrix and XSnpMatrix classes and methods
Classes and statistical methods for large SNP association studies. This extends the earlier snpMatrix package, allowing for uncertainty in genotypes.
Maintained by David Clayton. Last updated 5 months ago.
microarraysnpgeneticvariabilityzlib
5.4 match 9.41 score 674 scripts 17 dependents
m-jahn
WeightedTreemaps:Generate and Plot Voronoi or Sunburst Treemaps from Hierarchical Data
Treemaps are a visually appealing graphical representation of numerical data using a space-filling approach. A plane or 'map' is subdivided into smaller areas called cells. The cells in the map are scaled according to an underlying metric which allows to grasp the hierarchical organization and relative importance of many objects at once. This package contains two different implementations of treemaps, Voronoi treemaps and Sunburst treemaps. The Voronoi treemap function subdivides the plot area in polygonal cells according to the highest hierarchical level, then continues to subdivide those parental cells on the next lower hierarchical level, and so on. The Sunburst treemap is a computationally less demanding treemap that does not require iterative refinement, but simply generates circle sectors that are sized according to predefined weights. The Voronoi tesselation is based on functions from Paul Murrell (2012) <https://www.stat.auckland.ac.nz/~paul/Reports/VoronoiTreemap/voronoiTreeMap.html>.
Maintained by Michael Jahn. Last updated 3 months ago.
r-programmingrcppsunburst-treemapvoronoi-diagramvoronoi-treemapcpp
7.5 match 50 stars 6.73 score 18 scriptsr-gregmisc
gmodels:Various R Programming Tools for Model Fitting
Various R programming tools for model fitting.
Maintained by Gregory R. Warnes. Last updated 3 months ago.
5.0 match 1 stars 10.01 score 3.5k scripts 30 dependents
schweflo
lpSolveAPI:R Interface to 'lp_solve' Version 5.5.2.0
The lpSolveAPI package provides an R interface to 'lp_solve', a Mixed Integer Linear Programming (MILP) solver with support for pure linear, (mixed) integer/binary, semi-continuous and special ordered sets (SOS) models.
Maintained by Florian Schwendinger. Last updated 8 months ago.
6.4 match 7.83 score 640 scripts 79 dependentsr-forge
robustbase:Basic Robust Statistics
"Essential" Robust Statistics. Tools allowing to analyze data with robust methods. This includes regression methodology including model selections and multivariate statistics where we strive to cover the book "Robust Statistics, Theory and Methods" by 'Maronna, Martin and Yohai'; Wiley 2006.
Maintained by Martin Maechler. Last updated 4 months ago.
3.8 match 13.33 score 1.7k scripts 480 dependentsdbosak01
procs:Recreates Some 'SAS®' Procedures in 'R'
Contains functions to simulate the most commonly used 'SAS®' procedures. Specifically, the package aims to simulate the functionality of 'proc freq', 'proc means', 'proc ttest', 'proc reg', 'proc transpose', 'proc sort', and 'proc print'. The simulation will include recreating all statistics with the highest fidelity possible.
Maintained by David Bosak. Last updated 10 months ago.
6.6 match 6 stars 7.57 score 37 scripts 2 dependents
robinhankin
emulator:Bayesian Emulation of Computer Programs
Allows one to estimate the output of a computer program, as a function of the input parameters, without actually running it. The computer program is assumed to be a Gaussian process, whose parameters are estimated using Bayesian techniques that give a PDF of expected program output. This PDF is conditional on a training set of runs, each consisting of a point in parameter space and the model output at that point. The emphasis is on complex codes that take weeks or months to run, and that have a large number of undetermined input parameters; many climate prediction models fall into this class. The emulator essentially determines Bayesian posterior estimates of the PDF of the output of a model, conditioned on results from previous runs and a user-specified prior linear model. The package includes functionality to evaluate quadratic forms efficiently.
Maintained by Robin K. S. Hankin. Last updated 8 months ago.
5.9 match 4 stars 8.27 score 56 scripts 17 dependents
milesmcbain
fnmate:Create function definitions from function expressions
Convert any funcntion expression under the cursor to a definition contained in a file.
Maintained by Miles McBain. Last updated 14 days ago.
functional-programmingfunctions
7.5 match 100 stars 6.48 score 9 scripts 2 dependents
njtierney
maxcovr:A Set of Tools For Solving The Maximal Covering Location Problem
Solving the "maximal covering location problem" as described by Church can be difficult for users not familiar with linear programming. maxcovr provides functions to make it easy to solve this problem, and tools to calculate facility coverage.
Maintained by Nicholas Tierney. Last updated 4 months ago.
8.0 match 44 stars 6.06 score 43 scriptspharmaverse
admiralvaccine:Vaccine Extension Package for ADaM in 'R' Asset Library
Programming vaccine specific Clinical Data Interchange Standards Consortium (CDISC) compliant Analysis Data Model (ADaM) datasets in 'R'. Flat model is followed as per Center for Biologics Evaluation and Research (CBER) guidelines for creating vaccine specific domains. ADaM datasets are a mandatory part of any New Drug or Biologics License Application submitted to the United States Food and Drug Administration (FDA). Analysis derivations are implemented in accordance with the "Analysis Data Model Implementation Guide" (CDISC Analysis Data Model Team (2021), <https://www.cdisc.org/standards/foundational/adam/adamig-v1-3-release-package>). The package is an extension package of the 'admiral' package.
Maintained by Sukalpo Saha. Last updated 2 months ago.
6.5 match 6 stars 7.44 score 23 scripts
colinfay
attempt:Tools for Defensive Programming
Tools for defensive programming, inspired by 'purrr' mappers and based on 'rlang'.'attempt' extends and facilitates defensive programming by providing a consistent grammar, and provides a set of easy to use functions for common tests and conditions. 'attempt' only depends on 'rlang', and focuses on speed, so it can be easily integrated in other functions and used in data analysis.
Maintained by Colin Fay. Last updated 7 months ago.
4.1 match 126 stars 11.57 score 101 scripts 86 dependents
tsuchiya-lab
dsdp:Density Estimation with Semidefinite Programming
The models of probability density functions are Gaussian or exponential distributions with polynomial correction terms. Using a maximum likelihood method, 'dsdp' computes parameters of Gaussian or exponential distributions together with degrees of polynomials by a grid search, and coefficient of polynomials by a variant of semidefinite programming. It adopts Akaike Information Criterion for model selection. See a vignette for a tutorial and more on our 'Github' repository <https://github.com/tsuchiya-lab/dsdp/>.
Maintained by Satoshi Kakihara. Last updated 2 years ago.
density-estimationsemidefinite-programmingfortranopenblas
12.9 match 3.70 score 2 scripts
kkholst
mets:Analysis of Multivariate Event Times
Implementation of various statistical models for multivariate event history data <doi:10.1007/s10985-013-9244-x>. Including multivariate cumulative incidence models <doi:10.1002/sim.6016>, and bivariate random effects probit models (Liability models) <doi:10.1016/j.csda.2015.01.014>. Modern methods for survival analysis, including regression modelling (Cox, Fine-Gray, Ghosh-Lin, Binomial regression) with fast computation of influence functions.
Maintained by Klaus K. Holst. Last updated 23 hours ago.
multivariate-time-to-eventsurvival-analysistime-to-eventfortranopenblascpp
3.5 match 14 stars 13.47 score 236 scripts 42 dependentsstevecondylios
netstat:Retrieve Network Statistics Including Available TCP Ports
R interface for the 'netstat' command line utility used to retrieve and parse commonly used network statistics, including available and in-use transmission control protocol (TCP) ports. Primers offering technical background information on the 'netstat' command line utility are available in the "Linux System Administrator's Manual" by Michael Kerrisk (2014) <https://man7.org/linux/man-pages/man8/netstat.8.html>, and on the Microsoft website (2017) <https://docs.microsoft.com/en-us/windows-server/administration/windows-commands/netstat>.
Maintained by Steve Condylios. Last updated 2 years ago.
7.5 match 3 stars 6.27 score 260 scripts 2 dependentsdbosak01
common:Solutions for Common Problems in Base R
Contains functions for solving commonly encountered problems while programming in R. This package is intended to provide a lightweight supplement to Base R, and will be useful for almost any R user.
Maintained by David Bosak. Last updated 12 months ago.
5.7 match 6 stars 8.21 score 193 scripts 11 dependents
karlines
limSolve:Solving Linear Inverse Models
Functions that (1) find the minimum/maximum of a linear or quadratic function: min or max (f(x)), where f(x) = ||Ax-b||^2 or f(x) = sum(a_i*x_i) subject to equality constraints Ex=f and/or inequality constraints Gx>=h, (2) sample an underdetermined- or overdetermined system Ex=f subject to Gx>=h, and if applicable Ax~=b, (3) solve a linear system Ax=B for the unknown x. It includes banded and tridiagonal linear systems.
Maintained by Karline Soetaert. Last updated 1 years ago.
6.0 match 4 stars 7.85 score 158 scripts 52 dependents
elipousson
bcpss:Baltimore City Public Schools
Provides access to demographic, enrollment, and survey data on Baltimore City Public School System (BCPSS).
Maintained by Eli Pousson. Last updated 1 years ago.
13.3 match 3 stars 3.48 score 5 scripts
raim
dpseg:Piecewise Linear Segmentation by Dynamic Programming
Piecewise linear segmentation of ordered data by a dynamic programming algorithm. The algorithm was developed for time series data, e.g. growth curves, and for genome-wide read-count data from next generation sequencing, but is broadly applicable. Generic implementations of dynamic programming routines allow to scan for optimal segmentation parameters and test custom segmentation criteria ("scoring functions").
Maintained by Rainer Machne. Last updated 25 days ago.
9.8 match 4.71 score 17 scripts 1 dependentsprogram--
HSClientR:A HydroShare API client for R
A RESTful API wrapper for accessing <https://hydroshare.org> data in R.
Maintained by Justin Singh-Mohudpur. Last updated 4 years ago.
api-wrappercuashihydrologyhydrosharewater-resources
20.0 match 4 stars 2.30 score 2 scripts
miriamesteve
eat:Efficiency Analysis Trees
Functions are provided to determine production frontiers and technical efficiency measures through non-parametric techniques based upon regression trees. The package includes code for estimating radial input, output, directional and additive measures, plotting graphical representations of the scores and the production frontiers by means of trees, and determining rankings of importance of input variables in the analysis. Additionally, an adaptation of Random Forest by a set of individual Efficiency Analysis Trees for estimating technical efficiency is also included. More details in: <doi:10.1016/j.eswa.2020.113783>.
Maintained by Miriam Esteve. Last updated 3 years ago.
9.8 match 5 stars 4.68 score 19 scripts
jrdnbradford
readMDTable:Read Markdown Tables into Tibbles
Efficient reading of raw markdown tables into tibbles. Designed to accept content from strings, files, and URLs with the ability to extract and read multiple tables from markdown for analysis.
Maintained by Jordan Bradford. Last updated 1 months ago.
datadata-analysisdata-analyticsdata-extractiondata-miningdata-sciencemarkdownmarkdown-parsermarkdown-tabler-programming
7.5 match 7 stars 6.10 score 3 scripts 1 dependentscran
snowfall:Easier Cluster Computing (Based on 'snow')
Usability wrapper around snow for easier development of parallel R programs. This package offers e.g. extended error checks, and additional functions. All functions work in sequential mode, too, if no cluster is present or wished. Package is also designed as connector to the cluster management tool sfCluster, but can also used without it.
Maintained by Jochen Knaus. Last updated 1 years ago.
5.8 match 7.89 score 1.8k scripts 48 dependentsr-forge
linprog:Linear Programming / Optimization
Can be used to solve Linear Programming / Linear Optimization problems by using the simplex algorithm.
Maintained by Arne Henningsen. Last updated 3 years ago.
5.7 match 8.01 score 77 scripts 150 dependents
tetratech
baytrends:Long Term Water Quality Trend Analysis
Enable users to evaluate long-term trends using a Generalized Additive Modeling (GAM) approach. The model development includes selecting a GAM structure to describe nonlinear seasonally-varying changes over time, incorporation of hydrologic variability via either a river flow or salinity, the use of an intervention to deal with method or laboratory changes suspected to impact data values, and representation of left- and interval-censored data. The approach has been applied to water quality data in the Chesapeake Bay, a major estuary on the east coast of the United States to provide insights to a range of management- and research-focused questions. Methodology described in Murphy (2019) <doi:10.1016/j.envsoft.2019.03.027>.
Maintained by Erik W Leppo. Last updated 5 months ago.
6.8 match 12 stars 6.67 score 97 scriptscran
boot:Bootstrap Functions (Originally by Angelo Canty for S)
Functions and datasets for bootstrapping from the book "Bootstrap Methods and Their Application" by A. C. Davison and D. V. Hinkley (1997, CUP), originally written by Angelo Canty for S.
Maintained by Alessandra R. Brazzale. Last updated 7 months ago.
5.5 match 2 stars 8.21 score 2.3k dependents
alexkowa
EnvStats:Package for Environmental Statistics, Including US EPA Guidance
Graphical and statistical analyses of environmental data, with focus on analyzing chemical concentrations and physical parameters, usually in the context of mandated environmental monitoring. Major environmental statistical methods found in the literature and regulatory guidance documents, with extensive help that explains what these methods do, how to use them, and where to find them in the literature. Numerous built-in data sets from regulatory guidance documents and environmental statistics literature. Includes scripts reproducing analyses presented in the book "EnvStats: An R Package for Environmental Statistics" (Millard, 2013, Springer, ISBN 978-1-4614-8455-4, <doi:10.1007/978-1-4614-8456-1>).
Maintained by Alexander Kowarik. Last updated 15 days ago.
3.5 match 26 stars 12.80 score 2.4k scripts 46 dependents
tdaverse
ripserr:Calculate Persistent Homology with Ripser-Based Engines
Ports the Ripser <https://arxiv.org/abs/1908.02518> and Cubical Ripser <https://arxiv.org/abs/2005.12692> persistent homology calculation engines from C++. Can be used as a rapid calculation tool in topological data analysis pipelines.
Maintained by Raoul Wadhwa. Last updated 6 hours ago.
algebraic-topologycohomologycppcubical-complexpersistent-homologypixelpoint-cloudr-languager-programmingrcpprips-complexripsersimplicial-complexsimplicial-homologytopological-data-analysistopologyvietoris-complexvoxelcpp
7.5 match 7 stars 5.80 score 6 scriptsropensci
tarchetypes:Archetypes for Targets
Function-oriented Make-like declarative pipelines for Statistics and data science are supported in the 'targets' R package. As an extension to 'targets', the 'tarchetypes' package provides convenient user-side functions to make 'targets' easier to use. By establishing reusable archetypes for common kinds of targets and pipelines, these functions help express complicated reproducible pipelines concisely and compactly. The methods in this package were influenced by the 'targets' R package. by Will Landau (2018) <doi:10.21105/joss.00550>.
Maintained by William Michael Landau. Last updated 19 days ago.
data-sciencehigh-performance-computingpeer-reviewedpipeliner-targetopiareproducibilitytargetsworkflow
3.8 match 141 stars 11.43 score 1.7k scripts 10 dependents
stephenslab
mixsqp:Sequential Quadratic Programming for Fast Maximum-Likelihood Estimation of Mixture Proportions
Provides an optimization method based on sequential quadratic programming (SQP) for maximum likelihood estimation of the mixture proportions in a finite mixture model where the component densities are known. The algorithm is expected to obtain solutions that are at least as accurate as the state-of-the-art MOSEK interior-point solver (called by function "KWDual" in the 'REBayes' package), and they are expected to arrive at solutions more quickly when the number of samples is large and the number of mixture components is not too large. This implements the "mix-SQP" algorithm, with some improvements, described in Y. Kim, P. Carbonetto, M. Stephens & M. Anitescu (2020) <DOI:10.1080/10618600.2019.1689985>.
Maintained by Peter Carbonetto. Last updated 1 years ago.
4.9 match 11 stars 8.68 score 87 scripts 23 dependents
mariaguilleng
boostingDEA:A Boosting Approach to Data Envelopment Analysis
Includes functions to estimate production frontiers and make ideal output predictions in the Data Envelopment Analysis (DEA) context using both standard models from DEA and Free Disposal Hull (FDH) and boosting techniques. In particular, EATBoosting (Guillen et al., 2023 <doi:10.1016/j.eswa.2022.119134>) and MARSBoosting. Moreover, the package includes code for estimating several technical efficiency measures using different models such as the input and output-oriented radial measures, the input and output-oriented Russell measures, the Directional Distance Function (DDF), the Weighted Additive Measure (WAM) and the Slacks-Based Measure (SBM).
Maintained by Maria D. Guillen. Last updated 2 years ago.
10.5 match 2 stars 4.00 score 3 scriptscran
VFP:Variance Function Program
Variance function estimation for models proposed by W. Sadler in his variance function program ('VFP', www.aacb.asn.au/AACB/Resources/Variance-Function-Program). Here, the idea is to fit multiple variance functions to a data set and consequently assess which function reflects the relationship 'Var ~ Mean' best. For 'in-vitro diagnostic' ('IVD') assays modeling this relationship is of great importance when individual test-results are used for defining follow-up treatment of patients.
Maintained by Andre Schuetzenmeister. Last updated 2 months ago.
13.9 match 3.01 score 17 scripts
salvatoremangiafico
rcompanion:Functions to Support Extension Education Program Evaluation
Functions and datasets to support Summary and Analysis of Extension Program Evaluation in R, and An R Companion for the Handbook of Biological Statistics. Vignettes are available at <https://rcompanion.org>.
Maintained by Salvatore Mangiafico. Last updated 30 days ago.
5.2 match 4 stars 8.01 score 2.4k scripts 5 dependents
armcn
maybe:The Maybe Monad
The maybe type represents the possibility of some value or nothing. It is often used instead of throwing an error or returning `NULL`. The advantage of using a maybe type over `NULL` is that it is both composable and requires the developer to explicitly acknowledge the potential absence of a value, helping to avoid the existence of unexpected behaviour.
Maintained by Andrew McNeil. Last updated 2 years ago.
7.5 match 50 stars 5.48 score 9 scripts 4 dependentsbioc
methylMnM:detect different methylation level (DMR)
To give the exactly p-value and q-value of MeDIP-seq and MRE-seq data for different samples comparation.
Maintained by Yan Zhou. Last updated 5 months ago.
softwarednamethylationsequencing
9.4 match 4.38 score 2 scripts 1 dependentsdbosak01
logr:Creates Log Files
Contains functions to help create log files. The package aims to overcome the difficulty of the base R sink() command. The log_print() function will print to both the console and the file log, without interfering in other write operations.
Maintained by David Bosak. Last updated 1 months ago.
4.1 match 13 stars 10.03 score 265 scripts 3 dependents
bayesball
LearnBayes:Learning Bayesian Inference
Contains functions for summarizing basic one and two parameter posterior distributions and predictive distributions. It contains MCMC algorithms for summarizing posterior distributions defined by the user. It also contains functions for regression models, hierarchical models, Bayesian tests, and illustrations of Gibbs sampling.
Maintained by Jim Albert. Last updated 7 years ago.
3.6 match 38 stars 11.34 score 690 scripts 31 dependents
bodkan
slendr:A Simulation Framework for Spatiotemporal Population Genetics
A framework for simulating spatially explicit genomic data which leverages real cartographic information for programmatic and visual encoding of spatiotemporal population dynamics on real geographic landscapes. Population genetic models are then automatically executed by the 'SLiM' software by Haller et al. (2019) <doi:10.1093/molbev/msy228> behind the scenes, using a custom built-in simulation 'SLiM' script. Additionally, fully abstract spatial models not tied to a specific geographic location are supported, and users can also simulate data from standard, non-spatial, random-mating models. These can be simulated either with the 'SLiM' built-in back-end script, or using an efficient coalescent population genetics simulator 'msprime' by Baumdicker et al. (2022) <doi:10.1093/genetics/iyab229> with a custom-built 'Python' script bundled with the R package. Simulated genomic data is saved in a tree-sequence format and can be loaded, manipulated, and summarised using tree-sequence functionality via an R interface to the 'Python' module 'tskit' by Kelleher et al. (2019) <doi:10.1038/s41588-019-0483-y>. Complete model configuration, simulation and analysis pipelines can be therefore constructed without a need to leave the R environment, eliminating friction between disparate tools for population genetic simulations and data analysis.
Maintained by Martin Petr. Last updated 11 days ago.
popgenpopulation-geneticssimulationsspatial-statistics
4.5 match 56 stars 9.15 score 88 scriptsr-forge
Rglpk:R/GNU Linear Programming Kit Interface
R interface to the GNU Linear Programming Kit. 'GLPK' is open source software for solving large-scale linear programming (LP), mixed integer linear programming ('MILP') and other related problems.
Maintained by Stefan Theussl. Last updated 1 years ago.
5.6 match 7.20 score 240 scripts 52 dependents
moodymudskipper
inops:Infix Operators for Detection, Subsetting and Replacement
Infix operators to detect, subset, and replace the elements matched by a given condition. The functions have several variants of operator types, including subsets, ranges, regular expressions and others. Implemented operators work on vectors, matrices, and lists.
Maintained by Antoine Fabri. Last updated 5 years ago.
7.5 match 40 stars 5.34 score 11 scripts
nelson-gon
manymodelr:Build and Tune Several Models
Frequently one needs a convenient way to build and tune several models in one go.The goal is to provide a number of machine learning convenience functions. It provides the ability to build, tune and obtain predictions of several models in one function. The models are built using functions from 'caret' with easier to read syntax. Kuhn(2014) <arXiv:1405.6974>.
Maintained by Nelson Gonzabato. Last updated 3 years ago.
analysis-of-varianceanovacorrelationcorrelation-coefficientgeneralized-linear-modelsgradient-boosting-decision-treesknn-classificationlinear-modelslinear-regressionmachine-learningmissing-valuesmodelsr-programmingrandom-forest-algorithmregression-models
7.5 match 2 stars 5.30 score 50 scriptspharmaverse
admiralophtha:ADaM in R Asset Library - Ophthalmology
Aids the programming of Clinical Data Standards Interchange Consortium (CDISC) compliant Ophthalmology Analysis Data Model (ADaM) datasets in R. ADaM datasets are a mandatory part of any New Drug or Biologics License Application submitted to the United States Food and Drug Administration (FDA). Analysis derivations are implemented in accordance with the "Analysis Data Model Implementation Guide" (CDISC Analysis Data Model Team, 2021, <https://www.cdisc.org/standards/foundational/adam/adamig-v1-3-release-package>).
Maintained by Edoardo Mancini. Last updated 2 months ago.
5.0 match 15 stars 7.94 score 10 scripts
epiverse-trace
numberize:Convert Words to Numbers in Multiple Languages
Converts written out numbers into their equivalent numbers. Supports numbers written out in English, French, or Spanish.
Maintained by Bankole Ahadzie. Last updated 11 days ago.
7.5 match 4 stars 5.28 score 1 scripts 1 dependentshenrikbengtsson
R.oo:R Object-Oriented Programming with or without References
Methods and classes for object-oriented programming in R with or without references. Large effort has been made on making definition of methods as simple as possible with a minimum of maintenance for package developers. The package has been developed since 2001 and is now considered very stable. This is a cross-platform package implemented in pure R that defines standard S3 classes without any tricks.
Maintained by Henrik Bengtsson. Last updated 4 months ago.
3.4 match 20 stars 11.49 score 329 scripts 828 dependents
coatless-rpkg
errorist:Automatically Search Errors or Warnings
Provides environment hooks that obtain errors and warnings which occur during the execution of code to automatically search for solutions.
Maintained by James Balamuta. Last updated 1 years ago.
error-handlingerrorsr-programmingsearch-enginewarnings
7.5 match 27 stars 5.24 score 13 scripts
moderndive
moderndive:Tidyverse-Friendly Introductory Linear Regression
Datasets and wrapper functions for tidyverse-friendly introductory linear regression, used in "Statistical Inference via Data Science: A ModernDive into R and the Tidyverse" available at <https://moderndive.com/>.
Maintained by Albert Y. Kim. Last updated 3 months ago.
3.4 match 88 stars 11.35 score 1.8k scriptsdbosak01
fmtr:Easily Apply Formats to Data
Contains a set of functions that can be used to apply formats to data frames or vectors. The package aims to provide functionality similar to that of SAS® formats. Formats are assigned to the format attribute on data frame columns. Then when the fdata() function is called, a new data frame is created with the column data formatted as specified. The package also contains a value() function to create a user-defined format, similar to a SAS® user-defined format.
Maintained by David Bosak. Last updated 2 months ago.
fmtrformatformatsformattingcpp
4.4 match 12 stars 8.84 score 111 scripts 5 dependentshenrikbengtsson
port4me:Get the Same, Personal, Free 'TCP' Port over and over
An R implementation of the cross-platform, language-independent "port4me" algorithm (<https://github.com/HenrikBengtsson/port4me>), which (1) finds a free Transmission Control Protocol ('TCP') port in [1024,65535] that the user can open, (2) is designed to work in multi-user environments, (3), gives different users, different ports, (4) gives the user the same port over time with high probability, (5) gives different ports for different software tools, and (6) requires no configuration.
Maintained by Henrik Bengtsson. Last updated 1 years ago.
bashclihigh-performance-computinghpcmulti-tenantmulti-userportpypi-packagepythonr-languager-programmingtcputility
7.5 match 13 stars 5.11 score 5 scripts
opendp
opendp:R Bindings for the OpenDP Library
The OpenDP Library is a modular collection of statistical algorithms that adhere to the definition of differential privacy. It can be used to build applications of privacy-preserving computations, using a number of different models of privacy.
Maintained by Stefano Iacus. Last updated 22 days ago.
differential-privacydp-programming-frameworkopendpopendp-commonsprivacyrustcargo
6.7 match 343 stars 5.70 score 14 scripts
leobiazoli
capesData:Data on Scholarships in CAPES International Mobility Programs
Information on activities to promote scholarships in Brazil and abroad for international mobility programs, recorded in Capes' computerized payment systems. The CAPES database refers to international mobility programs for the period from 2010 to 2019 <https://dadosabertos.capes.gov.br/dataset/>.
Maintained by Leonardo Biazoli. Last updated 6 months ago.
10.7 match 1 stars 3.54 score 2 scriptsfchamroukhi
flamingos:Functional Latent Data Models for Clustering Heterogeneous Curves ('FLaMingos')
Provides a variety of original and flexible user-friendly statistical latent variable models for the simultaneous clustering and segmentation of heterogeneous functional data (i.e time series, or more generally longitudinal data, fitted by unsupervised algorithms, including EM algorithms. Functional Latent Data Models for Clustering heterogeneous curves ('FLaMingos') are originally introduced and written in 'Matlab' by Faicel Chamroukhi <https://github.com/fchamroukhi?utf8=?&tab=repositories&q=mix&type=public&language=matlab>. The references are mainly the following ones. Chamroukhi F. (2010) <https://chamroukhi.com/FChamroukhi-PhD.pdf>. Chamroukhi F., Same A., Govaert, G. and Aknin P. (2010) <doi:10.1016/j.neucom.2009.12.023>. Chamroukhi F., Same A., Aknin P. and Govaert G. (2011) <doi:10.1109/IJCNN.2011.6033590>. Same A., Chamroukhi F., Govaert G. and Aknin, P. (2011) <doi:10.1007/s11634-011-0096-5>. Chamroukhi F., and Glotin H. (2012) <doi:10.1109/IJCNN.2012.6252818>. Chamroukhi F., Glotin H. and Same A. (2013) <doi:10.1016/j.neucom.2012.10.030>. Chamroukhi F. (2015) <https://chamroukhi.com/FChamroukhi-HDR.pdf>. Chamroukhi F. and Nguyen H-D. (2019) <doi:10.1002/widm.1298>.
Maintained by Florian Lecocq. Last updated 5 years ago.
artificial-intelligencebaum-welch-algorithmcurve-clusteringdata-sciencedynamic-programmingem-algorithmfunctional-data-analysisfunctional-data-clusteringhidden-markov-modelshidden-process-regressionmixture-modelspiecewise-regressionstatistical-analysisstatistical-inferencestatistical-learningtime-series-analysisunsupervised-learningopenblascpp
7.5 match 6 stars 4.95 score 9 scripts
matthewblackwell
Amelia:A Program for Missing Data
A tool that "multiply imputes" missing data in a single cross-section (such as a survey), from a time series (like variables collected for each year in a country), or from a time-series-cross-sectional data set (such as collected by years for each of several countries). Amelia II implements our bootstrapping-based algorithm that gives essentially the same answers as the standard IP or EMis approaches, is usually considerably faster than existing approaches and can handle many more variables. Unlike Amelia I and other statistically rigorous imputation software, it virtually never crashes (but please let us know if you find to the contrary!). The program also generalizes existing approaches by allowing for trends in time series across observations within a cross-sectional unit, as well as priors that allow experts to incorporate beliefs they have about the values of missing cells in their data. Amelia II also includes useful diagnostics of the fit of multiple imputation models. The program works from the R command line or via a graphical user interface that does not require users to know R.
Maintained by Matthew Blackwell. Last updated 4 months ago.
4.1 match 1 stars 9.06 score 1.4k scripts 7 dependentsarmcn
quickcheck:Property Based Testing
Property based testing, inspired by the original 'QuickCheck'. This package builds on the property based testing framework provided by 'hedgehog' and is designed to seamlessly integrate with 'testthat'.
Maintained by Andrew McNeil. Last updated 1 years ago.
functional-programmingproperty-based-testing
7.5 match 25 stars 4.94 score 70 scriptsdbosak01
libr:Libraries, Data Dictionaries, and a Data Step for R
Contains a set of functions to create data libraries, generate data dictionaries, and simulate a data step. The libname() function will load a directory of data into a library in one line of code. The dictionary() function will generate data dictionaries for individual data frames or an entire library. And the datestep() function will perform row-by-row data processing.
Maintained by David Bosak. Last updated 3 months ago.
4.4 match 27 stars 8.34 score 48 scripts 2 dependents
gvegayon
ABCoptim:Implementation of Artificial Bee Colony (ABC) Optimization
An implementation of Karaboga (2005) Artificial Bee Colony Optimization algorithm <http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf>. This was developed upon the basic version programmed in C and available at the algorithm's official website.
Maintained by George Vega Yon. Last updated 2 years ago.
artificial-bee-colonyoptimizationr-programmingrcppstochastic-optimizerscpp
8.0 match 30 stars 4.54 score 23 scripts
pakjiddat
wordpredictor:Develop Text Prediction Models Based on N-Grams
A framework for developing n-gram models for text prediction. It provides data cleaning, data sampling, extracting tokens from text, model generation, model evaluation and word prediction. For information on how n-gram models work we referred to: "Speech and Language Processing" <https://web.archive.org/web/20240919222934/https%3A%2F%2Fweb.stanford.edu%2F~jurafsky%2Fslp3%2F3.pdf>. For optimizing R code and using R6 classes we referred to "Advanced R" <https://adv-r.hadley.nz/r6.html>. For writing R extensions we referred to "R Packages", <https://r-pkgs.org/index.html>.
Maintained by Nadir Latif. Last updated 5 months ago.
n-gram-language-modelsnatural-language-processingr-programming
7.5 match 6 stars 4.78 score 9 scripts
cfhammill
lenses:Elegant Data Manipulation with Lenses
Provides tools for creating and using lenses to simplify data manipulation. Lenses are composable getter/setter pairs for working with data in a purely functional way. Inspired by the 'Haskell' library 'lens' (Kmett, 2012) <https://hackage.haskell.org/package/lens>. For a fairly comprehensive (and highly technical) history of lenses please see the 'lens' wiki <https://github.com/ekmett/lens/wiki/History-of-Lenses>.
Maintained by Chris Hammill. Last updated 6 years ago.
7.5 match 27 stars 4.75 score 42 scripts
mpierrejean
jointseg:Joint Segmentation of Multivariate (Copy Number) Signals
Methods for fast segmentation of multivariate signals into piecewise constant profiles and for generating realistic copy-number profiles. A typical application is the joint segmentation of total DNA copy numbers and allelic ratios obtained from Single Nucleotide Polymorphism (SNP) microarrays in cancer studies. The methods are described in Pierre-Jean, Rigaill and Neuvial (2015) <doi:10.1093/bib/bbu026>.
Maintained by Morgane Pierre-Jean. Last updated 6 years ago.
5.5 match 6 stars 6.50 score 44 scripts 2 dependentssnoweye
pbdMPI:R Interface to MPI for HPC Clusters (Programming with Big Data Project)
A simplified, efficient, interface to MPI for HPC clusters. It is a derivation and rethinking of the Rmpi package. pbdMPI embraces the prevalent parallel programming style on HPC clusters. Beyond the interface, a collection of functions for global work with distributed data and resource-independent RNG reproducibility is included. It is based on S4 classes and methods.
Maintained by Wei-Chen Chen. Last updated 6 months ago.
5.0 match 2 stars 7.11 score 179 scripts 3 dependents
jyprojs
patentr:Access USPTO Bulk Data in Tidy Rectangular Format
Converts TXT and XML data curated by the United States Patent and Trademark Office (USPTO). Allows conversion of bulk data after downloading directly from the USPTO bulk data website, eliminating need for users to wrangle multiple data formats to get large patent databases in tidy, rectangular format. Data details can be found on the USPTO website <https://bulkdata.uspto.gov/>. Currently, all 3 formats: 1. TXT data (1976-2001); 2. XML format 1 data (2002-2004); and 3. XML format 2 data (2005-current) can be converted to rectangular, CSV format. Relevant literature that uses data from USPTO includes Wada (2020) <doi:10.1007/s11192-020-03674-4> and Plaza & Albert (2008) <doi:10.1007/s11192-007-1763-3>.
Maintained by Raoul Wadhwa. Last updated 3 years ago.
patentpatent-datapatentsr-programmingusptocpp
7.5 match 10 stars 4.70 score 5 scripts
wch
Rttf2pt1:'ttf2pt1' Program
Contains the program 'ttf2pt1', for use with the 'extrafont' package. This product includes software developed by the 'TTF2PT1' Project and its contributors.
Maintained by Winston Chang. Last updated 2 years ago.
4.3 match 14 stars 8.16 score 40 scripts 52 dependentspharmaverse
tidytlg:Create TLGs using the 'tidyverse'
Generate tables, listings, and graphs (TLG) using 'tidyverse.' Tables can be created functionally, using a standard TLG process, or by specifying table and column metadata to create generic analysis summaries. The 'envsetup' package can also be leveraged to create environments for table creation.
Maintained by Konrad Pagacz. Last updated 9 months ago.
4.3 match 33 stars 8.07 score 22 scripts
hcorrada
Rcsdp:R Interface to the CSDP Semidefinite Programming Library
R interface to the CSDP semidefinite programming library. Installs version 6.1.1 of CSDP from the COIN-OR website if required. An existing installation of CSDP may be used by passing the proper configure arguments to the installation command. See the INSTALL file for further details.
Maintained by Hector Corrada Bravo. Last updated 5 years ago.
7.0 match 1 stars 4.97 score 8 scripts 10 dependents
rossellhayes
crossmap:Apply Functions to All Combinations of List Elements
Provides an extension to the 'purrr' family of mapping functions to apply a function to each combination of elements in a list of inputs. Also includes functions for automatically detecting output type in mapping functions, finding every combination of elements of lists or rows of data frames, and applying multiple models to multiple subsets of a dataset.
Maintained by Alexander Rossell Hayes. Last updated 2 years ago.
functional-programmingtidyverse
7.5 match 20 stars 4.60 score 3 scripts
dmazarei
ntsDists:Neutrosophic Distributions
Computes the pdf, cdf, quantile function and generating random numbers for neutrosophic distributions. This family have been developed by different authors in the recent years. See Patro and Smarandache (2016) <doi:10.5281/zenodo.571153> and Rao et al (2023) <doi:10.5281/zenodo.7832786>.
Maintained by Danial Mazarei. Last updated 8 months ago.
distributiondistributionsneutrosophicneutrosophic-distributionsr-programming
7.5 match 2 stars 4.56 score 1 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.
2.0 match 164 stars 17.05 score 58k scripts 555 dependentsprogram--
logdec:Log Decorators: Create verbosity using only comments
Easily manage output for your Rscript using "#>>" comments with special identifying tags, such as "@info" or "@warning" to change the detail of your output.
Maintained by Justin Singh-Mohudpur. Last updated 3 years ago.
20.0 match 1 stars 1.70 scorebioc
Harshlight:A "corrective make-up" program for microarray chips
The package is used to detect extended, diffuse and compact blemishes on microarray chips. Harshlight automatically marks the areas in a collection of chips (affybatch objects) and a corrected AffyBatch object is returned, in which the defected areas are substituted with NAs or the median of the values of the same probe in the other chips in the collection. The new version handle the substitute value as whole matrix to solve the memory problem.
Maintained by Maurizio Pellegrino. Last updated 5 months ago.
microarrayqualitycontrolpreprocessingonechannelreportwriting
8.1 match 4.20 score 2 scripts
sergejruff
Virusparies:Visualize and Process Output from 'VirusHunterGatherer'
A collection of tools for downstream analysis of 'VirusHunterGatherer' output. Processing of hittables and plotting of results, enabling better interpretation, is made easier with the provided functions.
Maintained by Ruff Sergej. Last updated 3 months ago.
bioinformaticsdata-drivendiscoverdiscoveryggplot2graphical-tablehidden-markov-modelhmmlearnplotr-programmingsummary-statisticsvirusvirus-discoveryvirus-scanningvirusgatherervirushuntervirushuntergatherervisualization
7.5 match 1 stars 4.49 score 28 scriptspharmaverse
datacutr:SDTM Datacut
Supports the process of applying a cut to Standard Data Tabulation Model (SDTM), as part of the analysis of specific points in time of the data, normally as part of investigation into clinical trials. The functions support different approaches of cutting to the different domains of SDTM normally observed.
Maintained by Tim Barnett. Last updated 1 months ago.
4.5 match 14 stars 7.48 score 11 scriptsbioc
lpsymphony:Symphony integer linear programming solver in R
This package was derived from Rsymphony_0.1-17 from CRAN. These packages provide an R interface to SYMPHONY, an open-source linear programming solver written in C++. The main difference between this package and Rsymphony is that it includes the solver source code (SYMPHONY version 5.6), while Rsymphony expects to find header and library files on the users' system. Thus the intention of lpsymphony is to provide an easy to install interface to SYMPHONY. For Windows, precompiled DLLs are included in this package.
Maintained by Vladislav Kim. Last updated 5 months ago.
infrastructurethirdpartyclientcoinor-symphony
5.1 match 6.44 score 16 scripts 3 dependents
bldavies
nberwp:NBER Working Papers
Catalogue of NBER working papers published between June 1973 and December 2021.
Maintained by Benjamin Davies. Last updated 3 years ago.
7.5 match 23 stars 4.40 score 22 scripts
terrytangyuan
scaffolder:Scaffolding Interfaces to Packages in Other Programming Languages
Comprehensive set of tools for scaffolding R interfaces to modules, classes, functions, and documentations written in other programming languages, such as 'Python'.
Maintained by Yuan Tang. Last updated 2 years ago.
code-generationpythonreticulatescaffolding
5.3 match 27 stars 6.13 score 9 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 14 hours ago.
1.9 match 108 stars 17.13 score 1.1k scripts 1.8k dependents
centerforassessment
SGP:Student Growth Percentiles & Percentile Growth Trajectories
An analytic framework for the calculation of norm- and criterion-referenced academic growth estimates using large scale, longitudinal education assessment data as developed in Betebenner (2009) <doi:10.1111/j.1745-3992.2009.00161.x>.
Maintained by Damian W. Betebenner. Last updated 2 months ago.
percentile-growth-projectionsquantile-regressionsgpsgp-analysesstudent-growth-percentilesstudent-growth-projections
3.3 match 20 stars 9.69 score 88 scriptsbioc
lpNet:Linear Programming Model for Network Inference
lpNet aims at infering biological networks, in particular signaling and gene networks. For that it takes perturbation data, either steady-state or time-series, as input and generates an LP model which allows the inference of signaling networks. For parameter identification either leave-one-out cross-validation or stratified n-fold cross-validation can be used.
Maintained by Lars Kaderali. Last updated 5 months ago.
9.4 match 3.30 score
atlasoflivingaustralia
galah:Biodiversity Data from the GBIF Node Network
The Global Biodiversity Information Facility ('GBIF', <https://www.gbif.org>) sources data from an international network of data providers, known as 'nodes'. Several of these nodes - the "living atlases" (<https://living-atlases.gbif.org>) - maintain their own web services using software originally developed by the Atlas of Living Australia ('ALA', <https://www.ala.org.au>). 'galah' enables the R community to directly access data and resources hosted by 'GBIF' and its partner nodes.
Maintained by Martin Westgate. Last updated 1 months ago.
3.3 match 43 stars 9.17 score 275 scripts 1 dependents
rconsortium
S7:An Object Oriented System Meant to Become a Successor to S3 and S4
A new object oriented programming system designed to be a successor to S3 and S4. It includes formal class, generic, and method specification, and a limited form of multiple dispatch. It has been designed and implemented collaboratively by the R Consortium Object-Oriented Programming Working Group, which includes representatives from R-Core, 'Bioconductor', 'Posit'/'tidyverse', and the wider R community.
Maintained by Hadley Wickham. Last updated 4 months ago.
2.3 match 432 stars 13.15 score 86 scripts 22 dependents
radiant-rstats
radiant:Business Analytics using R and Shiny
A platform-independent browser-based interface for business analytics in R, based on the shiny package. The application combines the functionality of 'radiant.data', 'radiant.design', 'radiant.basics', 'radiant.model', and 'radiant.multivariate'.
Maintained by Vincent Nijs. Last updated 10 months ago.
3.8 match 460 stars 8.03 score 228 scripts
johnaponte
repana:Repeatable Analysis in R
Set of utilities to facilitate the reproduction of analysis in R. It allow to make_structure(), clean_structure(), and run and log programs in a predefined order to allow secondary files, analysis and reports be constructed in an ordered and reproducible form.
Maintained by John J. Aponte. Last updated 22 days ago.
5.0 match 5 stars 5.98 score 19 scripts
wlandau
crew:A Distributed Worker Launcher Framework
In computationally demanding analysis projects, statisticians and data scientists asynchronously deploy long-running tasks to distributed systems, ranging from traditional clusters to cloud services. The 'NNG'-powered 'mirai' R package by Gao (2023) <doi:10.5281/zenodo.7912722> is a sleek and sophisticated scheduler that efficiently processes these intense workloads. The 'crew' package extends 'mirai' with a unifying interface for third-party worker launchers. Inspiration also comes from packages. 'future' by Bengtsson (2021) <doi:10.32614/RJ-2021-048>, 'rrq' by FitzJohn and Ashton (2023) <https://github.com/mrc-ide/rrq>, 'clustermq' by Schubert (2019) <doi:10.1093/bioinformatics/btz284>), and 'batchtools' by Lang, Bischel, and Surmann (2017) <doi:10.21105/joss.00135>.
Maintained by William Michael Landau. Last updated 12 hours ago.
2.7 match 136 stars 11.19 score 243 scripts 2 dependents
cynkra
dm:Relational Data Models
Provides tools for working with multiple related tables, stored as data frames or in a relational database. Multiple tables (data and metadata) are stored in a compound object, which can then be manipulated with a pipe-friendly syntax.
Maintained by Kirill Müller. Last updated 2 months ago.
data-modeldata-warehousingdatawarehousingdbidbplyrrelational-databases
2.0 match 511 stars 14.81 score 410 scripts 8 dependents
nashjc
nlsr:Functions for Nonlinear Least Squares Solutions - Updated 2022
Provides tools for working with nonlinear least squares problems. For the estimation of models reliable and robust tools than nls(), where the the Gauss-Newton method frequently stops with 'singular gradient' messages. This is accomplished by using, where possible, analytic derivatives to compute the matrix of derivatives and a stabilization of the solution of the estimation equations. Tools for approximate or externally supplied derivative matrices are included. Bounds and masks on parameters are handled properly.
Maintained by John C Nash. Last updated 26 days ago.
4.2 match 7.02 score 94 scripts 5 dependentscran
goalp:Weighted and Lexicographic Goal Programming Interface
Solves goal programming problems of the weighted and lexicographic type, as well as combinations of the two, as described by Ignizio (1983) <doi:10.1016/0305-0548(83)90003-5>. Allows for a simple human-readable input describing the problem as a series of equations. Relies on the 'lpSolve' package to solve the underlying linear optimisation problem.
Maintained by David Palma. Last updated 2 years ago.
14.5 match 2.00 score
wanglabcsu
blit:Bioinformatics Library for Integrated Tools
An all-encompassing R toolkit designed to streamline the process of calling various bioinformatics software and then performing data analysis and visualization in R. With 'blit', users can easily integrate a wide array of bioinformatics command line tools into their workflows, leveraging the power of R for sophisticated data manipulation and graphical representation.
Maintained by Yun Peng. Last updated 1 days ago.
6.6 match 3 stars 4.38 score 3 scripts
atorus-research
metacore:A Centralized Metadata Object Focus on Clinical Trial Data Programming Workflows
Create an immutable container holding metadata for the purpose of better enabling programming activities and functionality of other packages within the clinical programming workflow.
Maintained by Christina Fillmore. Last updated 11 months ago.
3.6 match 35 stars 7.99 score 133 scripts 1 dependents
rywhale
kiwisR:A Wrapper for Querying KISTERS 'WISKI' Databases via the 'KiWIS' API
A wrapper for querying 'WISKI' databases via the 'KiWIS' 'REST' API. 'WISKI' is an 'SQL' relational database used for the collection and storage of water data developed by KISTERS and 'KiWIS' is a 'REST' service that provides access to 'WISKI' databases via HTTP requests (<https://www.kisters.eu/water-weather-and-environment/>). Contains a list of default databases (called 'hubs') and also allows users to provide their own 'KiWIS' URL. Supports the entire query process- from metadata to specific time series values. All data is returned as tidy tibbles.
Maintained by Ryan Whaley. Last updated 5 months ago.
api-wrapperhydrologyhydrometricskistersopen-datar-programming
7.5 match 13 stars 3.81 score 10 scriptspharmaverse
logrx:A Logging Utility Focus on Clinical Trial Programming Workflows
A utility to facilitate the logging and review of R programs in clinical trial programming workflows.
Maintained by Nathan Kosiba. Last updated 9 days ago.
3.8 match 41 stars 7.60 score 15 scripts
satijalab
Seurat:Tools for Single Cell Genomics
A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.
Maintained by Paul Hoffman. Last updated 1 years ago.
human-cell-atlassingle-cell-genomicssingle-cell-rna-seqcpp
1.7 match 2.4k stars 16.86 score 50k scripts 73 dependentscran
flexmix:Flexible Mixture Modeling
A general framework for finite mixtures of regression models using the EM algorithm is implemented. The E-step and all data handling are provided, while the M-step can be supplied by the user to easily define new models. Existing drivers implement mixtures of standard linear models, generalized linear models and model-based clustering.
Maintained by Bettina Gruen. Last updated 15 days ago.
3.4 match 5 stars 8.19 score 113 dependents
msuzen
Julia:Fractal Image Data Generator
Generates image data for fractals (Julia and Mandelbrot sets) on the complex plane in the given region and resolution. Benoit B Mandelbrot (1982).
Maintained by Mehmet Suzen. Last updated 8 months ago.
fractalsjuliajulia-fractaljulia-setsmandelbrot-fractalmandelbrot-renderermandelbrot-setr-programmingshape-analysis
7.5 match 1 stars 3.74 score 11 scripts
xoopr
R62S3:Automatic Method Generation from R6
After defining an R6 class, R62S3 is used to automatically generate optional S3/S4 generics and methods for dispatch. Also allows piping for R6 objects.
Maintained by Raphael Sonabend. Last updated 3 years ago.
dispatchobject-oriented-programmingoop
6.7 match 31 stars 4.19 score 1 scripts
profpetrie
regclass:Tools for an Introductory Class in Regression and Modeling
Contains basic tools for visualizing, interpreting, and building regression models. It has been designed for use with the book Introduction to Regression and Modeling with R by Adam Petrie, Cognella Publishers, ISBN: 978-1-63189-250-9 <https://titles.cognella.com/introduction-to-regression-and-modeling-with-r-9781631892509>.
Maintained by Adam Petrie. Last updated 5 years ago.
7.0 match 3.90 score 301 scripts 1 dependents
oxfordcontrol
clarabel:Interior Point Conic Optimization Solver
A versatile interior point solver that solves linear programs (LPs), quadratic programs (QPs), second-order cone programs (SOCPs), semidefinite programs (SDPs), and problems with exponential and power cone constraints (<https://clarabel.org/stable/>). For quadratic objectives, unlike interior point solvers based on the standard homogeneous self-dual embedding (HSDE) model, Clarabel handles quadratic objective without requiring any epigraphical reformulation of its objective function. It can therefore be significantly faster than other HSDE-based solvers for problems with quadratic objective functions. Infeasible problems are detected using using a homogeneous embedding technique.
Maintained by Balasubramanian Narasimhan. Last updated 25 days ago.
4.6 match 10 stars 5.95 score 4 scripts 2 dependentsropensci
qualR:An R package to download São Paulo and Rio de Janeiro air pollution data
A package to download information from CETESB QUALAR <https://cetesb.sp.gov.br/ar/qualar/> and MonitorAr <http://jeap.rio.rj.gov.br/je-metinfosmac/institucional/index.html> systems. It contains function to download different parameters, a set of criteria pollutants and the most frequent meteorological parameters used in air quality data analysis and air quality model evaluation.
Maintained by Mario Gavidia-Calderón. Last updated 25 days ago.
air-pollutantsair-quality-dataair-quality-measurementsbrazilcetesbrio-de-janeirosao-pauloweather-data
5.2 match 25 stars 5.20 score 21 scripts
timteafan
loopurrr:Tranlate purrr iterator functions to regular for loops
Makes learning, teaching and debugging iterator functions from the purrr package easy by translating them into regular for loops.
Maintained by Tim Tiefenbach. Last updated 2 years ago.
7.5 match 82 stars 3.61 score 3 scripts
jewellsean
LZeroSpikeInference:Exact Spike Train Inference via L0 Optimization
An implementation of algorithms described in Jewell and Witten (2017) <arXiv:1703.08644>.
Maintained by Sean Jewell. Last updated 6 years ago.
changepointdynamic-programminglassoneurosciencestatistics
7.5 match 8 stars 3.60 score 8 scriptstidyverse
tidyverse:Easily Install and Load the 'Tidyverse'
The 'tidyverse' is a set of packages that work in harmony because they share common data representations and 'API' design. This package is designed to make it easy to install and load multiple 'tidyverse' packages in a single step. Learn more about the 'tidyverse' at <https://www.tidyverse.org>.
Maintained by Hadley Wickham. Last updated 5 months ago.
1.3 match 1.7k stars 20.26 score 664k scripts 125 dependents
tbep-tech
tbeptools:Data and Indicators for the Tampa Bay Estuary Program
Several functions are provided for working with Tampa Bay Estuary Program data and indicators, including the water quality report card, tidal creek assessments, Tampa Bay Nekton Index, Tampa Bay Benthic Index, seagrass transect data, habitat report card, and fecal indicator bacteria. Additional functions are provided for miscellaneous tasks, such as reference library curation.
Maintained by Marcus Beck. Last updated 8 days ago.
data-analysistampa-baytbepwater-quality
3.4 match 10 stars 7.86 score 133 scripts
usepa
RAQSAPI:A Simple Interface to the US EPA Air Quality System Data Mart API
Retrieve air monitoring data and associated metadata from the US Environmental Protection Agency's Air Quality System service using functions. See <https://aqs.epa.gov/aqsweb/documents/data_api.html> for details about the US EPA Data Mart API.
Maintained by Clinton Mccrowey. Last updated 9 months ago.
united state environmental protection agencyenvironmental-data-retrievalair-quality-systemaqs-datamartair-monitoringenvironmental-monitoringairmonitoringaqsdatamartr03rprogrammingusepa
4.0 match 21 stars 6.64 score 32 scripts
schaubert
catdata:Categorical Data
This R-package contains examples from the book "Regression for Categorical Data", Tutz 2012, Cambridge University Press. The names of the examples refer to the chapter and the data set that is used.
Maintained by Gunther Schauberger. Last updated 1 years ago.
4.0 match 6.61 score 158 scripts 2 dependentselipousson
mapbaltimore:Make maps for Baltimore City with open data
This package provides data from the Baltimore City, the state of Maryland, and other sources, functions to access additional data, and function to create and modify simple maps of Baltimore neighborhoods using sf and ggplot2.
Maintained by Eli Pousson. Last updated 4 months ago.
6.8 match 17 stars 3.85 score 14 scriptsbioc
SRAdb:A compilation of metadata from NCBI SRA and tools
The Sequence Read Archive (SRA) is the largest public repository of sequencing data from the next generation of sequencing platforms including Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD System, Helicos Heliscope, and others. However, finding data of interest can be challenging using current tools. SRAdb is an attempt to make access to the metadata associated with submission, study, sample, experiment and run much more feasible. This is accomplished by parsing all the NCBI SRA metadata into a SQLite database that can be stored and queried locally. Fulltext search in the package make querying metadata very flexible and powerful. fastq and sra files can be downloaded for doing alignment locally. Beside ftp protocol, the SRAdb has funcitons supporting fastp protocol (ascp from Aspera Connect) for faster downloading large data files over long distance. The SQLite database is updated regularly as new data is added to SRA and can be downloaded at will for the most up-to-date metadata.
Maintained by Jack Zhu. Last updated 3 months ago.
infrastructuresequencingdataimport
3.3 match 2 stars 7.81 score 200 scripts
data-cleaning
errorlocate:Locate Errors with Validation Rules
Errors in data can be located and removed using validation rules from package 'validate'. See also Van der Loo and De Jonge (2018) <doi:10.1002/9781118897126>, chapter 7.
Maintained by Edwin de Jonge. Last updated 9 months ago.
data-cleaningerrorsinvalidation
4.3 match 22 stars 6.11 score 59 scripts
ablack3
icdpicr:'ICD' Programs for Injury Categorization in R
Categorization and scoring of injury severity typically involves trained personnel with access to injured persons or their medical records. 'icdpicr' contains a function that provides automated calculation of Abbreviated Injury Scale ('AIS') and Injury Severity Score ('ISS') from International Classification of Diseases ('ICD') codes and may be a useful substitute to manual injury severity scoring. 'ICDPIC' was originally developed in 'Stata', and 'icdpicr' is an open-access update that accepts both 'ICD-9' and 'ICD-10' codes.
Maintained by Adam Black. Last updated 3 years ago.
5.8 match 6 stars 4.48 score 10 scripts
ready4-dev
ready4:Develop and Use Modular Health Economic Models
A template model module, tools to help find model modules derived from this template and a programming syntax to use these modules in health economic analyses. These elements are the foundation for a prototype software framework for developing living and transferable models and using those models in reproducible health economic analyses. The software framework is extended by other R libraries. For detailed documentation about the framework and how to use it visit <https://www.ready4-dev.com/>. For a background to the methodological issues that the framework is attempting to help solve, see Hamilton et al. (2024) <doi:10.1007/s40273-024-01378-8>.
Maintained by Matthew Hamilton. Last updated 4 months ago.
computational-modelinghealth-economicssoftware-framework
3.8 match 2 stars 6.84 score 95 scripts
yukai-yang
R6DS:R6 Reference Class Based Data Structures
Provides reference classes implementing some useful data structures. The package implements these data structures by using the reference class R6. Therefore, the classes of the data structures are also reference classes which means that their instances are passed by reference. The implemented data structures include stack, queue, double-ended queue, doubly linked list, set, dictionary and binary search tree. See for example <https://en.wikipedia.org/wiki/Data_structure> for more information about the data structures.
Maintained by Yukai Yang. Last updated 2 years ago.
binary-search-treesdata-structuresdequedictionarydoubly-linked-listfunctional-programmingmapqueuereference-classstacktraversal
7.5 match 5 stars 3.40 score 5 scripts
k5cents
gluedown:Wrap Vectors in Markdown Formatting
Ease the transition between R vectors and markdown text. With 'gluedown' and 'rmarkdown', users can create traditional vectors in R, glue those strings together with the markdown syntax, and print those formatted vectors directly to the document. This package primarily uses GitHub Flavored Markdown (GFM), an offshoot of the unambiguous CommonMark specification by John MacFarlane (2019) <https://spec.commonmark.org/>.
Maintained by Kiernan Nicholls. Last updated 1 years ago.
3.3 match 115 stars 7.59 score 57 scriptstidyverse
ellmer:Chat with Large Language Models
Chat with large language models from a range of providers including 'Claude' <https://claude.ai>, 'OpenAI' <https://chatgpt.com>, and more. Supports streaming, asynchronous calls, tool calling, and structured data extraction.
Maintained by Hadley Wickham. Last updated 3 days ago.
2.0 match 388 stars 12.58 score 98 scripts 7 dependents
geobosh
gbutils:Utilities for Simulation, Plots, Quantile Functions and Programming
Plot density and distribution functions with automatic selection of suitable regions. Numerically invert (compute quantiles) distribution functions. Simulate real and complex numbers from distributions of their magnitude and arguments. Optionally, the magnitudes and/or arguments may be fixed in almost arbitrary ways. Create polynomials from roots given in Cartesian or polar form. Small programming utilities: check if an object is identical to NA, count positional arguments in a call, set intersection of more than two sets, check if an argument is unnamed, compute the graph of S4 classes in packages.
Maintained by Georgi N. Boshnakov. Last updated 3 years ago.
adjacency-matrixcomplex-numbersplotting-functionss4s4classsimulation
3.4 match 1 stars 7.32 score 29 scripts 56 dependents
bart1
move2:Processing and Analysing Animal Trajectories
Tools to handle, manipulate and explore trajectory data, with an emphasis on data from tracked animals. The package is designed to support large studies with several million location records and keep track of units where possible. Data import directly from 'movebank' <https://www.movebank.org/cms/movebank-main> and files is facilitated.
Maintained by Bart Kranstauber. Last updated 1 months ago.
3.3 match 7.51 score 169 scripts 1 dependents
pbs-software
PBSmodelling:GUI Tools Made Easy: Interact with Models and Explore Data
Provides software to facilitate the design, testing, and operation of computer models. It focuses particularly on tools that make it easy to construct and edit a customized graphical user interface ('GUI'). Although our simplified 'GUI' language depends heavily on the R interface to the 'Tcl/Tk' package, a user does not need to know 'Tcl/Tk'. Examples illustrate models built with other R packages, including 'PBSmapping', 'PBSddesolve', and 'BRugs'. A complete user's guide 'PBSmodelling-UG.pdf' shows how to use this package effectively.
Maintained by Rowan Haigh. Last updated 4 months ago.
3.7 match 2 stars 6.76 score 120 scripts 4 dependents
alexkz
kernlab:Kernel-Based Machine Learning Lab
Kernel-based machine learning methods for classification, regression, clustering, novelty detection, quantile regression and dimensionality reduction. Among other methods 'kernlab' includes Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes and a QP solver.
Maintained by Alexandros Karatzoglou. Last updated 7 months ago.
2.0 match 21 stars 12.26 score 7.8k scripts 487 dependentsbioc
BiocGenerics:S4 generic functions used in Bioconductor
The package defines many S4 generic functions used in Bioconductor.
Maintained by Hervé Pagès. Last updated 1 months ago.
infrastructurebioconductor-packagecore-package
1.7 match 12 stars 14.22 score 612 scripts 2.2k dependents
hongyuanjia
eplusr:A Toolkit for Using Whole Building Simulation Program 'EnergyPlus'
A rich toolkit of using the whole building simulation program 'EnergyPlus'(<https://energyplus.net>), which enables programmatic navigation, modification of 'EnergyPlus' models and makes it less painful to do parametric simulations and analysis.
Maintained by Hongyuan Jia. Last updated 8 months ago.
energy-simulationenergyplusenergyplus-modelseplusepwiddidfparametric-simulationr6simulation
3.4 match 72 stars 7.20 score 91 scripts 4 dependents
bradlindblad
tidyUSDA:A Minimal Tool Set for Gathering USDA Quick Stat Data for Analysis and Visualization
Provides a consistent API to pull United States Department of Agriculture census and survey data from the National Agricultural Statistics Service (NASS) QuickStats service.
Maintained by Brad Lindblad. Last updated 1 years ago.
3.8 match 43 stars 6.43 score 42 scripts
walkerke
tidycensus:Load US Census Boundary and Attribute Data as 'tidyverse' and 'sf'-Ready Data Frames
An integrated R interface to several United States Census Bureau APIs (<https://www.census.gov/data/developers/data-sets.html>) and the US Census Bureau's geographic boundary files. Allows R users to return Census and ACS data as tidyverse-ready data frames, and optionally returns a list-column with feature geometry for mapping and spatial analysis.
Maintained by Kyle Walker. Last updated 2 months ago.
1.7 match 647 stars 14.27 score 7.5k scripts 10 dependents
poissonconsulting
checkr:Check the Properties of Common R Objects
Expressive, assertive, pipe-friendly functions to check the properties of common R objects. In the case of failure the functions issue informative error messages. Superseded by the 'chk' package.
Maintained by Joe Thorley. Last updated 2 months ago.
3.3 match 13 stars 7.18 score 258 scripts 1 dependents
florianhartig
BayesianTools:General-Purpose MCMC and SMC Samplers and Tools for Bayesian Statistics
General-purpose MCMC and SMC samplers, as well as plots and diagnostic functions for Bayesian statistics, with a particular focus on calibrating complex system models. Implemented samplers include various Metropolis MCMC variants (including adaptive and/or delayed rejection MH), the T-walk, two differential evolution MCMCs, two DREAM MCMCs, and a sequential Monte Carlo (SMC) particle filter.
Maintained by Florian Hartig. Last updated 1 years ago.
bayesecological-modelsmcmcoptimizationsmcsystems-biologycpp
2.3 match 122 stars 10.17 score 580 scripts 5 dependents
kkawato
rdlearn:Safe Policy Learning under Regression Discontinuity Design with Multiple Cutoffs
Implements safe policy learning under regression discontinuity designs with multiple cutoffs, based on Zhang et al. (2022) <doi:10.48550/arXiv.2208.13323>. The learned cutoffs are guaranteed to perform no worse than the existing cutoffs in terms of overall outcomes. The 'rdlearn' package also includes features for visualizing the learned cutoffs relative to the baseline and conducting sensitivity analyses.
Maintained by Kentaro Kawato. Last updated 22 days ago.
4.5 match 1 stars 5.26 score 4 scripts
act-org
RSCAT:Shadow-Test Approach to Computerized Adaptive Testing
As an advanced approach to computerized adaptive testing (CAT), shadow testing (van der Linden(2005) <doi:10.1007/0-387-29054-0>) dynamically assembles entire shadow tests as a part of selecting items throughout the testing process. Selecting items from shadow tests guarantees the compliance of all content constraints defined by the blueprint. 'RSCAT' is an R package for the shadow-test approach to CAT. The objective of 'RSCAT' is twofold: 1) Enhancing the effectiveness of shadow-test CAT simulation; 2) Contributing to the academic and scientific community for CAT research. RSCAT is currently designed for dichotomous items based on the three-parameter logistic (3PL) model.
Maintained by Bingnan Jiang. Last updated 3 years ago.
computerized-adaptive-testingitem-response-theoryjavamixed-integer-programmingopen-sourceoptimizationshadow-testingshinyxpress-moselopenjdk
6.7 match 7 stars 3.54 score 6 scriptshadley
lazyeval:Lazy (Non-Standard) Evaluation
An alternative approach to non-standard evaluation using formulas. Provides a full implementation of LISP style 'quasiquotation', making it easier to generate code with other code.
Maintained by Hadley Wickham. Last updated 3 years ago.
1.5 match 131 stars 15.74 score 520 scripts 1.8k dependentsbioc
CellBench:Construct Benchmarks for Single Cell Analysis Methods
This package contains infrastructure for benchmarking analysis methods and access to single cell mixture benchmarking data. It provides a framework for organising analysis methods and testing combinations of methods in a pipeline without explicitly laying out each combination. It also provides utilities for sampling and filtering SingleCellExperiment objects, constructing lists of functions with varying parameters, and multithreaded evaluation of analysis methods.
Maintained by Shian Su. Last updated 5 months ago.
softwareinfrastructuresinglecellbenchmarkbioinformatics
2.7 match 30 stars 8.71 score 98 scripts
mhenderson
funcgeo:Functional Geometry in R
Peter Henderson's Functional Geometry in R.
Maintained by Matthew Henderson. Last updated 12 months ago.
functional-programminggeometrygraphics
7.5 match 8 stars 3.08 score 3 scriptsropensci
targets:Dynamic Function-Oriented 'Make'-Like Declarative Pipelines
Pipeline tools coordinate the pieces of computationally demanding analysis projects. The 'targets' package is a 'Make'-like pipeline tool for statistics and data science in R. The package skips costly runtime for tasks that are already up to date, orchestrates the necessary computation with implicit parallel computing, and abstracts files as R objects. If all the current output matches the current upstream code and data, then the whole pipeline is up to date, and the results are more trustworthy than otherwise. The methodology in this package borrows from GNU 'Make' (2015, ISBN:978-9881443519) and 'drake' (2018, <doi:10.21105/joss.00550>).
Maintained by William Michael Landau. Last updated 14 hours ago.
data-sciencehigh-performance-computingmakepeer-reviewedpipeliner-targetopiareproducibilityreproducible-researchtargetsworkflow
1.5 match 973 stars 15.20 score 4.6k scripts 22 dependents