Showing 149 of total 149 results (show query)
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 dependentsrstudio
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 dependentsthierryo
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.
qrcodeqrcode-generatorr-project
18.7 match 44 stars 7.56 score 456 scripts 7 dependents8-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.
analyticsapigooglegoogleanalyticsrgoogleauthr
13.3 match 262 stars 10.11 score 680 scripts 1 dependentsdmpe
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.
bitlyisgdshorten-urlsshortenershorturlurl
17.6 match 21 stars 6.70 score 53 scripts 1 dependentscoolbutuseless
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 scriptscran
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.
15.3 match 1 stars 6.35 score 36 dependentswrathematics
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-matrixhpclinear-algebramatrixfortranopenblasopenmp
8.7 match 46 stars 10.53 score 228 scripts 42 dependentseitsupi
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.
16.6 match 40 stars 4.86 score 1 scriptsbaddstats
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-bitclippercomputational-geometryminkowski-sumpolygon-clipping-algorithmpolygon-intersectionpolygon-offsettingpolygon-unionpolygonscpp
7.5 match 19 stars 10.31 score 27 scripts 553 dependentsmartinzaefferer
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 scriptsbioc
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.
infrastructuredataimporthdf5rhdf5opensslcurlzlibcpp
3.0 match 62 stars 15.93 score 4.2k scripts 232 dependentsspatstat
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-detectionconfidence-intervalshypothesis-testingk-functionroc-curvesscan-statisticssignificance-testingsimulation-envelopesspatial-analysisspatial-data-analysisspatial-sharpeningspatial-smoothingspatial-statistics
4.5 match 1 stars 10.17 score 67 scripts 148 dependentsrpolars
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.
3.6 match 499 stars 12.01 score 1.0k scripts 2 dependentsjeffreyevans
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.
biodiversityconservationecologyr-spatialrasterspatialvector
4.5 match 110 stars 9.55 score 736 scripts 2 dependentsrajarshi
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 dependentshsonne
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 dependentstrivialfis
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.
3.5 match 6 stars 11.70 score 13k scripts 112 dependentshwborchers
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 dependentsbioc
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.
workflowstepassaydomainproteomicsmassspectrometryimmunooncology
9.0 match 4.00 score 3 scriptshadley
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.
3.0 match 204 stars 11.85 score 1.9k scripts 56 dependentstrackage
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 scriptswasquith
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-analysisl-momentsmle-estimationmps-estimationprobability-distributionrainfall-frequency-analysisreliability-analysisrisk-analysissurvival-analysis
4.0 match 2 stars 8.06 score 458 scripts 38 dependentsazure
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.
amlcomputeazureazure-machine-learningazuremldsimachine-learningrstudiosdk-r
3.6 match 106 stars 8.91 score 221 scriptslangenbergstefan
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 scriptsemmanuelparadis
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.
1.8 match 64 stars 17.22 score 13k scripts 599 dependentslbraglia
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 scriptstidymodels
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.
1.3 match 1.5k stars 21.56 score 37k scripts 1.4k dependentsr-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 dependentsjpmonteagudo28
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 scriptsrorynolan
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 dependentsr-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.
3.0 match 84 stars 8.54 score 28 scripts 1 dependentsboydorr
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.
biodiversitydiversity-measurementpartitioning-diversity
3.7 match 8 stars 6.85 score 66 scripts 1 dependentspetolau
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-analysisdata-miningdata-mining-algorithmsdata-sciencerepresentationtime-seriestime-series-analysistime-series-classificationtime-series-clusteringtime-series-data-miningtime-series-representationscpp
3.5 match 97 stars 7.23 score 117 scriptsbioc
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.
dataimportsequencingcoveragealignmentqualitycontrolbioconductor-packagecore-packagecurlbzip2xz-utilszlibcpp
1.6 match 28 stars 15.42 score 3.2k scripts 566 dependentsropensci
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.
gbifspecimensapiweb-servicesoccurrencesspeciestaxonomybiodiversitydatalifewatchoscibiospocc
1.9 match 161 stars 13.26 score 2.1k scripts 20 dependentsbrodieg
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.
1.8 match 54 stars 14.18 score 136 scripts 11k dependentsms609
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.
phylogeneticstree-distancephylogenetic-treestree-distancestreescpp
2.3 match 32 stars 10.32 score 97 scripts 5 dependentspik-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 dependentsjaryan
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 dependentsrstudio
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 dependentsr-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.
1.8 match 11.30 score 316 scripts 141 dependentsjuanv66x
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 scriptsmmaechler
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 dependentsmlr-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-learningmiscellaneousmlr3
1.8 match 12 stars 10.28 score 302 scripts 42 dependentsbleutner
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.
ggplot2land-cover-mappingremote-sensingspectral-unmixingsupervised-classificationunsupervised-classificationopenblascpp
1.8 match 275 stars 10.10 score 1.1k scriptsgjmvanboxtel
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.
1.8 match 24 stars 10.03 score 133 scripts 34 dependentsropensci
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.
datadatasetfake-datafakerpeer-reviewed
1.8 match 296 stars 10.06 score 180 scripts 1 dependentsms609
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-biologyphylogenetic-treesphylogeneticscpp
1.7 match 21 stars 9.92 score 124 scripts 10 dependentscran
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.
2.0 match 2 stars 8.13 score 1.0k dependentsjefferis
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 dependentsrstudio
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.
1.3 match 108 stars 12.08 score 704 scripts 1 dependentswadpac
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.
accelerometeractivity-recognitioncircadian-rhythmmovement-sensorsleep
1.2 match 109 stars 13.20 score 342 scripts 3 dependentsreinhardfurrer
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.
1.7 match 1 stars 9.26 score 420 scripts 433 dependentsrorynolan
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 dependentsedwbaker
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.
2.0 match 6 stars 7.12 score 26 scriptsgermanrecordlinkage
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.
5.3 match 2 stars 2.64 score 22 scriptsflr
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.
fisheriesflrfisheries-modelling
1.6 match 16 stars 8.78 score 956 scripts 23 dependentsropensci
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.
gdalmodismodis-datamodis-land-productspeer-reviewedpreprocessingremote-sensingsatellite-imagerytime-series
1.7 match 156 stars 8.04 score 86 scripts 1 dependentsspkaluzny
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 dependentsreinhardfurrer
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.
5.0 match 2.58 score 25 scripts 3 dependentsflr
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.
1.8 match 2 stars 6.86 score 254 scripts 6 dependentsdongjli
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.
3.0 match 2 stars 4.08 score 3 scriptsmeyerp-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.
2.0 match 6.12 score 480 scripts 44 dependentsbioc
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.
softwaredatarepresentationgeneticsgraphandnetworkvisualizationkinshippedigree
2.0 match 2 stars 6.08 score 10 scriptsfreezenik
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.
2.0 match 1 stars 5.76 score 239 scripts 5 dependentsfilipezabala
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 scriptsrje42
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 dependentshanase
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 dependentsropensci
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 scriptsdaqana
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.
randomrandom-distributionsrandom-generationrandom-samplingrngcpp
0.8 match 42 stars 13.12 score 188 scripts 183 dependentsmatherion
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 scriptsshaunpwilkinson
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 scriptsfamuvie
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 scriptsbioc
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.
infrastructuregeneticsstatisticalmethodprincipalcomponentbioinformaticsgds-formatpcasimdsnpopenblascpp
0.8 match 104 stars 12.69 score 1.6k scripts 18 dependentsbenbruyneel
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-spectrometryproteomicsproteomics-data-analysis
3.2 match 2 stars 3.00 score 2 scriptsgtatters
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-physiologyheat-exchangeheat-fluximage-framestemperaturethermal-biologythermal-images
1.7 match 169 stars 5.85 score 83 scriptsbnaras
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 dependentsdata-cleaning
errorlocate:Locate Errors with Validation Rules
Errors in data can be located and removed using validation rules from package 'validate'. See also Van der Loo and De Jonge (2018) <doi:10.1002/9781118897126>, chapter 7.
Maintained by Edwin de Jonge. Last updated 9 months ago.
data-cleaningerrorsinvalidation
1.5 match 22 stars 6.11 score 59 scriptsr-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.
1.6 match 5.64 score 64 scripts 5 dependentsbioc
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.
infrastructuredataimportbioinformaticsgds-formatgenomicscpp
0.8 match 18 stars 11.34 score 920 scripts 29 dependentsbioc
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.
transcriptomicsspatialsinglecellcpp
1.7 match 1 stars 5.18 score 4 scriptsjabiru
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.
2.6 match 3.32 score 29 scriptsewouddt
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 dependentsmrc-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.
1.3 match 6.66 score 32 scripts 2 dependentsweiyangyu
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.
4.0 match 2.00 scorehughparsonage
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.
1.8 match 6 stars 4.42 score 11 scriptscoffeemuggler
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.
1.7 match 9 stars 4.42 score 58 scriptspepijn-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 scriptssoodoku
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 dependentsf-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 scriptsnatverse
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.
1.7 match 4.13 score 15 scripts 3 dependentsrobertschneiderfromuqar
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 scriptsr-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 dependentseddelbuettel
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.
datetimedatetimesnanosecond-resolutionnanosecondscpp
0.5 match 53 stars 10.91 score 134 scripts 17 dependentsvpetrosyan
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 scriptsbioc
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.
copynumbervariationmicroarraysoftware
1.2 match 2 stars 4.60 score 6 scriptsdaniel-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 dependentskwb-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.
1.6 match 3.00 score 7 scriptscdriveraus
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-equationstime-seriescpp
0.5 match 42 stars 9.58 score 366 scripts 1 dependentsrucknium
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 scriptsggseg
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 dependentsbnprks
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.
0.5 match 184 stars 7.48 score 172 scriptscoolbutuseless
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 scriptsjleivacuadrado
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.
1.8 match 2.00 score 33 scripts 1 dependentscran
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 scoreijayc
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 scoreerblast
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 dependentscran
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.
0.5 match 5.90 score 439 dependentscran
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 scriptscoolbutuseless
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 scriptsdipterix
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 scriptseddelbuettel
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.
0.5 match 17 stars 5.01 score 6 scripts 1 dependentswurli
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-enhancementsr-visualisation
0.5 match 29 stars 4.77 score 41 scriptsmlverse
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.
0.8 match 1 stars 2.70 score 6 scriptskolassa-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.
1.8 match 1.18 score 15 scriptswrathematics
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.
0.5 match 3.82 score 133 scriptsbpfaff
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 scriptspbiecek
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 scriptscran
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 scorereviewburner
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 scoreobreschkow
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 scorehypertidy
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 scriptscran
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 dependentssrika1919
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.
0.5 match 2.78 scorerogiersbart
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 scriptshaydarde
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 scriptsepiforecasts
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.
0.5 match 2 stars 2.00 score 1 scriptscran
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 scriptsskranz
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 scriptscran
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