R-universe search: bitly

r-lib

bit:Classes and Methods for Fast Memory-Efficient Boolean Selections

Provided are classes for boolean and skewed boolean vectors, fast boolean methods, fast unique and non-unique integer sorting, fast set operations on sorted and unsorted sets of integers, and foundations for ff (range index, compression, chunked processing).

Maintained by Michael Chirico. Last updated 6 days ago.

119.0 match 12 stars 15.15 score 131 scripts 3.2k 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.

20.0 match 845 stars 13.57 score 264 scripts 2 dependents

thierryo

qrcode:Generate QRcodes with R

Create static QR codes in R. The content of the QR code is exactly what the user defines. We don't add a redirect URL, making it impossible for us to track the usage of the QR code. This allows to generate fast, free to use and privacy friendly QR codes.

Maintained by Thierry Onkelinx. Last updated 6 months ago.

qrcode qrcode-generator r-project

18.7 match 44 stars 7.56 score 456 scripts 7 dependents

8-bit-sheep

googleAnalyticsR:Google Analytics API into R

Interact with the Google Analytics APIs <https://developers.google.com/analytics/>, including the Core Reporting API (v3 and v4), Management API, User Activity API GA4's Data API and Admin API and Multi-Channel Funnel API.

Maintained by Erik Grönroos. Last updated 6 months ago.

analytics api google googleanalyticsr googleauthr

13.3 match 262 stars 10.11 score 680 scripts 1 dependents

dmpe

urlshorteneR:R Wrapper for the 'Bit.ly' and 'Is.gd'/'v.gd' URL Shortening Services

Allows using two URL shortening services, which also provide expanding and analytic functions. Specifically developed for 'Bit.ly' (which requires OAuth 2.0) and 'is.gd' (no API key).

Maintained by John Malc. Last updated 28 days ago.

bitly isgd shorten-urls shortener shorturl url

17.6 match 21 stars 6.70 score 53 scripts 1 dependents

coolbutuseless

bitstreamio:Read and Write Bits from Files, Connections and Raw Vectors

Bit-level reading and writing are necessary when dealing with many file formats e.g. compressed data and binary files. Currently, R connections are manipulated at the byte level. This package wraps existing connections and raw vectors so that it is possible to read bits, bit sequences, unaligned bytes and low-bit representations of integers.

Maintained by Mike Cheng. Last updated 2 months ago.

25.1 match 3 stars 4.18 score 4 scripts

cran

compositions:Compositional Data Analysis

Provides functions for the consistent analysis of compositional data (e.g. portions of substances) and positive numbers (e.g. concentrations) in the way proposed by J. Aitchison and V. Pawlowsky-Glahn.

Maintained by K. Gerald van den Boogaart. Last updated 1 years ago.

openblas

15.3 match 1 stars 6.35 score 36 dependents

wrathematics

float:32-Bit Floats

R comes with a suite of utilities for linear algebra with "numeric" (double precision) vectors/matrices. However, sometimes single precision (or less!) is more than enough for a particular task. This package extends R's linear algebra facilities to include 32-bit float (single precision) data. Float vectors/matrices have half the precision of their "numeric"-type counterparts but are generally faster to numerically operate on, for a performance vs accuracy trade-off. The internal representation is an S4 class, which allows us to keep the syntax identical to that of base R's. Interaction between floats and base types for binary operators is generally possible; in these cases, type promotion always defaults to the higher precision. The package ships with copies of the single precision 'BLAS' and 'LAPACK', which are automatically built in the event they are not available on the system.

Maintained by Drew Schmidt. Last updated 7 days ago.

float-matrix hpc linear-algebra matrix fortran openblas openmp

8.7 match 46 stars 10.53 score 228 scripts 42 dependents

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 1 days ago.

rust cargo

16.6 match 40 stars 4.86 score 1 scripts

baddstats

polyclip:Polygon Clipping

R port of Angus Johnson's open source library 'Clipper'. Performs polygon clipping operations (intersection, union, set minus, set difference) for polygonal regions of arbitrary complexity, including holes. Computes offset polygons (spatial buffer zones, morphological dilations, Minkowski dilations) for polygonal regions and polygonal lines. Computes Minkowski Sum of general polygons. There is a function for removing self-intersections from polygon data.

Maintained by Adrian Baddeley. Last updated 8 months ago.

64-bit clipper computational-geometry minkowski-sum polygon-clipping-algorithm polygon-intersection polygon-offsetting polygon-union polygons cpp

7.5 match 19 stars 10.31 score 27 scripts 553 dependents

martinzaefferer

CEGO:Combinatorial Efficient Global Optimization

Model building, surrogate model based optimization and Efficient Global Optimization in combinatorial or mixed search spaces.

Maintained by Martin Zaefferer. Last updated 2 months ago.

17.2 match 1 stars 3.04 score 73 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

3.0 match 62 stars 15.93 score 4.2k scripts 232 dependents

spatstat

spatstat.explore:Exploratory Data Analysis for the 'spatstat' Family

Functionality for exploratory data analysis and nonparametric analysis of spatial data, mainly spatial point patterns, in the 'spatstat' family of packages. (Excludes analysis of spatial data on a linear network, which is covered by the separate package 'spatstat.linnet'.) Methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported.

Maintained by Adrian Baddeley. Last updated 1 months ago.

cluster-detection confidence-intervals hypothesis-testing k-function roc-curves scan-statistics significance-testing simulation-envelopes spatial-analysis spatial-data-analysis spatial-sharpening spatial-smoothing spatial-statistics

4.5 match 1 stars 10.17 score 67 scripts 148 dependents

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

3.6 match 499 stars 12.01 score 1.0k scripts 2 dependents

jeffreyevans

spatialEco:Spatial Analysis and Modelling Utilities

Utilities to support spatial data manipulation, query, sampling and modelling in ecological applications. Functions include models for species population density, spatial smoothing, multivariate separability, point process model for creating pseudo- absences and sub-sampling, Quadrant-based sampling and analysis, auto-logistic modeling, sampling models, cluster optimization, statistical exploratory tools and raster-based metrics.

Maintained by Jeffrey S. Evans. Last updated 13 days ago.

biodiversity conservation ecology r-spatial raster spatial vector

4.5 match 110 stars 9.55 score 736 scripts 2 dependents

rajarshi

fingerprint:Functions to Operate on Binary Fingerprint Data

Functions to manipulate binary fingerprints of arbitrary length. A fingerprint is represented by an object of S4 class 'fingerprint' which is internally represented a vector of integers, such that each element represents the position in the fingerprint that is set to 1. The bitwise logical functions in R are overridden so that they can be used directly with 'fingerprint' objects. A number of distance metrics are also available (many contributed by Michael Fadock). Fingerprints can be converted to Euclidean vectors (i.e., points on the unit hypersphere) and can also be folded using OR. Arbitrary fingerprint formats can be handled via line handlers. Currently handlers are provided for CDK, MOE and BCI fingerprint data.

Maintained by Rajarshi Guha. Last updated 7 years ago.

10.0 match 4.22 score 82 scripts 12 dependents

hsonne

odbc32:32-bit ODBC drivers for 64-bit R sessions

Tools for using 32-bit ODBC drivers from 64-bit R sessions. Based on socket connection between 64-bit R and host 32-bit R.

Maintained by Vaclav Hausenblas. Last updated 5 years ago.

11.8 match 3.54 score 6 scripts 23 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

3.5 match 6 stars 11.70 score 13k scripts 112 dependents

hwborchers

pracma:Practical Numerical Math Functions

Provides a large number of functions from numerical analysis and linear algebra, numerical optimization, differential equations, time series, plus some well-known special mathematical functions. Uses 'MATLAB' function names where appropriate to simplify porting.

Maintained by Hans W. Borchers. Last updated 1 years ago.

3.0 match 29 stars 12.34 score 6.6k scripts 931 dependents

bioc

pgca:PGCA: An Algorithm to Link Protein Groups Created from MS/MS Data

Protein Group Code Algorithm (PGCA) is a computationally inexpensive algorithm to merge protein summaries from multiple experimental quantitative proteomics data. The algorithm connects two or more groups with overlapping accession numbers. In some cases, pairwise groups are mutually exclusive but they may still be connected by another group (or set of groups) with overlapping accession numbers. Thus, groups created by PGCA from multiple experimental runs (i.e., global groups) are called "connected" groups. These identified global protein groups enable the analysis of quantitative data available for protein groups instead of unique protein identifiers.

Maintained by Gabriela Cohen-Freue. Last updated 5 months ago.

workflowstep assaydomain proteomics massspectrometry immunooncology

9.0 match 4.00 score 3 scripts

hadley

pryr:Tools for Computing on the Language

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

Maintained by Hadley Wickham. Last updated 1 years ago.

cpp

3.0 match 204 stars 11.85 score 1.9k scripts 56 dependents

truecluster

ff:Memory-Efficient Storage of Large Data on Disk and Fast Access Functions

The ff package provides data structures that are stored on disk but behave (almost) as if they were in RAM by transparently mapping only a section (pagesize) in main memory - the effective virtual memory consumption per ff object. ff supports R's standard atomic data types 'double', 'logical', 'raw' and 'integer' and non-standard atomic types boolean (1 bit), quad (2 bit unsigned), nibble (4 bit unsigned), byte (1 byte signed with NAs), ubyte (1 byte unsigned), short (2 byte signed with NAs), ushort (2 byte unsigned), single (4 byte float with NAs). For example 'quad' allows efficient storage of genomic data as an 'A','T','G','C' factor. The unsigned types support 'circular' arithmetic. There is also support for close-to-atomic types 'factor', 'ordered', 'POSIXct', 'Date' and custom close-to-atomic types. ff not only has native C-support for vectors, matrices and arrays with flexible dimorder (major column-order, major row-order and generalizations for arrays). There is also a ffdf class not unlike data.frames and import/export filters for csv files. ff objects store raw data in binary flat files in native encoding, and complement this with metadata stored in R as physical and virtual attributes. ff objects have well-defined hybrid copying semantics, which gives rise to certain performance improvements through virtualization. ff objects can be stored and reopened across R sessions. ff files can be shared by multiple ff R objects (using different data en/de-coding schemes) in the same process or from multiple R processes to exploit parallelism. A wide choice of finalizer options allows to work with 'permanent' files as well as creating/removing 'temporary' ff files completely transparent to the user. On certain OS/Filesystem combinations, creating the ff files works without notable delay thanks to using sparse file allocation. Several access optimization techniques such as Hybrid Index Preprocessing and Virtualization are implemented to achieve good performance even with large datasets, for example virtual matrix transpose without touching a single byte on disk. Further, to reduce disk I/O, 'logicals' and non-standard data types get stored native and compact on binary flat files i.e. logicals take up exactly 2 bits to represent TRUE, FALSE and NA. Beyond basic access functions, the ff package also provides compatibility functions that facilitate writing code for ff and ram objects and support for batch processing on ff objects (e.g. as.ram, as.ff, ffapply). ff interfaces closely with functionality from package 'bit': chunked looping, fast bit operations and coercions between different objects that can store subscript information ('bit', 'bitwhich', ff 'boolean', ri range index, hi hybrid index). This allows to work interactively with selections of large datasets and quickly modify selection criteria. Further high-performance enhancements can be made available upon request.

Maintained by Jens Oehlschlägel. Last updated 2 months ago.

cpp

2.9 match 27 stars 12.01 score 764 scripts 71 dependents

trackage

tripEstimation:Metropolis Sampler and Supporting Functions for Estimating Animal Movement from Archival Tags and Satellite Fixes

Data handling and estimation functions for animal movement estimation from archival or satellite tags. Helper functions are included for making image summaries binned by time interval from Markov Chain Monte Carlo simulations.

Maintained by Michael D. Sumner. Last updated 2 years ago.

7.8 match 4 stars 4.19 score 13 scripts

wasquith

lmomco:L-Moments, Censored L-Moments, Trimmed L-Moments, L-Comoments, and Many Distributions

Extensive functions for Lmoments (LMs) and probability-weighted moments (PWMs), distribution parameter estimation, LMs for distributions, LM ratio diagrams, multivariate Lcomoments, and asymmetric (asy) trimmed LMs (TLMs). Maximum likelihood and maximum product spacings estimation are available. Right-tail and left-tail LM censoring by threshold or indicator variable are available. LMs of residual (resid) and reversed (rev) residual life are implemented along with 13 quantile operators for reliability analyses. Exact analytical bootstrap estimates of order statistics, LMs, and LM var-covars are available. Harri-Coble Tau34-squared Normality Test is available. Distributions with L, TL, and added (+) support for right-tail censoring (RC) encompass: Asy Exponential (Exp) Power [L], Asy Triangular [L], Cauchy [TL], Eta-Mu [L], Exp. [L], Gamma [L], Generalized (Gen) Exp Poisson [L], Gen Extreme Value [L], Gen Lambda [L, TL], Gen Logistic [L], Gen Normal [L], Gen Pareto [L+RC, TL], Govindarajulu [L], Gumbel [L], Kappa [L], Kappa-Mu [L], Kumaraswamy [L], Laplace [L], Linear Mean Residual Quantile Function [L], Normal [L], 3p log-Normal [L], Pearson Type III [L], Polynomial Density-Quantile 3 and 4 [L], Rayleigh [L], Rev-Gumbel [L+RC], Rice [L], Singh Maddala [L], Slash [TL], 3p Student t [L], Truncated Exponential [L], Wakeby [L], and Weibull [L].

Maintained by William Asquith. Last updated 1 months ago.

flood-frequency-analysis l-moments mle-estimation mps-estimation probability-distribution rainfall-frequency-analysis reliability-analysis risk-analysis survival-analysis

4.0 match 2 stars 8.06 score 458 scripts 38 dependents

azure

azuremlsdk:Interface to the 'Azure Machine Learning' 'SDK'

Interface to the 'Azure Machine Learning' Software Development Kit ('SDK'). Data scientists can use the 'SDK' to train, deploy, automate, and manage machine learning models on the 'Azure Machine Learning' service. To learn more about 'Azure Machine Learning' visit the website: <https://docs.microsoft.com/en-us/azure/machine-learning/service/overview-what-is-azure-ml>.

Maintained by Diondra Peck. Last updated 3 years ago.

amlcompute azure azure-machine-learning azureml dsi machine-learning rstudio sdk-r

3.6 match 106 stars 8.91 score 221 scripts

langenbergstefan

sound:A Sound Interface for R

Basic functions for dealing with wav files and sound samples.

Maintained by Stefan Langenberg. Last updated 1 years ago.

8.0 match 3.79 score 124 scripts

emmanuelparadis

ape:Analyses of Phylogenetics and Evolution

Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.

Maintained by Emmanuel Paradis. Last updated 14 hours ago.

openblas cpp

1.8 match 64 stars 17.22 score 13k scripts 599 dependents

lbraglia

RStata:A Bit of Glue Between R and Stata

A simple R -> Stata interface allowing the user to execute Stata commands (both inline and from a .do file) from R.

Maintained by Luca Braglia. Last updated 4 years ago.

5.0 match 110 stars 5.76 score 105 scripts

tidymodels

broom:Convert Statistical Objects into Tidy Tibbles

Summarizes key information about statistical objects in tidy tibbles. This makes it easy to report results, create plots and consistently work with large numbers of models at once. Broom provides three verbs that each provide different types of information about a model. tidy() summarizes information about model components such as coefficients of a regression. glance() reports information about an entire model, such as goodness of fit measures like AIC and BIC. augment() adds information about individual observations to a dataset, such as fitted values or influence measures.

Maintained by Simon Couch. Last updated 4 months ago.

modeling tidy-data

1.3 match 1.5k stars 21.56 score 37k scripts 1.4k dependents

r-lib

bit64:A S3 Class for Vectors of 64bit Integers

Package 'bit64' provides serializable S3 atomic 64bit (signed) integers. These are useful for handling database keys and exact counting in +-2^63. WARNING: do not use them as replacement for 32bit integers, integer64 are not supported for subscripting by R-core and they have different semantics when combined with double, e.g. integer64 + double => integer64. Class integer64 can be used in vectors, matrices, arrays and data.frames. Methods are available for coercion from and to logicals, integers, doubles, characters and factors as well as many elementwise and summary functions. Many fast algorithmic operations such as 'match' and 'order' support inter- active data exploration and manipulation and optionally leverage caching.

Maintained by Michael Chirico. Last updated 4 days ago.

1.9 match 35 stars 14.91 score 1.5k scripts 3.2k dependents

jpmonteagudo28

despair:Motivational Quotes and Shakespearean Bard–bits for Personal Projects

Generate motivational quotes and Shakespearean word combinations (bard–bits) that a user can consider for their personal projects. Each of the package functions takes two arguments, cat which default to any, and a a numeric or character seed to ensure reproducible results.

Maintained by JP Monteagudo. Last updated 3 months ago.

7.3 match 3 stars 3.78 score 5 scripts

rorynolan

strex:Extra String Manipulation Functions

There are some things that I wish were easier with the 'stringr' or 'stringi' packages. The foremost of these is the extraction of numbers from strings. 'stringr' and 'stringi' make you figure out the regular expression for yourself; 'strex' takes care of this for you. There are many other handy functionalities in 'strex'. Contributions to this package are encouraged; it is intended as a miscellany of string manipulation functions that cannot be found in 'stringi' or 'stringr'.

Maintained by Rory Nolan. Last updated 6 months ago.

2.5 match 41 stars 10.59 score 1.2k scripts 18 dependents

r-lib

marquee:Markdown Parser and Renderer for R Graphics

Provides the mean to parse and render markdown text with grid along with facilities to define the styling of the text.

Maintained by Thomas Lin Pedersen. Last updated 2 months ago.

cpp

3.0 match 84 stars 8.54 score 28 scripts 1 dependents

boydorr

rdiversity:Measurement and Partitioning of Similarity-Sensitive Biodiversity

Provides a framework for the measurement and partitioning of the (similarity-sensitive) biodiversity of a metacommunity and its constituent subcommunities. Richard Reeve, et al. (2016) <arXiv:1404.6520v3>.

Maintained by Richard Reeve. Last updated 3 years ago.

biodiversity diversity-measurement partitioning-diversity

3.7 match 8 stars 6.85 score 66 scripts 1 dependents

petolau

TSrepr:Time Series Representations

Methods for representations (i.e. dimensionality reduction, preprocessing, feature extraction) of time series to help more accurate and effective time series data mining. Non-data adaptive, data adaptive, model-based and data dictated (clipped) representation methods are implemented. Also various normalisation methods (min-max, z-score, Box-Cox, Yeo-Johnson), and forecasting accuracy measures are implemented.

Maintained by Peter Laurinec. Last updated 5 years ago.

data-analysis data-mining data-mining-algorithms data-science representation time-series time-series-analysis time-series-classification time-series-clustering time-series-data-mining time-series-representations cpp

3.5 match 97 stars 7.23 score 117 scripts

bioc

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

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

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

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

1.6 match 28 stars 15.42 score 3.2k scripts 566 dependents

ropensci

rgbif:Interface to the Global Biodiversity Information Facility API

A programmatic interface to the Web Service methods provided by the Global Biodiversity Information Facility (GBIF; <https://www.gbif.org/developer/summary>). GBIF is a database of species occurrence records from sources all over the globe. rgbif includes functions for searching for taxonomic names, retrieving information on data providers, getting species occurrence records, getting counts of occurrence records, and using the GBIF tile map service to make rasters summarizing huge amounts of data.

Maintained by John Waller. Last updated 3 days ago.

gbif specimens api web-services occurrences species taxonomy biodiversity data lifewatch oscibio spocc

1.9 match 161 stars 13.26 score 2.1k scripts 20 dependents

brodieg

fansi:ANSI Control Sequence Aware String Functions

Counterparts to R string manipulation functions that account for the effects of ANSI text formatting control sequences.

Maintained by Brodie Gaslam. Last updated 10 months ago.

string-manipulation

1.8 match 54 stars 14.18 score 136 scripts 11k dependents

jhstaudacher

CoopGame:Important Concepts of Cooperative Game Theory

The theory of cooperative games with transferable utility offers useful insights into the way parties can share gains from cooperation and secure sustainable agreements, see e.g. one of the books by Chakravarty, Mitra and Sarkar (2015, ISBN:978-1107058798) or by Driessen (1988, ISBN:978-9027727299) for more details. A comprehensive set of tools for cooperative game theory with transferable utility is provided. Users can create special families of cooperative games, like e.g. bankruptcy games, cost sharing games and weighted voting games. There are functions to check various game properties and to compute five different set-valued solution concepts for cooperative games. A large number of point-valued solution concepts is available reflecting the diverse application areas of cooperative game theory. Some of these point-valued solution concepts can be used to analyze weighted voting games and measure the influence of individual voters within a voting body. There are routines for visualizing both set-valued and point-valued solutions in the case of three or four players.

Maintained by Jochen Staudacher. Last updated 4 years ago.

5.7 match 4.10 score 424 scripts 1 dependents

ms609

TreeDist:Calculate and Map Distances Between Phylogenetic Trees

Implements measures of tree similarity, including information-based generalized Robinson-Foulds distances (Phylogenetic Information Distance, Clustering Information Distance, Matching Split Information Distance; Smith 2020) <doi:10.1093/bioinformatics/btaa614>; Jaccard-Robinson-Foulds distances (Bocker et al. 2013) <doi:10.1007/978-3-642-40453-5_13>, including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>; the Matching Split Distance (Bogdanowicz & Giaro 2012) <doi:10.1109/TCBB.2011.48>; Maximum Agreement Subtree distances; the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the Nearest Neighbour Interchange (NNI) distance, approximated per Li et al. (1996) <doi:10.1007/3-540-61332-3_168>. Includes tools for visualizing mappings of tree space (Smith 2022) <doi:10.1093/sysbio/syab100>, for identifying islands of trees (Silva and Wilkinson 2021) <doi:10.1093/sysbio/syab015>, for calculating the median of sets of trees, and for computing the information content of trees and splits.

Maintained by Martin R. Smith. Last updated 1 months ago.

phylogenetics tree-distance phylogenetic-trees tree-distances trees cpp

2.3 match 32 stars 10.32 score 97 scripts 5 dependents

pik-piam

quitte:Bits and pieces of code to use with quitte-style data frames

A collection of functions for easily dealing with quitte-style data frames, doing multi-model comparisons and plots.

Maintained by Michaja Pehl. Last updated 3 days ago.

2.8 match 8.22 score 184 scripts 35 dependents

jaryan

mmap:Map Pages of Memory

R interface to POSIX mmap and Window's MapViewOfFile.

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

3.0 match 14 stars 7.40 score 44 scripts 3 dependents

rstudio

dygraphs:Interface to 'Dygraphs' Interactive Time Series Charting Library

An R interface to the 'dygraphs' JavaScript charting library (a copy of which is included in the package). Provides rich facilities for charting time-series data in R, including highly configurable series- and axis-display and interactive features like zoom/pan and series/point highlighting.

Maintained by Petr Shevtsov. Last updated 2 years ago.

1.6 match 365 stars 13.48 score 3.6k scripts 65 dependents

ericgiunta

Colossus:"Risk Model Regression and Analysis with Complex Non-Linear Models"

Performs survival analysis using general non-linear models. Risk models can be the sum or product of terms. Each term is the product of exponential/linear functions of covariates. Additionally sub-terms can be defined as a sum of exponential, linear threshold, and step functions. Cox Proportional hazards <https://en.wikipedia.org/wiki/Proportional_hazards_model>, Poisson <https://en.wikipedia.org/wiki/Poisson_regression>, and Fine-Gray competing risks <https://www.publichealth.columbia.edu/research/population-health-methods/competing-risk-analysis> regression are supported. This work was sponsored by NASA Grant 80NSSC19M0161 through a subcontract from the National Council on Radiation Protection and Measurements (NCRP). The computing for this project was performed on the Beocat Research Cluster at Kansas State University, which is funded in part by NSF grants CNS-1006860, EPS-1006860, EPS-0919443, ACI-1440548, CHE-1726332, and NIH P20GM113109.

Maintained by Eric Giunta. Last updated 3 days ago.

cpp openmp

3.0 match 1 stars 7.06 score 36 scripts

r-forge

Rmpfr:Interface R to MPFR - Multiple Precision Floating-Point Reliable

Arithmetic (via S4 classes and methods) for arbitrary precision floating point numbers, including transcendental ("special") functions. To this end, the package interfaces to the 'LGPL' licensed 'MPFR' (Multiple Precision Floating-Point Reliable) Library which itself is based on the 'GMP' (GNU Multiple Precision) Library.

Maintained by Martin Maechler. Last updated 4 months ago.

mpfr4 gmp

1.8 match 11.30 score 316 scripts 141 dependents

juanv66x

qvirus:Quantum Computing for Analyzing CD4 Lymphocytes and Antiretroviral Therapy

Resources, tutorials, and code snippets dedicated to exploring the intersection of quantum computing and artificial intelligence (AI) in the context of analyzing Cluster of Differentiation 4 (CD4) lymphocytes and optimizing antiretroviral therapy (ART) for human immunodeficiency virus (HIV). With the emergence of quantum artificial intelligence and the development of small-scale quantum computers, there's an unprecedented opportunity to revolutionize the understanding of HIV dynamics and treatment strategies. This project leverages the R package 'qsimulatR' (Ostmeyer and Urbach, 2023, <https://CRAN.R-project.org/package=qsimulatR>), a quantum computer simulator, to explore these applications in quantum computing techniques, addressing the challenges in studying CD4 lymphocytes and enhancing ART efficacy.

Maintained by Juan Pablo Acuña González. Last updated 11 days ago.

3.6 match 5.43 score 15 scripts

mmaechler

sfsmisc:Utilities from 'Seminar fuer Statistik' ETH Zurich

Useful utilities ['goodies'] from Seminar fuer Statistik ETH Zurich, some of which were ported from S-plus in the 1990s. For graphics, have pretty (Log-scale) axes eaxis(), an enhanced Tukey-Anscombe plot, combining histogram and boxplot, 2d-residual plots, a 'tachoPlot()', pretty arrows, etc. For robustness, have a robust F test and robust range(). For system support, notably on Linux, provides 'Sys.*()' functions with more access to system and CPU information. Finally, miscellaneous utilities such as simple efficient prime numbers, integer codes, Duplicated(), toLatex.numeric() and is.whole().

Maintained by Martin Maechler. Last updated 5 months ago.

1.8 match 11 stars 10.87 score 566 scripts 119 dependents

mlr-org

mlr3misc:Helper Functions for 'mlr3'

Frequently used helper functions and assertions used in 'mlr3' and its companion packages. Comes with helper functions for functional programming, for printing, to work with 'data.table', as well as some generally useful 'R6' classes. This package also supersedes the package 'BBmisc'.

Maintained by Marc Becker. Last updated 4 months ago.

machine-learning miscellaneous mlr3

1.8 match 12 stars 10.28 score 302 scripts 42 dependents

bleutner

RStoolbox:Remote Sensing Data Analysis

Toolbox for remote sensing image processing and analysis such as calculating spectral indexes, principal component transformation, unsupervised and supervised classification or fractional cover analyses.

Maintained by Konstantin Mueller. Last updated 1 months ago.

ggplot2 land-cover-mapping remote-sensing spectral-unmixing supervised-classification unsupervised-classification openblas cpp

1.8 match 275 stars 10.10 score 1.1k scripts

gjmvanboxtel

gsignal:Signal Processing

R implementation of the 'Octave' package 'signal', containing a variety of signal processing tools, such as signal generation and measurement, correlation and convolution, filtering, filter design, filter analysis and conversion, power spectrum analysis, system identification, decimation and sample rate change, and windowing.

Maintained by Geert van Boxtel. Last updated 2 months ago.

signal-processing signals cpp

1.8 match 24 stars 10.03 score 133 scripts 34 dependents

ropensci

charlatan:Make Fake Data

Make fake data that looks realistic, supporting addresses, person names, dates, times, colors, coordinates, currencies, digital object identifiers ('DOIs'), jobs, phone numbers, 'DNA' sequences, doubles and integers from distributions and within a range.

Maintained by Roel M. Hogervorst. Last updated 1 months ago.

data dataset fake-data faker peer-reviewed

1.8 match 296 stars 10.06 score 180 scripts 1 dependents

ms609

TreeTools:Create, Modify and Analyse Phylogenetic Trees

Efficient implementations of functions for the creation, modification and analysis of phylogenetic trees. Applications include: generation of trees with specified shapes; tree rearrangement; analysis of tree shape; rooting of trees and extraction of subtrees; calculation and depiction of split support; plotting the position of rogue taxa (Klopfstein & Spasojevic 2019) <doi:10.1371/journal.pone.0212942>; calculation of ancestor-descendant relationships, of 'stemwardness' (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>, and of tree balance (Mir et al. 2013, Lemant et al. 2022) <doi:10.1016/j.mbs.2012.10.005>, <doi:10.1093/sysbio/syac027>; artificial extinction (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>; import and export of trees from Newick, Nexus (Maddison et al. 1997) <doi:10.1093/sysbio/46.4.590>, and TNT <https://www.lillo.org.ar/phylogeny/tnt/> formats; and analysis of splits and cladistic information.

Maintained by Martin R. Smith. Last updated 1 months ago.

evolutionary-biology phylogenetic-trees phylogenetics cpp

1.7 match 21 stars 9.92 score 124 scripts 10 dependents

cran

RCurl:General Network (HTTP/FTP/...) Client Interface for R

A wrapper for 'libcurl' <https://curl.se/libcurl/> Provides functions to allow one to compose general HTTP requests and provides convenient functions to fetch URIs, get & post forms, etc. and process the results returned by the Web server. This provides a great deal of control over the HTTP/FTP/... connection and the form of the request while providing a higher-level interface than is available just using R socket connections. Additionally, the underlying implementation is robust and extensive, supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict, ldap, and also supports cookies, redirects, authentication, etc.

Maintained by CRAN Team. Last updated 8 months ago.

curl

2.0 match 2 stars 8.13 score 1.0k dependents

jefferis

bmp:Read Windows Bitmap (BMP) Images

Reads Windows BMP format images. Currently limited to 8 bit greyscale images and 24,32 bit (A)RGB images. Pure R implementation without external dependencies.

Maintained by Gregory Jefferis. Last updated 8 years ago.

2.5 match 1 stars 6.36 score 39 scripts 62 dependents

rstudio

shinytest2:Testing for Shiny Applications

Automated unit testing of Shiny applications through a headless 'Chromium' browser.

Maintained by Barret Schloerke. Last updated 1 months ago.

cpp

1.3 match 108 stars 12.08 score 704 scripts 1 dependents

wadpac

GGIR:Raw Accelerometer Data Analysis

A tool to process and analyse data collected with wearable raw acceleration sensors as described in Migueles and colleagues (JMPB 2019), and van Hees and colleagues (JApplPhysiol 2014; PLoSONE 2015). The package has been developed and tested for binary data from 'GENEActiv' <https://activinsights.com/>, binary (.gt3x) and .csv-export data from 'Actigraph' <https://theactigraph.com> devices, and binary (.cwa) and .csv-export data from 'Axivity' <https://axivity.com>. These devices are currently widely used in research on human daily physical activity. Further, the package can handle accelerometer data file from any other sensor brand providing that the data is stored in csv format. Also the package allows for external function embedding.

Maintained by Vincent T van Hees. Last updated 2 days ago.

accelerometer activity-recognition circadian-rhythm movement-sensor sleep

1.2 match 109 stars 13.20 score 342 scripts 3 dependents

reinhardfurrer

spam:SPArse Matrix

Set of functions for sparse matrix algebra. Differences with other sparse matrix packages are: (1) we only support (essentially) one sparse matrix format, (2) based on transparent and simple structure(s), (3) tailored for MCMC calculations within G(M)RF. (4) and it is fast and scalable (with the extension package spam64). Documentation about 'spam' is provided by vignettes included in this package, see also Furrer and Sain (2010) <doi:10.18637/jss.v036.i10>; see 'citation("spam")' for details.

Maintained by Reinhard Furrer. Last updated 2 months ago.

fortran openblas cpp

1.7 match 1 stars 9.26 score 420 scripts 433 dependents

rorynolan

filesstrings:Handy File and String Manipulation

This started out as a package for file and string manipulation. Since then, the 'fs' and 'strex' packages emerged, offering functionality previously given by this package (but it's done better in these new ones). Those packages have hence almost pushed 'filesstrings' into extinction. However, it still has a small number of unique, handy file manipulation functions which can be seen in the vignette. One example is a function to remove spaces from all file names in a directory.

Maintained by Rory Nolan. Last updated 1 years ago.

1.8 match 22 stars 8.59 score 632 scripts 4 dependents

edwbaker

sonicscrewdriver:Bioacoustic Analysis and Publication Tools

Provides tools for manipulating sound files for bioacoustic analysis, and preparing analyses these for publication. The package validates that values are physically possible wherever feasible.

Maintained by Ed Baker. Last updated 1 months ago.

bioacoustics ecoacoustics

2.0 match 6 stars 7.12 score 26 scripts

germanrecordlinkage

PPRL:Privacy Preserving Record Linkage

A toolbox for deterministic, probabilistic and privacy-preserving record linkage techniques. Combines the functionality of the 'Merge ToolBox' (<https://www.record-linkage.de>) with current privacy-preserving techniques.

Maintained by Dorothea Rukasz. Last updated 2 years ago.

cpp

5.3 match 2 stars 2.64 score 22 scripts

graemediack

ISO11784Tools:ISO11784 PIT Tag ID Format Converters

Some tools to assist with converting International Organization for Standardization (ISO) standard 11784 (ISO11784) animal ID codes between 4 recognised formats commonly displayed on Passive Integrated Transponder (PIT) tag readers. The most common formats are 15 digit decimal, e.g., 999123456789012, and 13 character hexadecimal 'dot' format, e.g., 3E7.1CBE991A14. These are referred to in this package as isodecimal and isodothex. The other two formats are the raw hexadecimal representation of the ISO11784 binary structure (see <https://en.wikipedia.org/wiki/ISO_11784_and_ISO_11785>). There are two 'flavours' of this format, a left and a right variation. Which flavour a reader happens to output depends on if the developers decided to reverse the binary number or not before converting to hexadecimal, a decision based on the fact that the PIT tags will transmit their binary code Least Significant Bit (LSB) first, or backwards basically.

Maintained by Graeme Diack. Last updated 20 days ago.

3.8 match 1 stars 3.70 score 6 scripts

flr

FLCore:Core Package of FLR, Fisheries Modelling in R

Core classes and methods for FLR, a framework for fisheries modelling and management strategy simulation in R. Developed by a team of fisheries scientists in various countries. More information can be found at <http://flr-project.org/>.

Maintained by Iago Mosqueira. Last updated 10 days ago.

fisheries flr fisheries-modelling

1.6 match 16 stars 8.78 score 956 scripts 23 dependents

ropensci

MODIStsp:Find, Download and Process MODIS Land Products Data

Allows automating the creation of time series of rasters derived from MODIS satellite land products data. It performs several typical preprocessing steps such as download, mosaicking, reprojecting and resizing data acquired on a specified time period. All processing parameters can be set using a user-friendly GUI. Users can select which layers of the original MODIS HDF files they want to process, which additional quality indicators should be extracted from aggregated MODIS quality assurance layers and, in the case of surface reflectance products, which spectral indexes should be computed from the original reflectance bands. For each output layer, outputs are saved as single-band raster files corresponding to each available acquisition date. Virtual files allowing access to the entire time series as a single file are also created. Command-line execution exploiting a previously saved processing options file is also possible, allowing users to automatically update time series related to a MODIS product whenever a new image is available. For additional documentation refer to the following article: Busetto and Ranghetti (2016) <doi:10.1016/j.cageo.2016.08.020>.

Maintained by Luigi Ranghetti. Last updated 8 months ago.

gdal modis modis-data modis-land-products peer-reviewed preprocessing remote-sensing satellite-imagery time-series

1.7 match 156 stars 8.04 score 86 scripts 1 dependents

spkaluzny

splus2R:Supplemental S-PLUS Functionality in R

Currently there are many functions in S-PLUS that are missing in R. To facilitate the conversion of S-PLUS packages to R packages, this package provides some missing S-PLUS functionality in R.

Maintained by Stephen Kaluzny. Last updated 1 years ago.

2.0 match 1 stars 6.56 score 82 scripts 30 dependents

reinhardfurrer

spam64:64-Bit Extension of the SPArse Matrix R Package 'spam'

Provides the Fortran code of the R package 'spam' with 64-bit integers. Loading this package together with the R package spam enables the sparse matrix class spam to handle huge sparse matrices with more than 2^31-1 non-zero elements. Documentation is provided in Gerber, Moesinger and Furrer (2017) <doi:10.1016/j.cageo.2016.11.015>.

Maintained by Reinhard Furrer. Last updated 1 years ago.

fortran openblas

5.0 match 2.58 score 25 scripts 3 dependents

flr

FLasher:Projection and Forecasting of Fish Populations, Stocks and Fleets

Projection of future population and fishery dynamics is carried out for a given set of management targets. A system of equations is solved, using Automatic Differentation (AD), for the levels of effort by fishery (fleet) that will result in the required abundances, catches or fishing mortalities.

Maintained by Iago Mosqueira. Last updated 10 days ago.

forecast fisheries flr cpp

1.8 match 2 stars 6.86 score 254 scripts 6 dependents

dongjli

bravo:Bayesian Screening and Variable Selection

Performs Bayesian variable screening and selection for ultra-high dimensional linear regression models.

Maintained by Dongjin Li. Last updated 4 months ago.

cpp

3.0 match 2 stars 4.08 score 3 scripts

meyerp-software

infotheo:Information-Theoretic Measures

Implements various measures of information theory based on several entropy estimators.

Maintained by Patrick E. Meyer. Last updated 3 years ago.

cpp

2.0 match 6.12 score 480 scripts 44 dependents

bioc

Pedixplorer:Pedigree Functions

Routines to handle family data with a Pedigree object. The initial purpose was to create correlation structures that describe family relationships such as kinship and identity-by-descent, which can be used to model family data in mixed effects models, such as in the coxme function. Also includes a tool for Pedigree drawing which is focused on producing compact layouts without intervention. Recent additions include utilities to trim the Pedigree object with various criteria, and kinship for the X chromosome.

Maintained by Louis Le Nezet. Last updated 1 days ago.

software datarepresentation genetics graphandnetwork visualization kinship pedigree

2.0 match 2 stars 6.08 score 10 scripts

philshea

binfunest:Estimates Parameters of Functions Driving Binomial Random Variables

Provides maximum likelihood estimates of the performance parameters that drive a binomial distribution of observed errors given signal-to-noise ratios, and takes full advantage of zero error observations. High performance communications systems typically have inherent noise sources and other performance limitations that need to be estimated. Measurements made at high signal to noise ratios typically result in zero errors due to limitation in available measurement time. Package includes theoretical performance functions for common modulation schemes (Proakis, "Digital Communications" (1995, <ISBN:0-07-051726-6>)), including polarization shifted QPSK (Agrell & Karlsson (2009, <DOI:10.1109/JLT.2009.2029064>)), and utility functions to work with the performance functions.

Maintained by Philip Shea. Last updated 2 years ago.

2.9 match 4.18 score 1 scripts

freezenik

bamlss:Bayesian Additive Models for Location, Scale, and Shape (and Beyond)

Infrastructure for estimating probabilistic distributional regression models in a Bayesian framework. The distribution parameters may capture location, scale, shape, etc. and every parameter may depend on complex additive terms (fixed, random, smooth, spatial, etc.) similar to a generalized additive model. The conceptual and computational framework is introduced in Umlauf, Klein, Zeileis (2019) <doi:10.1080/10618600.2017.1407325> and the R package in Umlauf, Klein, Simon, Zeileis (2021) <doi:10.18637/jss.v100.i04>.

Maintained by Nikolaus Umlauf. Last updated 5 months ago.

openblas

2.0 match 1 stars 5.76 score 239 scripts 5 dependents

filipezabala

voice:Voice Analysis, Speaker Recognition and Mood Inference via music theory

Voice analysis, speaker recognition and mood inference via music theory.

Maintained by Zabala Filipe J.. Last updated 2 hours ago.

2.0 match 20 stars 5.64 score 88 scripts

rje42

rje:Miscellaneous Useful Functions for Statistics

A series of functions in some way considered useful to the author. These include methods for subsetting tables and generating indices for arrays, conditioning and intervening in probability distributions, generating combinations, fast transformations, and more...

Maintained by Robin Evans. Last updated 12 months ago.

1.7 match 6.50 score 173 scripts 10 dependents

hanase

rlecuyer:R Interface to RNG with Multiple Streams

Provides an interface to the C implementation of the random number generator with multiple independent streams developed by L'Ecuyer et al (2002). The main purpose of this package is to enable the use of this random number generator in parallel R applications.

Maintained by Hana Sevcikova. Last updated 2 years ago.

1.8 match 2 stars 5.64 score 143 scripts 6 dependents

ropensci

dittodb:A Test Environment for Database Requests

Testing and documenting code that communicates with remote databases can be painful. Although the interaction with R is usually relatively simple (e.g. data(frames) passed to and from a database), because they rely on a separate service and the data there, testing them can be difficult to set up, unsustainable in a continuous integration environment, or impossible without replicating an entire production cluster. This package addresses that by allowing you to make recordings from your database interactions and then play them back while testing (or in other contexts) all without needing to spin up or have access to the database your code would typically connect to.

Maintained by Jonathan Keane. Last updated 11 months ago.

1.3 match 82 stars 8.04 score 49 scripts

daqana

dqrng:Fast Pseudo Random Number Generators

Several fast random number generators are provided as C++ header only libraries: The PCG family by O'Neill (2014 <https://www.cs.hmc.edu/tr/hmc-cs-2014-0905.pdf>) as well as the Xoroshiro / Xoshiro family by Blackman and Vigna (2021 <doi:10.1145/3460772>). In addition fast functions for generating random numbers according to a uniform, normal and exponential distribution are included. The latter two use the Ziggurat algorithm originally proposed by Marsaglia and Tsang (2000, <doi:10.18637/jss.v005.i08>). The fast sampling methods support unweighted sampling both with and without replacement. These functions are exported to R and as a C++ interface and are enabled for use with the default 64 bit generator from the PCG family, Xoroshiro128+/++/** and Xoshiro256+/++/** as well as the 64 bit version of the 20 rounds Threefry engine (Salmon et al., 2011, <doi:10.1145/2063384.2063405>) as provided by the package 'sitmo'.

Maintained by Ralf Stubner. Last updated 6 months ago.

random random-distributions random-generation random-sampling rng cpp

0.8 match 42 stars 13.12 score 188 scripts 183 dependents

matherion

limonaid:Working with 'LimeSurvey' Surveys and Responses

'LimeSurvey' is Free/Libre Open Source Software for the development and administrations of online studies, using sophisticated tailoring capabilities to support multiple study designs (see <https://www.limesurvey.org>). This package supports programmatic creation of surveys that can then be imported into 'LimeSurvey', as well as user friendly import of responses from 'LimeSurvey' studies.

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

3.3 match 3.00 score 6 scripts

shaunpwilkinson

insect:Informatic Sequence Classification Trees

Provides tools for probabilistic taxon assignment with informatic sequence classification trees. See Wilkinson et al (2018) <doi:10.7287/peerj.preprints.26812v1>.

Maintained by Shaun Wilkinson. Last updated 4 years ago.

1.7 match 14 stars 5.80 score 91 scripts

famuvie

breedR:Statistical Methods for Forest Genetic Resources Analysts

Statistical tools to build predictive models for the breeders community. It aims to assess the genetic value of individuals under a number of situations, including spatial autocorrelation, genetic/environment interaction and competition. It is under active development as part of the Trees4Future project, particularly developed having forest genetic trials in mind. But can be used for animals or other situations as well.

Maintained by Facundo Muñoz. Last updated 8 months ago.

1.8 match 33 stars 5.44 score 24 scripts

bioc

SNPRelate:Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data

Genome-wide association studies (GWAS) are widely used to investigate the genetic basis of diseases and traits, but they pose many computational challenges. We developed an R package SNPRelate to provide a binary format for single-nucleotide polymorphism (SNP) data in GWAS utilizing CoreArray Genomic Data Structure (GDS) data files. The GDS format offers the efficient operations specifically designed for integers with two bits, since a SNP could occupy only two bits. SNPRelate is also designed to accelerate two key computations on SNP data using parallel computing for multi-core symmetric multiprocessing computer architectures: Principal Component Analysis (PCA) and relatedness analysis using Identity-By-Descent measures. The SNP GDS format is also used by the GWASTools package with the support of S4 classes and generic functions. The extended GDS format is implemented in the SeqArray package to support the storage of single nucleotide variations (SNVs), insertion/deletion polymorphism (indel) and structural variation calls in whole-genome and whole-exome variant data.

Maintained by Xiuwen Zheng. Last updated 5 months ago.

infrastructure genetics statisticalmethod principalcomponent bioinformatics gds-format pca simd snp openblas cpp

0.8 match 104 stars 12.69 score 1.6k scripts 18 dependents

benbruyneel

proteinDiscover:ProteinDiscover

Provides an interface to the data contained in Proteome Discoverer (Thermo Scientific) results.

Maintained by Ben Bruyneel. Last updated 1 years ago.

mass-spectrometry proteomics proteomics-data-analysis

3.2 match 2 stars 3.00 score 2 scripts

gtatters

Thermimage:Thermal Image Analysis

A collection of functions and routines for inputting thermal image video files, plotting and converting binary raw data into estimates of temperature. First published 2015-03-26. Written primarily for research purposes in biological applications of thermal images. v1 included the base calculations for converting thermal image binary values to temperatures. v2 included additional equations for providing heat transfer calculations and an import function for thermal image files (v2.2.3 fixed error importing thermal image to windows OS). v3. Added numerous functions for converting thermal image, videos, rewriting and exporting. v3.1. Added new functions to convert files. v3.2. Fixed the various functions related to finding frame times. v4.0. fixed an error in atmospheric attenuation constants, affecting raw2temp and temp2raw functions. Recommend update for use with long distance calculations. v.4.1.3. changed to frameLocates to reflect change to as.character() to format().

Maintained by Glenn J. Tattersall. Last updated 3 years ago.

animal-physiology heat-exchange heat-flux image-frames temperature thermal-biology thermal-images

1.7 match 169 stars 5.85 score 83 scripts

bnaras

homomorpheR:Homomorphic Computations in R

Homomorphic computations in R for privacy-preserving applications. Currently only the Paillier Scheme is implemented.

Maintained by Balasubramanian Narasimhan. Last updated 3 years ago.

1.7 match 4 stars 5.73 score 18 scripts 1 dependents

data-cleaning

errorlocate:Locate Errors with Validation Rules

Errors in data can be located and removed using validation rules from package 'validate'. See also Van der Loo and De Jonge (2018) <doi:10.1002/9781118897126>, chapter 7.

Maintained by Edwin de Jonge. Last updated 9 months ago.

data-cleaning errors invalidation

1.5 match 22 stars 6.11 score 59 scripts

r-forge

lokern:Kernel Regression Smoothing with Local or Global Plug-in Bandwidth

Kernel regression smoothing with adaptive local or global plug-in bandwidth selection.

Maintained by Martin Maechler. Last updated 3 months ago.

fortran

1.6 match 5.64 score 64 scripts 5 dependents

bioc

gdsfmt:R Interface to CoreArray Genomic Data Structure (GDS) Files

Provides a high-level R interface to CoreArray Genomic Data Structure (GDS) data files. GDS is portable across platforms with hierarchical structure to store multiple scalable array-oriented data sets with metadata information. It is suited for large-scale datasets, especially for data which are much larger than the available random-access memory. The gdsfmt package offers the efficient operations specifically designed for integers of less than 8 bits, since a diploid genotype, like single-nucleotide polymorphism (SNP), usually occupies fewer bits than a byte. Data compression and decompression are available with relatively efficient random access. It is also allowed to read a GDS file in parallel with multiple R processes supported by the package parallel.

Maintained by Xiuwen Zheng. Last updated 2 days ago.

infrastructure dataimport bioinformatics gds-format genomics cpp

0.8 match 18 stars 11.34 score 920 scripts 29 dependents

bioc

smoppix:Analyze Single Molecule Spatial Omics Data Using the Probabilistic Index

Test for univariate and bivariate spatial patterns in spatial omics data with single-molecule resolution. The tests implemented allow for analysis of nested designs and are automatically calibrated to different biological specimens. Tests for aggregation, colocalization, gradients and vicinity to cell edge or centroid are provided.

Maintained by Stijn Hawinkel. Last updated 28 days ago.

transcriptomics spatial singlecell cpp

1.7 match 1 stars 5.18 score 4 scripts

jabiru

csvread:Fast Specialized CSV File Loader

Functions for loading large (10M+ lines) CSV and other delimited files, similar to read.csv, but typically faster and using less memory than the standard R loader. While not entirely general, it covers many common use cases when the types of columns in the CSV file are known in advance. In addition, the package provides a class 'int64', which represents 64-bit integers exactly when reading from a file. The latter is useful when working with 64-bit integer identifiers exported from databases. The CSV file loader supports common column types including 'integer', 'double', 'string', and 'int64', leaving further type transformations to the user.

Maintained by Sergei Izrailev. Last updated 4 months ago.

cpp

2.6 match 3.32 score 29 scripts

ewouddt

BiBitR:R Wrapper for Java Implementation of BiBit

A simple R wrapper for the Java BiBit algorithm from "A biclustering algorithm for extracting bit-patterns from binary datasets" from Domingo et al. (2011) <DOI:10.1093/bioinformatics/btr464>. An simple adaption for the BiBit algorithm which allows noise in the biclusters is also introduced as well as a function to guide the algorithm towards given (sub)patterns. Further, a workflow to derive noisy biclusters from discoverd larger column patterns is included as well.

Maintained by De Troyer Ewoud. Last updated 7 years ago.

2.2 match 1 stars 3.76 score 19 scripts 2 dependents

mrc-ide

dust2:Next Generation dust

Experimental sources for the next generation of dust, which will properly adopt the particle filter, have support for partial parameter updates, support for multiple parameter sets and hopefully better GPU/MPI support.

Maintained by Rich FitzJohn. Last updated 10 days ago.

cpp openmp

1.3 match 6.66 score 32 scripts 2 dependents

weiyangyu

HiGarrote:Nonnegative Garrote Method Incorporating Hierarchical Relationships

An implementation of the nonnegative garrote method that incorporates hierarchical relationships among variables. The core function, HiGarrote, offers an automated approach for analyzing experiments while respecting hierarchical structures among effects. For methodological details, refer to Yu and Joseph (2024) <https://arxiv.org/abs/2411.01383>. This work is supported by U.S. National Foundation grant DMS-2310637.

Maintained by Wei-Yang Yu. Last updated 4 months ago.

cpp

4.0 match 2.00 score

meer-1

PRNG:A Pseudo-Random Number Generator

Provides functions for generating pseudo-random numbers that follow a uniform distribution [0,1]. Randomness tests were conducted using the National Institute of Standards and Technology test suite<https://csrc.nist.gov/pubs/sp/800/22/r1/upd1/final>, along with additional tests. The sequence generated depends on the initial values and parameters. The package includes a linear congruence map as the decision map and three chaotic maps to generate the pseudo-random sequence, which follow a uniform distribution. Other distributions can be generated from the uniform distribution using the Inversion Principle Method and BOX-Muller transformation. Small perturbations in seed values result in entirely different sequences of numbers due to the sensitive nature of the maps being used. The chaotic nature of the maps helps achieve randomness in the generator. Additionally, the generator is capable of producing random bits.

Maintained by Sajad Ahmad Mir. Last updated 6 months ago.

2.5 match 3.18 score 5 scripts

hughparsonage

healthyAddress:Convert Addresses to Standard Inputs

Efficient tools for parsing and standardizing Australian addresses from textual data. It utilizes optimized algorithms to accurately identify and extract components of addresses, such as street names, types, and postcodes, especially for large batched data in contexts where sending addresses to internet services may be slow or inappropriate. The core functionality is built on fast string processing techniques to handle variations in address formats and abbreviations commonly found in Australian address data. Designed for data scientists, urban planners, and logistics analysts, the package facilitates the cleaning and normalization of address information, supporting better data integration and analysis in urban studies, geography, and related fields.

Maintained by Hugh Parsonage. Last updated 2 months ago.

openmp

1.8 match 6 stars 4.42 score 11 scripts

pbiecek

BetaBit:Mini Games from Adventures of Beta and Bit

Three games: proton, frequon and regression. Each one is a console-based data-crunching game for younger and older data scientists. Act as a data-hacker and find Slawomir Pietraszko's credentials to the Proton server. In proton you have to solve four data-based puzzles to find the login and password. There are many ways to solve these puzzles. You may use loops, data filtering, ordering, aggregation or other tools. Only basics knowledge of R is required to play the game, yet the more functions you know, the more approaches you can try. In frequon you will help to perform statistical cryptanalytic attack on a corpus of ciphered messages. This time seven sub-tasks are pushing the bar much higher. Do you accept the challenge? In regression you will test your modeling skills in a series of eight sub-tasks. Try only if ANOVA is your close friend. It's a part of Beta and Bit project. You will find more about the Beta and Bit project at <https://github.com/BetaAndBit/Charts>.

Maintained by Przemyslaw Biecek. Last updated 2 years ago.

3.8 match 1 stars 2.03 score 106 scripts

coffeemuggler

eseis:Environmental Seismology Toolbox

Environmental seismology is a scientific field that studies the seismic signals, emitted by Earth surface processes. This package provides all relevant functions to read/write seismic data files, prepare, analyse and visualise seismic data, and generate reports of the processing history.

Maintained by Michael Dietze. Last updated 4 months ago.

cpp

1.7 match 9 stars 4.42 score 58 scripts

pepijn-devries

AmigaFFH:Commodore Amiga File Format Handler

Modern software often poorly support older file formats. This package intends to handle many file formats that were native to the antiquated Commodore Amiga machine. This package focuses on file types from the older Amiga operating systems (<= 3.0). It will read and write specific file formats and coerces them into more contemporary data.

Maintained by Pepijn de Vries. Last updated 2 months ago.

1.8 match 4 stars 4.21 score 41 scripts

soodoku

aws.alexa:Client for the Amazon Alexa Web Information Services API

Use the Amazon Alexa Web Information Services API to find information about domains, including the kind of content that they carry, how popular are they---rank and traffic history, sites linking to them, among other things. See <https://aws.amazon.com/awis/> for more information.

Maintained by Gaurav Sood. Last updated 4 years ago.

2.0 match 3.65 score 9 scripts 1 dependents

f-silva-archaeo

skyscapeR:Data Analysis and Visualization for Skyscape Archaeology

Data reduction, visualization and statistical analysis of measurements of orientation of archaeological structures, following Silva (2020) <doi:10.1016/j.jas.2020.105138>.

Maintained by Silva Fabio. Last updated 6 months ago.

1.3 match 5 stars 5.31 score 41 scripts

natverse

nat.utils:File System Utility Functions for 'NeuroAnatomy Toolbox'

Utility functions that may be of general interest but are specifically required by the 'NeuroAnatomy Toolbox' ('nat'). Includes functions to provide a basic make style system to update files based on timestamp information, file locking and 'touch' utility. Convenience functions for working with file paths include 'abs2rel', 'split_path' and 'common_path'. Finally there are utility functions for working with 'zip' and 'gzip' files including integrity tests.

Maintained by Gregory Jefferis. Last updated 7 months ago.

nat neuroanatomy-toolbox

1.7 match 4.13 score 15 scripts 3 dependents

robertschneiderfromuqar

CTRing:Density Profiles of Wood from CT Scan Images

Computerized tomography (CT) can be used to assess certain wood properties when wood disks or logs are scanned. Wood density profiles (i.e. variations of wood density from pith to bark) can yield important information used for studies in forest resource assessment, wood quality and dendrochronology studies. The first step consists in transforming grey values from the scan images to density values. The packages then proposes a unique method to automatically locate the pith by combining an adapted Hough Transform method and a one-dimensional edge detector. Tree ring profiles (average ring density, earlywood and latewood density, ring width and percent latewood for each ring) are then obtained.

Maintained by Robert Schneider. Last updated 6 months ago.

3.4 match 2.00 score 2 scripts

r-lib

brio:Basic R Input Output

Functions to handle basic input output, these functions always read and write UTF-8 (8-bit Unicode Transformation Format) files and provide more explicit control over line endings.

Maintained by Gábor Csárdi. Last updated 7 months ago.

0.5 match 56 stars 12.00 score 39 scripts 526 dependents

eddelbuettel

nanotime:Nanosecond-Resolution Time Support for R

Full 64-bit resolution date and time functionality with nanosecond granularity is provided, with easy transition to and from the standard 'POSIXct' type. Three additional classes offer interval, period and duration functionality for nanosecond-resolution timestamps.

Maintained by Dirk Eddelbuettel. Last updated 1 months ago.

datetime datetimes nanosecond-resolution nanoseconds cpp

0.5 match 53 stars 10.91 score 134 scripts 17 dependents

allegropiano

GLDEX:Fitting Single and Mixture of Generalised Lambda Distributions

The fitting algorithms considered in this package have two major objectives. One is to provide a smoothing device to fit distributions to data using the weight and unweighted discretised approach based on the bin width of the histogram. The other is to provide a definitive fit to the data set using the maximum likelihood and quantile matching estimation. Other methods such as moment matching, starship method, L moment matching are also provided. Diagnostics on goodness of fit can be done via qqplots, KS-resample tests and comparing mean, variance, skewness and kurtosis of the data with the fitted distribution. References include the following: Karvanen and Nuutinen (2008) "Characterizing the generalized lambda distribution by L-moments" <doi:10.1016/j.csda.2007.06.021>, King and MacGillivray (1999) "A starship method for fitting the generalised lambda distributions" <doi:10.1111/1467-842X.00089>, Su (2005) "A Discretized Approach to Flexibly Fit Generalized Lambda Distributions to Data" <doi:10.22237/jmasm/1130803560>, Su (2007) "Nmerical Maximum Log Likelihood Estimation for Generalized Lambda Distributions" <doi:10.1016/j.csda.2006.06.008>, Su (2007) "Fitting Single and Mixture of Generalized Lambda Distributions to Data via Discretized and Maximum Likelihood Methods: GLDEX in R" <doi:10.18637/jss.v021.i09>, Su (2009) "Confidence Intervals for Quantiles Using Generalized Lambda Distributions" <doi:10.1016/j.csda.2009.02.014>, Su (2010) "Chapter 14: Fitting GLDs and Mixture of GLDs to Data using Quantile Matching Method" <doi:10.1201/b10159>, Su (2010) "Chapter 15: Fitting GLD to data using GLDEX 1.0.4 in R" <doi:10.1201/b10159>, Su (2015) "Flexible Parametric Quantile Regression Model" <doi:10.1007/s11222-014-9457-1>, Su (2021) "Flexible parametric accelerated failure time model"<doi:10.1080/10543406.2021.1934854>.

Maintained by Steve Su. Last updated 2 years ago.

1.8 match 3.05 score 93 scripts 2 dependents

vpetrosyan

CTD:A Method for 'Connecting The Dots' in Weighted Graphs

A method for pattern discovery in weighted graphs as outlined in Thistlethwaite et al. (2021) <doi:10.1371/journal.pcbi.1008550>. Two use cases are achieved: 1) Given a weighted graph and a subset of its nodes, do the nodes show significant connectedness? 2) Given a weighted graph and two subsets of its nodes, are the subsets close neighbors or distant?

Maintained by Varduhi Petrosyan. Last updated 7 months ago.

2.0 match 2.70 score 1 scripts

bioc

oncoscanR:Secondary analyses of CNV data (HRD and more)

The software uses the copy number segments from a text file and identifies all chromosome arms that are globally altered and computes various genome-wide scores. The following HRD scores (characteristic of BRCA-mutated cancers) are included: LST, HR-LOH, nLST and gLOH. the package is tailored for the ThermoFisher Oncoscan assay analyzed with their Chromosome Alteration Suite (ChAS) but can be adapted to any input.

Maintained by Yann Christinat. Last updated 5 months ago.

copynumbervariation microarray software

1.2 match 2 stars 4.60 score 6 scripts

obreschkow

cooltools:Practical Tools for Scientific Computations and Visualizations

Collection of routines for efficient scientific computations in physics and astrophysics. These routines include utility functions, numerical computation tools, as well as visualisation tools. They can be used, for example, for generating random numbers from spherical and custom distributions, information and entropy analysis, special Fourier transforms, two-point correlation estimation (e.g. as in Landy & Szalay (1993) <doi:10.1086/172900>), binning & gridding of point sets, 2D interpolation, Monte Carlo integration, vector arithmetic and coordinate transformations. Also included is a non-exhaustive list of important constants and cosmological conversion functions. The graphics routines can be used to produce and export publication-ready scientific plots and movies, e.g. as used in Obreschkow et al. (2020, MNRAS Vol 493, Issue 3, Pages 4551–4569). These routines include special color scales, projection functions, and bitmap handling routines.

Maintained by Danail Obreschkow. Last updated 3 months ago.

cpp

1.7 match 1 stars 3.17 score 21 scripts

daniel-dok

phenex:Auxiliary Functions for Phenological Data Analysis

Provides some easy-to-use functions for spatial analyses of (plant-) phenological data sets and satellite observations of vegetation.

Maintained by Daniel Doktor. Last updated 8 years ago.

2.3 match 2 stars 2.28 score 32 scripts 1 dependents

kwb-r

dwc.wells:A Package for Condition Predictions for Drinking Water Wells

This package allows to predict the condition of a drinking water well based on ML models. The models are trained with results from pump tests and a large set of input variables e.g. the well material, the age and the number of regenerations.

Maintained by Michael Rustler. Last updated 3 years ago.

machine-learning project-dwc

1.6 match 3.00 score 7 scripts

cdriveraus

ctsem:Continuous Time Structural Equation Modelling

Hierarchical continuous (and discrete) time state space modelling, for linear and nonlinear systems measured by continuous variables, with limited support for binary data. The subject specific dynamic system is modelled as a stochastic differential equation (SDE) or difference equation, measurement models are typically multivariate normal factor models. Linear mixed effects SDE's estimated via maximum likelihood and optimization are the default. Nonlinearities, (state dependent parameters) and random effects on all parameters are possible, using either max likelihood / max a posteriori optimization (with optional importance sampling) or Stan's Hamiltonian Monte Carlo sampling. See <https://github.com/cdriveraus/ctsem/raw/master/vignettes/hierarchicalmanual.pdf> for details. Priors may be used. For the conceptual overview of the hierarchical Bayesian linear SDE approach, see <https://www.researchgate.net/publication/324093594_Hierarchical_Bayesian_Continuous_Time_Dynamic_Modeling>. Exogenous inputs may also be included, for an overview of such possibilities see <https://www.researchgate.net/publication/328221807_Understanding_the_Time_Course_of_Interventions_with_Continuous_Time_Dynamic_Models> . Stan based functions are not available on 32 bit Windows systems at present. <https://cdriver.netlify.app/> contains some tutorial blog posts.

Maintained by Charles Driver. Last updated 12 days ago.

stochastic-differential-equations time-series cpp

0.5 match 42 stars 9.58 score 366 scripts 1 dependents

eddelbuettel

ulid:Generate Universally Unique 'Lexicographically' 'Sortable' Identifiers

Universally unique identifiers ('UUIDs') can be sub-optimal for many uses-cases because they are not the most character efficient way of encoding 128 bits of randomness; v1/v2 versions are impractical in many environments, as they require access to a unique, stable MAC address; v3/v5 versions require a unique seed and produce randomly distributed IDs, which can cause fragmentation in many data structures; v4 provides no other information than randomness which can cause fragmentation in many data structures. Providing an alternative, 'ULIDs' (<https://github.com/ulid/spec>) have 128-bit compatibility with 'UUID', 1.21e+24 unique 'ULIDs' per millisecond, support standard (text) sorting, canonically encoded as a 26 character string, as opposed to the 36 character 'UUID', use 'base32' encoding for better efficiency and readability (5 bits per character), are case insensitive, have no special characters (i.e. are 'URL' safe) and have a monotonic sort order (correctly detects and handles the same millisecond).

Maintained by Dirk Eddelbuettel. Last updated 9 months ago.

ulid uuid cpp

0.9 match 30 stars 4.91 score 6 scripts

rucknium

rbch:Extraction and Analysis of Data from the Bitcoin Cash (BCH) Blockchain

Issues RPC-JSON calls to 'bitcoind', the daemon of Bitcoin Cash (BCH), to extract transaction data from the blockchain. BCH is a fork of Bitcoin that permits a greater number of transactions per second. A BCH daemon is available under an MIT license from the Bitcoin Unlimited website <https://www.bitcoinunlimited.info>.

Maintained by Rucknium. Last updated 4 months ago.

1.7 match 3 stars 2.48 score 7 scripts

ggseg

ggseg3d:Tri-Surface Mesh Plots for Brain Atlases

Mainly contains a plotting function ggseg3d(), and data of two standard brain atlases (Desikan-Killiany and aseg). By far, the largest bit of the package is the data for each of the atlases. The functions and data enable users to plot tri-surface mesh plots of brain atlases, and customise these by projecting colours onto the brain segments based on values in their own data sets. Functions are wrappers for 'plotly'. Mowinckel & Vidal-Piñeiro (2020) <doi:10.1177/2515245920928009>.

Maintained by Athanasia Mo Mowinckel. Last updated 1 years ago.

0.5 match 36 stars 7.62 score 150 scripts 13 dependents

bnprks

BPCells:Single Cell Counts Matrices to PCA

> Efficient operations for single cell ATAC-seq fragments and RNA counts matrices. Interoperable with standard file formats, and introduces efficient bit-packed formats that allow large storage savings and increased read speeds.

Maintained by Benjamin Parks. Last updated 1 months ago.

zlib hdf5 cpp

0.5 match 184 stars 7.48 score 172 scripts

cran

adana:Adaptive Nature-Inspired Algorithms for Hybrid Genetic Optimization

The Genetic Algorithm (GA) is a type of optimization method of Evolutionary Algorithms. It uses the biologically inspired operators such as mutation, crossover, selection and replacement.Because of their global search and robustness abilities, GAs have been widely utilized in machine learning, expert systems, data science, engineering, life sciences and many other areas of research and business. However, the regular GAs need the techniques to improve their efficiency in computing time and performance in finding global optimum using some adaptation and hybridization strategies. The adaptive GAs (AGA) increase the convergence speed and success of regular GAs by setting the parameters crossover and mutation probabilities dynamically. The hybrid GAs combine the exploration strength of a stochastic GAs with the exact convergence ability of any type of deterministic local search algorithms such as simulated-annealing, in addition to other nature-inspired algorithms such as ant colony optimization, particle swarm optimization etc. The package 'adana' includes a rich working environment with its many functions that make possible to build and work regular GA, adaptive GA, hybrid GA and hybrid adaptive GA for any kind of optimization problems. Cebeci, Z. (2021, ISBN: 9786254397448).

Maintained by Erkut Tekeli. Last updated 3 years ago.

3.7 match 1.00 score 9 scripts

coolbutuseless

c64vice:Interface to Binary Monitor in VICE C64 Emulator

Interface to the binary monitor in VICE - the c64 emulator.

Maintained by mikefc. Last updated 1 years ago.

1.8 match 2 stars 2.08 score 12 scripts

jleivacuadrado

VeryLargeIntegers:Store and Operate with Arbitrarily Large Integers

Multi-precision library that allows to store and operate with arbitrarily big integers without loss of precision. It includes a large list of tools to work with them, like: - Arithmetic and logic operators - Modular-arithmetic operators - Computer Number Theory utilities - Probabilistic primality tests - Factorization algorithms - Random generators of diferent types of integers.

Maintained by Javier Leiva Cuadrado. Last updated 2 years ago.

cpp

1.8 match 2.00 score 33 scripts 1 dependents

cran

audiometry:Standard Conform Pure Tone Audiometry (PTA) Plots

Facilitates plotting audiometric data (mostly) by preparing the coordinate system according to standards, given e. g. in American Speech-Language-Hearing Association (2005), <doi:10.1044/policy.GL2005-00014>.

Maintained by Bernhard Lehnert. Last updated 4 years ago.

1.5 match 2.30 score

ijayc

shinyr:Data Insights Through Inbuilt R Shiny App

It builds dynamic R shiny based dashboards to analyze any CSV files. It provides simple dashboard design to subset the data, perform exploratory data analysis and preliminary machine learning (supervised and unsupervised). It also provides filters based on columns of interest.

Maintained by Jayachandra N. Last updated 1 months ago.

1.1 match 3.00 score

erblast

easyalluvial:Generate Alluvial Plots with a Single Line of Code

Alluvial plots are similar to sankey diagrams and visualise categorical data over multiple dimensions as flows. (Rosvall M, Bergstrom CT (2010) Mapping Change in Large Networks. PLoS ONE 5(1): e8694. <doi:10.1371/journal.pone.0008694> Their graphical grammar however is a bit more complex then that of a regular x/y plots. The 'ggalluvial' package made a great job of translating that grammar into 'ggplot2' syntax and gives you many options to tweak the appearance of an alluvial plot, however there still remains a multi-layered complexity that makes it difficult to use 'ggalluvial' for explorative data analysis. 'easyalluvial' provides a simple interface to this package that allows you to produce a decent alluvial plot from any dataframe in either long or wide format from a single line of code while also handling continuous data. It is meant to allow a quick visualisation of entire dataframes with a focus on different colouring options that can make alluvial plots a great tool for data exploration.

Maintained by Bjoern Koneswarakantha. Last updated 1 years ago.

0.5 match 110 stars 6.13 score 81 scripts 1 dependents

cran

dotCall64:Enhanced Foreign Function Interface Supporting Long Vectors

Provides .C64(), which is an enhanced version of .C() and .Fortran() from the foreign function interface. .C64() supports long vectors, arguments of type 64-bit integer, and provides a mechanism to avoid unnecessary copies of read-only and write-only arguments. This makes it a convenient and fast interface to C/C++ and Fortran code.

Maintained by Reinhard Furrer. Last updated 5 months ago.

fortran openmp

0.5 match 5.90 score 439 dependents

cran

thermocouple:Temperature Measurement with Thermocouples, RTD and IC Sensors

Temperature measurement data, equations and methods for thermocouples, wire RTD, thermistors, IC thermometers, bimetallic strips and the ITS-90.

Maintained by Jose Gama. Last updated 10 years ago.

1.8 match 1.68 score 48 scripts

coolbutuseless

fastpng:Read and Write PNG Files with Configurable Decoder/Encoder Options

Read and write PNG images with arrays, rasters, native rasters, numeric arrays, integer arrays, raw vectors and indexed values. This PNG encoder exposes configurable internal options enabling the user to select a speed-size tradeoff. For example, disabling compression can speed up writing PNG by a factor of 50. Multiple image formats are supported including raster, native rasters, and integer and numeric arrays at color depths of 1, 2, 3 or 4. 16-bit images are also supported. This implementation uses the 'libspng' 'C' library which is available from <https://github.com/randy408/libspng/>.

Maintained by Mike Cheng. Last updated 2 months ago.

0.5 match 18 stars 5.86 score 7 scripts

dipterix

rutabaga:Simple R Tools for Analysis and Visualizations

Provides functions (R, C++) to speed up array calculations. Includes various tools for prettier visualizations via R base plots.

Maintained by Zhengjia Wang. Last updated 3 years ago.

1.7 match 1.70 score 2 scripts

eddelbuettel

RcppBDT:'Rcpp' Bindings for the Boost Date_Time Library

Access to Boost Date_Time functionality for dates, durations (both for days and date time objects), time zones, and posix time ('ptime') is provided by using 'Rcpp modules'. The posix time implementation can support high-resolution of up to nano-second precision by using 96 bits (instead of 64 with R) to present a 'ptime' object (but this needs recompilation with a #define set).

Maintained by Dirk Eddelbuettel. Last updated 6 days ago.

cpp

0.5 match 17 stars 5.01 score 6 scripts 1 dependents

frenchrh

klovan:Geostatistics Methods and Klovan Data

A comprehensive set of geostatistical, visual, and analytical methods, in conjunction with the expanded version of the acclaimed J.E. Klovan's mining dataset, are included in 'klovan'. This makes the package an excellent learning resource for Principal Component Analysis (PCA), Factor Analysis (FA), kriging, and other geostatistical techniques. Originally published in the 1976 book 'Geological Factor Analysis', the included mining dataset was assembled by Professor J. E. Klovan of the University of Calgary. Being one of the first applications of FA in the geosciences, this dataset has significant historical importance. As a well-regarded and published dataset, it is an excellent resource for demonstrating the capabilities of PCA, FA, kriging, and other geostatistical techniques in geosciences. For those interested in these methods, the 'klovan' datasets provide a valuable and illustrative resource. Note that some methods require the 'RGeostats' package. Please refer to the README or Additional_repositories for installation instructions. This material is based upon research in the Materials Data Science for Stockpile Stewardship Center of Excellence (MDS3-COE), and supported by the Department of Energy's National Nuclear Security Administration under Award Number DE-NA0004104.

Maintained by Roger H French. Last updated 1 years ago.

1.0 match 2.48 score

wurli

ggborderline:Line Plots that Pop

A set of geometries to make line plots a little bit nicer. Use along with 'ggplot2' to: - Improve the clarity of line plots with many overlapping lines - Draw more realistic worms.

Maintained by Jacob Scott. Last updated 1 years ago.

ggplot2-enhancements r-visualisation

0.5 match 29 stars 4.77 score 41 scripts

mlverse

wav:Read and Write WAV Files

Efficiently read and write Waveform (WAV) audio files <https://en.wikipedia.org/wiki/WAV>. Support for unsigned 8 bit Pulse-code modulation (PCM), signed 12, 16, 24 and 32 bit PCM and other encodings.

Maintained by Daniel Falbel. Last updated 2 years ago.

audio wav cpp

0.8 match 1 stars 2.70 score 6 scripts

yongwoo-eg-kim

hightR:HIGHT Algorithm

HIGHT(HIGh security and light weigHT) algorithm is a block cipher encryption algorithm developed to provide confidentiality in computing environments that demand low power consumption and lightweight, such as RFID(Radio-Frequency Identification) and USN(Ubiquitous Sensor Network), or in mobile environments that require low power consumption and lightweight, such as smartphones and smart cards. Additionally, it is designed with a simple structure that enables it to be used with basic arithmetic operations, XOR, and circular shifts in 8-bit units. This algorithm was designed to consider both safety and efficiency in a very simple structure suitable for limited environments, compared to the former 128-bit encryption algorithm SEED. In December 2010, it became an ISO(International Organization for Standardization) standard. The detailed procedure is described in Hong et al. (2006) <doi:10.1007/11894063_4>.

Maintained by Yongwoo Kim. Last updated 2 years ago.

algorithm cryptography hight

0.8 match 1 stars 2.70 score

kolassa-dev

MultNonParam:Multivariate Nonparametric Methods

A collection of multivariate nonparametric methods, selected in part to support an MS level course in nonparametric statistical methods. Methods include adjustments for multiple comparisons, implementation of multivariate Mann-Whitney-Wilcoxon testing, inversion of these tests to produce a confidence region, some permutation tests for linear models, and some algorithms for calculating exact probabilities associated with one- and two- stage testing involving Mann-Whitney-Wilcoxon statistics. Supported by grant NSF DMS 1712839. See Kolassa and Seifu (2013) <doi:10.1016/j.acra.2013.03.006>.

Maintained by John E. Kolassa. Last updated 2 years ago.

fortran openblas

1.8 match 1.18 score 15 scripts

barcaroli

QGA:Quantum Genetic Algorithm

Function that implements the Quantum Genetic Algorithm, first proposed by Han and Kim in 2000. This is an R implementation of the 'python' application developed by Lahoz-Beltra (<https://github.com/ResearchCodesHub/QuantumGeneticAlgorithms>). Each optimization problem is represented as a maximization one, where each solution is a sequence of (qu)bits. Following the quantum paradigm, these qubits are in a superposition state: when measuring them, they collapse in a 0 or 1 state. After measurement, the fitness of the solution is calculated as in usual genetic algorithms. The evolution at each iteration is oriented by the application of two quantum gates to the amplitudes of the qubits: (1) a rotation gate (always); (2) a Pauli-X gate (optionally). The rotation is based on the theta angle values: higher values allow a quicker evolution, and lower values avoid local maxima. The Pauli-X gate is equivalent to the classical mutation operator and determines the swap between alfa and beta amplitudes of a given qubit. The package has been developed in such a way as to permit a complete separation between the engine, and the particular problem subject to combinatorial optimization.

Maintained by Giulio Barcaroli. Last updated 6 months ago.

0.5 match 4.00 score 18 scripts

wrathematics

kazaam:Tools for Tall Distributed Matrices

Many data science problems reduce to operations on very tall, skinny matrices. However, sometimes these matrices can be so tall that they are difficult to work with, or do not even fit into main memory. One strategy to deal with such objects is to distribute their rows across several processors. To this end, we offer an 'S4' class for tall, skinny, distributed matrices, called the 'shaq'. We also provide many useful numerical methods and statistics operations for operating on these distributed objects. The naming is a bit "tongue-in-cheek", with the class a play on the fact that 'Shaquille' 'ONeal' ('Shaq') is very tall, and he starred in the film 'Kazaam'.

Maintained by Drew Schmidt. Last updated 8 years ago.

openblas

0.5 match 3.82 score 133 scripts

bpfaff

rbtc:Bitcoin API

Implementation of the RPC-JSON API for Bitcoin and utility functions for address creation and content analysis of the blockchain.

Maintained by Bernhard Pfaff. Last updated 5 months ago.

1.7 match 1.15 score 14 scripts

pbiecek

proton:The Proton Game

'The Proton Game' is a console-based data-crunching game for younger and older data scientists. Act as a data-hacker and find Slawomir Pietraszko's credentials to the Proton server. You have to solve four data-based puzzles to find the login and password. There are many ways to solve these puzzles. You may use loops, data filtering, ordering, aggregation or other tools. Only basics knowledge of R is required to play the game, yet the more functions you know, the more approaches you can try. The knowledge of dplyr is not required but may be very helpful. This game is linked with the ,,Pietraszko's Cave'' story available at http://biecek.pl/BetaBit/Warsaw. It's a part of Beta and Bit series. You will find more about the Beta and Bit series at http://biecek.pl/BetaBit.

Maintained by Przemysław Biecek. Last updated 9 years ago.

0.8 match 2.49 score 312 scripts

terminological

roogledocs:R Wrapper For Googledocs Java Library

Programmatically substitute images, data and tables into a google doc or presentation. R library to perform limited interactions with google docs and slides in R via the Java API library. The purpose being to support google docs as a platform for interactive development and documentation of data analysis in R for scientific publication, although it is not limited to this purpose. The workflow supported is a parallel documentation and analysis where a team of people are working collaboratively on documentation, whilst at the same time analysis is being performed and results updated repeatedly as a result of new data. In this environment updating numeric results, tabular data and figures in word documents manually becomes annoying. With roogledocs you can automate this a bit like a RMarkdown document, but with the added benefit that the content can be updated independently of the analysis, by the wider team.

Maintained by Rob Challen. Last updated 11 months ago.

openjdk

0.5 match 4 stars 3.78 score 1 scripts

cran

Rdiagnosislist:Manipulate SNOMED CT Diagnosis Lists

Functions and methods for manipulating 'SNOMED CT' concepts. The package contains functions for loading the 'SNOMED CT' release into a convenient R environment, selecting 'SNOMED CT' concepts using regular expressions, and navigating the 'SNOMED CT' ontology. It provides the 'SNOMEDconcept' S3 class for a vector of 'SNOMED CT' concepts (stored as 64-bit integers) and the 'SNOMEDcodelist' S3 class for a table of concepts IDs with descriptions. The package can be used to construct sets of 'SNOMED CT' concepts for research (<doi:10.1093/jamia/ocac158>). For more information about 'SNOMED CT' visit <https://www.snomed.org/>.

Maintained by Anoop D. Shah. Last updated 2 months ago.

0.5 match 1 stars 3.60 score

reviewburner

AnimalSequences:Analyse Animal Sequential Behaviour and Communication

All animal behaviour occurs sequentially. The package has a number of functions to format sequence data from different sources, to analyse sequential behaviour and communication in animals. It also has functions to plot the data and to calculate the entropy of sequences.

Maintained by Alex Mielke. Last updated 6 months ago.

1.8 match 1.00 score

obreschkow

docore:Utility Functions for Scientific Coding

Basic routines used in scientific coding, such as timing routines, vector/array handing functions and I/O support routines.

Maintained by Danail Obreschkow. Last updated 3 years ago.

1.7 match 1.00 score

hypertidy

ximage:Draw Images of Raster Data and Related Adornments

Draw images easily and as if doing that was considered desirable or even essential to be able to do. Set up a plot with an image, specify where that image should be placed. Image plot by default reflects the index of the image data itself, or can be specified in simple extent terms 'xmin,xmax,ymin,ymax'. Numeric matrices, integer arrays, byte arrays, character arrays, and native rasters are (or will be) supported. A little bit like 'image()' and 'rasterImage()' from the 'graphics' package but with the good features celebrated and made easier to use.

Maintained by Michael D. Sumner. Last updated 7 months ago.

0.5 match 8 stars 3.25 score 22 scripts

jdench

rSHAPE:Simulated Haploid Asexual Population Evolution

In silico experimental evolution offers a cost-and-time effective means to test evolutionary hypotheses. Existing evolutionary simulation tools focus on simulations in a limited experimental framework, and tend to report on only the results presumed of interest by the tools designer. The R-package for Simulated Haploid Asexual Population Evolution ('rSHAPE') addresses these concerns by implementing a robust simulation framework that outputs complete population demographic and genomic information for in silico evolving communities. Allowing more than 60 parameters to be specified, 'rSHAPE' simulates evolution across discrete time-steps for an evolving community of haploid asexual populations with binary state genomes. These settings are for the current state of 'rSHAPE' and future steps will be to increase the breadth of evolutionary conditions permitted. At present, most effort was placed into permitting varied growth models to be simulated (such as constant size, exponential growth, and logistic growth) as well as various fitness landscape models to reflect the evolutionary landscape (e.g.: Additive, House of Cards - Stuart Kauffman and Simon Levin (1987) <doi:10.1016/S0022-5193(87)80029-2>, NK - Stuart A. Kauffman and Edward D. Weinberger (1989) <doi:10.1016/S0022-5193(89)80019-0>, Rough Mount Fuji - Neidhart, Johannes and Szendro, Ivan G and Krug, Joachim (2014) <doi:10.1534/genetics.114.167668>). This package includes numerous functions though users will only need defineSHAPE(), runSHAPE(), shapeExperiment() and summariseExperiment(). All other functions are called by these main functions and are likely only to be on interest for someone wishing to develop 'rSHAPE'. Simulation results will be stored in files which are exported to the directory referenced by the shape_workDir option (defaults to tempdir() but do change this by passing a folderpath argument for workDir when calling defineSHAPE() if you plan to make use of your results beyond your current session). 'rSHAPE' will generate numerous replicate simulations for your defined range of experimental parameters. The experiment will be built under the experimental working directory (i.e.: referenced by the option shape_workDir set using defineSHAPE() ) where individual replicate simulation results will be stored as well as processed results which I have made in an effort to facilitate analyses by automating collection and processing of the potentially thousands of files which will be created. On that note, 'rSHAPE' implements a robust and flexible framework with highly detailed output at the cost of computational efficiency and potentially requiring significant disk space (generally gigabytes but up to tera-bytes for very large simulation efforts). So, while 'rSHAPE' offers a single framework in which we can simulate evolution and directly compare the impacts of a wide range of parameters, it is not as quick to run as other in silico simulation tools which focus on a single scenario with limited output. There you have it, 'rSHAPE' offers you a less restrictive in silico evolutionary playground than other tools and I hope you enjoy testing your hypotheses.

Maintained by Jonathan Dench. Last updated 6 years ago.

1.6 match 1.00 score

cran

ufs:A Collection of Utilities

This is a new version of the 'userfriendlyscience' package, which has grown a bit unwieldy. Therefore, distinct functionalities are being 'consciously uncoupled' into different packages. This package contains the general-purpose tools and utilities (see the 'behaviorchange' package, the 'rosetta' package, and the soon-to-be-released 'scd' package for other functionality), and is the most direct 'successor' of the original 'userfriendlyscience' package. For example, this package contains a number of basic functions to create higher level plots, such as diamond plots, to easily plot sampling distributions, to generate confidence intervals, to plan study sample sizes for confidence intervals, and to do some basic operations such as (dis)attenuate effect size estimates.

Maintained by Gjalt-Jorn Peters. Last updated 1 years ago.

0.5 match 2.95 score 3 dependents

srika1919

pPCA:Partial Principal Component Analysis of Partitioned Large Sparse Matrices

Performs partial principal component analysis of a large sparse matrix. The matrix may be stored as a list of matrices to be concatenated (implicitly) horizontally. Useful application includes cases where the number of total nonzero entries exceed the capacity of 32 bit integers (e.g., with large Single Nucleotide Polymorphism data).

Maintained by Srika Raja. Last updated 5 months ago.

cpp

0.5 match 2.78 score

whateverliu

FLSSS:Mining Rigs for Problems in the Subset Sum Family

Specialized solvers for combinatorial optimization problems in the Subset Sum family. The solvers differ from the mainstream in the options of (i) restricting subset size, (ii) bounding subset elements, (iii) mining real-value multisets with predefined subset sum errors, (iv) finding one or more subsets in limited time. A novel algorithm for mining the one-dimensional Subset Sum induced algorithms for the multi-Subset Sum and the multidimensional Subset Sum. The multi-threaded framework for the latter offers exact algorithms to the multidimensional Knapsack and the Generalized Assignment problems. Historical updates include (a) renewed implementation of the multi-Subset Sum, multidimensional Knapsack and Generalized Assignment solvers; (b) availability of bounding solution space in the multidimensional Subset Sum; (c) fundamental data structure and architectural changes for enhanced cache locality and better chance of SIMD vectorization; (d) option of mapping floating-point instance to compressed 64-bit integer instance with user-controlled precision loss, which could yield substantial speedup due to the dimension reduction and efficient compressed integer arithmetic via bit-manipulations; (e) distributed computing infrastructure for multidimensional subset sum; (f) arbitrary-precision zero-margin-of-error multidimensional Subset Sum accelerated by a simplified Bloom filter. The package contains a copy of xxHash from <https://github.com/Cyan4973/xxHash>. Package vignette (<doi:10.48550/arXiv.1612.04484>) detailed a few historical updates. Functions prefixed with 'aux' (auxiliary) are independent implementations of published algorithms for solving optimization problems less relevant to Subset Sum.

Maintained by Charlie Wusuo Liu. Last updated 2 months ago.

gmp cpp

0.8 match 1 stars 1.78 score 20 scripts

rogiersbart

ti:A single-channel UINT8 TIFF toolkit

The {ti} package provides a set of tools for working with single-channel unsigned 8-bit integer TIFF images.

Maintained by Bart Rogiers. Last updated 9 months ago.

0.5 match 2.46 score 58 scripts

haydarde

CryptRndTest:Statistical Tests for Cryptographic Randomness

Performs cryptographic randomness tests on a sequence of random integers or bits. Included tests are greatest common divisor, birthday spacings, book stack, adaptive chi-square, topological binary, and three random walk tests (Ryabko and Monarev, 2005) <doi:10.1016/j.jspi.2004.02.010>. Tests except greatest common divisor and birthday spacings are not covered by standard test suites. In addition to the chi-square goodness-of-fit test, results of Anderson-Darling, Kolmogorov-Smirnov, and Jarque-Bera tests are also generated by some of the cryptographic randomness tests.

Maintained by Haydar Demirhan. Last updated 3 years ago.

0.5 match 2.20 score 16 scripts

epiforecasts

stanedit:Facilitate editing of stan models

Provides functionality for extracting particular bits of stan models as well as removing and adding lines.

Maintained by Sebastian Funk. Last updated 4 months ago.

probabilistic-programming stan

0.5 match 2 stars 2.00 score 1 scripts

cran

radlibs:Build Your Own Madlibs!

Make your phrase or sentence into something funny! Pass a string with the keywords in, and get out a bit of humor.

Maintained by Stephanie Kirmer. Last updated 5 years ago.

0.5 match 1.70 score 1 scripts

skranz

MetaStudies:Shiny app and function for Meta studies following Andrews and Kasy (2019).

This package mainly consists of Maximilan Kasy's code of his shiny app for MetaStudies on publication bias. I added some stuff, rewrote it a bit and put everything into an R package. The original code is here: https://github.com/maxkasy/MetaStudiesApp The code is based on Andrews and Kasy (2019). In particular, I added code to run misspecification tests that will be explained in Kranz and Pütz (2021). References: - Andrews, Isaiah and Maximilian Kasy. 2019. “Identification of and correction for publication bias.” American Economic Review 109 (8): 2766-94. - Kranz, Sebastian and Peter Pütz. 2021 “Rounding and other pitfalls in meta-studies on p-hacking and publication bias. A comment on Brodeur et al. (2020)”, working paper.

Maintained by Sebastian Kranz. Last updated 4 years ago.

0.5 match 1.70 score 5 scripts

cran

correlbinom:Correlated Binomial Probabilities

Calculates the probabilities of k successes given n trials of a binomial random variable with non-negative correlation across trials. The function takes as inputs the scalar values the level of correlation or association between trials, the success probability, the number of trials, an optional input specifying the number of bits of precision used in the calculation, and an optional input specifying whether the calculation approach to be used is from Witt (2014) <doi:10.1080/03610926.2012.725148> or from Kuk (2004) <doi:10.1046/j.1467-9876.2003.05369.x>. The output is a (trials+1)-dimensional vector containing the likelihoods of 0, 1, ..., trials successes.

Maintained by Gary Witt. Last updated 8 years ago.

0.5 match 1.00 score 1 scripts

cran

FITSio:FITS (Flexible Image Transport System) Utilities

Utilities to read and write files in the FITS (Flexible Image Transport System) format, a standard format in astronomy (see e.g. <https://en.wikipedia.org/wiki/FITS> for more information). Present low-level routines allow: reading, parsing, and modifying FITS headers; reading FITS images (multi-dimensional arrays); reading FITS binary and ASCII tables; and writing FITS images (multi-dimensional arrays). Higher-level functions allow: reading files composed of one or more headers and a single (perhaps multidimensional) image or single table; reading tables into data frames; generating vectors for image array axes; scaling and writing images as 16-bit integers. Known incompletenesses are reading random group extensions, as well as complex and array descriptor data types in binary tables.

Maintained by Andrew Harris. Last updated 4 years ago.

0.5 match 1 stars 1.00 score