R-universe search: serialization

qsbase

qs:Quick Serialization of R Objects

Provides functions for quickly writing and reading any R object to and from disk.

Maintained by Travers Ching. Last updated 9 days ago.

compression data-storage encoding serialization libzstd lz4 cpp

25.1 match 414 stars 13.91 score 2.5k scripts 51 dependents

sfcheung

manymome:Mediation, Moderation and Moderated-Mediation After Model Fitting

Computes indirect effects, conditional effects, and conditional indirect effects in a structural equation model or path model after model fitting, with no need to define any user parameters or label any paths in the model syntax, using the approach presented in Cheung and Cheung (2024) <doi:10.3758/s13428-023-02224-z>. Can also form bootstrap confidence intervals by doing bootstrapping only once and reusing the bootstrap estimates in all subsequent computations. Supports bootstrap confidence intervals for standardized (partially or completely) indirect effects, conditional effects, and conditional indirect effects as described in Cheung (2009) <doi:10.3758/BRM.41.2.425> and Cheung, Cheung, Lau, Hui, and Vong (2022) <doi:10.1037/hea0001188>. Model fitting can be done by structural equation modeling using lavaan() or regression using lm().

Maintained by Shu Fai Cheung. Last updated 22 days ago.

bootstrapping confidence-interval lavaan manymome mediation moderated-mediation moderation regression sem standardized-effect-size structural-equation-modeling

24.6 match 1 stars 8.06 score 172 scripts 4 dependents

coolbutuseless

serializer:Expose R's Serialization Interface

Expose R's serialization interface for serialing/unserializing R objects to/from raw vectors and connections.

Maintained by Mike Cheng. Last updated 8 months ago.

63.0 match 12 stars 3.08 score 7 scripts

ropensci

redland:RDF Library Bindings in R

Provides methods to parse, query and serialize information stored in the Resource Description Framework (RDF). RDF is described at <https://www.w3.org/TR/rdf-primer/>. This package supports RDF by implementing an R interface to the Redland RDF C library, described at <https://librdf.org/docs/api/index.html>. In brief, RDF provides a structured graph consisting of Statements composed of Subject, Predicate, and Object Nodes.

Maintained by Matthew B. Jones. Last updated 1 years ago.

redland

23.2 match 17 stars 7.85 score 98 scripts 13 dependents

mlverse

torch:Tensors and Neural Networks with 'GPU' Acceleration

Provides functionality to define and train neural networks similar to 'PyTorch' by Paszke et al (2019) <doi:10.48550/arXiv.1912.01703> but written entirely in R using the 'libtorch' library. Also supports low-level tensor operations and 'GPU' acceleration.

Maintained by Daniel Falbel. Last updated 6 days ago.

autograd deep-learning torch cpp

10.3 match 520 stars 16.52 score 1.4k scripts 38 dependents

eddelbuettel

RApiSerialize:R API Serialization

Access to the internal R serialization code is provided for use by other packages at the C function level by using the registration of native function mechanism. Client packages simply include a single header file RApiSerializeAPI.h provided by this package. This packages builds on the Rhpc package by Ei-ji Nakama and Junji Nakano which also includes a (partial) copy of the file src/main/serialize.c from R itself. The R Core group is the original author of the serialization code made available by this package.

Maintained by Dirk Eddelbuettel. Last updated 22 days ago.

serialization

17.8 match 11 stars 7.96 score 6 scripts 53 dependents

rstudio

plumber:An API Generator for R

Gives the ability to automatically generate and serve an HTTP API from R functions using the annotations in the R documentation around your functions.

Maintained by Barret Schloerke. Last updated 5 days ago.

api api-server plumber

8.4 match 1.4k stars 14.47 score 2.2k scripts 16 dependents

ycroissant

plm:Linear Models for Panel Data

A set of estimators for models and (robust) covariance matrices, and tests for panel data econometrics, including within/fixed effects, random effects, between, first-difference, nested random effects as well as instrumental-variable (IV) and Hausman-Taylor-style models, panel generalized method of moments (GMM) and general FGLS models, mean groups (MG), demeaned MG, and common correlated effects (CCEMG) and pooled (CCEP) estimators with common factors, variable coefficients and limited dependent variables models. Test functions include model specification, serial correlation, cross-sectional dependence, panel unit root and panel Granger (non-)causality. Typical references are general econometrics text books such as Baltagi (2021), Econometric Analysis of Panel Data (<doi:10.1007/978-3-030-53953-5>), Hsiao (2014), Analysis of Panel Data (<doi:10.1017/CBO9781139839327>), and Croissant and Millo (2018), Panel Data Econometrics with R (<doi:10.1002/9781119504641>).

Maintained by Kevin Tappe. Last updated 7 hours ago.

10.0 match 59 stars 12.06 score 39 dependents

mrc-ide

EpiEstim:Estimate Time Varying Reproduction Numbers from Epidemic Curves

Tools to quantify transmissibility throughout an epidemic from the analysis of time series of incidence as described in Cori et al. (2013) <doi:10.1093/aje/kwt133> and Wallinga and Teunis (2004) <doi:10.1093/aje/kwh255>.

Maintained by Anne Cori. Last updated 7 months ago.

9.0 match 95 stars 12.00 score 1.0k scripts 7 dependents

cran

serial:The Serial Interface Package

Enables reading and writing binary and ASCII data to RS232/RS422/RS485 or any other virtual serial interface of the computer.

Maintained by Martin Seilmayer. Last updated 5 years ago.

72.4 match 1.48 score 1 dependents

rstudio

keras3: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 4 days ago.

7.8 match 845 stars 13.57 score 264 scripts 2 dependents

qsbase

qs2:Efficient Serialization of R Objects

Streamlines and accelerates the process of saving and loading R objects, improving speed and compression compared to other methods. The package provides two compression formats: the 'qs2' format, which uses R serialization via the C API while optimizing compression and disk I/O, and the 'qdata' format, featuring custom serialization for slightly faster performance and better compression. Additionally, the 'qs2' format can be directly converted to the standard 'RDS' format, ensuring long-term compatibility with future versions of R.

Maintained by Travers Ching. Last updated 9 days ago.

compression data-storage serialization cpp

13.9 match 15 stars 7.57 score 25 scripts 2 dependents

shikokuchuo

sakura:Extension to R Serialization

Extends the functionality of R serialization by augmenting the built-in reference hook system. This enhanced implementation allows an integrated single-pass operation that combines R serialization with third-party serialization methods. Facilitates the serialization of even complex R objects, which contain non-system reference objects, such as those accessed via external pointers, to enable their use in parallel and distributed computing.

Maintained by Charlie Gao. Last updated 12 days ago.

marshalling serialization

24.2 match 12 stars 4.26 score

z267xu

ggmulti:High Dimensional Data Visualization

It provides materials (i.e. 'serial axes' objects, Andrew's plot, various glyphs for scatter plot) to visualize high dimensional data.

Maintained by Zehao Xu. Last updated 2 years ago.

16.3 match 6.11 score 36 scripts 4 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 9 hours ago.

geospatial raster spatial vector onetbb proj gdal geos cpp

4.9 match 559 stars 17.64 score 17k scripts 851 dependents

dankelley

oce:Analysis of Oceanographic Data

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

Maintained by Dan Kelley. Last updated 19 hours ago.

oceanography fortran cpp

5.5 match 146 stars 15.42 score 4.2k scripts 18 dependents

trivialfis

xgboost:Extreme Gradient Boosting

Extreme Gradient Boosting, which is an efficient implementation of the gradient boosting framework from Chen & Guestrin (2016) <doi:10.1145/2939672.2939785>. This package is its R interface. The package includes efficient linear model solver and tree learning algorithms. The package can automatically do parallel computation on a single machine which could be more than 10 times faster than existing gradient boosting packages. It supports various objective functions, including regression, classification and ranking. The package is made to be extensible, so that users are also allowed to define their own objectives easily.

Maintained by Jiaming Yuan. Last updated 8 months ago.

cpp openmp

7.0 match 6 stars 11.70 score 13k scripts 112 dependents

stochastictree

stochtree:Stochastic Tree Ensembles (XBART and BART) for Supervised Learning and Causal Inference

Flexible stochastic tree ensemble software. Robust implementations of Bayesian Additive Regression Trees (BART) Chipman, George, McCulloch (2010) <doi:10.1214/09-AOAS285> for supervised learning and Bayesian Causal Forests (BCF) Hahn, Murray, Carvalho (2020) <doi:10.1214/19-BA1195> for causal inference. Enables model serialization and parallel sampling and provides a low-level interface for custom stochastic forest samplers.

Maintained by Drew Herren. Last updated 17 days ago.

bart bayesian-machine-learning bayesian-methods decision-trees gradient-boosted-trees machine-learning probabilistic-models tree-ensembles cpp

9.2 match 20 stars 8.52 score 40 scripts

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 11 months ago.

6.4 match 10.82 score 10k scripts 54 dependents

fstpackage

fst:Lightning Fast Serialization of Data Frames

Multithreaded serialization of compressed data frames using the 'fst' format. The 'fst' format allows for full random access of stored data and a wide range of compression settings using the LZ4 and ZSTD compressors.

Maintained by Mark Klik. Last updated 6 months ago.

compression data-frame data-storage cpp

5.3 match 624 stars 13.14 score 1.9k scripts 55 dependents

ropensci

datapack:A Flexible Container to Transport and Manipulate Data and Associated Resources

Provides a flexible container to transport and manipulate complex sets of data. These data may consist of multiple data files and associated meta data and ancillary files. Individual data objects have associated system level meta data, and data files are linked together using the OAI-ORE standard resource map which describes the relationships between the files. The OAI- ORE standard is described at <https://www.openarchives.org/ore/>. Data packages can be serialized and transported as structured files that have been created following the BagIt specification. The BagIt specification is described at <https://tools.ietf.org/html/draft-kunze-bagit-08>.

Maintained by Matthew B. Jones. Last updated 3 years ago.

8.0 match 44 stars 8.56 score 195 scripts 4 dependents

bpfaff

vars:VAR Modelling

Estimation, lag selection, diagnostic testing, forecasting, causality analysis, forecast error variance decomposition and impulse response functions of VAR models and estimation of SVAR and SVEC models.

Maintained by Bernhard Pfaff. Last updated 12 months ago.

7.4 match 7 stars 8.68 score 2.8k scripts 44 dependents

renkun-ken

rlist:A Toolbox for Non-Tabular Data Manipulation

Provides a set of functions for data manipulation with list objects, including mapping, filtering, grouping, sorting, updating, searching, and other useful functions. Most functions are designed to be pipeline friendly so that data processing with lists can be chained.

Maintained by Kun Ren. Last updated 2 years ago.

4.5 match 206 stars 13.73 score 2.2k scripts 123 dependents

sfirke

janitor:Simple Tools for Examining and Cleaning Dirty Data

The main janitor functions can: perfectly format data.frame column names; provide quick counts of variable combinations (i.e., frequency tables and crosstabs); and explore duplicate records. Other janitor functions nicely format the tabulation results. These tabulate-and-report functions approximate popular features of SPSS and Microsoft Excel. This package follows the principles of the "tidyverse" and works well with the pipe function %>%. janitor was built with beginning-to-intermediate R users in mind and is optimized for user-friendliness.

Maintained by Sam Firke. Last updated 3 months ago.

data-analysis data-cleaning data-science dirty-data excel pivot-tables spss tabulations tidyverse

2.9 match 1.4k stars 19.15 score 35k scripts 231 dependents

eddelbuettel

RProtoBuf:R Interface to the 'Protocol Buffers' 'API' (Version 2 or 3)

Protocol Buffers are a way of encoding structured data in an efficient yet extensible format. Google uses Protocol Buffers for almost all of its internal 'RPC' protocols and file formats. Additional documentation is available in two included vignettes one of which corresponds to our 'JSS' paper (2016, <doi:10.18637/jss.v071.i02>. A sufficiently recent version of 'Protocol Buffers' library is required; currently version 3.3.0 from 2017 is the stated minimum.

Maintained by Dirk Eddelbuettel. Last updated 1 months ago.

c-plus-plus protocol-buffers protobuf cpp

4.8 match 73 stars 11.42 score 126 scripts 21 dependents

patakamuri

modifiedmk:Modified Versions of Mann Kendall and Spearman's Rho Trend Tests

Power of non-parametric Mann-Kendall test and Spearman’s Rho test is highly influenced by serially correlated data. To address this issue, trend tests may be applied on the modified versions of the time series data by Block Bootstrapping (BBS), Prewhitening (PW) , Trend Free Prewhitening (TFPW), Bias Corrected Prewhitening and Variance Correction Approach by calculating effective sample size. Mann, H. B. (1945).<doi:10.1017/CBO9781107415324.004>. Kendall, M. (1975). Multivariate analysis. Charles Griffin&Company Ltd,. sen, P. K. (1968).<doi:10.2307/2285891>. Önöz, B., & Bayazit, M. (2012) <doi:10.1002/hyp.8438>. Hamed, K. H. (2009).<doi:10.1016/j.jhydrol.2009.01.040>. Yue, S., & Wang, C. Y. (2002) <doi:10.1029/2001WR000861>. Yue, S., Pilon, P., Phinney, B., & Cavadias, G. (2002) <doi:10.1002/hyp.1095>. Hamed, K. H., & Ramachandra Rao, A. (1998) <doi:10.1016/S0022-1694(97)00125-X>. Yue, S., & Wang, C. Y. (2004) <doi:10.1023/B:WARM.0000043140.61082.60>.

Maintained by Sandeep Kumar Patakamuri. Last updated 4 years ago.

10.1 match 4 stars 5.36 score 38 scripts 1 dependents

sparklyr

sparklyr:R Interface to Apache Spark

R interface to Apache Spark, a fast and general engine for big data processing, see <https://spark.apache.org/>. This package supports connecting to local and remote Apache Spark clusters, provides a 'dplyr' compatible back-end, and provides an interface to Spark's built-in machine learning algorithms.

Maintained by Edgar Ruiz. Last updated 9 days ago.

apache-spark distributed dplyr ide livy machine-learning remote-clusters spark sparklyr

3.5 match 959 stars 15.16 score 4.0k scripts 21 dependents

mahshaaban

pcr:Analyzing Real-Time Quantitative PCR Data

Calculates the amplification efficiency and curves from real-time quantitative PCR (Polymerase Chain Reaction) data. Estimates the relative expression from PCR data using the double delta CT and the standard curve methods Livak & Schmittgen (2001) <doi:10.1006/meth.2001.1262>. Tests for statistical significance using two-group tests and linear regression Yuan et al. (2006) <doi: 10.1186/1471-2105-7-85>.

Maintained by Mahmoud Ahmed. Last updated 8 months ago.

data-analyses molecular-biology qpcr

7.2 match 28 stars 7.25 score 63 scripts

r-forge

randtoolbox:Toolbox for Pseudo and Quasi Random Number Generation and Random Generator Tests

Provides (1) pseudo random generators - general linear congruential generators, multiple recursive generators and generalized feedback shift register (SF-Mersenne Twister algorithm (<doi:10.1007/978-3-540-74496-2_36>) and WELL (<doi:10.1145/1132973.1132974>) generators); (2) quasi random generators - the Torus algorithm, the Sobol sequence, the Halton sequence (including the Van der Corput sequence) and (3) some generator tests - the gap test, the serial test, the poker test, see, e.g., Gentle (2003) <doi:10.1007/b97336>. Take a look at the Distribution task view of types and tests of random number generators. The package can be provided without the 'rngWELL' dependency on demand. Package in Memoriam of Diethelm and Barbara Wuertz.

Maintained by Christophe Dutang. Last updated 3 months ago.

5.0 match 1 stars 10.23 score 578 scripts 80 dependents

rstudio

pointblank:Data Validation and Organization of Metadata for Local and Remote Tables

Validate data in data frames, 'tibble' objects, 'Spark' 'DataFrames', and database tables. Validation pipelines can be made using easily-readable, consecutive validation steps. Upon execution of the validation plan, several reporting options are available. User-defined thresholds for failure rates allow for the determination of appropriate reporting actions. Many other workflows are available including an information management workflow, where the aim is to record, collect, and generate useful information on data tables.

Maintained by Richard Iannone. Last updated 9 days ago.

data-assertions data-checker data-dictionaries data-frames data-inference data-management data-profiler data-quality data-validation data-verification database-tables easy-to-understand reporting-tool schema-validation testing-tools yaml-configuration

4.7 match 932 stars 10.59 score 284 scripts

coolbutuseless

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

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

Maintained by Mike Cheng. Last updated 4 months ago.

zlib

4.8 match 147 stars 9.56 score 22 scripts 9 dependents

r-forge

copula:Multivariate Dependence with Copulas

Classes (S4) of commonly used elliptical, Archimedean, extreme-value and other copula families, as well as their rotations, mixtures and asymmetrizations. Nested Archimedean copulas, related tools and special functions. Methods for density, distribution, random number generation, bivariate dependence measures, Rosenblatt transform, Kendall distribution function, perspective and contour plots. Fitting of copula models with potentially partly fixed parameters, including standard errors. Serial independence tests, copula specification tests (independence, exchangeability, radial symmetry, extreme-value dependence, goodness-of-fit) and model selection based on cross-validation. Empirical copula, smoothed versions, and non-parametric estimators of the Pickands dependence function.

Maintained by Martin Maechler. Last updated 11 days ago.

3.8 match 11.83 score 1.2k scripts 86 dependents

jeroen

protolite:Highly Optimized Protocol Buffer Serializers

Pure C++ implementations for reading and writing several common data formats based on Google protocol-buffers. Currently supports 'rexp.proto' for serialized R objects, 'geobuf.proto' for binary geojson, and 'mvt.proto' for vector tiles. This package uses the auto-generated C++ code by protobuf-compiler, hence the entire serialization is optimized at compile time. The 'RProtoBuf' package on the other hand uses the protobuf runtime library to provide a general- purpose toolkit for reading and writing arbitrary protocol-buffer data in R.

Maintained by Jeroen Ooms. Last updated 1 months ago.

protobuf cpp

5.8 match 48 stars 7.82 score 27 scripts 19 dependents

bioc

pogos:PharmacOGenomics Ontology Support

Provide simple utilities for querying bhklab PharmacoDB, modeling API outputs, and integrating to cell and compound ontologies.

Maintained by VJ Carey. Last updated 2 months ago.

pharmacogenomics pooledscreens immunooncology

10.5 match 4.30 score 10 scripts

rstudio

bundle:Serialize Model Objects with a Consistent Interface

Typically, models in 'R' exist in memory and can be saved via regular 'R' serialization. However, some models store information in locations that cannot be saved using 'R' serialization alone. The goal of 'bundle' is to provide a common interface to capture this information, situate it within a portable object, and restore it for use in new settings.

Maintained by Julia Silge. Last updated 4 months ago.

5.5 match 30 stars 8.07 score 153 scripts 4 dependents

ai4ci

ggoutbreak:Estimate Incidence, Proportions and Exponential Growth Rates

Simple statistical models and visualisations for calculating the incidence, proportion, exponential growth rate, and reproduction number of infectious disease case time series. This toolkit was largely developed during the COVID-19 pandemic.

Maintained by Robert Challen. Last updated 1 months ago.

10.1 match 1 stars 4.30 score

mingdeyu

dgpsi:Interface to 'dgpsi' for Deep and Linked Gaussian Process Emulations

Interface to the 'python' package 'dgpsi' for Gaussian process, deep Gaussian process, and linked deep Gaussian process emulations of computer models and networks using stochastic imputation (SI). The implementations follow Ming & Guillas (2021) <doi:10.1137/20M1323771> and Ming, Williamson, & Guillas (2023) <doi:10.1080/00401706.2022.2124311> and Ming & Williamson (2023) <doi:10.48550/arXiv.2306.01212>. To get started with the package, see <https://mingdeyu.github.io/dgpsi-R/>.

Maintained by Deyu Ming. Last updated 30 days ago.

deep-gaussian-processes emulation gaussian-processes surrogate-models

7.0 match 5.99 score 76 scripts

wush978

Rcereal:"Cereal Headers for R and C++ Serialization"

To facilitate using 'cereal' with R via 'cpp11' or 'Rcpp'. 'cereal' is a header-only C++11 serialization library. 'cereal' takes arbitrary data types and reversibly turns them into different representations, such as compact binary encodings, 'XML', or 'JSON'. 'cereal' was designed to be fast, light-weight, and easy to extend - it has no external dependencies and can be easily bundled with other code or used standalone. Please see <https://uscilab.github.io/cereal/> for more information.

Maintained by Wush Wu. Last updated 6 months ago.

6.4 match 12 stars 6.42 score 4 scripts 4 dependents

polar-fhir

fhircrackr:Handling HL7 FHIR® Resources in R

Useful tools for conveniently downloading FHIR resources in xml format and converting them to R data.frames. The package uses FHIR-search to download bundles from a FHIR server, provides functions to save and read xml-files containing such bundles and allows flattening the bundles to data.frames using XPath expressions. FHIR® is the registered trademark of HL7 and is used with the permission of HL7. Use of the FHIR trademark does not constitute endorsement of this product by HL7.

Maintained by Julia Palm. Last updated 11 days ago.

fhir fhir-client

5.3 match 33 stars 7.63 score 46 scripts

bioc

updateObject:Find/fix old serialized S4 instances

A set of tools built around updateObject() to work with old serialized S4 instances. The package is primarily useful to package maintainers who want to update the serialized S4 instances included in their package. This is still work-in-progress.

Maintained by Hervé Pagès. Last updated 5 months ago.

infrastructure datarepresentation bioconductor-package core-package

8.9 match 1 stars 4.48 score 3 scripts

jeroen

jsonlite:A Simple and Robust JSON Parser and Generator for R

A reasonably fast JSON parser and generator, optimized for statistical data and the web. Offers simple, flexible tools for working with JSON in R, and is particularly powerful for building pipelines and interacting with a web API. The implementation is based on the mapping described in the vignette (Ooms, 2014). In addition to converting JSON data from/to R objects, 'jsonlite' contains functions to stream, validate, and prettify JSON data. The unit tests included with the package verify that all edge cases are encoded and decoded consistently for use with dynamic data in systems and applications.

Maintained by Jeroen Ooms. Last updated 22 days ago.

json parser

1.9 match 384 stars 21.15 score 27k scripts 8.6k dependents

shikokuchuo

mirai:Minimalist Async Evaluation Framework for R

Designed for simplicity, a 'mirai' evaluates an R expression asynchronously in a parallel process, locally or distributed over the network. The result is automatically available upon completion. Modern networking and concurrency, built on 'nanonext' and 'NNG' (Nanomsg Next Gen), ensures reliable and efficient scheduling over fast inter-process communications or TCP/IP secured by TLS. Distributed computing can launch remote resources via SSH or cluster managers. An inherently queued architecture handles many more tasks than available processes, and requires no storage on the file system. Innovative features include support for otherwise non-exportable reference objects, event-driven promises, and asynchronous parallel map.

Maintained by Charlie Gao. Last updated 2 days ago.

async asynchronous-tasks concurrency distributed-computing high-performance-computing parallel-computing

3.3 match 217 stars 11.94 score 130 scripts 7 dependents

jadahlke

schoenberg:Tools for 12-Tone Musical Composition

Functions for creating and manipulating 12-tone (i.e., dodecaphonic) musical matrices using Arnold Schoenberg's (1923) serialism technique. This package can generate random 12-tone matrices and can generate matrices using a pre-determined sequence of notes.

Maintained by Jeffrey A. Dahlke. Last updated 1 years ago.

music music-composition music-theory serialism

12.2 match 2 stars 3.00 score 8 scripts

rstudio

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 13 days ago.

reactive rstudio shiny web-app web-development

1.7 match 5.4k stars 21.28 score 108k scripts 1.8k dependents

yihui

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 3 days ago.

2.0 match 145 stars 18.18 score 916 scripts 4.4k dependents

npm27

lrd:A Package for Processing Lexical Response Data

Lexical response data is a package that can be used for processing cued-recall, free-recall, and sentence responses from memory experiments.

Maintained by Nicholas Maxwell. Last updated 3 years ago.

6.8 match 3 stars 5.30 score 33 scripts

eitsupi

neopolars:R Bindings for the 'polars' Rust Library

Lightning-fast 'DataFrame' library written in 'Rust'. Convert R data to 'Polars' data and vice versa. Perform fast, lazy, larger-than-memory and optimized data queries. 'Polars' is interoperable with the package 'arrow', as both are based on the 'Apache Arrow' Columnar Format.

Maintained by Tatsuya Shima. Last updated 17 hours ago.

rust cargo

7.3 match 40 stars 4.86 score 1 scripts

r-lib

cereal:Serialize 'vctrs' Objects to 'JSON'

The 'vctrs' package provides a concept of vector prototype that can be especially useful when deploying models and code. Serialize these object prototypes to 'JSON' so they can be used to check and coerce data in production systems, and deserialize 'JSON' back to the correct object prototypes.

Maintained by Julia Silge. Last updated 2 years ago.

7.1 match 25 stars 4.93 score 4 scripts 2 dependents

bioc

BiocParallel:Bioconductor facilities for parallel evaluation

This package provides modified versions and novel implementation of functions for parallel evaluation, tailored to use with Bioconductor objects.

Maintained by Martin Morgan. Last updated 25 days ago.

infrastructure bioconductor-package core-package u24ca289073 cpp

2.0 match 67 stars 17.40 score 7.3k scripts 1.1k dependents

r-lib

xml2:Parse XML

Bindings to 'libxml2' for working with XML data using a simple, consistent interface based on 'XPath' expressions. Also supports XML schema validation; for 'XSLT' transformations see the 'xslt' package.

Maintained by Jeroen Ooms. Last updated 2 days ago.

libxml2 xml cpp

1.9 match 220 stars 18.52 score 6.3k scripts 2.3k dependents

harrelfe

Hmisc:Harrell Miscellaneous

Contains many functions useful for data analysis, high-level graphics, utility operations, functions for computing sample size and power, simulation, importing and annotating datasets, imputing missing values, advanced table making, variable clustering, character string manipulation, conversion of R objects to LaTeX and html code, recoding variables, caching, simplified parallel computing, encrypting and decrypting data using a safe workflow, general moving window statistical estimation, and assistance in interpreting principal component analysis.

Maintained by Frank E Harrell Jr. Last updated 2 days ago.

fortran

1.9 match 210 stars 17.61 score 17k scripts 750 dependents

shikokuchuo

nanonext:NNG (Nanomsg Next Gen) Lightweight Messaging Library

R binding for NNG (Nanomsg Next Gen), a successor to ZeroMQ. NNG is a socket library for reliable, high-performance messaging over in-process, IPC, TCP, WebSocket and secure TLS transports. Implements 'Scalability Protocols', a standard for common communications patterns including publish/subscribe, request/reply and service discovery. As its own threaded concurrency framework, provides a toolkit for asynchronous programming and distributed computing. Intuitive 'aio' objects resolve automatically when asynchronous operations complete, and synchronisation primitives allow R to wait upon events signalled by concurrent threads.

Maintained by Charlie Gao. Last updated 1 days ago.

concurrency https ipc-message messaging-library nng rpc socket-communication synchronization-primitives tcp-protocol websocket mbedtls

3.3 match 60 stars 9.81 score 28 scripts 9 dependents

futureverse

marshal:Framework to Marshal Objects to be Used in Another R Process

Some types of R objects can be used only in the R session they were created. If used as-is in another R process, such objects often result in an immediate error or in obscure and hard-to-troubleshoot outcomes. Because of this, they cannot be saved to file and re-used at a later time. They can also not be exported to a worker in parallel processing. These objects are sometimes referred to as non-exportable or non-serializable objects. One solution to this problem is to use "marshalling" to encode the R object into an exportable representation that then can be used to re-create a copy of that object in another R process. This package provides a framework for marshalling and unmarshalling R objects such that they can be transferred using functions such as serialize() and unserialize() of base R.

Maintained by Henrik Bengtsson. Last updated 1 years ago.

marshalling parallel serialization

10.5 match 14 stars 3.10 score 18 scripts

henrikbengtsson

marshal:Framework to Marshal Objects to be Used in Another R Process

Some types of R objects can be used only in the R session they were created. If used as-is in another R process, such objects often result in an immediate error or in obscure and hard-to-troubleshoot outcomes. Because of this, they cannot be saved to file and re-used at a later time. They can also not be exported to a worker in parallel processing. These objects are sometimes referred to as non-exportable or non-serializable objects. One solution to this problem is to use "marshalling" to encode the R object into an exportable representation that then can be used to re-create a copy of that object in another R process. This package provides a framework for marshalling and unmarshalling R objects such that they can be transferred using functions such as serialize() and unserialize() of base R.

Maintained by Henrik Bengtsson. Last updated 1 years ago.

marshalling parallel serialization

10.5 match 14 stars 3.10 score 18 scripts

bioc

RImmPort:RImmPort: Enabling Ready-for-analysis Immunology Research Data

The RImmPort package simplifies access to ImmPort data for analysis in the R environment. It provides a standards-based interface to the ImmPort study data that is in a proprietary format.

Maintained by Zicheng Hu. Last updated 5 months ago.

biomedicalinformatics dataimport datarepresentation

7.4 match 4.33 score 27 scripts

statist7

sitar:Super Imposition by Translation and Rotation Growth Curve Analysis

Functions for fitting and plotting SITAR (Super Imposition by Translation And Rotation) growth curve models. SITAR is a shape-invariant model with a regression B-spline mean curve and subject-specific random effects on both the measurement and age scales. The model was first described by Lindstrom (1995) <doi:10.1002/sim.4780141807> and developed as the SITAR method by Cole et al (2010) <doi:10.1093/ije/dyq115>.

Maintained by Tim Cole. Last updated 2 months ago.

3.6 match 13 stars 8.69 score 58 scripts 3 dependents

sybig

RPPanalyzer:Reads, Annotates, and Normalizes Reverse Phase Protein Array Data

Reads in sample description and slide description files and annotates the expression values taken from GenePix results files (text file format used by many microarray scanner and software providers). After normalization data can be visualized as boxplot, heatmap or dotplot.

Maintained by Torsten Schoeps. Last updated 1 years ago.

8.6 match 1 stars 3.63 score 71 scripts

sfcheung

modelbpp:Model BIC Posterior Probability

Fits the neighboring models of a fitted structural equation model and assesses the model uncertainty of the fitted model based on BIC posterior probabilities, using the method presented in Wu, Cheung, and Leung (2020) <doi:10.1080/00273171.2019.1574546>.

Maintained by Shu Fai Cheung. Last updated 6 months ago.

lavaan model-comparison model-comparison-and-selection model-selection structural-equation-modeling

6.8 match 4.54 score 2 scripts

ropensci

vcr:Record 'HTTP' Calls to Disk

Record test suite 'HTTP' requests and replays them during future runs. A port of the Ruby gem of the same name (<https://github.com/vcr/vcr/>). Works by hooking into the 'webmockr' R package for matching 'HTTP' requests by various rules ('HTTP' method, 'URL', query parameters, headers, body, etc.), and then caching real 'HTTP' responses on disk in 'cassettes'. Subsequent 'HTTP' requests matching any previous requests in the same 'cassette' use a cached 'HTTP' response.

Maintained by Scott Chamberlain. Last updated 12 days ago.

http https api web-services curl mock mocking http-mocking testing testing-tools tdd unit-testing vcr

3.0 match 77 stars 10.06 score 165 scripts

jsugarelli

xmlconvert:Comfortably Converting XML Documents to Dataframes and Vice Versa

Converts XML documents to R dataframes and dataframes to XML documents. A wide variety of options allows for different XML formats and flexible control of the conversion process. Results can be exported to CSV and Excel, if desired. Also converts XML data to R lists.

Maintained by Joachim Zuckarelli. Last updated 4 years ago.

conversion dataframe xml xml-serialization

7.5 match 20 stars 4.00 score 7 scripts

ropensci

geojson:Classes for 'GeoJSON'

Classes for 'GeoJSON' to make working with 'GeoJSON' easier. Includes S3 classes for 'GeoJSON' classes with brief summary output, and a few methods such as extracting and adding bounding boxes, properties, and coordinate reference systems; working with newline delimited 'GeoJSON'; and serializing to/from 'Geobuf' binary 'GeoJSON' format.

Maintained by Michael Sumner. Last updated 2 years ago.

geojson geospatial conversion data input-output bbox polygon geobuf crs ndgeojson spatial

2.8 match 32 stars 10.56 score 166 scripts 14 dependents

jameslamb

lightgbm:Light Gradient Boosting Machine

Tree based algorithms can be improved by introducing boosting frameworks. 'LightGBM' is one such framework, based on Ke, Guolin et al. (2017) <https://papers.nips.cc/paper/6907-lightgbm-a-highly-efficient-gradient-boosting-decision>. This package offers an R interface to work with it. It is designed to be distributed and efficient with the following advantages: 1. Faster training speed and higher efficiency. 2. Lower memory usage. 3. Better accuracy. 4. Parallel learning supported. 5. Capable of handling large-scale data. In recognition of these advantages, 'LightGBM' has been widely-used in many winning solutions of machine learning competitions. Comparison experiments on public datasets suggest that 'LightGBM' can outperform existing boosting frameworks on both efficiency and accuracy, with significantly lower memory consumption. In addition, parallel experiments suggest that in certain circumstances, 'LightGBM' can achieve a linear speed-up in training time by using multiple machines.

Maintained by James Lamb. Last updated 30 days ago.

cpp openmp

3.4 match 1 stars 8.47 score 1.6k scripts 6 dependents

achetverikov

circhelp:Circular Analyses Helper Functions

Light-weight functions for computing descriptive statistics in different circular spaces (e.g., 2pi, 180, or 360 degrees), to handle angle-dependent biases, pad circular data, and more. Specifically aimed for psychologists and neuroscientists analyzing circular data. Basic methods are based on Jammalamadaka and SenGupta (2001) <doi:10.1142/4031>, removal of cardinal biases is based on the approach introduced in van Bergen, Ma, Pratte, & Jehee (2015) <doi:10.1038/nn.4150> and Chetverikov and Jehee (2023) <doi:10.1038/s41467-023-43251-w>.

Maintained by Andrey Chetverikov. Last updated 5 months ago.

6.0 match 1 stars 4.78 score 6 scripts

s-u

Cairo:R Graphics Device using Cairo Graphics Library for Creating High-Quality Bitmap (PNG, JPEG, TIFF), Vector (PDF, SVG, PostScript) and Display (X11 and Win32) Output

R graphics device using cairographics library that can be used to create high-quality vector (PDF, PostScript and SVG) and bitmap output (PNG,JPEG,TIFF), and high-quality rendering in displays (X11 and Win32). Since it uses the same back-end for all output, copying across formats is WYSIWYG. Files are created without the dependence on X11 or other external programs. This device supports alpha channel (semi-transparent drawing) and resulting images can contain transparent and semi-transparent regions. It is ideal for use in server environments (file output) and as a replacement for other devices that don't have Cairo's capabilities such as alpha support or anti-aliasing. Backends are modular such that any subset of backends is supported.

Maintained by Simon Urbanek. Last updated 7 months ago.

freetype cairo libx11 libjpeg-turbo harfbuzz icu tiff

2.3 match 14 stars 12.52 score 3.9k scripts 71 dependents

cran

RJSONIO:Serialize R Objects to JSON, JavaScript Object Notation

This is a package that allows conversion to and from data in Javascript object notation (JSON) format. This allows R objects to be inserted into Javascript/ECMAScript/ActionScript code and allows R programmers to read and convert JSON content to R objects. This is an alternative to rjson package. Originally, that was too slow for converting large R objects to JSON and was not extensible. rjson's performance is now similar to this package, and perhaps slightly faster in some cases. This package uses methods and is readily extensible by defining methods for different classes, vectorized operations, and C code and callbacks to R functions for deserializing JSON objects to R. The two packages intentionally share the same basic interface. This package (RJSONIO) has many additional options to allow customizing the generation and processing of JSON content. This package uses libjson rather than implementing yet another JSON parser. The aim is to support other general projects by building on their work, providing feedback and benefit from their ongoing development.

Maintained by CRAN Team. Last updated 1 years ago.

cpp

4.6 match 2 stars 6.04 score 78 dependents

jsugarelli

xml2relational:Converting XML Documents into Relational Data Models

Import an XML document with nested object structures and convert it into a relational data model. The result is a set of R dataframes with foreign key relationships. The data model and the data can be exported as SQL code of different SQL flavors.

Maintained by Joachim Zuckarelli. Last updated 3 years ago.

relational-database relational-model sql xml xml-serialization

7.5 match 10 stars 3.70 score 5 scripts

coolbutuseless

zstdlite:Fast Compression and Serialization with 'Zstandard' Algorithm

Fast, compressed serialization of R objects using the 'Zstandard' algorithm. The included zstandard connection ('zstdfile()') can be used to read/write compressed data by any code which supports R's built-in 'connections' mechanism. Dictionaries are supported for more effective compression of small data, and functions are provided for training these dictionaries. This implementation provides an R interface to advanced features of the 'Zstandard' 'C' library (available from <https://github.com/facebook/zstd>).

Maintained by Mike Cheng. Last updated 2 months ago.

zstd

5.2 match 30 stars 4.95 score 7 scripts

ramnathv

htmlwidgets:HTML Widgets for R

A framework for creating HTML widgets that render in various contexts including the R console, 'R Markdown' documents, and 'Shiny' web applications.

Maintained by Carson Sievert. Last updated 1 years ago.

1.3 match 791 stars 19.05 score 7.4k scripts 3.1k dependents

tsutatsuta

MDSS:Modeling Human Dentin Serial Sectioning

Modeling microstructures of human tooth dentin and horizontal serial-sectioning of the dentin. Corresponding age range of dentin serial sections, that is used in stable isotope analyses, can be calculated by using this package.

Maintained by Takumi Tsutaya. Last updated 3 years ago.

12.6 match 2.00 score

bioc

Spectra:Spectra Infrastructure for Mass Spectrometry Data

The Spectra package defines an efficient infrastructure for storing and handling mass spectrometry spectra and functionality to subset, process, visualize and compare spectra data. It provides different implementations (backends) to store mass spectrometry data. These comprise backends tuned for fast data access and processing and backends for very large data sets ensuring a small memory footprint.

Maintained by RforMassSpectrometry Package Maintainer. Last updated 9 days ago.

infrastructure proteomics massspectrometry metabolomics bioconductor hacktoberfest mass-spectrometry

1.9 match 41 stars 13.01 score 254 scripts 35 dependents

epiforecasts

EpiSoon:Forecast Cases Using Reproduction Numbers

To forecast the time-varying reproduction number and use this to forecast reported case counts. Includes tools to evaluate a range of models across samples and time series using proper scoring rules.

Maintained by Sam Abbott. Last updated 2 years ago.

case-forecasts forecasts

5.8 match 7 stars 4.26 score 25 scripts 1 dependents

oswaldogressani

EpiLPS:A Fast and Flexible Bayesian Tool for Estimating Epidemiological Parameters

Estimation of epidemiological parameters with Laplacian-P-splines following the methodology of Gressani et al. (2022) <doi:10.1371/journal.pcbi.1010618>.

Maintained by Oswaldo Gressani. Last updated 5 months ago.

openblas cpp openmp

5.3 match 19 stars 4.69 score 17 scripts

franzmohr

prais:Prais-Winsten Estimator for AR(1) Serial Correlation

The Prais-Winsten estimator (Prais & Winsten, 1954) takes into account AR(1) serial correlation of the errors in a linear regression model. The procedure recursively estimates the coefficients and the error autocorrelation of the specified model until sufficient convergence of the AR(1) coefficient is attained.

Maintained by Franz X. Mohr. Last updated 4 months ago.

prais-winsten prais-winsten-estimator

5.1 match 6 stars 4.77 score 48 scripts

ropensci

rdflib:Tools to Manipulate and Query Semantic Data

The Resource Description Framework, or 'RDF' is a widely used data representation model that forms the cornerstone of the Semantic Web. 'RDF' represents data as a graph rather than the familiar data table or rectangle of relational databases. The 'rdflib' package provides a friendly and concise user interface for performing common tasks on 'RDF' data, such as reading, writing and converting between the various serializations of 'RDF' data, including 'rdfxml', 'turtle', 'nquads', 'ntriples', and 'json-ld'; creating new 'RDF' graphs, and performing graph queries using 'SPARQL'. This package wraps the low level 'redland' R package which provides direct bindings to the 'redland' C library. Additionally, the package supports the newer and more developer friendly 'JSON-LD' format through the 'jsonld' package. The package interface takes inspiration from the Python 'rdflib' library.

Maintained by Carl Boettiger. Last updated 7 months ago.

peer-reviewed

2.5 match 57 stars 9.59 score 123 scripts 7 dependents

alexkowa

EnvStats:Package for Environmental Statistics, Including US EPA Guidance

Graphical and statistical analyses of environmental data, with focus on analyzing chemical concentrations and physical parameters, usually in the context of mandated environmental monitoring. Major environmental statistical methods found in the literature and regulatory guidance documents, with extensive help that explains what these methods do, how to use them, and where to find them in the literature. Numerous built-in data sets from regulatory guidance documents and environmental statistics literature. Includes scripts reproducing analyses presented in the book "EnvStats: An R Package for Environmental Statistics" (Millard, 2013, Springer, ISBN 978-1-4614-8455-4, <doi:10.1007/978-1-4614-8456-1>).

Maintained by Alexander Kowarik. Last updated 16 days ago.

1.9 match 26 stars 12.80 score 2.4k scripts 46 dependents

sarahleavitt

nbTransmission:Naive Bayes Transmission Analysis

Estimates the relative transmission probabilities between cases in an infectious disease outbreak or cluster using naive Bayes. Included are various functions to use these probabilities to estimate transmission parameters such as the generation/serial interval and reproductive number as well as finding the contribution of covariates to the probabilities and visualizing results. The ideal use is for an infectious disease dataset with metadata on the majority of cases but more informative data such as contact tracing or pathogen whole genome sequencing on only a subset of cases. For a detailed description of the methods see Leavitt et al. (2020) <doi:10.1093/ije/dyaa031>.

Maintained by Sarah V Leavitt. Last updated 4 days ago.

5.3 match 4 stars 4.45 score 14 scripts

tobadia

R0:Estimation of R0 and Real-Time Reproduction Number from Epidemics

Estimation of reproduction numbers for disease outbreak, based on incidence data. The R0 package implements several documented methods. It is therefore possible to compare estimations according to the methods used. Depending on the methods requested by user, basic reproduction number (commonly denoted as R0) or real-time reproduction number (referred to as R(t)) is computed, along with a 95% Confidence Interval. Plotting outputs will give different graphs depending on the methods requested : basic reproductive number estimations will only show the epidemic curve (collected data) and an adjusted model, whereas real-time methods will also show the R(t) variations throughout the outbreak time period. Sensitivity analysis tools are also provided, and allow for investigating effects of varying Generation Time distribution or time window on estimates.

Maintained by Thomas Obadia. Last updated 18 days ago.

4.0 match 4 stars 5.87 score 186 scripts

johnasher

transplantr:Audit and Research Functions for Transplantation

A set of vectorised functions to calculate medical equations used in transplantation, focused mainly on transplantation of abdominal organs. These functions include donor and recipient risk indices as used by NHS Blood & Transplant, OPTN/UNOS and Eurotransplant, tools for quantifying HLA mismatches, functions for calculating estimated glomerular filtration rate (eGFR), a function to calculate the APRI (AST to platelet ratio) score used in initial screening of suitability to receive a transplant from a hepatitis C seropositive donor and some biochemical unit converter functions. All functions are designed to work with either US or international units. References for the equations are provided in the vignettes and function documentation.

Maintained by John Asher. Last updated 5 years ago.

4.6 match 2 stars 5.05 score 28 scripts

r-simmer

simmer.json:Translates JSON into a simmer environment

Define a simmer simulation problem using JSON syntax. This makes for easy sharing of simulation definitions and for easily digesting a simulation definition through an API.

Maintained by Bart Smeets. Last updated 9 years ago.

discrete-event json serialization simulation

10.0 match 4 stars 2.30 score 4 scripts

bioc

annotate:Annotation for microarrays

Using R enviroments for annotation.

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

annotation pathways go

2.0 match 11.41 score 812 scripts 243 dependents

peekxc

simplextree:Provides Tools for Working with General Simplicial Complexes

Provides an interface to a Simplex Tree data structure, which is a data structure aimed at enabling efficient manipulation of simplicial complexes of any dimension. The Simplex Tree data structure was originally introduced by Jean-Daniel Boissonnat and Clément Maria (2014) <doi:10.1007/s00453-014-9887-3>.

Maintained by Matt Piekenbrock. Last updated 1 years ago.

rcpp simplicial-complex topological-data-analysis topology cpp

5.0 match 15 stars 4.56 score 16 scripts 1 dependents

schochastics

networkdata:Repository of Network Datasets

The package contains a large collection of network dataset with different context. This includes social networks, animal networks and movie networks. All datasets are in 'igraph' format.

Maintained by David Schoch. Last updated 12 months ago.

dataset network-analysis

4.5 match 143 stars 5.01 score 143 scripts

tercen

rtson:Typed JSON

TSON, short for Typed JSON, is a binary-encoded serialization of JSON like document that support JavaScript typed data (https://github.com/tercen/TSON).

Maintained by Alexandre Maurel. Last updated 6 years ago.

5.0 match 17 stars 4.47 score 35 scripts

sgiannerini

tseriesEntropy:Entropy Based Analysis and Tests for Time Series

Implements an Entropy measure of dependence based on the Bhattacharya-Hellinger-Matusita distance. Can be used as a (nonlinear) autocorrelation/crosscorrelation function for continuous and categorical time series. The package includes tests for serial dependence and nonlinearity based on it. Some routines have a parallel version that can be used in a multicore/cluster environment. The package makes use of S4 classes.

Maintained by Simone Giannerini. Last updated 4 years ago.

fortran

7.5 match 3.00 score 20 scripts

bioc

miaViz:Microbiome Analysis Plotting and Visualization

The miaViz package implements functions to visualize TreeSummarizedExperiment objects especially in the context of microbiome analysis. Part of the mia family of R/Bioconductor packages.

Maintained by Tuomas Borman. Last updated 23 hours ago.

microbiome software visualization bioconductor microbiome-analysis plotting

2.6 match 10 stars 8.65 score 81 scripts 1 dependents

cran

mcmc:Markov Chain Monte Carlo

Simulates continuous distributions of random vectors using Markov chain Monte Carlo (MCMC). Users specify the distribution by an R function that evaluates the log unnormalized density. Algorithms are random walk Metropolis algorithm (function metrop), simulated tempering (function temper), and morphometric random walk Metropolis (Johnson and Geyer, 2012, <doi:10.1214/12-AOS1048>, function morph.metrop), which achieves geometric ergodicity by change of variable.

Maintained by Charles J. Geyer. Last updated 1 years ago.

3.0 match 7.41 score 154 dependents

dtkaplan

LSTbook:Data and Software for "Lessons in Statistical Thinking"

"Lessons in Statistical Thinking" D.T. Kaplan (2014) <https://dtkaplan.github.io/Lessons-in-statistical-thinking/> is a textbook for a first or second course in statistics that embraces data wrangling, causal reasoning, modeling, statistical adjustment, and simulation. 'LSTbook' supports the student-centered, tidy, pipeline-oriented computing style featured in the book.

Maintained by Daniel Kaplan. Last updated 15 hours ago.

3.5 match 4 stars 6.29 score 27 scripts

jeffreyracine

np:Nonparametric Kernel Smoothing Methods for Mixed Data Types

Nonparametric (and semiparametric) kernel methods that seamlessly handle a mix of continuous, unordered, and ordered factor data types. We would like to gratefully acknowledge support from the Natural Sciences and Engineering Research Council of Canada (NSERC, <https://www.nserc-crsng.gc.ca/>), the Social Sciences and Humanities Research Council of Canada (SSHRC, <https://www.sshrc-crsh.gc.ca/>), and the Shared Hierarchical Academic Research Computing Network (SHARCNET, <https://sharcnet.ca/>). We would also like to acknowledge the contributions of the GNU GSL authors. In particular, we adapt the GNU GSL B-spline routine gsl_bspline.c adding automated support for quantile knots (in addition to uniform knots), providing missing functionality for derivatives, and for extending the splines beyond their endpoints.

Maintained by Jeffrey S. Racine. Last updated 1 months ago.

1.7 match 49 stars 12.64 score 672 scripts 44 dependents

s-fleck

lgrExtra:Extra Appenders for 'lgr'

Additional appenders for the logging package 'lgr' that support logging to databases, email and push notifications.

Maintained by Stefan Fleck. Last updated 6 months ago.

6.0 match 7 stars 3.54 score 3 scripts

cmjt

stelfi:Hawkes and Log-Gaussian Cox Point Processes Using Template Model Builder

Fit Hawkes and log-Gaussian Cox process models with extensions. Introduced in Hawkes (1971) <doi:10.2307/2334319> a Hawkes process is a self-exciting temporal point process where the occurrence of an event immediately increases the chance of another. We extend this to consider self-inhibiting process and a non-homogeneous background rate. A log-Gaussian Cox process is a Poisson point process where the log-intensity is given by a Gaussian random field. We extend this to a joint likelihood formulation fitting a marked log-Gaussian Cox model. In addition, the package offers functionality to fit self-exciting spatiotemporal point processes. Models are fitted via maximum likelihood using 'TMB' (Template Model Builder). Where included 1) random fields are assumed to be Gaussian and are integrated over using the Laplace approximation and 2) a stochastic partial differential equation model, introduced by Lindgren, Rue, and Lindström. (2011) <doi:10.1111/j.1467-9868.2011.00777.x>, is defined for the field(s).

Maintained by Charlotte M. Jones-Todd. Last updated 5 months ago.

cpp openmp

3.6 match 8 stars 5.90 score 4 scripts

bioc

rhdf5:R Interface to HDF5

This package provides an interface between HDF5 and R. HDF5's main features are the ability to store and access very large and/or complex datasets and a wide variety of metadata on mass storage (disk) through a completely portable file format. The rhdf5 package is thus suited for the exchange of large and/or complex datasets between R and other software package, and for letting R applications work on datasets that are larger than the available RAM.

Maintained by Mike Smith. Last updated 2 months ago.

infrastructure dataimport hdf5 rhdf5 openssl curl zlib cpp

1.3 match 62 stars 15.93 score 4.2k scripts 232 dependents

johnihrie

MPN:Most Probable Number and Other Microbial Enumeration Techniques

Calculates the Most Probable Number (MPN) to quantify the concentration (density) of microbes in serial dilutions of a laboratory sample (described in Jarvis, 2010 <doi:10.1111/j.1365-2672.2010.04792.x>). Also calculates the Aerobic Plate Count (APC) for similar microbial enumeration experiments.

Maintained by John Ihrie. Last updated 5 months ago.

6.4 match 3.30 score 10 scripts

amutak

cosinor2:Extended Tools for Cosinor Analysis of Rhythms

Statistical procedures for calculating population–mean cosinor, non–stationary cosinor, estimation of best–fitting period, tests of population rhythm differences and more. See Cornélissen, G. (2014). <doi:10.1186/1742-4682-11-16>.

Maintained by Augustin Mutak. Last updated 6 years ago.

3.8 match 5 stars 5.63 score 19 scripts 5 dependents

ropensci

phylotaR:Automated Phylogenetic Sequence Cluster Identification from 'GenBank'

A pipeline for the identification, within taxonomic groups, of orthologous sequence clusters from 'GenBank' <https://www.ncbi.nlm.nih.gov/genbank/> as the first step in a phylogenetic analysis. The pipeline depends on a local alignment search tool and is, therefore, not dependent on differences in gene naming conventions and naming errors.

Maintained by Shixiang Wang. Last updated 8 months ago.

blastn genbank peer-reviewed phylogenetics sequence-alignment

3.6 match 23 stars 5.86 score 156 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 4 days ago.

array hdfs s3 storage-manager tiledb cpp

1.8 match 107 stars 11.96 score 306 scripts 4 dependents

apache

nanoarrow:Interface to the 'nanoarrow' 'C' Library

Provides an 'R' interface to the 'nanoarrow' 'C' library and the 'Apache Arrow' application binary interface. Functions to import and export 'ArrowArray', 'ArrowSchema', and 'ArrowArrayStream' 'C' structures to and from 'R' objects are provided alongside helpers to facilitate zero-copy data transfer among 'R' bindings to libraries implementing the 'Arrow' 'C' data interface.

Maintained by Dewey Dunnington. Last updated 1 days ago.

cpp

1.8 match 183 stars 11.79 score 37 scripts 27 dependents

chrisaberson

pwr2ppl:Power Analyses for Common Designs (Power to the People)

Statistical power analysis for designs including t-tests, correlations, multiple regression, ANOVA, mediation, and logistic regression. Functions accompany Aberson (2019) <doi:10.4324/9781315171500>.

Maintained by Chris Aberson. Last updated 3 years ago.

5.0 match 17 stars 4.16 score 17 scripts

rpolars

polars:Lightning-Fast 'DataFrame' Library

Lightning-fast 'DataFrame' library written in 'Rust'. Convert R data to 'Polars' data and vice versa. Perform fast, lazy, larger-than-memory and optimized data queries. 'Polars' is interoperable with the package 'arrow', as both are based on the 'Apache Arrow' Columnar Format.

Maintained by Soren Welling. Last updated 3 days ago.

arrow polars rust

1.7 match 499 stars 12.01 score 1.0k scripts 2 dependents

seth-mg

rosetteApi:'Rosette' API

'Rosette' is an API for multilingual text analysis and information extraction. More information can be found at <https://developer.rosette.com>.

Maintained by Seth Gransky. Last updated 5 years ago.

7.5 match 2.70 score 4 scripts

bioc

gwascat:representing and modeling data in the EMBL-EBI GWAS catalog

Represent and model data in the EMBL-EBI GWAS catalog.

Maintained by VJ Carey. Last updated 5 months ago.

genetics

3.3 match 6.05 score 110 scripts 2 dependents

bioc

graph:graph: A package to handle graph data structures

A package that implements some simple graph handling capabilities.

Maintained by Bioconductor Package Maintainer. Last updated 10 days ago.

graphandnetwork

1.7 match 11.78 score 764 scripts 342 dependents

cynkra

dm:Relational Data Models

Provides tools for working with multiple related tables, stored as data frames or in a relational database. Multiple tables (data and metadata) are stored in a compound object, which can then be manipulated with a pipe-friendly syntax.

Maintained by Kirill Müller. Last updated 2 months ago.

data-model data-warehousing datawarehousing dbi dbplyr relational-databases

1.3 match 511 stars 14.81 score 410 scripts 8 dependents

bioc

MuData:Serialization for MultiAssayExperiment Objects

Save MultiAssayExperiments to h5mu files supported by muon and mudata. Muon is a Python framework for multimodal omics data analysis. It uses an HDF5-based format for data storage.

Maintained by Ilia Kats. Last updated 20 days ago.

dataimport anndata bioconductor mudata multi-omics multimodal-omics scrna-seq

3.3 match 5 stars 5.89 score 26 scripts

bioc

matter:Out-of-core statistical computing and signal processing

Toolbox for larger-than-memory scientific computing and visualization, providing efficient out-of-core data structures using files or shared memory, for dense and sparse vectors, matrices, and arrays, with applications to nonuniformly sampled signals and images.

Maintained by Kylie A. Bemis. Last updated 3 months ago.

infrastructure datarepresentation dataimport dimensionreduction preprocessing cpp

2.0 match 57 stars 9.52 score 64 scripts 2 dependents

david-cortes

isotree:Isolation-Based Outlier Detection

Fast and multi-threaded implementation of isolation forest (Liu, Ting, Zhou (2008) <doi:10.1109/ICDM.2008.17>), extended isolation forest (Hariri, Kind, Brunner (2018) <doi:10.48550/arXiv.1811.02141>), SCiForest (Liu, Ting, Zhou (2010) <doi:10.1007/978-3-642-15883-4_18>), fair-cut forest (Cortes (2021) <doi:10.48550/arXiv.2110.13402>), robust random-cut forest (Guha, Mishra, Roy, Schrijvers (2016) <http://proceedings.mlr.press/v48/guha16.html>), and customizable variations of them, for isolation-based outlier detection, clustered outlier detection, distance or similarity approximation (Cortes (2019) <doi:10.48550/arXiv.1910.12362>), isolation kernel calculation (Ting, Zhu, Zhou (2018) <doi:10.1145/3219819.3219990>), and imputation of missing values (Cortes (2019) <doi:10.48550/arXiv.1911.06646>), based on random or guided decision tree splitting, and providing different metrics for scoring anomalies based on isolation depth or density (Cortes (2021) <doi:10.48550/arXiv.2111.11639>). Provides simple heuristics for fitting the model to categorical columns and handling missing data, and offers options for varying between random and guided splits, and for using different splitting criteria.

Maintained by David Cortes. Last updated 14 days ago.

anomaly-detection imputation isolation-forest outlier-detection cpp openmp

1.8 match 203 stars 10.41 score 115 scripts 6 dependents

rcurtin

mlpack:'Rcpp' Integration for the 'mlpack' Library

A fast, flexible machine learning library, written in C++, that aims to provide fast, extensible implementations of cutting-edge machine learning algorithms. See also Curtin et al. (2023) <doi:10.21105/joss.05026>.

Maintained by Ryan Curtin. Last updated 3 months ago.

openblas cpp openmp

4.9 match 3.71 score 20 scripts 8 dependents

neonscience

neonUtilities:Utilities for Working with NEON Data

NEON data packages can be accessed through the NEON Data Portal <https://www.neonscience.org> or through the NEON Data API (see <https://data.neonscience.org/data-api> for documentation). Data delivered from the Data Portal are provided as monthly zip files packaged within a parent zip file, while individual files can be accessed from the API. This package provides tools that aid in discovering, downloading, and reformatting data prior to use in analyses. This includes downloading data via the API, merging data tables by type, and converting formats. For more information, see the readme file at <https://github.com/NEONScience/NEON-utilities>.

Maintained by Claire Lunch. Last updated 1 months ago.

1.7 match 57 stars 10.66 score 944 scripts 15 dependents

bnaras

distcomp:Computations over Distributed Data without Aggregation

Implementing algorithms and fitting models when sites (possibly remote) share computation summaries rather than actual data over HTTP with a master R process (using 'opencpu', for example). A stratified Cox model and a singular value decomposition are provided. The former makes direct use of code from the R 'survival' package. (That is, the underlying Cox model code is derived from that in the R 'survival' package.) Sites may provide data via several means: CSV files, Redcap API, etc. An extensible design allows for new methods to be added in the future and includes facilities for local prototyping and testing. Web applications are provided (via 'shiny') for the implemented methods to help in designing and deploying the computations.

Maintained by Balasubramanian Narasimhan. Last updated 9 months ago.

3.3 match 9 stars 5.33 score 47 scripts

lightbluetitan

crimedatasets:A Comprehensive Collection of Crime-Related Datasets

A comprehensive collection of datasets exclusively focused on crimes, criminal activities, and related topics. This package serves as a valuable resource for researchers, analysts, and students interested in crime analysis, criminology, social and economic studies related to criminal behavior. Datasets span global and local contexts, with a mix of tabular and spatial data.

Maintained by Renzo Caceres Rossi. Last updated 3 months ago.

3.6 match 8 stars 4.90 score 3 scripts

pecanproject

PEcAn.remote:PEcAn Model Execution Utilities

This package contains utilities for communicating with and executing code on local and remote hosts. In particular, it has PEcAn-specific utilities for starting ecosystem model runs.

Maintained by Rob Kooper. Last updated 2 days ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants

1.8 match 216 stars 9.66 score 13 scripts 32 dependents

cloudyr

googleComputeEngineR:R Interface with Google Compute Engine

Interact with the 'Google Compute Engine' API in R. Lets you create, start and stop instances in the 'Google Cloud'. Support for preconfigured instances, with templates for common R needs.

Maintained by Mark Edmondson. Last updated 13 hours ago.

api cloud-computing cloudyr google-cloud googleauthr launching-virtual-machines

1.8 match 152 stars 9.73 score 235 scripts

sym33

RecordLinkage:Record Linkage Functions for Linking and Deduplicating Data Sets

Provides functions for linking and deduplicating data sets. Methods based on a stochastic approach are implemented as well as classification algorithms from the machine learning domain. For details, see our paper "The RecordLinkage Package: Detecting Errors in Data" Sariyar M / Borg A (2010) <doi:10.32614/RJ-2010-017>.

Maintained by Murat Sariyar. Last updated 2 years ago.

1.9 match 6 stars 9.00 score 454 scripts 8 dependents

swihart

repeated:Non-Normal Repeated Measurements Models

Various functions to fit models for non-normal repeated measurements, such as Binary Random Effects Models with Two Levels of Nesting, Bivariate Beta-binomial Regression Models, Marginal Bivariate Binomial Regression Models, Cormack capture-recapture models, Continuous-time Hidden Markov Chain Models, Discrete-time Hidden Markov Chain Models, Changepoint Location Models using a Continuous-time Two-state Hidden Markov Chain, generalized nonlinear autoregression models, multivariate Gaussian copula models, generalized non-linear mixed models with one random effect, generalized non-linear mixed models using h-likelihood for one random effect, Repeated Measurements Models for Counts with Frailty or Serial Dependence, Repeated Measurements Models for Continuous Variables with Frailty or Serial Dependence, Ordinal Random Effects Models with Dropouts, marginal homogeneity models for square contingency tables, correlated negative binomial models with Kalman update. References include Lindsey's text books, JK Lindsey (2001) <isbn:10-0198508123> and JK Lindsey (1999) <isbn:10-0198505590>.

Maintained by Bruce Swihart. Last updated 5 months ago.

fortran

4.2 match 3.97 score 31 scripts

bodkan

slendr:A Simulation Framework for Spatiotemporal Population Genetics

A framework for simulating spatially explicit genomic data which leverages real cartographic information for programmatic and visual encoding of spatiotemporal population dynamics on real geographic landscapes. Population genetic models are then automatically executed by the 'SLiM' software by Haller et al. (2019) <doi:10.1093/molbev/msy228> behind the scenes, using a custom built-in simulation 'SLiM' script. Additionally, fully abstract spatial models not tied to a specific geographic location are supported, and users can also simulate data from standard, non-spatial, random-mating models. These can be simulated either with the 'SLiM' built-in back-end script, or using an efficient coalescent population genetics simulator 'msprime' by Baumdicker et al. (2022) <doi:10.1093/genetics/iyab229> with a custom-built 'Python' script bundled with the R package. Simulated genomic data is saved in a tree-sequence format and can be loaded, manipulated, and summarised using tree-sequence functionality via an R interface to the 'Python' module 'tskit' by Kelleher et al. (2019) <doi:10.1038/s41588-019-0483-y>. Complete model configuration, simulation and analysis pipelines can be therefore constructed without a need to leave the R environment, eliminating friction between disparate tools for population genetic simulations and data analysis.

Maintained by Martin Petr. Last updated 12 days ago.

popgen population-genetics simulations spatial-statistics

1.8 match 56 stars 9.15 score 88 scripts

rte-antares-rpackage

antaresEditObject:Edit an 'Antares' Simulation

Edit an 'Antares' simulation before running it : create new areas, links, thermal clusters or binding constraints or edit existing ones. Update 'Antares' general & optimization settings. 'Antares' is an open source power system generator, more information available here : <https://antares-simulator.org/>.

Maintained by Tatiana Vargas. Last updated 27 days ago.

antares-simulation cluster energy monte-carlo-simulation rte

1.9 match 8 stars 8.76 score 101 scripts

lalvarezmat

EpiInvert:Variational Techniques in Epidemiology

Using variational techniques we address some epidemiological problems as the incidence curve decomposition by inverting the renewal equation as described in Alvarez et al. (2021) <doi:10.1073/pnas.2105112118> and Alvarez et al. (2022) <doi:10.3390/biology11040540> or the estimation of the functional relationship between epidemiological indicators. We also propose a learning method for the short time forecast of the trend incidence curve as described in Morel et al. (2022) <doi:10.1101/2022.11.05.22281904>.

Maintained by Luis Alvarez. Last updated 1 years ago.

cpp

5.2 match 3 stars 3.18 score 3 scripts

tdhock

directlabels:Direct Labels for Multicolor Plots

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

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

1.5 match 83 stars 10.62 score 1.8k scripts 16 dependents

aagillet

MorphoRegions:Analysis of Regionalization Patterns in Serially Homologous Structures

Computes the optimal number of regions (or subdivisions) and their position in serial structures without a priori assumptions and to visualize the results. After reducing data dimensionality with the built-in function for data ordination, regions are fitted as segmented linear regressions along the serial structure. Every region boundary position and increasing number of regions are iteratively fitted and the best model (number of regions and boundary positions) is selected with an information criterion. This package expands on the previous 'regions' package (Jones et al. (2018) <doi:10.1126/science.aar3126>) with improved computation and more fitting and plotting options.

Maintained by Amandine Gillet. Last updated 4 months ago.

3.7 match 4.30 score 6 scripts

bioc

scviR:experimental inferface from R to scvi-tools

This package defines interfaces from R to scvi-tools. A vignette works through the totalVI tutorial for analyzing CITE-seq data. Another vignette compares outputs of Chapter 12 of the OSCA book with analogous outputs based on totalVI quantifications. Future work will address other components of scvi-tools, with a focus on building understanding of probabilistic methods based on variational autoencoders.

Maintained by Vincent Carey. Last updated 5 months ago.

infrastructure singlecell dataimport bioconductor cite-seq scverse

2.8 match 6 stars 5.60 score 11 scripts

sritchie73

NetRep:Permutation Testing Network Module Preservation Across Datasets

Functions for assessing the replication/preservation of a network module's topology across datasets through permutation testing; Ritchie et al. (2015) <doi: 10.1016/j.cels.2016.06.012>.

Maintained by Scott Ritchie. Last updated 4 years ago.

openblas cpp

2.3 match 12 stars 6.84 score 16 scripts 3 dependents

markusfritsch

pdynmc:Moment Condition Based Estimation of Linear Dynamic Panel Data Models

Linear dynamic panel data modeling based on linear and nonlinear moment conditions as proposed by Holtz-Eakin, Newey, and Rosen (1988) <doi:10.2307/1913103>, Ahn and Schmidt (1995) <doi:10.1016/0304-4076(94)01641-C>, and Arellano and Bover (1995) <doi:10.1016/0304-4076(94)01642-D>. Estimation of the model parameters relies on the Generalized Method of Moments (GMM) and instrumental variables (IV) estimation, numerical optimization (when nonlinear moment conditions are employed) and the computation of closed form solutions (when estimation is based on linear moment conditions). One-step, two-step and iterated estimation is available. For inference and specification testing, Windmeijer (2005) <doi:10.1016/j.jeconom.2004.02.005> and doubly corrected standard errors (Hwang, Kang, Lee, 2021 <doi:10.1016/j.jeconom.2020.09.010>) are available. Additionally, serial correlation tests, tests for overidentification, and Wald tests are provided. Functions for visualizing panel data structures and modeling results obtained from GMM estimation are also available. The plot methods include functions to plot unbalanced panel structure, coefficient ranges and coefficient paths across GMM iterations (the latter is implemented according to the plot shown in Hansen and Lee, 2021 <doi:10.3982/ECTA16274>). For a more detailed description of the GMM-based functionality, please see Fritsch, Pua, Schnurbus (2021) <doi:10.32614/RJ-2021-035>. For more details on the IV-based estimation routines, see Fritsch, Pua, and Schnurbus (WP, 2024) and Han and Phillips (2010) <doi:10.1017/S026646660909063X>.

Maintained by Markus Fritsch. Last updated 13 days ago.

2.3 match 4 stars 6.65 score 106 scripts

cran

XML:Tools for Parsing and Generating XML Within R and S-Plus

Many approaches for both reading and creating XML (and HTML) documents (including DTDs), both local and accessible via HTTP or FTP. Also offers access to an 'XPath' "interpreter".

Maintained by CRAN Team. Last updated 2 months ago.

libxml2

1.7 match 3 stars 8.87 score 1.3k dependents

pecanproject

PEcAn.LPJGUESS:PEcAn Package for Integration of the LPJ-GUESS Model

This module provides functions to link LPJ-GUESS to PEcAn.

Maintained by Istem Fer. Last updated 2 days ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants cpp

2.0 match 216 stars 7.56 score 1 scripts

snoweye

pbdZMQ:Programming with Big Data -- Interface to 'ZeroMQ'

'ZeroMQ' is a well-known library for high-performance asynchronous messaging in scalable, distributed applications. This package provides high level R wrapper functions to easily utilize 'ZeroMQ'. We mainly focus on interactive client/server programming frameworks. For convenience, a minimal 'ZeroMQ' library (4.2.2) is shipped with 'pbdZMQ', which can be used if no system installation of 'ZeroMQ' is available. A few wrapper functions compatible with 'rzmq' are also provided.

Maintained by Wei-Chen Chen. Last updated 6 months ago.

zeromq3

1.5 match 17 stars 9.92 score 46 scripts 26 dependents

bioc

tenXplore:ontological exploration of scRNA-seq of 1.3 million mouse neurons from 10x genomics

Perform ontological exploration of scRNA-seq of 1.3 million mouse neurons from 10x genomics.

Maintained by VJ Carey. Last updated 5 months ago.

immunooncology dimensionreduction principalcomponent transcriptomics singlecell

3.6 match 4.18 score 7 scripts

vegawidget

vegawidget:'Htmlwidget' for 'Vega' and 'Vega-Lite'

'Vega' and 'Vega-Lite' parse text in 'JSON' notation to render chart-specifications into 'HTML'. This package is used to facilitate the rendering. It also provides a means to interact with signals, events, and datasets in a 'Vega' chart using 'JavaScript' or 'Shiny'.

Maintained by Ian Lyttle. Last updated 1 years ago.

1.8 match 68 stars 8.04 score 49 scripts 4 dependents

datastorm-open

rAmCharts:JavaScript Charts Tool

Provides an R interface for using 'AmCharts' Library. Based on 'htmlwidgets', it provides a global architecture to generate 'JavaScript' source code for charts. Most of classes in the library have their equivalent in R with S4 classes; for those classes, not all properties have been referenced but can easily be added in the constructors. Complex properties (e.g. 'JavaScript' object) can be passed as named list. See examples at <https://datastorm-open.github.io/introduction_ramcharts/> and <https://www.amcharts.com/> for more information about the library. The package includes the free version of 'AmCharts' Library. Its only limitation is a small link to the web site displayed on your charts. If you enjoy this library, do not hesitate to refer to this page <https://www.amcharts.com/online-store/> to purchase a licence, and thus support its creators and get a period of Priority Support. See also <https://www.amcharts.com/about/> for more information about 'AmCharts' company.

Maintained by Benoit Thieurmel. Last updated 2 months ago.

2.0 match 49 stars 7.17 score 153 scripts 4 dependents

hrbrmstr

tdigest:Wicked Fast, Accurate Quantiles Using t-Digests

The t-Digest construction algorithm, by Dunning et al., (2019) <doi:10.48550/arXiv.1902.04023>, uses a variant of 1-dimensional k-means clustering to produce a very compact data structure that allows accurate estimation of quantiles. This t-Digest data structure can be used to estimate quantiles, compute other rank statistics or even to estimate related measures like trimmed means. The advantage of the t-Digest over previous digests for this purpose is that the t-Digest handles data with full floating point resolution. The accuracy of quantile estimates produced by t-Digests can be orders of magnitude more accurate than those produced by previous digest algorithms. Methods are provided to create and update t-Digests and retrieve quantiles from the accumulated distributions.

Maintained by Bob Rudis. Last updated 9 months ago.

quantile t-digest

2.6 match 37 stars 5.35 score 10 scripts 4 dependents

xinweihuang-stat

Copula.Markov.survival:Copula Markov Model with Dependent Censoring

Perform likelihood estimation and corresponding analysis under the copula-based Markov chain model for serially dependent event times with a dependent terminal event. Available are statistical methods in Huang, Wang and Emura (2020, JJSD accepted).

Maintained by Xin-Wei Huang. Last updated 5 years ago.

13.5 match 1.00 score

bioc

ORFik:Open Reading Frames in Genomics

R package for analysis of transcript and translation features through manipulation of sequence data and NGS data like Ribo-Seq, RNA-Seq, TCP-Seq and CAGE. It is generalized in the sense that any transcript region can be analysed, as the name hints to it was made with investigation of ribosomal patterns over Open Reading Frames (ORFs) as it's primary use case. ORFik is extremely fast through use of C++, data.table and GenomicRanges. Package allows to reassign starts of the transcripts with the use of CAGE-Seq data, automatic shifting of RiboSeq reads, finding of Open Reading Frames for whole genomes and much more.

Maintained by Haakon Tjeldnes. Last updated 27 days ago.

immunooncology software sequencing riboseq rnaseq functionalgenomics coverage alignment dataimport cpp

1.3 match 33 stars 10.63 score 115 scripts 2 dependents

trevorld

datetimeoffset:Datetimes with Optional UTC Offsets and/or Heterogeneous Time Zones

Supports import/export for a number of datetime string standards and R datetime classes often including lossless re-export of any original reduced precision including 'ISO 8601' <https://en.wikipedia.org/wiki/ISO_8601> and 'pdfmark' <https://opensource.adobe.com/dc-acrobat-sdk-docs/library/pdfmark/> datetime strings. Supports local/global datetimes with optional UTC offsets and/or (possibly heterogeneous) time zones with up to nanosecond precision.

Maintained by Trevor L. Davis. Last updated 2 months ago.

2.5 match 6 stars 5.26 score 1 scripts 2 dependents

mikejohnson51

climateR:climateR

Find, subset, and retrive geospatial data by AOI.

Maintained by Mike Johnson. Last updated 3 months ago.

aoi climate dataset geospatial gridded-climate-data weather

1.5 match 187 stars 8.74 score 156 scripts 1 dependents

jaredsmurray

bcf:Causal Inference for a Binary Treatment and Continuous Outcome using Bayesian Causal Forests

Causal inference for a binary treatment and continuous outcome using Bayesian Causal Forests. See Hahn, Murray and Carvalho (2020) <https://projecteuclid.org/journals/bayesian-analysis/volume-15/issue-3/Bayesian-Regression-Tree-Models-for-Causal-Inference--Regularization-Confounding/10.1214/19-BA1195.full> for additional information. This implementation relies on code originally accompanying Pratola et. al. (2013) <arXiv:1309.1906>.

Maintained by Jared S. Murray. Last updated 1 years ago.

openblas cpp

1.6 match 41 stars 8.12 score 46 scripts

stephematician

literanger:Random Forests for Multiple Imputation Based on 'ranger'

An updated implementation of R package 'ranger' by Wright et al, (2017) <doi:10.18637/jss.v077.i01> for training and predicting from random forests, particularly suited to high-dimensional data, and for embedding in 'Multiple Imputation by Chained Equations' (MICE) by van Buuren (2007) <doi:10.1177/0962280206074463>. Ensembles of classification and regression trees are currently supported. Sparse data of class 'dgCMatrix' (R package 'Matrix') can be directly analyzed. Conventional bagged predictions are available alongside an efficient prediction for MICE via the algorithm proposed by Doove et al (2014) <doi:10.1016/j.csda.2013.10.025>. Survival and probability forests are not supported in the update, nor is data of class 'gwaa.data' (R package 'GenABEL'); use the original 'ranger' package for these analyses.

Maintained by Stephen Wade. Last updated 6 months ago.

cpp

3.9 match 3.26 score 2 scripts

namgillee

VARshrink:Shrinkage Estimation Methods for Vector Autoregressive Models

Vector autoregressive (VAR) model is a fundamental and effective approach for multivariate time series analysis. Shrinkage estimation methods can be applied to high-dimensional VAR models with dimensionality greater than the number of observations, contrary to the standard ordinary least squares method. This package is an integrative package delivering nonparametric, parametric, and semiparametric methods in a unified and consistent manner, such as the multivariate ridge regression in Golub, Heath, and Wahba (1979) <doi:10.2307/1268518>, a James-Stein type nonparametric shrinkage method in Opgen-Rhein and Strimmer (2007) <doi:10.1186/1471-2105-8-S2-S3>, and Bayesian estimation methods using noninformative and informative priors in Lee, Choi, and S.-H. Kim (2016) <doi:10.1016/j.csda.2016.03.007> and Ni and Sun (2005) <doi:10.1198/073500104000000622>.

Maintained by Namgil Lee. Last updated 5 years ago.

4.0 match 3 stars 3.18 score 6 scripts

philips-software

latrend:A Framework for Clustering Longitudinal Data

A framework for clustering longitudinal datasets in a standardized way. The package provides an interface to existing R packages for clustering longitudinal univariate trajectories, facilitating reproducible and transparent analyses. Additionally, standard tools are provided to support cluster analyses, including repeated estimation, model validation, and model assessment. The interface enables users to compare results between methods, and to implement and evaluate new methods with ease. The 'akmedoids' package is available from <https://github.com/MAnalytics/akmedoids>.

Maintained by Niek Den Teuling. Last updated 2 months ago.

cluster-analysis clustering-evaluation clustering-methods data-science longitudinal-clustering longitudinal-data mixture-models time-series-analysis

1.8 match 30 stars 6.77 score 26 scripts

mrc-ide

epireview:Tools to update and summarise the latest pathogen data from the Pathogen Epidemiology Review Group (PERG)

Contains the latest open access pathogen data from the Pathogen Epidemiology Review Group (PERG). Tools are available to update pathogen databases with new peer-reviewed data as it becomes available, and to summarise the latest data using tables and figures.

Maintained by Sangeeta Bhatia. Last updated 2 days ago.

1.8 match 30 stars 6.76 score 6 scripts

zdk123

pulsar:Parallel Utilities for Lambda Selection along a Regularization Path

Model selection for penalized graphical models using the Stability Approach to Regularization Selection ('StARS'), with options for speed-ups including Bounded StARS (B-StARS), batch computing, and other stability metrics (e.g., graphlet stability G-StARS). Christian L. Müller, Richard Bonneau, Zachary Kurtz (2016) <arXiv:1605.07072>.

Maintained by Zachary Kurtz. Last updated 1 years ago.

graphical-models

1.9 match 10 stars 6.16 score 65 scripts

dmmelamed

catregs:Post-Estimation Functions for Generalized Linear Mixed Models

Several functions for working with mixed effects regression models for limited dependent variables. The functions facilitate post-estimation of model predictions or margins, and comparisons between model predictions for assessing or probing moderation. Additional helper functions facilitate model comparisons and implements simulation-based inference for model predictions of alternative-specific outcome models. See also, Melamed and Doan (2024, ISBN: 978-1032509518).

Maintained by David Melamed. Last updated 8 months ago.

3.4 match 3.40 score 28 scripts

thiloklein

matchingMarkets:Analysis of Stable Matchings

Implements structural estimators to correct for the sample selection bias from observed outcomes in matching markets. This includes one-sided matching of agents into groups as well as two-sided matching of students to schools. The package also contains algorithms to find stable matchings in the three most common matching problems: the stable roommates problem, the college admissions problem, and the house allocation problem.

Maintained by Thilo Klein. Last updated 5 years ago.

openblas cpp openmp openjdk

1.9 match 40 stars 5.99 score 49 scripts

tonyfischetti

libbib:Various Utilities for Library Science/Assessment and Cataloging

Provides functions for validating and normalizing bibliographic codes such as ISBN, ISSN, and LCCN. Also includes functions to communicate with the WorldCat API, translate Call numbers (Library of Congress and Dewey Decimal) to their subject classifications or subclassifications, and provides various loadable data files such call number / subject crosswalks and code tables.

Maintained by Tony Fischetti. Last updated 2 years ago.

3.5 match 3.20 score 32 scripts

rformassspectrometry

MsIO:Serializing and restoring/importing mass spectrometry data objects

The serialization mechanism of R allows to save and load R data objects in a binary format, that can however not be read by other programming languages or software. The MsIO package supports serializing and restoring or importing mass spectrometry data objects to and from language agnostic file formats. A variety of different file types, including HDF5 and JSON-based formats defined by the Bioconductor *alabaster* package are supported. The file type can be defined and configured through a second argument `param` of the export/import methods.

Maintained by Johannes Rainer. Last updated 5 months ago.

infrastructure massspectrometry metabolomics dataimport proteomics mass-spectrometry

3.6 match 2 stars 3.08 score 5 scripts

bioc

ontoProc:processing of ontologies of anatomy, cell lines, and so on

Support harvesting of diverse bioinformatic ontologies, making particular use of the ontologyIndex package on CRAN. We provide snapshots of key ontologies for terms about cells, cell lines, chemical compounds, and anatomy, to help analyze genome-scale experiments, particularly cell x compound screens. Another purpose is to strengthen development of compelling use cases for richer interfaces to emerging ontologies.

Maintained by Vincent Carey. Last updated 3 days ago.

infrastructure go bioinformatics genomics ontology

1.7 match 3 stars 6.37 score 75 scripts 2 dependents

ostirrup

covBM:Brownian Motion Processes for 'nlme'-Models

Allows Brownian motion, fractional Brownian motion, and integrated Ornstein-Uhlenbeck process components to be added to linear and non-linear mixed effects models using the structures and methods of the 'nlme' package.

Maintained by Oliver Stirrup. Last updated 9 years ago.

3.6 match 3.00 score 10 scripts

mlverse

cuda.ml:R Interface for the RAPIDS cuML Suite of Libraries

R interface for RAPIDS cuML (<https://github.com/rapidsai/cuml>), a suite of GPU-accelerated machine learning libraries powered by CUDA (<https://en.wikipedia.org/wiki/CUDA>).

Maintained by Daniel Falbel. Last updated 3 years ago.

gpu machine-learning cpp

2.0 match 33 stars 5.27 score 57 scripts

justinmshea

wooldridge:115 Data Sets from "Introductory Econometrics: A Modern Approach, 7e" by Jeffrey M. Wooldridge

Students learning both econometrics and R may find the introduction to both challenging. The wooldridge data package aims to lighten the task by efficiently loading any data set found in the text with a single command. Data sets have been compressed to a fraction of their original size. Documentation files contain page numbers, the original source, time of publication, and notes from the author suggesting avenues for further analysis and research. If one needs an introduction to R model syntax, a vignette contains solutions to examples from chapters of the text. Data sets are from the 7th edition (Wooldridge 2020, ISBN-13 978-1-337-55886-0), and are backwards compatible with all previous versions of the text.

Maintained by Justin M. Shea. Last updated 3 months ago.

econometrics

1.1 match 203 stars 9.38 score 1.4k scripts

lebebr01

simglm:Simulate Models Based on the Generalized Linear Model

Simulates regression models, including both simple regression and generalized linear mixed models with up to three level of nesting. Power simulations that are flexible allowing the specification of missing data, unbalanced designs, and different random error distributions are built into the package.

Maintained by Brandon LeBeau. Last updated 10 months ago.

power simulation

1.3 match 43 stars 7.87 score 87 scripts

bioc

xenLite:Simple classes and methods for managing Xenium datasets

Define a relatively light class for managing Xenium data using Bioconductor. Address use of parquet for coordinates, SpatialExperiment for assay and sample data. Address serialization and use of cloud storage.

Maintained by Vincent Carey. Last updated 5 months ago.

infrastructure

2.3 match 1 stars 4.48 score 4 scripts

bpfaff

rneos:XML-RPC Interface to NEOS

Within this package the XML-RPC API to NEOS <https://neos-server.org/neos/> is implemented. This enables the user to pass optimization problems to NEOS and retrieve results within R.

Maintained by Bernhard Pfaff. Last updated 5 years ago.

4.0 match 2.54 score 25 scripts 4 dependents

ecor

RMAWGEN:Multi-Site Auto-Regressive Weather GENerator

S3 and S4 functions are implemented for spatial multi-site stochastic generation of daily time series of temperature and precipitation. These tools make use of Vector AutoRegressive models (VARs). The weather generator model is then saved as an object and is calibrated by daily instrumental "Gaussianized" time series through the 'vars' package tools. Once obtained this model, it can it can be used for weather generations and be adapted to work with several climatic monthly time series.

Maintained by Emanuele Cordano. Last updated 26 days ago.

1.8 match 3 stars 5.62 score 115 scripts 4 dependents

cmilando

WhiteLabRt:Novel Methods for Reproduction Number Estimation, Back-Calculation, and Forecasting

A collection of functions related to novel methods for estimating R(t), created by the lab of Professor Laura White. Currently implemented methods include two-step Bayesian back-calculation and now-casting for line-list data with missing reporting delays, adapted in 'STAN' from Li (2021) <doi:10.1371/journal.pcbi.1009210>, and calculation of time-varying reproduction number assuming a flux between various adjacent states, adapted into 'STAN' from Zhou (2021) <doi:10.1371/journal.pcbi.1010434>.

Maintained by Chad Milando. Last updated 7 months ago.

cpp

1.9 match 6 stars 5.38 score 4 scripts

chriswweibo

mojson:A Serialization-Style Flattening and Description for JSON

Support JSON flattening in a long data frame way, where the nesting keys will be stored in the absolute path. It also provides an easy way to summarize the basic description of a JSON list. The idea of 'mojson' is to transform a JSON object in an absolute serialization way, which means the early key-value pairs will appear in the heading rows of the resultant data frame. 'mojson' also provides an alternative way of comparing two different JSON lists, returning the left/inner/right-join style results.

Maintained by Bo Wei. Last updated 4 years ago.

3.5 match 1 stars 2.88 score 15 scripts

openpharma

graphicalMCP:Graphical Multiple Comparison Procedures

Multiple comparison procedures (MCPs) control the familywise error rate in clinical trials. Graphical MCPs include many commonly used procedures as special cases; see Bretz et al. (2011) <doi:10.1002/bimj.201000239>, Lu (2016) <doi:10.1002/sim.6985>, and Xi et al. (2017) <doi:10.1002/bimj.201600233>. This package is a low-dependency implementation of graphical MCPs which allow mixed types of tests. It also includes power simulations and visualization of graphical MCPs.

Maintained by Dong Xi. Last updated 4 months ago.

1.3 match 17 stars 7.35 score 18 scripts

aphalo

ooacquire:Acquire Data from OO Spectrometers

Functions to acquire data directly from Ocean Optics spectrometers, and functions to read similar data from files. Functions to convert raw-counts into counts-per-second and physical quantities. Data are saved in objects of classes defined in package 'photobiology'. The instrument settings, instrument description, date-time of acquisition and optionally goecode are stored as attributes.

Maintained by Pedro J. Aphalo. Last updated 2 months ago.

data-acquisition data-import r4photobiology spectra cpp

1.9 match 1 stars 5.17 score 93 scripts

medewitt

intervalcalc:Calculations for Epidemiological Intervals

Calculating epidemiological intervals

Maintained by Michael DeWitt. Last updated 4 years ago.

3.5 match 2.70 score 2 scripts

meghapsimatrix

simhelpers:Helper Functions for Simulation Studies

Calculates performance criteria measures and associated Monte Carlo standard errors for simulation results. Includes functions to help run simulation studies, following a general simulation workflow that closely aligns with the approach described by Morris, White, and Crowther (2019) <DOI:10.1002/sim.8086>. Also includes functions for calculating bootstrap confidence intervals (including normal, basic, studentized, percentile, bias-corrected, and bias-corrected-and-accelerated) with tidy output, as well as for extrapolating confidence interval coverage rates and hypothesis test rejection rates following techniques suggested by Boos and Zhang (2000) <DOI:10.1080/01621459.2000.10474226>.

Maintained by Megha Joshi. Last updated 2 months ago.

1.3 match 11 stars 7.07 score 40 scripts

ropensci

rrricanes:Web Scraper for Atlantic and East Pacific Hurricanes and Tropical Storms

Get archived data of past and current hurricanes and tropical storms for the Atlantic and eastern Pacific oceans. Data is available for storms since 1998. Datasets are updated via the rrricanesdata package. Currently, this package is about 6MB of datasets. See the README or view `vignette("drat")` for more information.

Maintained by Elin Waring. Last updated 1 years ago.

hurricane peer-reviewed weather

2.0 match 21 stars 4.66 score 55 scripts

juba

robservable:Import an Observable Notebook as HTML Widget

Allows loading and displaying an Observable notebook (online JavaScript notebooks powered by <https://observablehq.com>) as an HTML Widget in an R session, 'shiny' application or 'rmarkdown' document.

Maintained by Julien Barnier. Last updated 7 months ago.

htmlwidgets observable

1.3 match 165 stars 7.00 score 40 scripts

dyfanjones

sagemaker.mlcore:sagemaker machine learning core classes and methods

`sagemaker` machine learning core classes and methods.

Maintained by Dyfan Jones. Last updated 3 years ago.

amazon-sagemaker aws machine-learning sagemaker sdk

3.5 match 2.65 score 3 dependents

ralmond

RNetica:R interface to Netica(R) Bayesian Network Engine

This provides an R interface to the Netica (http://norsys.com/) Bayesian network library API.

Maintained by Russell Almond. Last updated 2 months ago.

bayesian-network

1.9 match 2 stars 4.92 score 14 scripts 2 dependents

byzheng

weaana:Analysis the Weather Data

Functions are collected to analyse weather data for agriculture purposes including to read weather records in multiple formats, calculate extreme climate index.

Maintained by Bangyou Zheng. Last updated 1 months ago.

1.7 match 3 stars 5.32 score 23 scripts 1 dependents

mikiya0417

msgpackR:A library to serialize or unserialize data in MessagePack format

This is the library that can serialize or unserialize MessagePack format data.

Maintained by Mikiya TANIZAWA. Last updated 11 years ago.

8.9 match 1.00 score

cmilando

linelistBayes:Bayesian Analysis of Epidemic Data Using Line List and Case Count Approaches

Provides tools for performing Bayesian inference on epidemiological data to estimate the time-varying reproductive number and other related metrics. These methods were published in Li and White (2021) <doi:10.1371/journal.pcbi.1009210>. This package supports analyses based on aggregated case count data and individual line list data, facilitating enhanced surveillance and intervention planning for infectious diseases like COVID-19.

Maintained by Chad Milando. Last updated 11 months ago.

openblas cpp

1.8 match 4 stars 5.00 score 2 scripts

c-monaghan

lwc2022:Langa-Weir Classification of Cognitive Function for 2022 HRS Data

Generates the Langa-Weir classification of cognitive function for the 2022 Health and Retirement Study (HRS) cognition data. It is particularly useful for researchers studying cognitive aging who wish to work with the most recent release of HRS data. The package provides user-friendly functions for data preprocessing, scoring, and classification allowing users to easily apply the Langa-Weir classification system. For details regarding the; HRS <https://hrsdata.isr.umich.edu/> and Langa-Weir classifications <https://hrsdata.isr.umich.edu/data-products/langa-weir-classification-cognitive-function-1995-2020>.

Maintained by Cormac Monaghan. Last updated 4 months ago.

1.9 match 4.48 score 4 scripts

swihart

event:Event History Procedures and Models

Functions for setting up and analyzing event history data.

Maintained by Bruce Swihart. Last updated 8 years ago.

fortran

1.8 match 1 stars 4.74 score 548 scripts

cran

TSA:Time Series Analysis

Contains R functions and datasets detailed in the book "Time Series Analysis with Applications in R (second edition)" by Jonathan Cryer and Kung-Sik Chan.

Maintained by Kung-Sik Chan. Last updated 3 years ago.

1.8 match 2 stars 4.47 score 5 dependents

ocbe-uio

contingencytables:Statistical Analysis of Contingency Tables

Provides functions to perform statistical inference of data organized in contingency tables. This package is a companion to the "Statistical Analysis of Contingency Tables" book by Fagerland et al. <ISBN 9781466588172>.

Maintained by Waldir Leoncio. Last updated 7 months ago.

contingency-table

1.9 match 3 stars 4.13 score 8 scripts 1 dependents

rcppcore

RcppParallel:Parallel Programming Tools for 'Rcpp'

High level functions for parallel programming with 'Rcpp'. For example, the 'parallelFor()' function can be used to convert the work of a standard serial "for" loop into a parallel one and the 'parallelReduce()' function can be used for accumulating aggregate or other values.

Maintained by Kevin Ushey. Last updated 2 months ago.

onetbb cpp

0.5 match 173 stars 14.89 score 215 scripts 790 dependents

inbo

etn:Access Data from the European Tracking Network

Package with functions to access and process data from the European Tracking Network hosted by VLIZ.

Maintained by Pieter Huybrechts. Last updated 2 months ago.

animal-movement animal-tracking biologging data-access fish lifewatch oscibio

1.8 match 8 stars 4.15 score 14 scripts

surajitstat

Modalclust:Hierarchical Modal Clustering

Performs Modal Clustering (MAC) including Hierarchical Modal Clustering (HMAC) along with their parallel implementation (PHMAC) over several processors. These model-based non-parametric clustering techniques can extract clusters in very high dimensions with arbitrary density shapes. By default clustering is performed over several resolutions and the results are summarised as a hierarchical tree. Associated plot functions are also provided. There is a package vignette that provides many examples. This version adheres to CRAN policy of not spanning more than two child processes by default.

Maintained by Surajit Ray. Last updated 6 years ago.

3.5 match 2.08 score 12 scripts

martakarass

arctools:Processing and Physical Activity Summaries of Minute Level Activity Data

Provides functions to process minute level actigraphy-measured activity counts data and extract commonly used physical activity volume and fragmentation metrics.

Maintained by Marta Karas. Last updated 2 years ago.

1.8 match 1 stars 3.98 score 19 scripts

cran

preregr:Specify (Pre)Registrations and Export Them Human- And Machine-Readably

Preregistrations, or more generally, registrations, enable explicit timestamped and (often but not necessarily publicly) frozen documentation of plans and expectations as well as decisions and justifications. In research, preregistrations are commonly used to clearly document plans and facilitate justifications of deviations from those plans, as well as decreasing the effects of publication bias by enabling identification of research that was conducted but not published. Like reporting guidelines, (pre)registration forms often have specific structures that facilitate systematic reporting of important items. The 'preregr' package facilitates specifying (pre)registrations in R and exporting them to a human-readable format (using R Markdown partials or exporting to an 'HTML' file) as well as human-readable embedded data (using 'JSON'), as well as importing such exported (pre)registration specifications from such embedded 'JSON'.

Maintained by Gjalt-Jorn Peters. Last updated 2 years ago.

1.8 match 3.98 score 1 scripts

tanaylab

misha:Toolkit for Analysis of Genomic Data

A toolkit for analysis of genomic data. The 'misha' package implements an efficient data structure for storing genomic data, and provides a set of functions for data extraction, manipulation and analysis. Some of the 2D genome algorithms were described in Yaffe and Tanay (2011) <doi:10.1038/ng.947>.

Maintained by Aviezer Lifshitz. Last updated 5 days ago.

genomic-data-analysis cpp

1.2 match 4 stars 5.86 score

cran

SeqDetect:Sequence and Latent Process Detector

Sequence detector in this package contains a specific automaton model that can be used to learn and detect data and process sequences. Automaton model in this package is capable of learning and tracing sequences. Automaton model can be found in Krleža, Vrdoljak, Brčić (2019) <doi:10.1109/ACCESS.2019.2955245>. This research has been partly supported under Competitiveness and Cohesion Operational Programme from the European Regional and Development Fund, as part of the Integrated Anti-Fraud System project no. KK.01.2.1.01.0041. This research has also been partly supported by the European Regional Development Fund under the grant KK.01.1.1.01.0009.

Maintained by Dalibor Krleža. Last updated 5 years ago.

cpp

3.4 match 2.00 score 2 scripts

s-fleck

rotor:Log Rotation and Conditional Backups

Conditionally rotate or back-up files based on their size or the date of the last backup; inspired by the 'Linux' utility 'logrotate'.

Maintained by Stefan Fleck. Last updated 2 years ago.

backup logging logrotate logrotation

1.8 match 12 stars 3.78 score 10 scripts

rubens2005

criticalpath:An Implementation of the Critical Path Method

An R implementation of the Critical Path Method (CPM). CPM is a method used to estimate the minimum project duration and determine the amount of scheduling flexibility on the logical network paths within the schedule model. The flexibility is in terms of early start, early finish, late start, late finish, total float and free float. Beside, it permits to quantify the complexity of network diagram through the analysis of topological indicators. Finally, it permits to change the activities duration to perform what-if scenario analysis. The package was built based on following references: To make topological sorting and other graph operation, we use Csardi, G. & Nepusz, T. (2005) <https://www.researchgate.net/publication/221995787_The_Igraph_Software_Package_for_Complex_Network_Research>; For schedule concept, the reference was Project Management Institute (2017) <https://www.pmi.org/pmbok-guide-standards/foundational/pmbok>; For standards terms, we use Project Management Institute (2017) <https://www.pmi.org/pmbok-guide-standards/lexicon>; For algorithms on Critical Path Method development, we use Vanhoucke, M. (2013) <doi:10.1007/978-3-642-40438-2> and Vanhoucke, M. (2014) <doi:10.1007/978-3-319-04331-9>; And, finally, for topological definitions, we use Vanhoucke, M. (2009) <doi:10.1007/978-1-4419-1014-1>.

Maintained by Rubens Jose Rosa. Last updated 3 years ago.

1.8 match 1 stars 3.70 score 5 scripts

cran

astrochron:A Computational Tool for Astrochronology

Routines for astrochronologic testing, astronomical time scale construction, and time series analysis <doi:10.1016/j.earscirev.2018.11.015>. Also included are a range of statistical analysis and modeling routines that are relevant to time scale development and paleoclimate analysis.

Maintained by Stephen Meyers. Last updated 6 months ago.

fortran

1.7 match 5 stars 3.85 score 141 scripts

cran

Copula.Markov:Copula-Based Estimation and Statistical Process Control for Serially Correlated Time Series

Estimation and statistical process control are performed under copula-based time-series models. Available are statistical methods in Long and Emura (2014 JCSA), Emura et al. (2017 Commun Stat-Simul) <DOI:10.1080/03610918.2015.1073303>, Huang and Emura (2021 Commun Stat-Simul) <DOI:10.1080/03610918.2019.1602647>, Lin et al. (2021 Comm Stat-Simul) <DOI:10.1080/03610918.2019.1652318>, Sun et al. (2020 JSS Series in Statistics)<DOI:10.1007/978-981-15-4998-4>, and Huang and Emura (2021, in revision).

Maintained by Takeshi Emura. Last updated 3 years ago.

4.4 match 3 stars 1.48 score

raven-computing

raven.rdf:An R Interface for Raven DataFrames (Beta0)

Provides an I/O interface between R data.frames and Raven DataFrames. Defines functions to both read and write DataFrame files, as well as serialize/deserialize data.frames/DataFrames.

Maintained by Phil Gaiser. Last updated 4 years ago.

2.2 match 2.70 score

cran

deident:Persistent Data Anonymization Pipeline

A framework for the replicable removal of personally identifiable data (PID) in data sets. The package implements a suite of methods to suit different data types based on the suggestions of Garfinkel (2015) <doi:10.6028/NIST.IR.8053> and the ICO "Guidelines on Anonymization" (2012) <https://ico.org.uk/media/1061/anonymisation-code.pdf>.

Maintained by Robert Cook. Last updated 4 months ago.

1.9 match 3.16 score 16 scripts

ropensci

emld:Ecological Metadata as Linked Data

This is a utility for transforming Ecological Metadata Language ('EML') files into 'JSON-LD' and back into 'EML.' Doing so creates a list-based representation of 'EML' in R, so that 'EML' data can easily be manipulated using standard 'R' tools. This makes this package an effective backend for other 'R'-based tools working with 'EML.' By abstracting away the complexity of 'XML' Schema, developers can build around native 'R' list objects and not have to worry about satisfying many of the additional constraints of set by the schema (such as element ordering, which is handled automatically). Additionally, the 'JSON-LD' representation enables the use of developer-friendly 'JSON' parsing and serialization that may facilitate the use of 'EML' in contexts outside of 'R,' as well as the informatics-friendly serializations such as 'RDF' and 'SPARQL' queries.

Maintained by Carl Boettiger. Last updated 4 years ago.

0.8 match 13 stars 7.63 score 69 scripts 8 dependents

aphalo

rOmniDriver:Omni Driver R wrapper

This package is a wrapper of the OmniDriver java driver for Ocean Optics spectrometers.

Maintained by Pedro J. Aphalo. Last updated 7 months ago.

data-acquisition spectroscopy openjdk

1.9 match 1 stars 3.00 score 6 scripts

cran

gasanalyzer:Import, Recompute and Analyze Data from Portable Gas Analyzers

The gasanalyzer R package offers methods for importing, preprocessing, and analyzing data related to photosynthetic characteristics (gas exchange, chlorophyll fluorescence and isotope ratios). It translates variable names into a standard format, and can recalculate derived, physiological quantities using imported or predefined equations. The package also allows users to assess the sensitivity of their results to different assumptions used in the calculations. See also Tholen (2024) <doi:10.1093/aobpla/plae035>.

Maintained by Danny Tholen. Last updated 2 months ago.

1.6 match 1 stars 3.30 score

lechmadeyski

reproducer:Reproduce Statistical Analyses and Meta-Analyses

Includes data analysis and meta-analysis functions (e.g., to calculate effect sizes and 95% Confidence Intervals (CI) on Standardised Effect Sizes (d) for AB/BA cross-over repeated-measures experimental designs), data presentation functions (e.g., density curve overlaid on histogram),and the data sets analyzed in different research papers in software engineering (e.g., related to software defect prediction or multi- site experiment concerning the extent to which structured abstracts were clearer and more complete than conventional abstracts) to streamline reproducible research in software engineering.

Maintained by Lech Madeyski. Last updated 1 years ago.

1.5 match 3.50 score 63 scripts

r-lib

urlchecker:Run CRAN URL Checks from Older R Versions

Provide the URL checking tools available in R 4.1+ as a package for earlier versions of R. Also uses concurrent requests so can be much faster than the serial versions.

Maintained by Gábor Csárdi. Last updated 7 months ago.

0.5 match 47 stars 10.00 score 15 scripts 151 dependents

reconhub

earlyR:Estimation of Transmissibility in the Early Stages of a Disease Outbreak

Implements a simple, likelihood-based estimation of the reproduction number (R0) using a branching process with a Poisson likelihood. This model requires knowledge of the serial interval distribution, and dates of symptom onsets. Infectiousness is determined by weighting R0 by the probability mass function of the serial interval on the corresponding day. It is a simplified version of the model introduced by Cori et al. (2013) <doi:10.1093/aje/kwt133>.

Maintained by Thibaut Jombart. Last updated 4 years ago.

0.8 match 9 stars 6.59 score 96 scripts

coolbutuseless

lz4lite:Extremely Fast Compression with LZ4

Extremely fast compression of R objects with LZ4.

Maintained by mikefc. Last updated 4 years ago.

1.7 match 20 stars 3.00 score 7 scripts

mayooran1987

grabsampling:Probability of detection for grab sample selection

The goal of grabsampling package is to enable probability of detection calculation for grab samples selection by using two different methods such as systematic or random based on two-state Markov chain in bulk production process.

Maintained by Mayooran Thevaraja. Last updated 2 years ago.

1.9 match 1 stars 2.70 score 1 scripts

ralmond

mongo:Higher level interface to Mongo database

This is a wrapper for the jsonlite and mongolite packages which offers both an R6 object for managing the connection as well as some mechanisms for saving and restoring S4 objects to a Mongo database.

Maintained by Russell Almond. Last updated 10 months ago.

1.2 match 4.13 score 3 dependents

dyfanjones

sagemaker.core:Sagemaker core classes, methods and functions

Contains core classes, methods and functions that support `AWS Sagemaker R Software Development Kit (SDK)`.

Maintained by Dyfan Jones. Last updated 3 years ago.

amazon-sagemaker aws machine-learning sagemaker sdk

1.7 match 2.88 score 1 scripts 5 dependents

kjetil1001

BayesDA:Functions and Datasets for the book "Bayesian Data Analysis"

Functions for Bayesian Data Analysis, with datasets from the book "Bayesian data Analysis (second edition)" by Gelman, Carlin, Stern and Rubin. Not all datasets yet, hopefully completed soon.

Maintained by Kjetil Halvorsen. Last updated 13 years ago.

4.0 match 1.23 score 17 scripts

bachfisch

PHENTHAUproc:Phenology Modelling of Thaumetopoea Processionea

Methods to calculate and present 'PHENTHAUproc', an early warning and decision support system for hazard assessment and control of oak processionary moth (OPM) using local and spatial temperature data. It was created by Halbig et al. 2024 (<doi:10.1016/j.foreco.2023.121525>) at FVA (<https://www.fva-bw.de/en/homepage/>) Forest Research Institute Baden-Wuerttemberg, Germany and at BOKU - University of Natural Ressources and Life Sciences, Vienna, Austria.

Maintained by Lorenz Bachfischer. Last updated 9 months ago.

1.7 match 2.70 score 3 scripts

fastverse

fastverse:A Suite of High-Performance Packages for Statistics and Data Manipulation

Easy installation, loading and management, of high-performance packages for statistical computing and data manipulation in R. The core 'fastverse' consists of 4 packages: 'data.table', 'collapse', 'kit' and 'magrittr', that jointly only depend on 'Rcpp'. The 'fastverse' can be freely and permanently extended with additional packages, both globally or for individual projects. Separate package verses can also be created. Fast packages for many common tasks such as time series, dates and times, strings, spatial data, statistics, data serialization, larger-than-memory processing, and compilation of R code are listed in the README file: <https://github.com/fastverse/fastverse#suggested-extensions>.

Maintained by Sebastian Krantz. Last updated 25 days ago.

c cpp data-aggregation data-manipulation data-science data-transformation high-performance low-dependency panel-data statistical-computing time-series weights

0.5 match 264 stars 8.90 score 222 scripts

tguillerme

dispRity:Measuring Disparity

A modular package for measuring disparity (multidimensional space occupancy). Disparity can be calculated from any matrix defining a multidimensional space. The package provides a set of implemented metrics to measure properties of the space and allows users to provide and test their own metrics. The package also provides functions for looking at disparity in a serial way (e.g. disparity through time) or per groups as well as visualising the results. Finally, this package provides several statistical tests for disparity analysis.

Maintained by Thomas Guillerme. Last updated 2 days ago.

disparity ecology multidimensionality palaeobiology

0.5 match 26 stars 8.69 score 220 scripts 1 dependents

bioc

alabaster.base:Save Bioconductor Objects to File

Save Bioconductor data structures into file artifacts, and load them back into memory. This is a more robust and portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

Maintained by Aaron Lun. Last updated 11 days ago.

datarepresentation dataimport zlib cpp

0.5 match 3 stars 8.47 score 60 scripts 15 dependents

dyfanjones

sagemaker.mlframework:sagemaker machine learning developed by amazon

`sagemaker` machine learning developed by amazon.

Maintained by Dyfan Jones. Last updated 3 years ago.

amazon-sagemaker aws machine-learning sagemaker sdk

1.8 match 2.48 score 2 dependents

kurthornik

OAIHarvester:Harvest Metadata Using OAI-PMH Version 2.0

Harvest metadata using the Open Archives Initiative Protocol for Metadata Harvesting (OAI-PMH) version 2.0 (for more information, see <https://www.openarchives.org/OAI/openarchivesprotocol.html>).

Maintained by Kurt Hornik. Last updated 4 months ago.

1.9 match 2.24 score 9 scripts

shikokuchuo

secretbase:Cryptographic Hash, Extendable-Output and Base64 Functions

Fast and memory-efficient streaming hash functions and base64 encoding / decoding. Hashes strings and raw vectors directly. Stream hashes files which can be larger than memory, as well as in-memory objects through R's serialization mechanism. Implementations include the SHA-256, SHA-3 and 'Keccak' cryptographic hash functions, SHAKE256 extendable-output function (XOF), and 'SipHash' pseudo-random function.

Maintained by Charlie Gao. Last updated 2 days ago.

base64 cryptographic-hash-functions extendable-output-functions keccak sha256 sha3 shake256 siphash

0.5 match 11 stars 8.14 score 8 scripts 24 dependents

bioc

DEScan2:Differential Enrichment Scan 2

Integrated peak and differential caller, specifically designed for broad epigenomic signals.

Maintained by Dario Righelli. Last updated 5 months ago.

immunooncology peakdetection epigenetics software sequencing coverage cpp

1.3 match 3.30 score 2 scripts

anloor7

ctsfeatures:Analyzing Categorical Time Series

An implementation of several functions for feature extraction in categorical time series datasets. Specifically, some features related to marginal distributions and serial dependence patterns can be computed. These features can be used to feed clustering and classification algorithms for categorical time series, among others. The package also includes some interesting datasets containing biological sequences. Practitioners from a broad variety of fields could benefit from the general framework provided by 'ctsfeatures'.

Maintained by Angel Lopez-Oriona. Last updated 1 years ago.

3.9 match 1 stars 1.00 score 1 scripts