Showing 200 of total 2367 results (show query)
cynkra
constructive:Display Idiomatic Code to Construct Most R Objects
Prints code that can be used to recreate R objects. In a sense it is similar to 'base::dput()' or 'base::deparse()' but 'constructive' strives to use idiomatic constructors.
Maintained by Antoine Fabri. Last updated 3 days ago.
111.8 match 151 stars 8.68 score 20 scripts
jbkunst
highcharter:A Wrapper for the 'Highcharts' Library
A wrapper for the 'Highcharts' library including shortcut functions to plot R objects. 'Highcharts' <https://www.highcharts.com/> is a charting library offering numerous chart types with a simple configuration syntax.
Maintained by Joshua Kunst. Last updated 1 years ago.
highchartshtmlwidgetsshinyshiny-rvisualizationwrapper
62.8 match 725 stars 13.93 score 4.9k scripts 18 dependents
dgkf
options:Simple, Consistent Package Options
Simple mechanisms for defining and interpreting package options. Provides helpers for interpreting environment variables, global options, defining default values and more.
Maintained by Doug Kelkhoff. Last updated 5 days ago.
72.4 match 7.14 score 1.2k scripts
rstudio
gt:Easily Create Presentation-Ready Display Tables
Build display tables from tabular data with an easy-to-use set of functions. With its progressive approach, we can construct display tables with a cohesive set of table parts. Table values can be formatted using any of the included formatting functions. Footnotes and cell styles can be precisely added through a location targeting system. The way in which 'gt' handles things for you means that you don't often have to worry about the fine details.
Maintained by Richard Iannone. Last updated 28 days ago.
docxeasy-to-usehtmllatexrtfsummary-tables
26.8 match 2.1k stars 18.36 score 20k scripts 112 dependents
henrikbengtsson
R.utils:Various Programming Utilities
Utility functions useful when programming and developing R packages.
Maintained by Henrik Bengtsson. Last updated 1 years ago.
34.9 match 63 stars 13.74 score 5.7k scripts 814 dependents
coolbutuseless
yyjsonr:Fast 'JSON', 'NDJSON' and 'GeoJSON' Parser and Generator
A fast 'JSON' parser, generator and validator which converts 'JSON', 'NDJSON' (Newline Delimited 'JSON') and 'GeoJSON' (Geographic 'JSON') data to/from R objects. The standard R data types are supported (e.g. logical, numeric, integer) with configurable handling of NULL and NA values. Data frames, atomic vectors and lists are all supported as data containers translated to/from 'JSON'. 'GeoJSON' data is read in as 'simple features' objects. This implementation wraps the 'yyjson' 'C' library which is available from <https://github.com/ibireme/yyjson>.
Maintained by Mike Cheng. Last updated 5 months ago.
44.1 match 147 stars 9.56 score 22 scripts 9 dependents
datastorm-open
visNetwork:Network Visualization using 'vis.js' Library
Provides an R interface to the 'vis.js' JavaScript charting library. It allows an interactive visualization of networks.
Maintained by Benoit Thieurmel. Last updated 2 years ago.
25.7 match 550 stars 15.25 score 4.1k scripts 196 dependents
cran
futile.options:Futile Options Management
A scoped options management framework. Used in other packages.
Maintained by Brian Lee Yung Rowe. Last updated 7 years ago.
49.8 match 7.15 score 1.2k dependents
epiforecasts
EpiNow2:Estimate Real-Time Case Counts and Time-Varying Epidemiological Parameters
Estimates the time-varying reproduction number, rate of spread, and doubling time using a range of open-source tools (Abbott et al. (2020) <doi:10.12688/wellcomeopenres.16006.1>), and current best practices (Gostic et al. (2020) <doi:10.1101/2020.06.18.20134858>). It aims to help users avoid some of the limitations of naive implementations in a framework that is informed by community feedback and is actively supported.
Maintained by Sebastian Funk. Last updated 1 months ago.
backcalculationcovid-19gaussian-processesopen-sourcereproduction-numberstancpp
29.2 match 123 stars 11.86 score 210 scripts
jokergoo
GlobalOptions:Generate Functions to Get or Set Global Options
It provides more configurations on the option values such as validation and filtering on the values, making options invisible or private.
Maintained by Zuguang Gu. Last updated 9 months ago.
35.8 match 9 stars 9.54 score 40 scripts 221 dependents
antoinechampion
optional:Optional Types and Pattern Matching
Introduces optional types with some() and none, as well as match_with() from functional languages.
Maintained by Antoine Champion. Last updated 3 years ago.
librarynullableoptionalpattern-matching
79.0 match 1 stars 4.29 score 39 scripts
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 4 hours ago.
dynamic-documentsknitrliterate-programmingrmarkdownsweave
14.1 match 2.4k stars 23.62 score 116k scripts 4.2k dependents
billdenney
PKNCA:Perform Pharmacokinetic Non-Compartmental Analysis
Compute standard Non-Compartmental Analysis (NCA) parameters for typical pharmacokinetic analyses and summarize them.
Maintained by Bill Denney. Last updated 1 months ago.
ncanoncompartmental-analysispharmacokinetics
26.4 match 73 stars 12.53 score 214 scripts 4 dependents
rvlenth
emmeans:Estimated Marginal Means, aka Least-Squares Means
Obtain estimated marginal means (EMMs) for many linear, generalized linear, and mixed models. Compute contrasts or linear functions of EMMs, trends, and comparisons of slopes. Plots and other displays. Least-squares means are discussed, and the term "estimated marginal means" is suggested, in Searle, Speed, and Milliken (1980) Population marginal means in the linear model: An alternative to least squares means, The American Statistician 34(4), 216-221 <doi:10.1080/00031305.1980.10483031>.
Maintained by Russell V. Lenth. Last updated 1 days ago.
16.4 match 380 stars 19.25 score 13k scripts 188 dependents
jinseob2kim
jstable:Create Tables from Different Types of Regression
Create regression tables from generalized linear model(GLM), generalized estimating equation(GEE), generalized linear mixed-effects model(GLMM), Cox proportional hazards model, survey-weighted generalized linear model(svyglm) and survey-weighted Cox model results for publication.
Maintained by Jinseob Kim. Last updated 5 days ago.
28.0 match 28 stars 10.08 score 199 scripts 1 dependents
ahudde
greeks:Sensitivities of Prices of Financial Options and Implied Volatilities
Methods to calculate sensitivities of financial option prices for European, geometric and arithmetic Asian, and American options, with various payoff functions in the Black Scholes model, and in more general jump diffusion models. A shiny app to interactively plot the results is included. Furthermore, methods to compute implied volatilities are provided for a wide range of option types and custom payoff functions. Classical formulas are implemented for European options in the Black Scholes Model, as is presented in Hull, J. C. (2017), Options, Futures, and Other Derivatives. In the case of Asian options, Malliavin Monte Carlo Greeks are implemented, see Hudde, A. & Rüschendorf, L. (2023). European and Asian Greeks for exponential Lévy processes. <doi:10.1007/s11009-023-10014-5>. For American options, the Binomial Tree Method is implemented, as is presented in Hull, J. C. (2017).
Maintained by Anselm Hudde. Last updated 20 days ago.
asian-optiongreeksimplied-volatilityoptioncpp
48.9 match 7 stars 5.75 score 6 scripts
dreamrs
toastui:Interactive Tables, Calendars and Charts for the Web
Create interactive tables, calendars and charts with 'TOAST UI' <https://ui.toast.com/> libraries to integrate in 'shiny' applications or 'rmarkdown' 'HTML' documents.
Maintained by Victor Perrier. Last updated 10 hours ago.
28.0 match 87 stars 9.82 score 144 scripts 8 dependents
biomodhub
biomod2:Ensemble Platform for Species Distribution Modeling
Functions for species distribution modeling, calibration and evaluation, ensemble of models, ensemble forecasting and visualization. The package permits to run consistently up to 10 single models on a presence/absences (resp presences/pseudo-absences) dataset and to combine them in ensemble models and ensemble projections. Some bench of other evaluation and visualisation tools are also available within the package.
Maintained by Maya Guéguen. Last updated 18 hours ago.
19.7 match 95 stars 13.91 score 536 scripts 8 dependents
apache
arrow:Integration to 'Apache' 'Arrow'
'Apache' 'Arrow' <https://arrow.apache.org/> is a cross-language development platform for in-memory data. It specifies a standardized language-independent columnar memory format for flat and hierarchical data, organized for efficient analytic operations on modern hardware. This package provides an interface to the 'Arrow C++' library.
Maintained by Jonathan Keane. Last updated 2 months ago.
13.8 match 15k stars 19.25 score 10k scripts 82 dependentsdreamrs
apexcharter:Create Interactive Chart with the JavaScript 'ApexCharts' Library
Provides an 'htmlwidgets' interface to 'apexcharts.js'. 'Apexcharts' is a modern JavaScript charting library to build interactive charts and visualizations with simple API. 'Apexcharts' examples and documentation are available here: <https://apexcharts.com/>.
Maintained by Victor Perrier. Last updated 1 months ago.
29.9 match 144 stars 8.43 score 247 scripts
trafficonese
leaflet.extras:Extra Functionality for 'leaflet' Package
The 'leaflet' JavaScript library provides many plugins some of which are available in the core 'leaflet' package, but there are many more. It is not possible to support them all in the core 'leaflet' package. This package serves as an add-on to the 'leaflet' package by providing extra functionality via 'leaflet' plugins.
Maintained by Sebastian Gatscha. Last updated 3 months ago.
data-visualizationgeospatialleaflet
18.4 match 218 stars 13.27 score 2.5k scripts 25 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 5 months ago.
31.0 match 2 stars 6.76 score 120 scripts 4 dependents
trevorld
optparse:Command Line Option Parser
A command line parser inspired by Python's 'optparse' library to be used with Rscript to write "#!" shebang scripts that accept short and long flag/options.
Maintained by Trevor L. Davis. Last updated 11 months ago.
16.1 match 150 stars 12.86 score 13k scripts 32 dependentsrstudio
shiny:Web Application Framework for R
Makes it incredibly easy to build interactive web applications with R. Automatic "reactive" binding between inputs and outputs and extensive prebuilt widgets make it possible to build beautiful, responsive, and powerful applications with minimal effort.
Maintained by Winston Chang. Last updated 8 days ago.
reactiverstudioshinyweb-appweb-development
9.7 match 5.5k stars 21.31 score 108k scripts 1.8k dependents
ropensci
crul:HTTP Client
A simple HTTP client, with tools for making HTTP requests, and mocking HTTP requests. The package is built on R6, and takes inspiration from Ruby's 'faraday' gem (<https://rubygems.org/gems/faraday>). The package name is a play on curl, the widely used command line tool for HTTP, and this package is built on top of the R package 'curl', an interface to 'libcurl' (<https://curl.se/libcurl/>).
Maintained by Scott Chamberlain. Last updated 8 months ago.
httphttpsapiweb-servicescurldownloadlibcurlasyncmockingcaching
14.6 match 107 stars 14.07 score 240 scripts 168 dependents
jacob-long
jtools:Analysis and Presentation of Social Scientific Data
This is a collection of tools for more efficiently understanding and sharing the results of (primarily) regression analyses. There are also a number of miscellaneous functions for statistical and programming purposes. Support for models produced by the survey and lme4 packages are points of emphasis.
Maintained by Jacob A. Long. Last updated 7 months ago.
13.1 match 167 stars 14.48 score 4.0k scripts 14 dependents
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 17 days ago.
11.0 match 107 stars 17.17 score 1.1k scripts 1.8k dependentsdreamrs
shinyWidgets:Custom Inputs Widgets for Shiny
Collection of custom input controls and user interface components for 'Shiny' applications. Give your applications a unique and colorful style !
Maintained by Victor Perrier. Last updated 29 days ago.
11.0 match 849 stars 17.05 score 8.1k scripts 218 dependents
eddelbuettel
RQuantLib:R Interface to the 'QuantLib' Library
The 'RQuantLib' package makes parts of 'QuantLib' accessible from R The 'QuantLib' project aims to provide a comprehensive software framework for quantitative finance. The goal is to provide a standard open source library for quantitative analysis, modeling, trading, and risk management of financial assets.
Maintained by Dirk Eddelbuettel. Last updated 8 days ago.
21.0 match 123 stars 8.44 score 194 scripts
mayoverse
arsenal:An Arsenal of 'R' Functions for Large-Scale Statistical Summaries
An Arsenal of 'R' functions for large-scale statistical summaries, which are streamlined to work within the latest reporting tools in 'R' and 'RStudio' and which use formulas and versatile summary statistics for summary tables and models. The primary functions include tableby(), a Table-1-like summary of multiple variable types 'by' the levels of one or more categorical variables; paired(), a Table-1-like summary of multiple variable types paired across two time points; modelsum(), which performs simple model fits on one or more endpoints for many variables (univariate or adjusted for covariates); freqlist(), a powerful frequency table across many categorical variables; comparedf(), a function for comparing data.frames; and write2(), a function to output tables to a document.
Maintained by Ethan Heinzen. Last updated 8 months ago.
baseline-characteristicsdescriptive-statisticsmodelingpaired-comparisonsreportingstatisticstableone
13.3 match 225 stars 13.40 score 1.2k scripts 15 dependents
nandp1
nser:Bhavcopy and Live Market Data from National Stock Exchange (NSE) & Bombay Stock Exchange (BSE) India
Download Current & Historical Bhavcopy. Get Live Market data from NSE India of Equities and Derivatives (F&O) segment. Data source <https://www.nseindia.com/>.
Maintained by Nandan Patil. Last updated 5 months ago.
bhavbhavcopybhavcopy-downloaderfinancial-datamarket-datanational-stock-exchangensense-stock-dataoption-pricingoptionchainrseleniumstock-prices
23.3 match 8 stars 7.61 score 76 scripts
r-tmap
tmap:Thematic Maps
Thematic maps are geographical maps in which spatial data distributions are visualized. This package offers a flexible, layer-based, and easy to use approach to create thematic maps, such as choropleths and bubble maps.
Maintained by Martijn Tennekes. Last updated 18 hours ago.
choropleth-mapsmapsspatialthematic-mapsvisualisation
10.8 match 879 stars 16.23 score 13k scripts 24 dependents
r-lib
ymlthis:Write 'YAML' for 'R Markdown', 'bookdown', 'blogdown', and More
Write 'YAML' front matter for R Markdown and related documents. Work with 'YAML' objects more naturally and write the resulting 'YAML' to your clipboard or to 'YAML' files related to your project.
Maintained by Malcolm Barrett. Last updated 3 years ago.
17.2 match 165 stars 9.92 score 196 scripts 14 dependents
omelnikov
QFRM:Pricing of Vanilla and Exotic Option Contracts
Option pricing (financial derivatives) techniques mainly following textbook 'Options, Futures and Other Derivatives', 9ed by John C.Hull, 2014. Prentice Hall. Implementations are via binomial tree option model (BOPM), Black-Scholes model, Monte Carlo simulations, etc. This package is a result of Quantitative Financial Risk Management course (STAT 449 and STAT 649) at Rice University, Houston, TX, USA, taught by Oleg Melnikov, statistics PhD student, as of Spring 2015.
Maintained by Oleg Melnikov. Last updated 10 years ago.
63.4 match 2 stars 2.67 score 47 scriptsrstudio
rmarkdown:Dynamic Documents for R
Convert R Markdown documents into a variety of formats.
Maintained by Yihui Xie. Last updated 3 days ago.
literate-programmingmarkdownpandocrmarkdown
7.3 match 2.9k stars 21.80 score 14k scripts 3.7k dependents
markvanderloo
settings:Software Option Settings Manager for R
Provides option settings management that goes beyond R's default 'options' function. With this package, users can define their own option settings manager holding option names, default values and (if so desired) ranges or sets of allowed option values that will be automatically checked. Settings can then be retrieved, altered and reset to defaults with ease. For R programmers and package developers it offers cloning and merging functionality which allows for conveniently defining global and local options, possibly in a multilevel options hierarchy. See the package vignette for some examples concerning functions, S4 classes, and reference classes. There are convenience functions to reset par() and options() to their 'factory defaults'.
Maintained by Mark van der Loo. Last updated 10 months ago.
16.9 match 7 stars 9.32 score 1.0k scripts 36 dependents
mrc-ide
naomi.options:Contains model and calibration options and helper functions for Naomi
Contains model and calibration option JSON and default values and helper functions for Naomi.
Maintained by Robert Ashton. Last updated 5 months ago.
45.7 match 3.43 score 1 scripts 3 dependents
nlmixr2
rxode2:Facilities for Simulating from ODE-Based Models
Facilities for running simulations from ordinary differential equation ('ODE') models, such as pharmacometrics and other compartmental models. A compilation manager translates the ODE model into C, compiles it, and dynamically loads the object code into R for improved computational efficiency. An event table object facilitates the specification of complex dosing regimens (optional) and sampling schedules. NB: The use of this package requires both C and Fortran compilers, for details on their use with R please see Section 6.3, Appendix A, and Appendix D in the "R Administration and Installation" manual. Also the code is mostly released under GPL. The 'VODE' and 'LSODA' are in the public domain. The information is available in the inst/COPYRIGHTS.
Maintained by Matthew L. Fidler. Last updated 2 months ago.
13.4 match 40 stars 11.24 score 220 scripts 13 dependentsyihui
xfun:Supporting Functions for Packages Maintained by 'Yihui Xie'
Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.
Maintained by Yihui Xie. Last updated 5 hours ago.
8.2 match 147 stars 18.21 score 916 scripts 4.4k dependents
bioc
MOFA2:Multi-Omics Factor Analysis v2
The MOFA2 package contains a collection of tools for training and analysing multi-omic factor analysis (MOFA). MOFA is a probabilistic factor model that aims to identify principal axes of variation from data sets that can comprise multiple omic layers and/or groups of samples. Additional time or space information on the samples can be incorporated using the MEFISTO framework, which is part of MOFA2. Downstream analysis functions to inspect molecular features underlying each factor, vizualisation, imputation etc are available.
Maintained by Ricard Argelaguet. Last updated 5 months ago.
dimensionreductionbayesianvisualizationfactor-analysismofamulti-omics
14.8 match 326 stars 10.03 score 502 scriptsbioc
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
16.3 match 57 stars 9.03 score 90 scripts 1 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 1 months ago.
literate-programmingmarkdownpandocpandoc-markdownreproducible-researchrmarkdowncpp
8.6 match 298 stars 16.76 score 7.6k scripts 110 dependents
femiguez
apsimx:Inspect, Read, Edit and Run 'APSIM' "Next Generation" and 'APSIM' Classic
The functions in this package inspect, read, edit and run files for 'APSIM' "Next Generation" ('JSON') and 'APSIM' "Classic" ('XML'). The files with an 'apsim' extension correspond to 'APSIM' Classic (7.x) - Windows only - and the ones with an 'apsimx' extension correspond to 'APSIM' "Next Generation". For more information about 'APSIM' see (<https://www.apsim.info/>) and for 'APSIM' next generation (<https://apsimnextgeneration.netlify.app/>).
Maintained by Fernando Miguez. Last updated 14 days ago.
14.6 match 59 stars 9.72 score 68 scripts 2 dependentsr-lib
callr:Call R from R
It is sometimes useful to perform a computation in a separate R process, without affecting the current R process at all. This packages does exactly that.
Maintained by Gábor Csárdi. Last updated 1 months ago.
9.3 match 300 stars 15.24 score 289 scripts 1.2k dependents
dcomtois
summarytools:Tools to Quickly and Neatly Summarize Data
Data frame summaries, cross-tabulations, weight-enabled frequency tables and common descriptive (univariate) statistics in concise tables available in a variety of formats (plain ASCII, Markdown and HTML). A good point-of-entry for exploring data, both for experienced and new R users.
Maintained by Dominic Comtois. Last updated 2 days ago.
descriptive-statisticsfrequency-tablehtml-reportmarkdownpanderpandocpandoc-markdownrmarkdownrstudio
9.5 match 528 stars 14.69 score 2.9k scripts 6 dependents
jirotubuyaki
Jdmbs:Monte Carlo Option Pricing Algorithms for Jump Diffusion Models with Correlational Companies
Option is a one of the financial derivatives and its pricing is an important problem in practice. The process of stock prices are represented as Geometric Brownian motion [Black (1973) <doi:10.1086/260062>] or jump diffusion processes [Kou (2002) <doi:10.1287/mnsc.48.8.1086.166>]. In this package, algorithms and visualizations are implemented by Monte Carlo method in order to calculate European option price for three equations by Geometric Brownian motion and jump diffusion processes and furthermore a model that presents jumps among companies affect each other.
Maintained by Masashi Okada. Last updated 5 years ago.
black-scholesbrownian-motioncomputational-financederivativesfinancefinancial-analysisfinancial-engineeringjump-diffusionmonte-carlooptionoption-pricingsdestochastic-differential-equationsstochastic-processesstock-market
27.1 match 27 stars 5.13 score 6 scripts
martin3141
spant:MR Spectroscopy Analysis Tools
Tools for reading, visualising and processing Magnetic Resonance Spectroscopy data. The package includes methods for spectral fitting: Wilson (2021) <DOI:10.1002/mrm.28385> and spectral alignment: Wilson (2018) <DOI:10.1002/mrm.27605>.
Maintained by Martin Wilson. Last updated 6 days ago.
brainmrimrsmrshubspectroscopyfortran
15.3 match 25 stars 8.52 score 81 scriptstrafficonese
leaflet.extras2:Extra Functionality for 'leaflet' Package
Several 'leaflet' plugins are integrated, which are available as extension to the 'leaflet' package.
Maintained by Gatscha Sebastian. Last updated 29 days ago.
data-visualizationgeospatialgeospatial-visualizationleafletleaflet-plugins
13.1 match 87 stars 9.70 score 432 scripts 1 dependents
khamidieh
RND:Risk Neutral Density Extraction Package
Extract the implied risk neutral density from options using various methods.
Maintained by Kam Hamidieh. Last updated 8 years ago.
43.0 match 1 stars 2.80 score 70 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 7 hours ago.
data-sciencehigh-performance-computingmakepeer-reviewedpipeliner-targetopiareproducibilityreproducible-researchtargetsworkflow
7.9 match 979 stars 15.18 score 4.6k scripts 22 dependents
usdaforestservice
FIESTAutils:Utility Functions for Forest Inventory Estimation and Analysis
A set of tools for data wrangling, spatial data analysis, statistical modeling (including direct, model-assisted, photo-based, and small area tools), and USDA Forest Service data base tools. These tools are aimed to help Foresters, Analysts, and Scientists extract and perform analyses on USDA Forest Service data.
Maintained by Grayson White. Last updated 8 days ago.
18.5 match 9 stars 6.40 score 1 dependents
alexanderlynl
safestats:Safe Anytime-Valid Inference
Functions to design and apply tests that are anytime valid. The functions can be used to design hypothesis tests in the prospective/randomised control trial setting or in the observational/retrospective setting. The resulting tests remain valid under both optional stopping and optional continuation. The current version includes safe t-tests and safe tests of two proportions. For details on the theory of safe tests, see Grunwald, de Heide and Koolen (2019) "Safe Testing" <arXiv:1906.07801>, for details on safe logrank tests see ter Schure, Perez-Ortiz, Ly and Grunwald (2020) "The Safe Logrank Test: Error Control under Continuous Monitoring with Unlimited Horizon" <arXiv:2011.06931v3> and Turner, Ly and Grunwald (2021) "Safe Tests and Always-Valid Confidence Intervals for contingency tables and beyond" <arXiv:2106.02693> for details on safe contingency table tests.
Maintained by Alexander Ly. Last updated 2 years ago.
evalueshacktoberfestsafe-testingstatistics
22.5 match 6 stars 5.23 score 14 scripts
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 15 hours ago.
cdiscclinical-trialsopen-source
8.1 match 239 stars 13.93 score 486 scripts 4 dependents
doi-usgs
EGRET:Exploration and Graphics for RivEr Trends
Statistics and graphics for streamflow history, water quality trends, and the statistical modeling algorithm: Weighted Regressions on Time, Discharge, and Season (WRTDS).
Maintained by Laura DeCicco. Last updated 4 months ago.
usgswater-qualitywater-quality-data
10.2 match 90 stars 10.67 score 362 scripts 1 dependents
insightsengineering
teal:Exploratory Web Apps for Analyzing Clinical Trials Data
A 'shiny' based interactive exploration framework for analyzing clinical trials data. 'teal' currently provides a dynamic filtering facility and different data viewers. 'teal' 'shiny' applications are built using standard 'shiny' modules.
Maintained by Dawid Kaledkowski. Last updated 1 months ago.
clinical-trialsnestshinywebapp
8.5 match 206 stars 12.65 score 176 scripts 5 dependents
decisionpatterns
optigrab:Command-Line Parsing for an R World
Parse options from the command-line using a simple, clean syntax. It requires little or no specification and supports short and long options, GNU-, Java- or Microsoft- style syntaxes, verb commands and more.
Maintained by Christopher Brown. Last updated 6 years ago.
18.4 match 8 stars 5.80 score 39 scripts
snoweye
cubfits:Codon Usage Bias Fits
Estimating mutation and selection coefficients on synonymous codon bias usage based on models of ribosome overhead cost (ROC). Multinomial logistic regression and Markov Chain Monte Carlo are used to estimate and predict protein production rates with/without the presence of expressions and measurement errors. Work flows with examples for simulation, estimation and prediction processes are also provided with parallelization speedup. The whole framework is tested with yeast genome and gene expression data of Yassour, et al. (2009) <doi:10.1073/pnas.0812841106>.
Maintained by Wei-Chen Chen. Last updated 3 years ago.
22.0 match 7 stars 4.83 score 32 scripts
uupharmacometrics
xpose:Diagnostics for Pharmacometric Models
Diagnostics for non-linear mixed-effects (population) models from 'NONMEM' <https://www.iconplc.com/solutions/technologies/nonmem/>. 'xpose' facilitates data import, creation of numerical run summary and provide 'ggplot2'-based graphics for data exploration and model diagnostics.
Maintained by Benjamin Guiastrennec. Last updated 3 months ago.
diagnosticsggplot2nonmempharmacometricsxpose
9.6 match 62 stars 11.02 score 183 scripts 6 dependents
pyfe
FER:Financial Engineering in R
R implementations of standard financial engineering codes; vanilla option pricing models such as Black-Scholes, Bachelier, CEV, and SABR.
Maintained by Jaehyuk Choi. Last updated 4 years ago.
bachelierblack-scholesderivativesfinancial-engineeringmathematical-financeoption-pricingquantitative-finance
22.2 match 12 stars 4.76 score 12 scripts
tiledb-inc
tiledb:Modern Database Engine for Complex Data Based on Multi-Dimensional Arrays
The modern database 'TileDB' introduces a powerful on-disk format for storing and accessing any complex data based on multi-dimensional arrays. It supports dense and sparse arrays, dataframes and key-values stores, cloud storage ('S3', 'GCS', 'Azure'), chunked arrays, multiple compression, encryption and checksum filters, uses a fully multi-threaded implementation, supports parallel I/O, data versioning ('time travel'), metadata and groups. It is implemented as an embeddable cross-platform C++ library with APIs from several languages, and integrations. This package provides the R support.
Maintained by Isaiah Norton. Last updated 6 days ago.
arrayhdfss3storage-managertiledbcpp
8.8 match 108 stars 11.79 score 306 scripts 4 dependents
rmcd1024
derivmkts:Functions and R Code to Accompany Derivatives Markets
A set of pricing and expository functions that should be useful in teaching a course on financial derivatives.
Maintained by Robert McDonald. Last updated 3 years ago.
19.5 match 36 stars 5.20 score 75 scriptstrevorld
ggpattern:'ggplot2' Pattern Geoms
Provides 'ggplot2' geoms filled with various patterns. Includes a patterned version of every 'ggplot2' geom that has a region that can be filled with a pattern. Provides a suite of 'ggplot2' aesthetics and scales for controlling pattern appearances. Supports over a dozen builtin patterns (every pattern implemented by 'gridpattern') as well as allowing custom user-defined patterns.
Maintained by Trevor L. Davis. Last updated 2 months ago.
8.2 match 370 stars 12.36 score 1.7k scripts 3 dependents
cjvanlissa
tidySEM:Tidy Structural Equation Modeling
A tidy workflow for generating, estimating, reporting, and plotting structural equation models using 'lavaan', 'OpenMx', or 'Mplus'. Throughout this workflow, elements of syntax, results, and graphs are represented as 'tidy' data, making them easy to customize. Includes functionality to estimate latent class analyses, and to plot 'dagitty' and 'igraph' objects.
Maintained by Caspar J. van Lissa. Last updated 25 days ago.
9.4 match 58 stars 10.69 score 330 scripts 1 dependents
acorg
Racmacs:Antigenic Cartography Macros
A toolkit for making antigenic maps from immunological assay data, in order to quantify and visualize antigenic differences between different pathogen strains as described in Smith et al. (2004) <doi:10.1126/science.1097211> and used in the World Health Organization influenza vaccine strain selection process. Additional functions allow for the diagnostic evaluation of antigenic maps and an interactive viewer is provided to explore antigenic relationships amongst several strains and incorporate the visualization of associated genetic information.
Maintained by Sam Wilks. Last updated 9 months ago.
12.5 match 21 stars 8.06 score 362 scripts
workflowr
workflowr:A Framework for Reproducible and Collaborative Data Science
Provides a workflow for your analysis projects by combining literate programming ('knitr' and 'rmarkdown') and version control ('Git', via 'git2r') to generate a website containing time-stamped, versioned, and documented results.
Maintained by John Blischak. Last updated 4 months ago.
gitproject-managementrmarkdownwebsiteworkflow
8.7 match 848 stars 11.53 score 566 scripts
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 19 hours ago.
4.3 match 3.7k stars 23.47 score 230k scripts 4.6k dependentsbioc
geva:Gene Expression Variation Analysis (GEVA)
Statistic methods to evaluate variations of differential expression (DE) between multiple biological conditions. It takes into account the fold-changes and p-values from previous differential expression (DE) results that use large-scale data (*e.g.*, microarray and RNA-seq) and evaluates which genes would react in response to the distinct experiments. This evaluation involves an unique pipeline of statistical methods, including weighted summarization, quantile detection, cluster analysis, and ANOVA tests, in order to classify a subset of relevant genes whose DE is similar or dependent to certain biological factors.
Maintained by Itamar José Guimarães Nunes. Last updated 5 months ago.
classificationdifferentialexpressiongeneexpressionmicroarraymultiplecomparisonrnaseqsystemsbiologytranscriptomics
23.1 match 2 stars 4.30 score 4 scripts
joshuaulrich
quantmod:Quantitative Financial Modelling Framework
Specify, build, trade, and analyse quantitative financial trading strategies.
Maintained by Joshua M. Ulrich. Last updated 5 days ago.
algorithmic-tradingchartingdata-importfinancetime-series
6.0 match 840 stars 16.18 score 8.1k scripts 343 dependents
tidyverse
tibble:Simple Data Frames
Provides a 'tbl_df' class (the 'tibble') with stricter checking and better formatting than the traditional data frame.
Maintained by Kirill Müller. Last updated 2 days ago.
4.3 match 697 stars 22.88 score 47k scripts 11k dependents
yixuan
prettydoc:Creating Pretty Documents from R Markdown
Creating tiny yet beautiful documents and vignettes from R Markdown. The package provides the 'html_pretty' output format as an alternative to the 'html_document' and 'html_vignette' engines that convert R Markdown into HTML pages. Various themes and syntax highlight styles are supported.
Maintained by Yixuan Qiu. Last updated 4 years ago.
7.5 match 486 stars 12.90 score 550 scripts 8 dependentsrstudio
learnr:Interactive Tutorials for R
Create interactive tutorials using R Markdown. Use a combination of narrative, figures, videos, exercises, and quizzes to create self-paced tutorials for learning about R and R packages.
Maintained by Garrick Aden-Buie. Last updated 7 months ago.
interactivepythonrmarkdownshinysqlteachingtutorial
6.4 match 714 stars 14.80 score 6.5k scripts 29 dependents
glin
reactable:Interactive Data Tables for R
Interactive data tables for R, based on the 'React Table' JavaScript library. Provides an HTML widget that can be used in 'R Markdown' or 'Quarto' documents, 'Shiny' applications, or viewed from an R console.
Maintained by Greg Lin. Last updated 2 months ago.
6.5 match 648 stars 14.57 score 3.3k scripts 158 dependents
ngreifer
cobalt:Covariate Balance Tables and Plots
Generate balance tables and plots for covariates of groups preprocessed through matching, weighting or subclassification, for example, using propensity scores. Includes integration with 'MatchIt', 'WeightIt', 'MatchThem', 'twang', 'Matching', 'optmatch', 'CBPS', 'ebal', 'cem', 'sbw', and 'designmatch' for assessing balance on the output of their preprocessing functions. Users can also specify data for balance assessment not generated through the above packages. Also included are methods for assessing balance in clustered or multiply imputed data sets or data sets with multi-category, continuous, or longitudinal treatments.
Maintained by Noah Greifer. Last updated 12 months ago.
causal-inferencepropensity-scores
7.6 match 76 stars 12.41 score 1.0k scripts 8 dependents
great-northern-diver
loon:Interactive Statistical Data Visualization
An extendable toolkit for interactive data visualization and exploration.
Maintained by R. Wayne Oldford. Last updated 2 years ago.
data-analysisdata-sciencedata-visualizationexploratory-analysisexploratory-data-analysishigh-dimensional-datainteractive-graphicsinteractive-visualizationsloonpythonstatistical-analysisstatistical-graphicsstatisticstcl-extensiontk
10.5 match 48 stars 9.00 score 93 scripts 5 dependentsrstudio
leaflet:Create Interactive Web Maps with the JavaScript 'Leaflet' Library
Create and customize interactive maps using the 'Leaflet' JavaScript library and the 'htmlwidgets' package. These maps can be used directly from the R console, from 'RStudio', in Shiny applications and R Markdown documents.
Maintained by Joe Cheng. Last updated 30 days ago.
5.5 match 821 stars 17.20 score 39k scripts 178 dependentsropensci
beautier:'BEAUti' from R
'BEAST2' (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'BEAUti 2' (which is part of 'BEAST2') is a GUI tool that allows users to specify the many possible setups and generates the XML file 'BEAST2' needs to run. This package provides a way to create 'BEAST2' input files without active user input, but using R function calls instead.
Maintained by Richèl J.C. Bilderbeek. Last updated 1 months ago.
bayesianbeastbeast2beautiphylogenetic-inferencephylogenetics
10.7 match 13 stars 8.76 score 198 scripts 5 dependentscran
ragtop:Pricing Equity Derivatives with Extensions of Black-Scholes
Algorithms to price American and European equity options, convertible bonds and a variety of other financial derivatives. It uses an extension of the usual Black-Scholes model in which jump to default may occur at a probability specified by a power-law link between stock price and hazard rate as found in the paper by Takahashi, Kobayashi, and Nakagawa (2001) <doi:10.3905/jfi.2001.319302>. We use ideas and techniques from Andersen and Buffum (2002) <doi:10.2139/ssrn.355308> and Linetsky (2006) <doi:10.1111/j.1467-9965.2006.00271.x>.
Maintained by Brian K. Boonstra. Last updated 5 years ago.
34.1 match 2.70 scorejokergoo
GetoptLong:Parsing Command-Line Arguments and Simple Variable Interpolation
This is a command-line argument parser which wraps the powerful Perl module Getopt::Long and with some adaptations for easier use in R. It also provides a simple way for variable interpolation in R.
Maintained by Zuguang Gu. Last updated 3 years ago.
8.3 match 17 stars 11.08 score 478 scripts 160 dependents
juba
obsplot:Create Charts with 'Observable Plot'
Creation of charts with the 'Observable Plot' 'JavaScript' library.
Maintained by Julien Barnier. Last updated 2 years ago.
18.0 match 60 stars 5.08 score 10 scripts
jestonblu
RobinHood:Interface for the RobinHood.com No Commission Investing Platform
Execute API calls to the RobinHood <https://robinhood.com> investing platform. Functionality includes accessing account data and current holdings, retrieving investment statistics and quotes, placing and canceling orders, getting market trading hours, searching investments by popular tag, and interacting with watch lists.
Maintained by Joseph Blubaugh. Last updated 2 years ago.
algotradingapirobinhoodrobinhood-apitrade
20.0 match 45 stars 4.58 score 17 scripts
jeroen
curl:A Modern and Flexible Web Client for R
Bindings to 'libcurl' <https://curl.se/libcurl/> for performing fully configurable HTTP/FTP requests where responses can be processed in memory, on disk, or streaming via the callback or connection interfaces. Some knowledge of 'libcurl' is recommended; for a more-user-friendly web client see the 'httr2' package which builds on this package with http specific tools and logic.
Maintained by Jeroen Ooms. Last updated 2 days ago.
4.5 match 221 stars 20.06 score 4.0k scripts 5.9k dependents
martynplummer
coda:Output Analysis and Diagnostics for MCMC
Provides functions for summarizing and plotting the output from Markov Chain Monte Carlo (MCMC) simulations, as well as diagnostic tests of convergence to the equilibrium distribution of the Markov chain.
Maintained by Martyn Plummer. Last updated 1 years ago.
8.0 match 6 stars 11.38 score 8.3k scripts 1.1k dependents
hauselin
ollamar:'Ollama' Language Models
An interface to easily run local language models with 'Ollama' <https://ollama.com> server and API endpoints (see <https://github.com/ollama/ollama/blob/main/docs/api.md> for details). It lets you run open-source large language models locally on your machine.
Maintained by Hause Lin. Last updated 10 days ago.
9.7 match 89 stars 9.32 score 74 scripts 5 dependents
aphalo
photobiology:Photobiological Calculations
Definitions of classes, methods, operators and functions for use in photobiology and radiation meteorology and climatology. Calculation of effective (weighted) and not-weighted irradiances/doses, fluence rates, transmittance, reflectance, absorptance, absorbance and diverse ratios and other derived quantities from spectral data. Local maxima and minima: peaks, valleys and spikes. Conversion between energy-and photon-based units. Wavelength interpolation. Astronomical calculations related solar angles and day length. Colours and vision. This package is part of the 'r4photobiology' suite, Aphalo, P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Maintained by Pedro J. Aphalo. Last updated 4 days ago.
lightphotobiologyquantificationr4photobiology-suiteradiationspectrasun-position
9.8 match 4 stars 9.20 score 604 scripts 12 dependents
tconwell
pgTools:Functions for Generating PostgreSQL Statements/Scripts
Create PostgreSQL statements/scripts from R, optionally executing the SQL statements. Common SQL operations are included, although not every configurable option is available at this time. SQL output is intended to be compliant with PostgreSQL syntax specifications. PostgreSQL documentation is available here <https://www.postgresql.org/docs/current/index.html>.
Maintained by Timothy Conwell. Last updated 2 years ago.
43.8 match 1 stars 2.00 score 3 scripts
neuroshepherd
ordinalsimr:Compare Ordinal Endpoints Using Simulations
Simultaneously evaluate multiple ordinal outcome measures. Applied data analysts in particular are faced with uncertainty in choosing appropriate statistical tests for ordinal data. The included 'shiny' application allows users to simulate outcomes given different ordinal data distributions.
Maintained by Pat Callahan. Last updated 1 months ago.
16.7 match 1 stars 5.26 score 5 scripts
ikosmidis
enrichwith:Methods to Enrich R Objects with Extra Components
Provides the "enrich" method to enrich list-like R objects with new, relevant components. The current version has methods for enriching objects of class 'family', 'link-glm', 'lm', 'glm' and 'betareg'. The resulting objects preserve their class, so all methods associated with them still apply. The package also provides the 'enriched_glm' function that has the same interface as 'glm' but results in objects of class 'enriched_glm'. In addition to the usual components in a `glm` object, 'enriched_glm' objects carry an object-specific simulate method and functions to compute the scores, the observed and expected information matrix, the first-order bias, as well as model densities, probabilities, and quantiles at arbitrary parameter values. The package can also be used to produce customizable source code templates for the structured implementation of methods to compute new components and enrich arbitrary objects.
Maintained by Ioannis Kosmidis. Last updated 5 years ago.
11.7 match 6 stars 7.40 score 16 scripts 13 dependents
rspatial
terra:Spatial Data Analysis
Methods for spatial data analysis with vector (points, lines, polygons) and raster (grid) data. Methods for vector data include geometric operations such as intersect and buffer. Raster methods include local, focal, global, zonal and geometric operations. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/> to get started. 'terra' replaces the 'raster' package ('terra' can do more, and it is faster and easier to use).
Maintained by Robert J. Hijmans. Last updated 11 hours ago.
geospatialrasterspatialvectoronetbbprojgdalgeoscpp
4.9 match 560 stars 17.61 score 17k scripts 860 dependents
walkerke
tigris:Load Census TIGER/Line Shapefiles
Download TIGER/Line shapefiles from the United States Census Bureau (<https://www.census.gov/geographies/mapping-files/time-series/geo/tiger-line-file.html>) and load into R as 'sf' objects.
Maintained by Kyle Walker. Last updated 5 months ago.
6.6 match 331 stars 12.87 score 5.3k scripts 16 dependents
igraph
igraph:Network Analysis and Visualization
Routines for simple graphs and network analysis. It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.
Maintained by Kirill Müller. Last updated 1 days ago.
complex-networksgraph-algorithmsgraph-theorymathematicsnetwork-analysisnetwork-graphfortranlibxml2glpkopenblascpp
4.0 match 584 stars 21.14 score 31k scripts 1.9k dependents
markedmondson1234
googleAuthR:Authenticate and Create Google APIs
Create R functions that interact with OAuth2 Google APIs <https://developers.google.com/apis-explorer/> easily, with auto-refresh and Shiny compatibility.
Maintained by Erik Grönroos. Last updated 11 months ago.
apiauthenticationgooglegoogleauthroauth2-flowshiny
6.5 match 178 stars 12.85 score 804 scripts 13 dependents
tbates
umx:Structural Equation Modeling and Twin Modeling in R
Quickly create, run, and report structural equation models, and twin models. See '?umx' for help, and umx_open_CRAN_page("umx") for NEWS. Timothy C. Bates, Michael C. Neale, Hermine H. Maes, (2019). umx: A library for Structural Equation and Twin Modelling in R. Twin Research and Human Genetics, 22, 27-41. <doi:10.1017/thg.2019.2>.
Maintained by Timothy C. Bates. Last updated 2 days ago.
behavior-geneticsgeneticsopenmxpsychologysemstatisticsstructural-equation-modelingtutorialstwin-modelsumx
8.9 match 44 stars 9.32 score 472 scriptsr-lib
rlang:Functions for Base Types and Core R and 'Tidyverse' Features
A toolbox for working with base types, core R features like the condition system, and core 'Tidyverse' features like tidy evaluation.
Maintained by Lionel Henry. Last updated 17 hours ago.
4.0 match 517 stars 20.58 score 9.8k scripts 15k dependentsr-lib
httr:Tools for Working with URLs and HTTP
Useful tools for working with HTTP organised by HTTP verbs (GET(), POST(), etc). Configuration functions make it easy to control additional request components (authenticate(), add_headers() and so on).
Maintained by Hadley Wickham. Last updated 1 years ago.
4.0 match 989 stars 20.56 score 29k scripts 4.3k dependents
davidgohel
ggiraph:Make 'ggplot2' Graphics Interactive
Create interactive 'ggplot2' graphics using 'htmlwidgets'.
Maintained by David Gohel. Last updated 6 days ago.
5.6 match 822 stars 14.37 score 4.1k scripts 35 dependents
dbosak01
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.
10.5 match 6 stars 7.57 score 37 scripts 2 dependents
stan-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 5 days ago.
bayesian-data-analysisbayesian-inferencebayesian-statisticsmcmcstancpp
4.2 match 1.1k stars 18.86 score 14k scripts 281 dependents
thinkr-open
golem:A Framework for Robust Shiny Applications
An opinionated framework for building a production-ready 'Shiny' application. This package contains a series of tools for building a robust 'Shiny' application from start to finish.
Maintained by Colin Fay. Last updated 7 months ago.
golemversehacktoberfestshinyshiny-appsshiny-rshinyapps
5.5 match 921 stars 14.21 score 167 scripts 63 dependents
enricoschumann
NMOF:Numerical Methods and Optimization in Finance
Functions, examples and data from the first and the second edition of "Numerical Methods and Optimization in Finance" by M. Gilli, D. Maringer and E. Schumann (2019, ISBN:978-0128150658). The package provides implementations of optimisation heuristics (Differential Evolution, Genetic Algorithms, Particle Swarm Optimisation, Simulated Annealing and Threshold Accepting), and other optimisation tools, such as grid search and greedy search. There are also functions for the valuation of financial instruments such as bonds and options, for portfolio selection and functions that help with stochastic simulations.
Maintained by Enrico Schumann. Last updated 5 days ago.
black-scholesdifferential-evolutiongenetic-algorithmgrid-searchheuristicsimplied-volatilitylocal-searchoptimizationparticle-swarm-optimizationsimulated-annealingthreshold-accepting
8.4 match 37 stars 9.27 score 101 scripts 3 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 12 days ago.
data-aggregationdata-analysisdata-manipulationdata-processingdata-sciencedata-transformationeconometricshigh-performancepanel-datascientific-computingstatisticstime-seriesweightedweightscppopenmp
4.7 match 672 stars 16.68 score 708 scripts 99 dependents
obiba
opalr:'Opal' Data Repository Client and 'DataSHIELD' Utils
Data integration Web application for biobanks by 'OBiBa'. 'Opal' is the core database application for biobanks. Participant data, once collected from any data source, must be integrated and stored in a central data repository under a uniform model. 'Opal' is such a central repository. It can import, process, validate, query, analyze, report, and export data. 'Opal' is typically used in a research center to analyze the data acquired at assessment centres. Its ultimate purpose is to achieve seamless data-sharing among biobanks. This 'Opal' client allows to interact with 'Opal' web services and to perform operations on the R server side. 'DataSHIELD' administration tools are also provided.
Maintained by Yannick Marcon. Last updated 3 months ago.
10.0 match 3 stars 7.76 score 179 scripts 2 dependentsbioc
GRaNIE:GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using single-cell or bulk chromatin accessibility and RNA-seq data
Genetic variants associated with diseases often affect non-coding regions, thus likely having a regulatory role. To understand the effects of genetic variants in these regulatory regions, identifying genes that are modulated by specific regulatory elements (REs) is crucial. The effect of gene regulatory elements, such as enhancers, is often cell-type specific, likely because the combinations of transcription factors (TFs) that are regulating a given enhancer have cell-type specific activity. This TF activity can be quantified with existing tools such as diffTF and captures differences in binding of a TF in open chromatin regions. Collectively, this forms a gene regulatory network (GRN) with cell-type and data-specific TF-RE and RE-gene links. Here, we reconstruct such a GRN using single-cell or bulk RNAseq and open chromatin (e.g., using ATACseq or ChIPseq for open chromatin marks) and optionally (Capture) Hi-C data. Our network contains different types of links, connecting TFs to regulatory elements, the latter of which is connected to genes in the vicinity or within the same chromatin domain (TAD). We use a statistical framework to assign empirical FDRs and weights to all links using a permutation-based approach.
Maintained by Christian Arnold. Last updated 5 months ago.
softwaregeneexpressiongeneregulationnetworkinferencegenesetenrichmentbiomedicalinformaticsgeneticstranscriptomicsatacseqrnaseqgraphandnetworkregressiontranscriptionchipseq
14.3 match 5.40 score 24 scripts
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 22 days ago.
bayesian-inferencebayesian-methodshierarchical-modelsmcmcprobabilistic-programmingopenblascpp
5.9 match 169 stars 12.97 score 2.6k scripts 19 dependents
dcousin3
superb:Summary Plots with Adjusted Error Bars
Computes standard error and confidence interval of various descriptive statistics under various designs and sampling schemes. The main function, superb(), return a plot. It can also be used to obtain a dataframe with the statistics and their precision intervals so that other plotting environments (e.g., Excel) can be used. See Cousineau and colleagues (2021) <doi:10.1177/25152459211035109> or Cousineau (2017) <doi:10.5709/acp-0214-z> for a review as well as Cousineau (2005) <doi:10.20982/tqmp.01.1.p042>, Morey (2008) <doi:10.20982/tqmp.04.2.p061>, Baguley (2012) <doi:10.3758/s13428-011-0123-7>, Cousineau & Laurencelle (2016) <doi:10.1037/met0000055>, Cousineau & O'Brien (2014) <doi:10.3758/s13428-013-0441-z>, Calderini & Harding <doi:10.20982/tqmp.15.1.p001> for specific references.
Maintained by Denis Cousineau. Last updated 2 months ago.
error-barsplottingstatisticssummary-plotssummary-statisticsvisualization
7.9 match 19 stars 9.53 score 155 scripts 2 dependentsbioc
RnBeads:RnBeads
RnBeads facilitates comprehensive analysis of various types of DNA methylation data at the genome scale.
Maintained by Fabian Mueller. Last updated 2 months ago.
dnamethylationmethylationarraymethylseqepigeneticsqualitycontrolpreprocessingbatcheffectdifferentialmethylationsequencingcpgislandimmunooncologytwochanneldataimport
10.9 match 6.85 score 169 scripts 1 dependents
spatstat
spatstat.geom:Geometrical Functionality of the 'spatstat' Family
Defines spatial data types and supports geometrical operations on them. Data types include point patterns, windows (domains), pixel images, line segment patterns, tessellations and hyperframes. Capabilities include creation and manipulation of data (using command line or graphical interaction), plotting, geometrical operations (rotation, shift, rescale, affine transformation), convex hull, discretisation and pixellation, Dirichlet tessellation, Delaunay triangulation, pairwise distances, nearest-neighbour distances, distance transform, morphological operations (erosion, dilation, closing, opening), quadrat counting, geometrical measurement, geometrical covariance, colour maps, calculus on spatial domains, Gaussian blur, level sets of images, transects of images, intersections between objects, minimum distance matching. (Excludes spatial data on a network, which are supported by the package 'spatstat.linnet'.)
Maintained by Adrian Baddeley. Last updated 9 days ago.
classes-and-objectsdistance-calculationgeometrygeometry-processingimagesmensurationplottingpoint-patternsspatial-dataspatial-data-analysis
6.1 match 7 stars 12.14 score 241 scripts 229 dependents
rinterface
shinyMobile:Mobile Ready 'shiny' Apps with Standalone Capabilities
Develop outstanding 'shiny' apps for 'iOS' and 'Android' as well as beautiful 'shiny' gadgets. 'shinyMobile' is built on top of the latest 'Framework7' template <https://framework7.io>. Discover 14 new input widgets (sliders, vertical sliders, stepper, grouped action buttons, toggles, picker, smart select, ...), 2 themes (light and dark), 12 new widgets (expandable cards, badges, chips, timelines, gauges, progress bars, ...) combined with the power of server-side notifications such as alerts, modals, toasts, action sheets, sheets (and more) as well as 3 layouts (single, tabs and split).
Maintained by David Granjon. Last updated 2 months ago.
androidhacktoberfest2022pwashinyshinyappstemplate
6.2 match 410 stars 11.85 score 1.1k scripts 2 dependents
bnosac
udpipe:Tokenization, Parts of Speech Tagging, Lemmatization and Dependency Parsing with the 'UDPipe' 'NLP' Toolkit
This natural language processing toolkit provides language-agnostic 'tokenization', 'parts of speech tagging', 'lemmatization' and 'dependency parsing' of raw text. Next to text parsing, the package also allows you to train annotation models based on data of 'treebanks' in 'CoNLL-U' format as provided at <https://universaldependencies.org/format.html>. The techniques are explained in detail in the paper: 'Tokenizing, POS Tagging, Lemmatizing and Parsing UD 2.0 with UDPipe', available at <doi:10.18653/v1/K17-3009>. The toolkit also contains functionalities for commonly used data manipulations on texts which are enriched with the output of the parser. Namely functionalities and algorithms for collocations, token co-occurrence, document term matrix handling, term frequency inverse document frequency calculations, information retrieval metrics (Okapi BM25), handling of multi-word expressions, keyword detection (Rapid Automatic Keyword Extraction, noun phrase extraction, syntactical patterns) sentiment scoring and semantic similarity analysis.
Maintained by Jan Wijffels. Last updated 2 years ago.
conlldependency-parserlemmatizationnatural-language-processingnlppos-taggingr-pkgrcpptext-miningtokenizerudpipecpp
6.2 match 215 stars 11.83 score 1.2k scripts 9 dependentsbioc
AnnotationHub:Client to access AnnotationHub resources
This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, Ensembl) can be discovered. The resource includes metadata about each resource, e.g., a textual description, tags, and date of modification. The client creates and manages a local cache of files retrieved by the user, helping with quick and reproducible access.
Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.
infrastructuredataimportguithirdpartyclientcore-packageu24ca289073
5.3 match 17 stars 13.88 score 2.7k scripts 104 dependents
statnet
ergm:Fit, Simulate and Diagnose Exponential-Family Models for Networks
An integrated set of tools to analyze and simulate networks based on exponential-family random graph models (ERGMs). 'ergm' is a part of the Statnet suite of packages for network analysis. See Hunter, Handcock, Butts, Goodreau, and Morris (2008) <doi:10.18637/jss.v024.i03> and Krivitsky, Hunter, Morris, and Klumb (2023) <doi:10.18637/jss.v105.i06>.
Maintained by Pavel N. Krivitsky. Last updated 24 days ago.
4.8 match 100 stars 15.36 score 1.4k scripts 36 dependents
plotly
plotly:Create Interactive Web Graphics via 'plotly.js'
Create interactive web graphics from 'ggplot2' graphs and/or a custom interface to the (MIT-licensed) JavaScript library 'plotly.js' inspired by the grammar of graphics.
Maintained by Carson Sievert. Last updated 4 months ago.
d3jsdata-visualizationggplot2javascriptplotlyshinywebgl
3.8 match 2.6k stars 19.43 score 93k scripts 797 dependentsr-lib
cli:Helpers for Developing Command Line Interfaces
A suite of tools to build attractive command line interfaces ('CLIs'), from semantic elements: headings, lists, alerts, paragraphs, etc. Supports custom themes via a 'CSS'-like language. It also contains a number of lower level 'CLI' elements: rules, boxes, trees, and 'Unicode' symbols with 'ASCII' alternatives. It support ANSI colors and text styles as well.
Maintained by Gábor Csárdi. Last updated 17 days ago.
3.8 match 664 stars 19.34 score 1.4k scripts 14k dependentsr-lib
gargle:Utilities for Working with Google APIs
Provides utilities for working with Google APIs <https://developers.google.com/apis-explorer>. This includes functions and classes for handling common credential types and for preparing, executing, and processing HTTP requests.
Maintained by Jennifer Bryan. Last updated 2 years ago.
4.8 match 113 stars 14.90 score 266 scripts 192 dependents
inlabru-org
inlabru:Bayesian Latent Gaussian Modelling using INLA and Extensions
Facilitates spatial and general latent Gaussian modeling using integrated nested Laplace approximation via the INLA package (<https://www.r-inla.org>). Additionally, extends the GAM-like model class to more general nonlinear predictor expressions, and implements a log Gaussian Cox process likelihood for modeling univariate and spatial point processes based on ecological survey data. Model components are specified with general inputs and mapping methods to the latent variables, and the predictors are specified via general R expressions, with separate expressions for each observation likelihood model in multi-likelihood models. A prediction method based on fast Monte Carlo sampling allows posterior prediction of general expressions of the latent variables. Ecology-focused introduction in Bachl, Lindgren, Borchers, and Illian (2019) <doi:10.1111/2041-210X.13168>.
Maintained by Finn Lindgren. Last updated 5 hours ago.
5.7 match 97 stars 12.59 score 832 scripts 6 dependents
stla
shinyChakraUI:A Wrapper of the 'React' Library 'Chakra UI' for 'Shiny'
Makes the 'React' library 'Chakra UI' usable in 'Shiny' apps. 'Chakra UI' components include alert dialogs, drawers (sliding panels), menus, modals, popovers, sliders, and more.
Maintained by Stéphane Laurent. Last updated 3 years ago.
14.3 match 22 stars 4.98 score 87 scripts
bcgov
fasstr:Analyze, Summarize, and Visualize Daily Streamflow Data
The Flow Analysis Summary Statistics Tool for R, 'fasstr', provides various functions to tidy and screen daily stream discharge data, calculate and visualize various summary statistics and metrics, and compute annual trending and volume frequency analyses. It features useful function arguments for filtering of and handling dates, customizing data and metrics, and the ability to pull daily data directly from the Water Survey of Canada hydrometric database (<https://collaboration.cmc.ec.gc.ca/cmc/hydrometrics/www/>).
Maintained by Jon Goetz. Last updated 6 months ago.
bcgovforfrequency-analysishydathydrologystreamflowsummary-statisticstrendswater
9.5 match 57 stars 7.48 score 89 scripts
winvector
rquery:Relational Query Generator for Data Manipulation at Scale
A piped query generator based on Edgar F. Codd's relational algebra, and on production experience using 'SQL' and 'dplyr' at big data scale. The design represents an attempt to make 'SQL' more teachable by denoting composition by a sequential pipeline notation instead of nested queries or functions. The implementation delivers reliable high performance data processing on large data systems such as 'Spark', databases, and 'data.table'. Package features include: data processing trees or pipelines as observable objects (able to report both columns produced and columns used), optimized 'SQL' generation as an explicit user visible table modeling step, plus explicit query reasoning and checking.
Maintained by John Mount. Last updated 2 years ago.
7.4 match 110 stars 9.53 score 126 scripts 3 dependents
r-spatial
leafem:'leaflet' Extensions for 'mapview'
Provides extensions for packages 'leaflet' & 'mapdeck', many of which are used by package 'mapview'. Focus is on functionality readily available in Geographic Information Systems such as 'Quantum GIS'. Includes functions to display coordinates of mouse pointer position, query image values via mouse pointer and zoom-to-layer buttons. Additionally, provides a feature type agnostic function to add points, lines, polygons to a map.
Maintained by Tim Appelhans. Last updated 1 months ago.
5.7 match 108 stars 12.41 score 704 scripts 55 dependentsstan-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 4 days ago.
bayesbayesianmarkov-chain-monte-carlomaximum-likelihoodmcmcstanvariational-inference
5.5 match 145 stars 12.65 score 5.2k scripts 9 dependents
deepayan
lattice:Trellis Graphics for R
A powerful and elegant high-level data visualization system inspired by Trellis graphics, with an emphasis on multivariate data. Lattice is sufficient for typical graphics needs, and is also flexible enough to handle most nonstandard requirements. See ?Lattice for an introduction.
Maintained by Deepayan Sarkar. Last updated 3 days ago.
4.0 match 69 stars 17.35 score 27k scripts 13k dependents
atorus-research
Tplyr:A Traceability Focused Grammar of Clinical Data Summary
A traceability focused tool created to simplify the data manipulation necessary to create clinical summaries.
Maintained by Mike Stackhouse. Last updated 1 years ago.
7.3 match 95 stars 9.49 score 138 scripts 2 dependentsbioc
scMultiSim:Simulation of Multi-Modality Single Cell Data Guided By Gene Regulatory Networks and Cell-Cell Interactions
scMultiSim simulates paired single cell RNA-seq, single cell ATAC-seq and RNA velocity data, while incorporating mechanisms of gene regulatory networks, chromatin accessibility and cell-cell interactions. It allows users to tune various parameters controlling the amount of each biological factor, variation of gene-expression levels, the influence of chromatin accessibility on RNA sequence data, and so on. It can be used to benchmark various computational methods for single cell multi-omics data, and to assist in experimental design of wet-lab experiments.
Maintained by Hechen Li. Last updated 5 months ago.
singlecelltranscriptomicsgeneexpressionsequencingexperimentaldesign
9.7 match 23 stars 7.08 score 11 scripts
insightsengineering
tern:Create Common TLGs Used in Clinical Trials
Table, Listings, and Graphs (TLG) library for common outputs used in clinical trials.
Maintained by Joe Zhu. Last updated 3 months ago.
clinical-trialsgraphslistingsnestoutputstables
5.5 match 83 stars 12.50 score 186 scripts 9 dependents
plangfelder
WGCNA:Weighted Correlation Network Analysis
Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data as originally described in Horvath and Zhang (2005) <doi:10.2202/1544-6115.1128> and Langfelder and Horvath (2008) <doi:10.1186/1471-2105-9-559>. Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits. Also includes a number of utility functions for data manipulation and visualization.
Maintained by Peter Langfelder. Last updated 7 months ago.
7.1 match 54 stars 9.65 score 5.3k scripts 32 dependentsbioc
ComplexHeatmap:Make Complex Heatmaps
Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential patterns. Here the ComplexHeatmap package provides a highly flexible way to arrange multiple heatmaps and supports various annotation graphics.
Maintained by Zuguang Gu. Last updated 1 days ago.
softwarevisualizationsequencingclusteringcomplex-heatmapsheatmap
4.0 match 1.4k stars 17.11 score 16k scripts 153 dependents
brodieg
diffobj:Diffs for R Objects
Generate a colorized diff of two R objects for an intuitive visualization of their differences.
Maintained by Brodie Gaslam. Last updated 3 years ago.
5.2 match 231 stars 13.17 score 107 scripts 494 dependents
natverse
nat:NeuroAnatomy Toolbox for Analysis of 3D Image Data
NeuroAnatomy Toolbox (nat) enables analysis and visualisation of 3D biological image data, especially traced neurons. Reads and writes 3D images in NRRD and 'Amira' AmiraMesh formats and reads surfaces in 'Amira' hxsurf format. Traced neurons can be imported from and written to SWC and 'Amira' LineSet and SkeletonGraph formats. These data can then be visualised in 3D via 'rgl', manipulated including applying calculated registrations, e.g. using the 'CMTK' registration suite, and analysed. There is also a simple representation for neurons that have been subjected to 3D skeletonisation but not formally traced; this allows morphological comparison between neurons including searches and clustering (via the 'nat.nblast' extension package).
Maintained by Gregory Jefferis. Last updated 6 months ago.
3dconnectomicsimage-analysisneuroanatomyneuroanatomy-toolboxneuronneuron-morphologyneurosciencevisualisation
6.8 match 67 stars 9.94 score 436 scripts 2 dependents
risktoollib
RTL:Risk Tool Library - Trading, Risk, Analytics for Commodities
A toolkit for Commodities 'analytics', risk management and trading professionals. Includes functions for API calls to <https://commodities.morningstar.com/#/>, <https://developer.genscape.com/>, and <https://www.bankofcanada.ca/valet/docs>.
Maintained by Philippe Cote. Last updated 1 months ago.
analyticsapicommoditiescommodities-apifinancegenscapemorningstarpythonrisk-managementcpp
8.9 match 30 stars 7.51 score 198 scripts
ajrgodfrey
BrailleR:Improved Access for Blind Users
Blind users do not have access to the graphical output from R without printing the content of graphics windows to an embosser of some kind. This is not as immediate as is required for efficient access to statistical output. The functions here are created so that blind people can make even better use of R. This includes the text descriptions of graphs, convenience functions to replace the functionality offered in many GUI front ends, and experimental functionality for optimising graphical content to prepare it for embossing as tactile images.
Maintained by A. Jonathan R. Godfrey. Last updated 12 months ago.
7.5 match 123 stars 8.90 score 143 scripts
crunch-io
crunch:Crunch.io Data Tools
The Crunch.io service <https://crunch.io/> provides a cloud-based data store and analytic engine, as well as an intuitive web interface. Using this package, analysts can interact with and manipulate Crunch datasets from within R. Importantly, this allows technical researchers to collaborate naturally with team members, managers, and clients who prefer a point-and-click interface.
Maintained by Greg Freedman Ellis. Last updated 12 days ago.
6.4 match 9 stars 10.47 score 200 scripts 2 dependents
rmojab63
ldt:Automated Uncertainty Analysis
Methods and tools for model selection and multi-model inference (Burnham and Anderson (2002) <doi:10.1007/b97636>, among others). 'SUR' (for parameter estimation), 'logit'/'probit' (for binary classification), and 'VARMA' (for time-series forecasting) are implemented. Evaluations are both in-sample and out-of-sample. It is designed to be efficient in terms of CPU usage and memory consumption.
Maintained by Ramin Mojab. Last updated 9 months ago.
26.8 match 2.48 score 7 scriptsrstudio
bslib:Custom 'Bootstrap' 'Sass' Themes for 'shiny' and 'rmarkdown'
Simplifies custom 'CSS' styling of both 'shiny' and 'rmarkdown' via 'Bootstrap' 'Sass'. Supports 'Bootstrap' 3, 4 and 5 as well as their various 'Bootswatch' themes. An interactive widget is also provided for previewing themes in real time.
Maintained by Carson Sievert. Last updated 28 days ago.
bootstraphtmltoolsrmarkdownsassshiny
3.7 match 511 stars 18.02 score 5.1k scripts 4.3k dependents
predictiveecology
reproducible:Enhance Reproducibility of R Code
A collection of high-level, machine- and OS-independent tools for making reproducible and reusable content in R. The two workhorse functions are Cache() and prepInputs(). Cache() allows for nested caching, is robust to environments and objects with environments (like functions), and deals with some classes of file-backed R objects e.g., from terra and raster packages. Both functions have been developed to be foundational components of data retrieval and processing in continuous workflow situations. In both functions, efforts are made to make the first and subsequent calls of functions have the same result, but faster at subsequent times by way of checksums and digesting. Several features are still under development, including cloud storage of cached objects allowing for sharing between users. Several advanced options are available, see ?reproducibleOptions().
Maintained by Eliot J B McIntire. Last updated 2 months ago.
reproducibilityreproducible-research
6.2 match 41 stars 10.52 score 122 scripts 15 dependents
ericdunipace
causalOT:Optimal Transport Weights for Causal Inference
Uses optimal transport distances to find probabilistic matching estimators for causal inference. These methods are described in Dunipace, Eric (2021) <arXiv:2109.01991>. The package will build the weights, estimate treatment effects, and calculate confidence intervals via the methods described in the paper. The package also supports several other methods as described in the help files.
Maintained by Eric Dunipace. Last updated 8 months ago.
12.0 match 6 stars 5.38 score 20 scriptsbioc
MEIGOR:MEIGOR - MEtaheuristics for bIoinformatics Global Optimization
MEIGOR provides a comprehensive environment for performing global optimization tasks in bioinformatics and systems biology. It leverages advanced metaheuristic algorithms to efficiently search the solution space and is specifically tailored to handle the complexity and high-dimensionality of biological datasets. This package supports various optimization routines and is integrated with Bioconductor's infrastructure for a seamless analysis workflow.
Maintained by Jose A. Egea. Last updated 5 months ago.
systemsbiologyoptimizationsoftware
15.7 match 4.12 score 44 scripts
ycphs
openxlsx:Read, Write and Edit xlsx Files
Simplifies the creation of Excel .xlsx files by providing a high level interface to writing, styling and editing worksheets. Through the use of 'Rcpp', read/write times are comparable to the 'xlsx' and 'XLConnect' packages with the added benefit of removing the dependency on Java.
Maintained by Jan Marvin Garbuszus. Last updated 2 months ago.
3.4 match 232 stars 19.09 score 20k scripts 277 dependents
jiefei-wang
aws.ecx:Communicating with AWS EC2 and ECS using AWS REST APIs
Providing the functions for communicating with Amazon Web Services(AWS) Elastic Compute Cloud(EC2) and Elastic Container Service(ECS). The functions will have the prefix 'ecs_' or 'ec2_' depending on the class of the API. The request will be sent via the REST API and the parameters are given by the function argument. The credentials can be set via 'aws_set_credentials'. The EC2 documentation can be found at <https://docs.aws.amazon.com/AWSEC2/latest/APIReference/Welcome.html> and ECS can be found at <https://docs.aws.amazon.com/AmazonECS/latest/APIReference/Welcome.html>.
Maintained by Jiefei Wang. Last updated 3 years ago.
15.4 match 1 stars 4.18 score 2 scriptsbioc
PathoStat:PathoStat Statistical Microbiome Analysis Package
The purpose of this package is to perform Statistical Microbiome Analysis on metagenomics results from sequencing data samples. In particular, it supports analyses on the PathoScope generated report files. PathoStat provides various functionalities including Relative Abundance charts, Diversity estimates and plots, tests of Differential Abundance, Time Series visualization, and Core OTU analysis.
Maintained by Solaiappan Manimaran. Last updated 5 months ago.
microbiomemetagenomicsgraphandnetworkmicroarraypatternlogicprincipalcomponentsequencingsoftwarevisualizationrnaseqimmunooncology
10.8 match 8 stars 5.90 score 8 scriptsrstudio
dygraphs:Interface to 'Dygraphs' Interactive Time Series Charting Library
An R interface to the 'dygraphs' JavaScript charting library (a copy of which is included in the package). Provides rich facilities for charting time-series data in R, including highly configurable series- and axis-display and interactive features like zoom/pan and series/point highlighting.
Maintained by Petr Shevtsov. Last updated 2 years ago.
4.7 match 366 stars 13.55 score 3.6k scripts 67 dependents
wviechtb
metafor:Meta-Analysis Package for R
A comprehensive collection of functions for conducting meta-analyses in R. The package includes functions to calculate various effect sizes or outcome measures, fit equal-, fixed-, random-, and mixed-effects models to such data, carry out moderator and meta-regression analyses, and create various types of meta-analytical plots (e.g., forest, funnel, radial, L'Abbe, Baujat, bubble, and GOSH plots). For meta-analyses of binomial and person-time data, the package also provides functions that implement specialized methods, including the Mantel-Haenszel method, Peto's method, and a variety of suitable generalized linear (mixed-effects) models (i.e., mixed-effects logistic and Poisson regression models). Finally, the package provides functionality for fitting meta-analytic multivariate/multilevel models that account for non-independent sampling errors and/or true effects (e.g., due to the inclusion of multiple treatment studies, multiple endpoints, or other forms of clustering). Network meta-analyses and meta-analyses accounting for known correlation structures (e.g., due to phylogenetic relatedness) can also be conducted. An introduction to the package can be found in Viechtbauer (2010) <doi:10.18637/jss.v036.i03>.
Maintained by Wolfgang Viechtbauer. Last updated 6 days ago.
meta-analysismixed-effectsmultilevel-modelsmultivariate
3.9 match 250 stars 16.32 score 4.9k scripts 92 dependentsbioc
ExperimentHub:Client to access ExperimentHub resources
This package provides a client for the Bioconductor ExperimentHub web resource. ExperimentHub provides a central location where curated data from experiments, publications or training courses can be accessed. Each resource has associated metadata, tags and date of modification. The client creates and manages a local cache of files retrieved enabling quick and reproducible access.
Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.
infrastructuredataimportguithirdpartyclientcore-packageu24ca289073
5.3 match 10 stars 11.94 score 764 scripts 57 dependentsnlmixr2
nlmixr2est:Nonlinear Mixed Effects Models in Population PK/PD, Estimation Routines
Fit and compare nonlinear mixed-effects models in differential equations with flexible dosing information commonly seen in pharmacokinetics and pharmacodynamics (Almquist, Leander, and Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation solving is by compiled C code provided in the 'rxode2' package (Wang, Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Maintained by Matthew Fidler. Last updated 16 days ago.
7.5 match 9 stars 8.33 score 26 scripts 9 dependentsnlmixr2
nlmixr2:Nonlinear Mixed Effects Models in Population PK/PD
Fit and compare nonlinear mixed-effects models in differential equations with flexible dosing information commonly seen in pharmacokinetics and pharmacodynamics (Almquist, Leander, and Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation solving is by compiled C code provided in the 'rxode2' package (Wang, Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Maintained by Matthew Fidler. Last updated 2 days ago.
7.5 match 52 stars 8.32 score 120 scripts 3 dependentsmrc-ide
hipercow:High Performance Computing
Set up cluster environments and jobs. Moo.
Maintained by Rich FitzJohn. Last updated 5 days ago.
9.5 match 1 stars 6.57 score 45 scripts 1 dependents
kassambara
ggpubr:'ggplot2' Based Publication Ready Plots
The 'ggplot2' package is excellent and flexible for elegant data visualization in R. However the default generated plots requires some formatting before we can send them for publication. Furthermore, to customize a 'ggplot', the syntax is opaque and this raises the level of difficulty for researchers with no advanced R programming skills. 'ggpubr' provides some easy-to-use functions for creating and customizing 'ggplot2'- based publication ready plots.
Maintained by Alboukadel Kassambara. Last updated 2 years ago.
3.7 match 1.2k stars 16.68 score 65k scripts 409 dependents
emf-creaf
meteospain:Access to Spanish Meteorological Stations Services
Access to different Spanish meteorological stations data services and APIs (AEMET, SMC, MG, Meteoclimatic...).
Maintained by Victor Granda. Last updated 6 months ago.
9.5 match 8 stars 6.46 score 52 scripts
r-lum
Luminescence:Comprehensive Luminescence Dating Data Analysis
A collection of various R functions for the purpose of Luminescence dating data analysis. This includes, amongst others, data import, export, application of age models, curve deconvolution, sequence analysis and plotting of equivalent dose distributions.
Maintained by Sebastian Kreutzer. Last updated 12 hours ago.
bayesian-statisticsdata-sciencegeochronologyluminescenceluminescence-datingopen-scienceoslplottingradiofluorescencetlxsygcpp
5.7 match 16 stars 10.66 score 178 scripts 8 dependentsr-lib
styler:Non-Invasive Pretty Printing of R Code
Pretty-prints R code without changing the user's formatting intent.
Maintained by Lorenz Walthert. Last updated 18 hours ago.
3.8 match 753 stars 16.13 score 940 scripts 63 dependents
danchaltiel
crosstable:Crosstables for Descriptive Analyses
Create descriptive tables for continuous and categorical variables. Apply summary statistics and counting function, with or without a grouping variable, and create beautiful reports using 'rmarkdown' or 'officer'. You can also compute effect sizes and statistical tests if needed.
Maintained by Dan Chaltiel. Last updated 2 months ago.
descriptive-statisticsflextablefrequency-tablehtml-reportmswordofficer
5.8 match 116 stars 10.40 score 340 scriptsbioc
TCGAbiolinks:TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
The aim of TCGAbiolinks is : i) facilitate the GDC open-access data retrieval, ii) prepare the data using the appropriate pre-processing strategies, iii) provide the means to carry out different standard analyses and iv) to easily reproduce earlier research results. In more detail, the package provides multiple methods for analysis (e.g., differential expression analysis, identifying differentially methylated regions) and methods for visualization (e.g., survival plots, volcano plots, starburst plots) in order to easily develop complete analysis pipelines.
Maintained by Tiago Chedraoui Silva. Last updated 1 months ago.
dnamethylationdifferentialmethylationgeneregulationgeneexpressionmethylationarraydifferentialexpressionpathwaysnetworksequencingsurvivalsoftwarebiocbioconductorgdcintegrative-analysistcgatcga-datatcgabiolinks
4.2 match 310 stars 14.47 score 1.6k scripts 6 dependents
darwin-eu
CodelistGenerator:Identify Relevant Clinical Codes and Evaluate Their Use
Generate a candidate code list for the Observational Medical Outcomes Partnership (OMOP) common data model based on string matching. For a given search strategy, a candidate code list will be returned.
Maintained by Edward Burn. Last updated 7 days ago.
6.0 match 14 stars 9.94 score 165 scripts 4 dependents
ocbe-uio
BayesMallows:Bayesian Preference Learning with the Mallows Rank Model
An implementation of the Bayesian version of the Mallows rank model (Vitelli et al., Journal of Machine Learning Research, 2018 <https://jmlr.org/papers/v18/15-481.html>; Crispino et al., Annals of Applied Statistics, 2019 <doi:10.1214/18-AOAS1203>; Sorensen et al., R Journal, 2020 <doi:10.32614/RJ-2020-026>; Stein, PhD Thesis, 2023 <https://eprints.lancs.ac.uk/id/eprint/195759>). Both Metropolis-Hastings and sequential Monte Carlo algorithms for estimating the models are available. Cayley, footrule, Hamming, Kendall, Spearman, and Ulam distances are supported in the models. The rank data to be analyzed can be in the form of complete rankings, top-k rankings, partially missing rankings, as well as consistent and inconsistent pairwise preferences. Several functions for plotting and studying the posterior distributions of parameters are provided. The package also provides functions for estimating the partition function (normalizing constant) of the Mallows rank model, both with the importance sampling algorithm of Vitelli et al. and asymptotic approximation with the IPFP algorithm (Mukherjee, Annals of Statistics, 2016 <doi:10.1214/15-AOS1389>).
Maintained by Oystein Sorensen. Last updated 2 months ago.
mallows-modelopenblascppopenmp
7.4 match 21 stars 7.91 score 36 scripts 1 dependentsrstudio
r2d3:Interface to 'D3' Visualizations
Suite of tools for using 'D3', a library for producing dynamic, interactive data visualizations. Supports translating objects into 'D3' friendly data structures, rendering 'D3' scripts, publishing 'D3' visualizations, incorporating 'D3' in R Markdown, creating interactive 'D3' applications with Shiny, and distributing 'D3' based 'htmlwidgets' in R packages.
Maintained by Nick Strayer. Last updated 3 years ago.
4.8 match 519 stars 11.88 score 498 scripts 10 dependents
stan-dev
rstanarm:Bayesian Applied Regression Modeling via Stan
Estimates previously compiled regression models using the 'rstan' package, which provides the R interface to the Stan C++ library for Bayesian estimation. Users specify models via the customary R syntax with a formula and data.frame plus some additional arguments for priors.
Maintained by Ben Goodrich. Last updated 15 days ago.
bayesianbayesian-data-analysisbayesian-inferencebayesian-methodsbayesian-statisticsmultilevel-modelsrstanrstanarmstanstatistical-modelingcpp
3.6 match 393 stars 15.70 score 5.0k scripts 13 dependentsr-spatial
sf:Simple Features for R
Support for simple feature access, a standardized way to encode and analyze spatial vector data. Binds to 'GDAL' <doi:10.5281/zenodo.5884351> for reading and writing data, to 'GEOS' <doi:10.5281/zenodo.11396894> for geometrical operations, and to 'PROJ' <doi:10.5281/zenodo.5884394> for projection conversions and datum transformations. Uses by default the 's2' package for geometry operations on geodetic (long/lat degree) coordinates.
Maintained by Edzer Pebesma. Last updated 18 hours ago.
2.5 match 1.4k stars 22.44 score 117k scripts 1.2k dependentsropensci
beastier:Call 'BEAST2'
'BEAST2' (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'BEAST2' is a command-line tool. This package provides a way to call 'BEAST2' from an 'R' function call.
Maintained by Richèl J.C. Bilderbeek. Last updated 1 months ago.
bayesianbeastbeast2phylogenetic-inferencephylogeneticsopenjdk
7.2 match 11 stars 7.87 score 47 scripts 4 dependents
rmi-pacta
pacta.multi.loanbook:Run 'PACTA' on Multiple Loan Books Easily
Run Paris Agreement Capital Transition Assessment ('PACTA') analyses on multiple loan books in a structured way. Provides access to standard 'PACTA' metrics and additional 'PACTA'-related metrics for multiple loan books. Results take the form of 'csv' files and plots and are exported to user-specified project paths.
Maintained by Jacob Kastl. Last updated 20 days ago.
climate-changepactapactaversesustainable-finance
8.7 match 6.48 score 4 scripts
gforge
htmlTable:Advanced Tables for Markdown/HTML
Tables with state-of-the-art layout elements such as row spanners, column spanners, table spanners, zebra striping, and more. While allowing advanced layout, the underlying css-structure is simple in order to maximize compatibility with common word processors. The package also contains a few text formatting functions that help outputting text compatible with HTML/LaTeX.
Maintained by Max Gordon. Last updated 9 months ago.
3.7 match 79 stars 15.33 score 1.3k scripts 767 dependents
aryoda
tryCatchLog:Advanced 'tryCatch()' and 'try()' Functions
Advanced tryCatch() and try() functions for better error handling (logging, stack trace with source code references and support for post-mortem analysis via dump files).
Maintained by Juergen Altfeld. Last updated 2 years ago.
6.4 match 72 stars 8.72 score 116 scripts 9 dependentsrstudio
rsconnect:Deploy Docs, Apps, and APIs to 'Posit Connect', 'shinyapps.io', and 'RPubs'
Programmatic deployment interface for 'RPubs', 'shinyapps.io', and 'Posit Connect'. Supported content types include R Markdown documents, Shiny applications, Plumber APIs, plots, and static web content.
Maintained by Aron Atkins. Last updated 13 hours ago.
3.8 match 141 stars 14.88 score 3.1k scripts 6 dependentspredictiveecology
Require:Installing and Loading R Packages for Reproducible Workflows
A single key function, 'Require' that makes rerun-tolerant versions of 'install.packages' and `require` for CRAN packages, packages no longer on CRAN (i.e., archived), specific versions of packages, and GitHub packages. This approach is developed to create reproducible workflows that are flexible and fast enough to use while in development stages, while able to build snapshots once a stable package collection is found. As with other functions in a reproducible workflow, this package emphasizes functions that return the same result whether it is the first or subsequent times running the function, with subsequent times being sufficiently fast that they can be run every time without undue waiting burden on the user or developer.
Maintained by Eliot J B McIntire. Last updated 1 months ago.
5.9 match 22 stars 9.38 score 144 scripts 14 dependents
tagteam
riskRegression:Risk Regression Models and Prediction Scores for Survival Analysis with Competing Risks
Implementation of the following methods for event history analysis. Risk regression models for survival endpoints also in the presence of competing risks are fitted using binomial regression based on a time sequence of binary event status variables. A formula interface for the Fine-Gray regression model and an interface for the combination of cause-specific Cox regression models. A toolbox for assessing and comparing performance of risk predictions (risk markers and risk prediction models). Prediction performance is measured by the Brier score and the area under the ROC curve for binary possibly time-dependent outcome. Inverse probability of censoring weighting and pseudo values are used to deal with right censored data. Lists of risk markers and lists of risk models are assessed simultaneously. Cross-validation repeatedly splits the data, trains the risk prediction models on one part of each split and then summarizes and compares the performance across splits.
Maintained by Thomas Alexander Gerds. Last updated 1 months ago.
4.3 match 47 stars 13.07 score 736 scripts 37 dependents
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 15 hours ago.
multivariate-time-to-eventsurvival-analysistime-to-eventfortranopenblascpp
4.1 match 14 stars 13.44 score 236 scripts 42 dependentsdreamrs
esquisse:Explore and Visualize Your Data Interactively
A 'shiny' gadget to create 'ggplot2' figures interactively with drag-and-drop to map your variables to different aesthetics. You can quickly visualize your data accordingly to their type, export in various formats, and retrieve the code to reproduce the plot.
Maintained by Victor Perrier. Last updated 1 months ago.
addindata-visualizationggplot2rstudio-addinvisualization
4.2 match 1.8k stars 13.31 score 1.1k scripts 1 dependents
bbolker
bbmle:Tools for General Maximum Likelihood Estimation
Methods and functions for fitting maximum likelihood models in R. This package modifies and extends the 'mle' classes in the 'stats4' package.
Maintained by Ben Bolker. Last updated 2 months ago.
4.1 match 25 stars 13.36 score 1.4k scripts 117 dependents
khliland
pls:Partial Least Squares and Principal Component Regression
Multivariate regression methods Partial Least Squares Regression (PLSR), Principal Component Regression (PCR) and Canonical Powered Partial Least Squares (CPPLS).
Maintained by Kristian Hovde Liland. Last updated 2 months ago.
4.0 match 37 stars 13.60 score 3.2k scripts 85 dependents
wlandau
crew.cluster:Crew Launcher Plugins for Traditional High-Performance Computing Clusters
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 'crew.cluster' package extends the 'mirai'-powered 'crew' package with worker launcher plugins for traditional high-performance computing systems. Inspiration also comes from packages 'mirai' by Gao (2023) <https://github.com/shikokuchuo/mirai>, '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, Bischl, and Surmann (2017). <doi:10.21105/joss.00135>.
Maintained by William Michael Landau. Last updated 6 days ago.
crewhigh-performance-computing
8.0 match 29 stars 6.80 score 68 scripts
projectmosaic
mosaic:Project MOSAIC Statistics and Mathematics Teaching Utilities
Data sets and utilities from Project MOSAIC (<http://www.mosaic-web.org>) used to teach mathematics, statistics, computation and modeling. Funded by the NSF, Project MOSAIC is a community of educators working to tie together aspects of quantitative work that students in science, technology, engineering and mathematics will need in their professional lives, but which are usually taught in isolation, if at all.
Maintained by Randall Pruim. Last updated 1 years ago.
4.0 match 93 stars 13.32 score 7.2k scripts 7 dependentsr-lib
withr:Run Code 'With' Temporarily Modified Global State
A set of functions to run code 'with' safely and temporarily modified global state. Many of these functions were originally a part of the 'devtools' package, this provides a simple package with limited dependencies to provide access to these functions.
Maintained by Lionel Henry. Last updated 1 months ago.
3.0 match 176 stars 17.96 score 1.2k scripts 12k dependentsdreamrs
vchartr:Interactive Charts with the 'JavaScript' 'VChart' Library
Provides an 'htmlwidgets' interface to 'VChart.js'. 'VChart', more than just a cross-platform charting library, but also an expressive data storyteller. 'VChart' examples and documentation are available here: <https://www.visactor.io/vchart>.
Maintained by Victor Perrier. Last updated 3 months ago.
7.8 match 9 stars 6.89 score 96 scripts
dfsp-spirit
fsbrain:Managing and Visualizing Brain Surface Data
Provides high-level access to neuroimaging data from standard software packages like 'FreeSurfer' <http://freesurfer.net/> on the level of subjects and groups. Load morphometry data, surfaces and brain parcellations based on atlases. Mask data using labels, load data for specific atlas regions only, and visualize data and statistical results directly in 'R'.
Maintained by Tim Schäfer. Last updated 4 months ago.
3dbraindtifreesurfermeshmrineuroimagingresearchsurfacevisualizationvoxel
8.3 match 68 stars 6.49 score 15 scripts
ipums
ipumsr:An R Interface for Downloading, Reading, and Handling IPUMS Data
An easy way to work with census, survey, and geographic data provided by IPUMS in R. Generate and download data through the IPUMS API and load IPUMS files into R with their associated metadata to make analysis easier. IPUMS data describing 1.4 billion individuals drawn from over 750 censuses and surveys is available free of charge from the IPUMS website <https://www.ipums.org>.
Maintained by Derek Burk. Last updated 1 months ago.
4.8 match 30 stars 11.05 score 720 scripts 2 dependentsbioc
gpuMagic:An openCL compiler with the capacity to compile R functions and run the code on GPU
The package aims to help users write openCL code with little or no effort. It is able to compile an user-defined R function and run it on a device such as a CPU or a GPU. The user can also write and run their openCL code directly by calling .kernel function.
Maintained by Jiefei Wang. Last updated 5 months ago.
9.6 match 10 stars 5.60 score 1 scripts
mlopez-ibanez
irace:Iterated Racing for Automatic Algorithm Configuration
Iterated race is an extension of the Iterated F-race method for the automatic configuration of optimization algorithms, that is, (offline) tuning their parameters by finding the most appropriate settings given a set of instances of an optimization problem. M. López-Ibáñez, J. Dubois-Lacoste, L. Pérez Cáceres, T. Stützle, and M. Birattari (2016) <doi:10.1016/j.orp.2016.09.002>.
Maintained by Manuel López-Ibáñez. Last updated 2 months ago.
algorithm-configurationhyperparameter-tuningiraceoptimization-algorithms
5.2 match 63 stars 10.20 score 103 scripts 1 dependents
t-kalinowski
keras:R Interface to 'Keras'
Interface to 'Keras' <https://keras.io>, a high-level neural networks 'API'. 'Keras' was developed with a focus on enabling fast experimentation, supports both convolution based networks and recurrent networks (as well as combinations of the two), and runs seamlessly on both 'CPU' and 'GPU' devices.
Maintained by Tomasz Kalinowski. Last updated 12 months ago.
4.9 match 10.93 score 10k scripts 55 dependentskkholst
lava:Latent Variable Models
A general implementation of Structural Equation Models with latent variables (MLE, 2SLS, and composite likelihood estimators) with both continuous, censored, and ordinal outcomes (Holst and Budtz-Joergensen (2013) <doi:10.1007/s00180-012-0344-y>). Mixture latent variable models and non-linear latent variable models (Holst and Budtz-Joergensen (2020) <doi:10.1093/biostatistics/kxy082>). The package also provides methods for graph exploration (d-separation, back-door criterion), simulation of general non-linear latent variable models, and estimation of influence functions for a broad range of statistical models.
Maintained by Klaus K. Holst. Last updated 3 months ago.
latent-variable-modelssimulationstatisticsstructural-equation-models
4.1 match 33 stars 12.87 score 610 scripts 478 dependents
mandymejia
ciftiTools:Tools for Reading, Writing, Viewing and Manipulating CIFTI Files
CIFTI files contain brain imaging data in "grayordinates," which represent the gray matter as cortical surface vertices (left and right) and subcortical voxels (cerebellum, basal ganglia, and other deep gray matter). 'ciftiTools' provides a unified environment for reading, writing, visualizing and manipulating CIFTI-format data. It supports the "dscalar," "dlabel," and "dtseries" intents. Grayordinate data is read in as a "xifti" object, which is structured for convenient access to the data and metadata, and includes support for surface geometry files to enable spatially-dependent functionality such as static or interactive visualizations and smoothing.
Maintained by Amanda Mejia. Last updated 2 months ago.
6.0 match 47 stars 8.84 score 176 scripts 4 dependentsbioc
dada2:Accurate, high-resolution sample inference from amplicon sequencing data
The dada2 package infers exact amplicon sequence variants (ASVs) from high-throughput amplicon sequencing data, replacing the coarser and less accurate OTU clustering approach. The dada2 pipeline takes as input demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier, and species-level assignment to 16S rRNA gene fragments by exact matching.
Maintained by Benjamin Callahan. Last updated 5 months ago.
immunooncologymicrobiomesequencingclassificationmetagenomicsampliconbioconductorbioinformaticsmetabarcodingtaxonomycpp
4.0 match 487 stars 13.17 score 3.0k scripts 4 dependents
alexrecuenco
TexExamRandomizer:Personalizes and Randomizes Exams Written in 'LaTeX'
Randomizing exams with 'LaTeX'. If you can compile your main document with 'LaTeX', the program should be able to compile the randomized versions without much extra effort when creating the document.
Maintained by Alejandro Gonzalez Recuenco. Last updated 1 years ago.
11.6 match 1 stars 4.52 score 22 scripts
novonordisk-opensource
zephyr:Structured Messages and Options
Provides a structured framework for consistent user communication and configuration management for package developers.
Maintained by Aksel Thomsen. Last updated 21 days ago.
11.0 match 2 stars 4.75 score 2 scripts
rte-antares-rpackage
antaresRead:Import, Manipulate and Explore the Results of an 'Antares' Simulation
Import, manipulate and explore results generated by 'Antares', a powerful open source software developed by RTE (Réseau de Transport d’Électricité) to simulate and study electric power systems (more information about 'Antares' here : <https://antares-simulator.org/>).
Maintained by Tatiana Vargas. Last updated 7 days ago.
infrastructuredataimportadequacybilanelectricityenergyhdf5linear-algebramonte-carlo-simulationoptimisationprevisionnelrhdf5rtesimulationtyndp
5.6 match 13 stars 9.32 score 148 scripts 3 dependentsrstudio
httpuv:HTTP and WebSocket Server Library
Provides low-level socket and protocol support for handling HTTP and WebSocket requests directly from within R. It is primarily intended as a building block for other packages, rather than making it particularly easy to create complete web applications using httpuv alone. httpuv is built on top of the libuv and http-parser C libraries, both of which were developed by Joyent, Inc. (See LICENSE file for libuv and http-parser license information.)
Maintained by Winston Chang. Last updated 15 days ago.
3.4 match 236 stars 15.42 score 708 scripts 2.1k dependentsrstudio
sass:Syntactically Awesome Style Sheets ('Sass')
An 'SCSS' compiler, powered by the 'LibSass' library. With this, R developers can use variables, inheritance, and functions to generate dynamic style sheets. The package uses the 'Sass CSS' extension language, which is stable, powerful, and CSS compatible.
Maintained by Carson Sievert. Last updated 1 days ago.
3.3 match 100 stars 15.63 score 252 scripts 4.3k dependents
sollano
forestmangr:Forest Mensuration and Management
Processing forest inventory data with methods such as simple random sampling, stratified random sampling and systematic sampling. There are also functions for yield and growth predictions and model fitting, linear and nonlinear grouped data fitting, and statistical tests. References: Kershaw Jr., Ducey, Beers and Husch (2016). <doi:10.1002/9781118902028>.
Maintained by Sollano Rabelo Braga. Last updated 4 months ago.
6.6 match 17 stars 7.89 score 378 scriptsdfsp-spirit
pkgfilecache:Download and Manage Optional Package Data
Manage optional data for your package. The data can be hosted anywhere, and you have to give a Uniform Resource Locator (URL) for each file. File integrity checks are supported. This is useful for package authors who need to ship more than the 5 Megabyte of data currently allowed by the the Comprehensive R Archive Network (CRAN).
Maintained by Tim Schäfer. Last updated 1 years ago.
cachechecksumdeveloper-toolsdownloadfilesfilestoragehome-directory
8.7 match 7 stars 6.01 score 3 scripts 9 dependents
mihaiconstantin
parabar:Progress Bar for Parallel Tasks
A simple interface in the form of R6 classes for executing tasks in parallel, tracking their progress, and displaying accurate progress bars.
Maintained by Mihai Constantin. Last updated 4 months ago.
parallel-computingprogress-bar
6.9 match 20 stars 7.56 score 20 scripts 5 dependentstrafficonese
leaflet.esri:'ESRI' Bindings for the 'leaflet' Package
An add-on package to the 'leaflet' package, which provides bindings for 'ESRI' services. This package allows a user to add 'ESRI' provided services such as 'MapService', 'ImageMapService', 'TiledMapService' etc. to a 'leaflet' map.
Maintained by Bhaskar Karambelkar. Last updated 4 years ago.
data-visualizationesriesri-leafletgeospatialleaflet
8.3 match 36 stars 6.28 score 106 scriptsyihui
litedown:A Lightweight Version of R Markdown
Render R Markdown to Markdown (without using 'knitr'), and Markdown to lightweight HTML or 'LaTeX' documents with the 'commonmark' package (instead of 'Pandoc'). Some missing Markdown features in 'commonmark' are also supported, such as raw HTML or 'LaTeX' blocks, 'LaTeX' math, superscripts, subscripts, footnotes, element attributes, and appendices, but not all 'Pandoc' Markdown features are (or will be) supported. With additional JavaScript and CSS, you can also create HTML slides and articles. This package can be viewed as a trimmed-down version of R Markdown and 'knitr'. It does not aim at rich Markdown features or a large variety of output formats (the primary formats are HTML and 'LaTeX'). Book and website projects of multiple input documents are also supported.
Maintained by Yihui Xie. Last updated 1 days ago.
litedownmarkdownr-markdownreport-generatorreproducible-research
3.9 match 201 stars 13.36 score 16 scripts 164 dependents
bschneidr
svrep:Tools for Creating, Updating, and Analyzing Survey Replicate Weights
Provides tools for creating and working with survey replicate weights, extending functionality of the 'survey' package from Lumley (2004) <doi:10.18637/jss.v009.i08>. Implements bootstrap methods for complex surveys, including the generalized survey bootstrap as described by Beaumont and Patak (2012) <doi:10.1111/j.1751-5823.2011.00166.x>. Methods are provided for applying nonresponse adjustments to both full-sample and replicate weights as described by Rust and Rao (1996) <doi:10.1177/096228029600500305>. Implements methods for sample-based calibration described by Opsomer and Erciulescu (2021) <https://www150.statcan.gc.ca/n1/pub/12-001-x/2021002/article/00006-eng.htm>. Diagnostic functions are included to compare weights and weighted estimates from different sets of replicate weights.
Maintained by Ben Schneider. Last updated 24 days ago.
6.3 match 8 stars 8.12 score 54 scripts 3 dependentsr-lib
lintr:A 'Linter' for R Code
Checks adherence to a given style, syntax errors and possible semantic issues. Supports on the fly checking of R code edited with 'RStudio IDE', 'Emacs', 'Vim', 'Sublime Text', 'Atom' and 'Visual Studio Code'.
Maintained by Michael Chirico. Last updated 1 days ago.
3.0 match 1.2k stars 16.97 score 916 scripts 33 dependentsyihui
animation:A Gallery of Animations in Statistics and Utilities to Create Animations
Provides functions for animations in statistics, covering topics in probability theory, mathematical statistics, multivariate statistics, non-parametric statistics, sampling survey, linear models, time series, computational statistics, data mining and machine learning. These functions may be helpful in teaching statistics and data analysis. Also provided in this package are a series of functions to save animations to various formats, e.g. Flash, 'GIF', HTML pages, 'PDF' and videos. 'PDF' animations can be inserted into 'Sweave' / 'knitr' easily.
Maintained by Yihui Xie. Last updated 2 years ago.
animationstatistical-computingstatistical-graphicsstatistics
4.1 match 208 stars 12.13 score 2.5k scripts 28 dependents