Showing 157 of total 157 results (show query)
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.
151.3 match 499 stars 12.01 score 1.0k scripts 2 dependentstrinker
lexicon:Lexicons for Text Analysis
A collection of lexical hash tables, dictionaries, and word lists.
Maintained by Tyler Rinker. Last updated 3 years ago.
hashlexiconlookupnames-frequentstopwordstext-dictionariestext-mining
35.1 match 111 stars 8.80 score 224 scripts 25 dependentsadokter
bioRad:Biological Analysis and Visualization of Weather Radar Data
Extract, visualize and summarize aerial movements of birds and insects from weather radar data. See Dokter, A. M. et al. (2018) "bioRad: biological analysis and visualization of weather radar data" <doi:10.1111/ecog.04028> for a software paper describing package and methodologies.
Maintained by Adriaan M. Dokter. Last updated 20 days ago.
aeroecologyenrameumetnet-operalifewatchmovement-ecologynexradoscibioradarweather-radarwsr-88d
30.3 match 29 stars 8.65 score 56 scriptseitsupi
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.
45.5 match 40 stars 4.86 score 1 scriptstrinker
sentimentr:Calculate Text Polarity Sentiment
Calculate text polarity sentiment at the sentence level and optionally aggregate by rows or grouping variable(s).
Maintained by Tyler Rinker. Last updated 3 years ago.
amplifierpolaritysentimentsentiment-analysisvalence-shifter
21.2 match 432 stars 9.43 score 680 scripts 2 dependentstrinker
qdap:Bridging the Gap Between Qualitative Data and Quantitative Analysis
Automates many of the tasks associated with quantitative discourse analysis of transcripts containing discourse including frequency counts of sentence types, words, sentences, turns of talk, syllables and other assorted analysis tasks. The package provides parsing tools for preparing transcript data. Many functions enable the user to aggregate data by any number of grouping variables, providing analysis and seamless integration with other R packages that undertake higher level analysis and visualization of text. This affords the user a more efficient and targeted analysis. 'qdap' is designed for transcript analysis, however, many functions are applicable to other areas of Text Mining/ Natural Language Processing.
Maintained by Tyler Rinker. Last updated 4 years ago.
qdapquantitative-discourse-analysistext-analysistext-miningtext-plottingopenjdk
19.4 match 176 stars 9.61 score 1.3k scripts 3 dependentsbioc
Spectra:Spectra Infrastructure for Mass Spectrometry Data
The Spectra package defines an efficient infrastructure for storing and handling mass spectrometry spectra and functionality to subset, process, visualize and compare spectra data. It provides different implementations (backends) to store mass spectrometry data. These comprise backends tuned for fast data access and processing and backends for very large data sets ensuring a small memory footprint.
Maintained by RforMassSpectrometry Package Maintainer. Last updated 9 days ago.
infrastructureproteomicsmassspectrometrymetabolomicsbioconductorhacktoberfestmass-spectrometry
10.0 match 41 stars 13.01 score 254 scripts 35 dependentsetiennebacher
tidypolars:Get the Power of Polars with the Syntax of the Tidyverse
Polars is a cross-language tool for manipulating very large data. However, one drawback is that the R implementation has a syntax that will look odd to many R users who are not used to Python syntax. The objective of tidypolars is to improve the ease-of-use of Polars in R by providing tidyverse syntax to polars.
Maintained by Etienne Bacher. Last updated 6 days ago.
16.5 match 198 stars 7.86 score 30 scriptspolar-fhir
fhircrackr:Handling HL7 FHIR® Resources in R
Useful tools for conveniently downloading FHIR resources in xml format and converting them to R data.frames. The package uses FHIR-search to download bundles from a FHIR server, provides functions to save and read xml-files containing such bundles and allows flattening the bundles to data.frames using XPath expressions. FHIR® is the registered trademark of HL7 and is used with the permission of HL7. Use of the FHIR trademark does not constitute endorsement of this product by HL7.
Maintained by Julia Palm. Last updated 11 days ago.
15.0 match 33 stars 7.63 score 46 scriptskatrionagoldmann
volcano3D:3D Volcano Plots and Polar Plots for Three-Class Data
Generates interactive plots for analysing and visualising three-class high dimensional data. It is particularly suited to visualising differences in continuous attributes such as gene/protein/biomarker expression levels between three groups. Differential gene/biomarker expression analysis between two classes is typically shown as a volcano plot. However, with three groups this type of visualisation is particularly difficult to interpret. This package generates 3D volcano plots and 3-way polar plots for easier interpretation of three-class data.
Maintained by Katriona Goldmann. Last updated 2 years ago.
bioinformaticsdifferential-expressiondifferential-expression-analysisgene-expressioninteractiveomicsplotlyrna-seqtranscriptomicsvolcanoplots
15.1 match 36 stars 5.90 score 37 scriptshwborchers
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.
7.1 match 29 stars 12.34 score 6.6k scripts 931 dependentsbioc
xcms:LC-MS and GC-MS Data Analysis
Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. Preprocesses data for high-throughput, untargeted analyte profiling.
Maintained by Steffen Neumann. Last updated 2 days ago.
immunooncologymassspectrometrymetabolomicsbioconductorfeature-detectionmass-spectrometrypeak-detectioncpp
6.0 match 196 stars 14.31 score 984 scripts 11 dependentsopenair-project
openairmaps:Create Maps of Air Pollution Data
Combine the air quality data analysis methods of 'openair' with the JavaScript 'Leaflet' (<https://leafletjs.com/>) library. Functionality includes plotting site maps, "directional analysis" figures such as polar plots, and air mass trajectories.
Maintained by Jack Davison. Last updated 1 days ago.
12.9 match 21 stars 6.04 score 47 scriptsstefanocoretta
rticulate:Articulatory Data Processing in R
A tool for processing Articulate Assistant Advanced™ (AAA) ultrasound tongue imaging data and Carstens AG500/1 electro-magnetic articulographic data.
Maintained by Stefano Coretta. Last updated 24 days ago.
phoneticssoftwaretongue-imageultrasoundultrasound-tongue-imaging
11.9 match 5 stars 5.88 score 17 scriptsopenair-project
openair:Tools for the Analysis of Air Pollution Data
Tools to analyse, interpret and understand air pollution data. Data are typically regular time series and air quality measurement, meteorological data and dispersion model output can be analysed. The package is described in Carslaw and Ropkins (2012, <doi:10.1016/j.envsoft.2011.09.008>) and subsequent papers.
Maintained by David Carslaw. Last updated 25 days ago.
air-qualityair-quality-datameteorologyopenaircpp
5.2 match 311 stars 12.91 score 1.2k scripts 12 dependentsmlverse
mall:Run Multiple Large Language Model Predictions Against a Table, or Vectors
Run multiple 'Large Language Model' predictions against a table. The predictions run row-wise over a specified column. It works using a one-shot prompt, along with the current row's content. The prompt that is used will depend of the type of analysis needed.
Maintained by Edgar Ruiz. Last updated 3 months ago.
data-sciencedplyrllmpolarspython
10.0 match 86 stars 6.61 score 94 scriptsdavidcsterratt
retistruct:Retinal Reconstruction Program
Reconstructs retinae by morphing a flat surface with cuts (a dissected flat-mount retina) onto a curvilinear surface (the standard retinal shape). It can estimate the position of a point on the intact adult retina to within 8 degrees of arc (3.6% of nasotemporal axis). The coordinates in reconstructed retinae can be transformed to visuotopic coordinates. For more details see Sterratt, D. C., Lyngholm, D., Willshaw, D. J. and Thompson, I. D. (2013) <doi:10.1371/journal.pcbi.1002921>.
Maintained by David C. Sterratt. Last updated 9 days ago.
14.2 match 8 stars 4.60 scoreallancameron
geomtextpath:Curved Text in 'ggplot2'
A 'ggplot2' extension that allows text to follow curved paths. Curved text makes it easier to directly label paths or neatly annotate in polar co-ordinates.
Maintained by Allan Cameron. Last updated 2 months ago.
5.3 match 631 stars 12.04 score 960 scripts 5 dependentsbioc
ProtGenerics:Generic infrastructure for Bioconductor mass spectrometry packages
S4 generic functions and classes needed by Bioconductor proteomics packages.
Maintained by Laurent Gatto. Last updated 2 months ago.
infrastructureproteomicsmassspectrometrybioconductormass-spectrometrymetabolomics
6.0 match 8 stars 9.43 score 4 scripts 188 dependentstidyverse
ggplot2:Create Elegant Data Visualisations Using the Grammar of Graphics
A system for 'declaratively' creating graphics, based on "The Grammar of Graphics". You provide the data, tell 'ggplot2' how to map variables to aesthetics, what graphical primitives to use, and it takes care of the details.
Maintained by Thomas Lin Pedersen. Last updated 9 days ago.
data-visualisationvisualisation
2.3 match 6.6k stars 25.10 score 645k scripts 7.5k dependentsbioc
fgsea:Fast Gene Set Enrichment Analysis
The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.
Maintained by Alexey Sergushichev. Last updated 3 months ago.
geneexpressiondifferentialexpressiongenesetenrichmentpathwayscpp
3.4 match 387 stars 16.25 score 3.9k scripts 101 dependentsmlverse
torch:Tensors and Neural Networks with 'GPU' Acceleration
Provides functionality to define and train neural networks similar to 'PyTorch' by Paszke et al (2019) <doi:10.48550/arXiv.1912.01703> but written entirely in R using the 'libtorch' library. Also supports low-level tensor operations and 'GPU' acceleration.
Maintained by Daniel Falbel. Last updated 6 days ago.
3.3 match 520 stars 16.52 score 1.4k scripts 38 dependentsdankelley
oce:Analysis of Oceanographic Data
Supports the analysis of Oceanographic data, including 'ADCP' measurements, measurements made with 'argo' floats, 'CTD' measurements, sectional data, sea-level time series, coastline and topographic data, etc. Provides specialized functions for calculating seawater properties such as potential temperature in either the 'UNESCO' or 'TEOS-10' equation of state. Produces graphical displays that conform to the conventions of the Oceanographic literature. This package is discussed extensively by Kelley (2018) "Oceanographic Analysis with R" <doi:10.1007/978-1-4939-8844-0>.
Maintained by Dan Kelley. Last updated 1 days ago.
3.5 match 146 stars 15.42 score 4.2k scripts 18 dependentskjhealy
gssrdoc:Document General Social Survey Variable
The General Social Survey (GSS) is a long-running, mostly annual survey of US households. It is administered by the National Opinion Research Center (NORC). This package contains the a tibble with information on the survey variables, together with every variable documented as an R help page. For more information on the GSS see \url{http://gss.norc.org}.
Maintained by Kieran Healy. Last updated 11 months ago.
21.9 match 2.28 score 38 scriptsrpolars
polarssql:A 'polars' backend for 'DBI'.
DBI-compliant interface to 'polars'.
Maintained by Tatsuya Shima. Last updated 7 months ago.
14.0 match 26 stars 3.41 score 3 scriptsdcgerard
tensr:Covariance Inference and Decompositions for Tensor Datasets
A collection of functions for Kronecker structured covariance estimation and testing under the array normal model. For estimation, maximum likelihood and Bayesian equivariant estimation procedures are implemented. For testing, a likelihood ratio testing procedure is available. This package also contains additional functions for manipulating and decomposing tensor data sets. This work was partially supported by NSF grant DMS-1505136. Details of the methods are described in Gerard and Hoff (2015) <doi:10.1016/j.jmva.2015.01.020> and Gerard and Hoff (2016) <doi:10.1016/j.laa.2016.04.033>.
Maintained by David Gerard. Last updated 2 years ago.
7.1 match 5 stars 6.53 score 56 scripts 4 dependentsdavidcsterratt
geometry:Mesh Generation and Surface Tessellation
Makes the 'Qhull' library <http://www.qhull.org> available in R, in a similar manner as in Octave and MATLAB. Qhull computes convex hulls, Delaunay triangulations, halfspace intersections about a point, Voronoi diagrams, furthest-site Delaunay triangulations, and furthest-site Voronoi diagrams. It runs in 2D, 3D, 4D, and higher dimensions. It implements the Quickhull algorithm for computing the convex hull. Qhull does not support constrained Delaunay triangulations, or mesh generation of non-convex objects, but the package does include some R functions that allow for this.
Maintained by David C. Sterratt. Last updated 1 months ago.
3.5 match 16 stars 12.98 score 776 scripts 139 dependentsbioc
LOBSTAHS:Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences
LOBSTAHS is a multifunction package for screening, annotation, and putative identification of mass spectral features in large, HPLC-MS lipid datasets. In silico data for a wide range of lipids, oxidized lipids, and oxylipins can be generated from user-supplied structural criteria with a database generation function. LOBSTAHS then applies these databases to assign putative compound identities to features in any high-mass accuracy dataset that has been processed using xcms and CAMERA. Users can then apply a series of orthogonal screening criteria based on adduct ion formation patterns, chromatographic retention time, and other properties, to evaluate and assign confidence scores to this list of preliminary assignments. During the screening routine, LOBSTAHS rejects assignments that do not meet the specified criteria, identifies potential isomers and isobars, and assigns a variety of annotation codes to assist the user in evaluating the accuracy of each assignment.
Maintained by Henry Holm. Last updated 5 months ago.
immunooncologymassspectrometrymetabolomicslipidomicsdataimportadductalgaebioconductorhplc-esi-mslipidmass-spectrometryoxidative-stress-biomarkersoxidized-lipidsoxylipinsplankton
6.0 match 8 stars 6.56 score 9 scriptsshixiangwang
ggpolar:Dots and Their Connections in Polar Coordinate System
Provides basic graphing functions to fully demonstrate point-to-point connections in a polar coordinate space.
Maintained by Shixiang Wang. Last updated 2 years ago.
8.3 match 9 stars 4.65 score 7 scriptsbioc
MSnbase:Base Functions and Classes for Mass Spectrometry and Proteomics
MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data.
Maintained by Laurent Gatto. Last updated 2 days ago.
immunooncologyinfrastructureproteomicsmassspectrometryqualitycontroldataimportbioconductorbioinformaticsmass-spectrometryproteomics-datavisualisationcpp
3.0 match 130 stars 12.81 score 772 scripts 36 dependentsjohncoene
echarts4r:Create Interactive Graphs with 'Echarts JavaScript' Version 5
Easily create interactive charts by leveraging the 'Echarts Javascript' library which includes 36 chart types, themes, 'Shiny' proxies and animations.
Maintained by David Munoz Tord. Last updated 3 days ago.
echartshacktoberfesthtmlwidgethtmlwidgetsvisualization
3.3 match 603 stars 11.45 score 1.3k scripts 11 dependentswillgearty
deeptime:Plotting Tools for Anyone Working in Deep Time
Extends the functionality of other plotting packages (notably 'ggplot2') to help facilitate the plotting of data over long time intervals, including, but not limited to, geological, evolutionary, and ecological data. The primary goal of 'deeptime' is to enable users to add highly customizable timescales to their visualizations. Other functions are also included to assist with other areas of deep time visualization.
Maintained by William Gearty. Last updated 3 months ago.
geologyggplot2paleontologyvisualization
3.5 match 92 stars 10.61 score 207 scripts 3 dependentsfchen365
epca:Exploratory Principal Component Analysis
Exploratory principal component analysis for large-scale dataset, including sparse principal component analysis and sparse matrix approximation.
Maintained by Fan Chen. Last updated 11 months ago.
community-detectionexploratory-data-analysismatrix-decompositionspcaprincipal-component-analysissparse-matrix
7.6 match 11 stars 4.74 score 8 scriptsquanteda
quanteda.textmodels:Scaling Models and Classifiers for Textual Data
Scaling models and classifiers for sparse matrix objects representing textual data in the form of a document-feature matrix. Includes original implementations of 'Laver', 'Benoit', and Garry's (2003) <doi:10.1017/S0003055403000698>, 'Wordscores' model, the Perry and 'Benoit' (2017) <doi:10.48550/arXiv.1710.08963> class affinity scaling model, and the 'Slapin' and 'Proksch' (2008) <doi:10.1111/j.1540-5907.2008.00338.x> 'wordfish' model, as well as methods for correspondence analysis, latent semantic analysis, and fast Naive Bayes and linear 'SVMs' specially designed for sparse textual data.
Maintained by Kenneth Benoit. Last updated 1 months ago.
3.5 match 42 stars 9.56 score 432 scriptskoheiw
LSX:Semi-Supervised Algorithm for Document Scaling
A word embeddings-based semi-supervised model for document scaling Watanabe (2020) <doi:10.1080/19312458.2020.1832976>. LSS allows users to analyze large and complex corpora on arbitrary dimensions with seed words exploiting efficiency of word embeddings (SVD, Glove). It can generate word vectors on a users-provided corpus or incorporate a pre-trained word vectors.
Maintained by Kohei Watanabe. Last updated 2 months ago.
lsaquantedasentiment-analysistext-analysis
5.5 match 55 stars 6.09 score 14 scriptstyy20
KEPTED:Kernel-Embedding-of-Probability Test for Elliptical Distribution
Provides an implementation of a kernel-embedding of probability test for elliptical distribution. This is an asymptotic test for elliptical distribution under general alternatives, and the location and shape parameters are assumed to be unknown. Some side-products are posted, including the transformation between rectangular and polar coordinates and two product-type kernel functions. See Tang and Li (2024) <doi:10.48550/arXiv.2306.10594> for details.
Maintained by Yin Tang. Last updated 11 months ago.
7.9 match 4.18 scoreouhscbbmc
Wats:Wrap Around Time Series Graphics
Wrap-around Time Series (WATS) plots for interrupted time series designs with seasonal patterns. Longitudinal trajectories are shown in both Cartesian and polar coordinates. In many scenarios, a WATS plot more clearly shows the existence and effect size of of an intervention. This package accompanies "Graphical Data Analysis on the Circle: Wrap-Around Time Series Plots for (Interrupted) Time Series Designs" by Rodgers, Beasley, & Schuelke (2014) <doi:10.1080/00273171.2014.946589>; see 'citation("Wats")' for details.
Maintained by Will Beasley. Last updated 20 days ago.
graphical-analysisoklahoma-city-bombingpublicationseasonaltime-series
5.3 match 7 stars 6.14 score 44 scriptssfeuerriegel
SentimentAnalysis:Dictionary-Based Sentiment Analysis
Performs a sentiment analysis of textual contents in R. This implementation utilizes various existing dictionaries, such as Harvard IV, or finance-specific dictionaries. Furthermore, it can also create customized dictionaries. The latter uses LASSO regularization as a statistical approach to select relevant terms based on an exogenous response variable.
Maintained by Nicolas Proellochs. Last updated 2 years ago.
3.8 match 149 stars 8.34 score 242 scripts 1 dependentsssnn-airr
alakazam:Immunoglobulin Clonal Lineage and Diversity Analysis
Provides methods for high-throughput adaptive immune receptor repertoire sequencing (AIRR-Seq; Rep-Seq) analysis. In particular, immunoglobulin (Ig) sequence lineage reconstruction, lineage topology analysis, diversity profiling, amino acid property analysis and gene usage. Citations: Gupta and Vander Heiden, et al (2017) <doi:10.1093/bioinformatics/btv359>, Stern, Yaari and Vander Heiden, et al (2014) <doi:10.1126/scitranslmed.3008879>.
Maintained by Susanna Marquez. Last updated 3 months ago.
3.3 match 9.09 score 424 scripts 7 dependentsropensci
spatsoc:Group Animal Relocation Data by Spatial and Temporal Relationship
Detects spatial and temporal groups in GPS relocations (Robitaille et al. (2019) <doi:10.1111/2041-210X.13215>). It can be used to convert GPS relocations to gambit-of-the-group format to build proximity-based social networks In addition, the randomizations function provides data-stream randomization methods suitable for GPS data.
Maintained by Alec L. Robitaille. Last updated 1 months ago.
3.0 match 24 stars 9.97 score 145 scripts 3 dependentsnmartinkova
diemr:Diagnostic Index Expectation Maximisation in R
Likelihood-based genome polarisation finds which alleles of genomic markers belong to which side of the barrier. Co-estimates which individuals belong to either side of the barrier and barrier strength. Uses expectation maximisation in likelihood framework. The method is described in Baird et al. (2023) <doi:10.1111/2041-210X.14010>.
Maintained by Natalia Martinkova. Last updated 2 months ago.
9.1 match 3.26 score 1 scriptsgeobosh
gbutils:Utilities for Simulation, Plots, Quantile Functions and Programming
Plot density and distribution functions with automatic selection of suitable regions. Numerically invert (compute quantiles) distribution functions. Simulate real and complex numbers from distributions of their magnitude and arguments. Optionally, the magnitudes and/or arguments may be fixed in almost arbitrary ways. Create polynomials from roots given in Cartesian or polar form. Small programming utilities: check if an object is identical to NA, count positional arguments in a call, set intersection of more than two sets, check if an argument is unnamed, compute the graph of S4 classes in packages.
Maintained by Georgi N. Boshnakov. Last updated 3 years ago.
adjacency-matrixcomplex-numbersplotting-functionss4s4classsimulation
4.0 match 1 stars 7.32 score 29 scripts 56 dependentsadokter
vol2birdR:Vertical Profiles of Biological Signals in Weather Radar Data
'R' implementation of the 'vol2bird' software for generating vertical profiles of birds and other biological signals in weather radar data. See Dokter et al. (2011) <doi:10.1098/rsif.2010.0116> for a paper describing the methodology.
Maintained by Adriaan M. Dokter. Last updated 10 days ago.
4.4 match 6 stars 6.61 score 19 scriptsjokergoo
circlize:Circular Visualization
Circular layout is an efficient way for the visualization of huge amounts of information. Here this package provides an implementation of circular layout generation in R as well as an enhancement of available software. The flexibility of the package is based on the usage of low-level graphics functions such that self-defined high-level graphics can be easily implemented by users for specific purposes. Together with the seamless connection between the powerful computational and visual environment in R, it gives users more convenience and freedom to design figures for better understanding complex patterns behind multiple dimensional data. The package is described in Gu et al. 2014 <doi:10.1093/bioinformatics/btu393>.
Maintained by Zuguang Gu. Last updated 1 years ago.
1.9 match 983 stars 15.62 score 10k scripts 213 dependentsropensci
GLMMcosinor:Fit a Cosinor Model Using a Generalized Mixed Modeling Framework
Allows users to fit a cosinor model using the 'glmmTMB' framework. This extends on existing cosinor modeling packages, including 'cosinor' and 'circacompare', by including a wide range of available link functions and the capability to fit mixed models. The cosinor model is described by Cornelissen (2014) <doi:10.1186/1742-4682-11-16>.
Maintained by Rex Parsons. Last updated 4 months ago.
5.0 match 1 stars 5.77 score 22 scriptsrmendels
rerddapXtracto:Extracts Environmental Data from 'ERDDAP™' Web Services
Contains three functions that access environmental data from any 'ERDDAP™' data web service. The rxtracto() function extracts data along a trajectory for a given "radius" around the point. The rxtracto_3D() function extracts data in a box. The rxtractogon() function extracts data in a polygon. All of those three function use the 'rerddap' package to extract the data, and should work with any 'ERDDAP™' server. There are also two functions, plotBBox() and plotTrack() that use the 'plotdap' package to simplify the creation of maps of the data.
Maintained by Roy Mendelssohn. Last updated 18 days ago.
4.9 match 14 stars 5.79 score 44 scriptssvmiller
peacesciencer:Tools and Data for Quantitative Peace Science Research
These are useful tools and data sets for the study of quantitative peace science. The goal for this package is to include tools and data sets for doing original research that mimics well what a user would have to previously get from a software package that may not be well-sourced or well-supported. Those software bundles were useful the extent to which they encourage replications of long-standing analyses by starting the data-generating process from scratch. However, a lot of the functionality can be done relatively quickly and more transparently in the R programming language.
Maintained by Steve Miller. Last updated 3 days ago.
5.1 match 29 stars 5.49 score 211 scriptsandrewljackson
SIBER:Stable Isotope Bayesian Ellipses in R
Fits bi-variate ellipses to stable isotope data using Bayesian inference with the aim being to describe and compare their isotopic niche.
Maintained by Andrew Jackson. Last updated 10 months ago.
community-ecologyecologyniche-modellingstable-isotopesjagscpp
3.0 match 36 stars 9.13 score 187 scripts 1 dependentsiainmstott
popdemo:Demographic Modelling Using Projection Matrices
Tools for modelling populations and demography using matrix projection models, with deterministic and stochastic model implementations. Includes population projection, indices of short- and long-term population size and growth, perturbation analysis, convergence to stability or stationarity, and diagnostic and manipulation tools.
Maintained by Iain Stott. Last updated 3 years ago.
5.3 match 5.16 score 172 scripts 7 dependentsyunuuuu
ggalign:A 'ggplot2' Extension for Consistent Axis Alignment
A 'ggplot2' extension offers various tools the creation of complex, multi-plot visualizations. Built on the familiar grammar of graphics, it provides intuitive tools to align and organize plots, making it ideal for complex visualizations. It excels in multi-omics research—such as genomics and microbiomes—by simplifying the visualization of intricate relationships between datasets, for example, linking genes to pathways. Whether you need to stack plots, arrange them around a central figure, or create a circular layout, 'ggalign' delivers flexibility and accuracy with minimal effort.
Maintained by Yun Peng. Last updated 18 hours ago.
complex-heatmapsdendrogramdendrogram-heatmapggplotggplot-extensionggplot2heatmapheatmap-visualizationheatmapsmarginal-plotsoncoplotoncoprinttanglegramupsetupsetplot
3.8 match 267 stars 7.08 score 27 scriptsgreat-northern-diver
loon.ggplot:A Grammar of Interactive Graphics
Provides a bridge between the 'loon' and 'ggplot2' packages. Extends the grammar of ggplot to add clauses to create interactive 'loon' plots. Existing ggplot(s) can be turned into interactive 'loon' plots and 'loon' plots into static ggplot(s); the function 'loon.ggplot()' is the bridge from one plot structure to the other.
Maintained by Zehao Xu. Last updated 10 months ago.
data-analysisggplotggplot-featuresgraphicsinteractive-plotsloonvisualizations
3.7 match 24 stars 7.11 score 9 scripts 3 dependentsbioc
Rcpi:Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery
A molecular informatics toolkit with an integration of bioinformatics and chemoinformatics tools for drug discovery.
Maintained by Nan Xiao. Last updated 5 months ago.
softwaredataimportdatarepresentationfeatureextractioncheminformaticsbiomedicalinformaticsproteomicsgosystemsbiologybioconductorbioinformaticsdrug-discoveryfeature-extractionfingerprintmolecular-descriptorsprotein-sequences
3.4 match 37 stars 7.81 score 29 scriptsnilsmechtel
MetAlyzer:Read and Analyze 'MetIDQ™' Software Output Files
The 'MetAlyzer' S4 object provides methods to read and reformat metabolomics data for convenient data handling, statistics and downstream analysis. The resulting format corresponds to input data of the Shiny app 'MetaboExtract' (<https://www.metaboextract.shiny.dkfz.de/MetaboExtract/>).
Maintained by Nils Mechtel. Last updated 3 months ago.
4.9 match 3 stars 5.35 score 4 scriptsdmurdoch
plotrix:Various Plotting Functions
Lots of plots, various labeling, axis and color scaling functions. The author/maintainer died in September 2023.
Maintained by Duncan Murdoch. Last updated 1 years ago.
2.3 match 5 stars 11.31 score 9.2k scripts 361 dependentsgaboraszabo
sherlock:Graphical Displays for Structured Problem Solving and Diagnosis
Powerful graphical displays and statistical tools for structured problem solving and diagnosis. The functions of the 'sherlock' package are especially useful for applying the process of elimination as a problem diagnosis technique. The 'sherlock' package was designed to seamlessly work with the 'tidyverse' set of packages and provides a collection of graphical displays built on top of the 'ggplot' and 'plotly' packages, such as different kinds of small multiple plots as well as helper functions such as adding reference lines, normalizing observations, reading in data or saving analysis results in an Excel file. References: David Hartshorne (2019, ISBN: 978-1-5272-5139-7). Stefan H. Steiner, R. Jock MacKay (2005, ISBN: 0873896467).
Maintained by Gabor Szabo. Last updated 4 months ago.
5.5 match 7 stars 4.42 score 15 scriptsglenndavis52
spacesXYZ:CIE XYZ and some of Its Derived Color Spaces
Functions for converting among CIE XYZ, xyY, Lab, and Luv. Calculate Correlated Color Temperature (CCT) and the Planckian and daylight loci. The XYZs of some standard illuminants and some standard linear chromatic adaptation transforms (CATs) are included. Three standard color difference metrics are included, plus the forward direction of the 'CIECAM02' color appearance model.
Maintained by Glenn Davis. Last updated 1 months ago.
3.4 match 7.03 score 21 scripts 32 dependentstrinker
qdapDictionaries:Dictionaries and Word Lists for the 'qdap' Package
A collection of text analysis dictionaries and word lists for use with the 'qdap' package.
Maintained by Tyler Rinker. Last updated 7 years ago.
4.0 match 4 stars 5.99 score 113 scripts 6 dependentsemanuelhuber
RConics:Computations on Conics
Solve some conic related problems (intersection of conics with lines and conics, arc length of an ellipse, polar lines, etc.).
Maintained by Emanuel Huber. Last updated 27 days ago.
conicsellipseellipticgeometryintersection
5.6 match 4.20 score 53 scripts 2 dependentsbioc
CluMSID:Clustering of MS2 Spectra for Metabolite Identification
CluMSID is a tool that aids the identification of features in untargeted LC-MS/MS analysis by the use of MS2 spectra similarity and unsupervised statistical methods. It offers functions for a complete and customisable workflow from raw data to visualisations and is interfaceable with the xmcs family of preprocessing packages.
Maintained by Tobias Depke. Last updated 5 months ago.
metabolomicspreprocessingclustering
3.9 match 10 stars 6.04 score 22 scriptsspatstat
spatstat.geom:Geometrical Functionality of the 'spatstat' Family
Defines spatial data types and supports geometrical operations on them. Data types include point patterns, windows (domains), pixel images, line segment patterns, tessellations and hyperframes. Capabilities include creation and manipulation of data (using command line or graphical interaction), plotting, geometrical operations (rotation, shift, rescale, affine transformation), convex hull, discretisation and pixellation, Dirichlet tessellation, Delaunay triangulation, pairwise distances, nearest-neighbour distances, distance transform, morphological operations (erosion, dilation, closing, opening), quadrat counting, geometrical measurement, geometrical covariance, colour maps, calculus on spatial domains, Gaussian blur, level sets of images, transects of images, intersections between objects, minimum distance matching. (Excludes spatial data on a network, which are supported by the package 'spatstat.linnet'.)
Maintained by Adrian Baddeley. Last updated 2 days ago.
classes-and-objectsdistance-calculationgeometrygeometry-processingimagesmensurationplottingpoint-patternsspatial-dataspatial-data-analysis
1.9 match 7 stars 12.11 score 241 scripts 227 dependentsmpru
ggcleveland:Implementation of Plots from Cleveland's Visualizing Data Book
William S. Cleveland's book 'Visualizing Data' is a classic piece of literature on Exploratory Data Analysis. Although it was written several decades ago, its content is still relevant as it proposes several tools which are useful to discover patterns and relationships among the data under study, and also to assess the goodness of fit of a model. This package provides functions to produce the 'ggplot2' versions of the visualization tools described in this book and is thought to be used in the context of courses on Exploratory Data Analysis.
Maintained by Marcos Prunello. Last updated 3 years ago.
4.5 match 9 stars 4.83 score 15 scriptstalgalili
dendextend:Extending 'dendrogram' Functionality in R
Offers a set of functions for extending 'dendrogram' objects in R, letting you visualize and compare trees of 'hierarchical clusterings'. You can (1) Adjust a tree's graphical parameters - the color, size, type, etc of its branches, nodes and labels. (2) Visually and statistically compare different 'dendrograms' to one another.
Maintained by Tal Galili. Last updated 2 months ago.
1.2 match 154 stars 17.02 score 6.0k scripts 164 dependentsbioc
bettr:A Better Way To Explore What Is Best
bettr provides a set of interactive visualization methods to explore the results of a benchmarking study, where typically more than a single performance measures are computed. The user can weight the performance measures according to their preferences. Performance measures can also be grouped and aggregated according to additional annotations.
Maintained by Charlotte Soneson. Last updated 4 months ago.
3.9 match 3 stars 5.26 score 3 scriptsbioc
flowcatchR:Tools to analyze in vivo microscopy imaging data focused on tracking flowing blood cells
flowcatchR is a set of tools to analyze in vivo microscopy imaging data, focused on tracking flowing blood cells. It guides the steps from segmentation to calculation of features, filtering out particles not of interest, providing also a set of utilities to help checking the quality of the performed operations (e.g. how good the segmentation was). It allows investigating the issue of tracking flowing cells such as in blood vessels, to categorize the particles in flowing, rolling and adherent. This classification is applied in the study of phenomena such as hemostasis and study of thrombosis development. Moreover, flowcatchR presents an integrated workflow solution, based on the integration with a Shiny App and Jupyter notebooks, which is delivered alongside the package, and can enable fully reproducible bioimage analysis in the R environment.
Maintained by Federico Marini. Last updated 3 months ago.
softwarevisualizationcellbiologyclassificationinfrastructureguishinyappsbioconductorfluorescencemicroscopyparticlestracking
3.6 match 4 stars 5.62 score 8 scriptsanimint
animint2:Animated Interactive Grammar of Graphics
Functions are provided for defining animated, interactive data visualizations in R code, and rendering on a web page. The 2018 Journal of Computational and Graphical Statistics paper, <doi:10.1080/10618600.2018.1513367> describes the concepts implemented.
Maintained by Toby Hocking. Last updated 27 days ago.
2.3 match 64 stars 8.87 score 173 scriptsicosa-grid
icosa:Global Triangular and Penta-Hexagonal Grids Based on Tessellated Icosahedra
Implementation of icosahedral grids in three dimensions. The spherical-triangular tessellation can be set to create grids with custom resolutions. Both the primary triangular and their inverted penta-hexagonal grids can be calculated. Additional functions are provided that allow plotting of the grids and associated data, the interaction of the grids with other raster and vector objects, and treating the grids as a graphs.
Maintained by Adam T. Kocsis. Last updated 7 months ago.
3.5 match 4 stars 5.41 score 65 scriptsimehlhaff
CPC:Implementation of Cluster-Polarization Coefficient
Implements cluster-polarization coefficient for measuring distributional polarization in single or multiple dimensions, as well as associated functions. Contains support for hierarchical clustering, k-means, partitioning around medoids, density-based spatial clustering with noise, and manually imposed cluster membership. Mehlhaff (forthcoming) <doi:10.1017/S0003055423001041>.
Maintained by Isaac Mehlhaff. Last updated 5 months ago.
5.9 match 3.18 score 9 scriptsbioc
piano:Platform for integrative analysis of omics data
Piano performs gene set analysis using various statistical methods, from different gene level statistics and a wide range of gene-set collections. Furthermore, the Piano package contains functions for combining the results of multiple runs of gene set analyses.
Maintained by Leif Varemo Wigge. Last updated 5 months ago.
microarraypreprocessingqualitycontroldifferentialexpressionvisualizationgeneexpressiongenesetenrichmentpathwaysbioconductorbioconductor-packagebioinformaticsgene-set-enrichmenttranscriptomics
2.3 match 13 stars 8.30 score 183 scripts 7 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
1.9 match 21 stars 9.92 score 124 scripts 10 dependentskarlines
ReacTran:Reactive Transport Modelling in 1d, 2d and 3d
Routines for developing models that describe reaction and advective-diffusive transport in one, two or three dimensions. Includes transport routines in porous media, in estuaries, and in bodies with variable shape.
Maintained by Karline Soetaert. Last updated 8 years ago.
4.0 match 6 stars 4.57 score 52 scriptsroaldarbol
animovement:An R toolbox for analysing animal movement across space and time
An R toolbox for analysing animal movement across space and time.
Maintained by Mikkel Roald-Arbøl. Last updated 2 months ago.
animal-behaviouranimal-movementneuroethologyneuroscience
3.8 match 10 stars 4.81 score 8 scriptsreneschulenberg
dineq:Decomposition of (Income) Inequality
Decomposition of (income) inequality by population sub groups. For a decomposition on a single variable the mean log deviation can be used (see Mookherjee Shorrocks (1982) <DOI:10.2307/2232673>. For a decomposition on multiple variables a regression based technique can be used (see Fields (2003) <DOI:10.1016/s0147-9121(03)22001-x>). Recentered influence function regression for marginal effects of the (income or wealth) distribution (see Firpo et al. (2009) <DOI:10.3982/ECTA6822>). Some extensions to inequality functions to handle weights and/or missings.
Maintained by René Schulenberg. Last updated 7 years ago.
4.5 match 3 stars 4.00 score 112 scripts 1 dependentsemilhvitfeldt
textdata:Download and Load Various Text Datasets
Provides a framework to download, parse, and store text datasets on the disk and load them when needed. Includes various sentiment lexicons and labeled text data sets for classification and analysis.
Maintained by Emil Hvitfeldt. Last updated 10 months ago.
1.8 match 75 stars 9.66 score 1.4k scripts 1 dependentsmrc-ide
dust:Iterate Multiple Realisations of Stochastic Models
An Engine for simulation of stochastic models. Includes support for running stochastic models in parallel, either with shared or varying parameters. Simulations are run efficiently in compiled code and can be run with a fraction of simulated states returned to R, allowing control over memory usage. Support is provided for building bootstrap particle filter for performing Sequential Monte Carlo (e.g., Gordon et al. 1993 <doi:10.1049/ip-f-2.1993.0015>). The core of the simulation engine is the 'xoshiro256**' algorithm (Blackman and Vigna <arXiv:1805.01407>), and the package is further described in FitzJohn et al 2021 <doi:10.12688/wellcomeopenres.16466.2>.
Maintained by Rich FitzJohn. Last updated 6 months ago.
2.2 match 18 stars 7.84 score 60 scripts 3 dependentscran
DER:Income Polarization Index
The DER (or PaF) income polarization index as proposed by Duclos J. Y., Esteban, J. and Ray D. (2004). "Polarization: concepts, measurement, estimation". Econometrica, 72(6): 1737--1772. <doi:10.1111/j.1468-0262.2004.00552.x>. The index may be computed for a single or for a range of values of the alpha-parameter. Bootstrapping is also available.
Maintained by Michail Tsagris. Last updated 20 days ago.
16.9 match 1.00 scoreshulele
RoundAndRound:Plot Objects Moving in Orbits
Visualize the objects in orbits in 2D and 3D. The packages is under developing to plot the orbits of objects in polar coordinate system. See the examples in demo.
Maintained by Lele Shu. Last updated 5 years ago.
5.9 match 2.81 score 13 scriptsf-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.
3.1 match 5 stars 5.31 score 41 scriptsshikokuchuo
mirai:Minimalist Async Evaluation Framework for R
Designed for simplicity, a 'mirai' evaluates an R expression asynchronously in a parallel process, locally or distributed over the network. The result is automatically available upon completion. Modern networking and concurrency, built on 'nanonext' and 'NNG' (Nanomsg Next Gen), ensures reliable and efficient scheduling over fast inter-process communications or TCP/IP secured by TLS. Distributed computing can launch remote resources via SSH or cluster managers. An inherently queued architecture handles many more tasks than available processes, and requires no storage on the file system. Innovative features include support for otherwise non-exportable reference objects, event-driven promises, and asynchronous parallel map.
Maintained by Charlie Gao. Last updated 2 days ago.
asyncasynchronous-tasksconcurrencydistributed-computinghigh-performance-computingparallel-computing
1.3 match 217 stars 11.94 score 130 scripts 7 dependentscardiomoon
ggiraphExtra:Make Interactive 'ggplot2'. Extension to 'ggplot2' and 'ggiraph'
Collection of functions to enhance 'ggplot2' and 'ggiraph'. Provides functions for exploratory plots. All plot can be a 'static' plot or an 'interactive' plot using 'ggiraph'.
Maintained by Keon-Woong Moon. Last updated 4 years ago.
1.6 match 48 stars 8.93 score 402 scripts 3 dependentsadelmofilho
tenispolaR:Provides ZENIT-POLAR Substitution Cipher Method of Encryption
Implementation of ZENIT-POLAR substitution cipher method of encryption using by default the TENIS-POLAR cipher. This last cipher of encryption became famous through the collection of Brazilian books "Os Karas" by the author Pedro Bandeira. For more details, see "A Cryptographic Dictionary" (GC&CS, 1944).
Maintained by Adelmo Filho. Last updated 6 years ago.
5.4 match 2.70 score 3 scriptsmmaechler
supclust:Supervised Clustering of Predictor Variables Such as Genes
Methodology for supervised grouping aka "clustering" of potentially many predictor variables, such as genes etc, implementing algorithms 'PELORA' and 'WILMA'.
Maintained by Martin Maechler. Last updated 7 months ago.
3.4 match 2 stars 4.15 score 28 scriptspwarncke77
ResIN:Response Item Networks
Contains various tools to perform and visualize Response Item Networks ('ResIN's'). 'ResIN' binarizes ordered-categorical and qualitative response choices from (survey) data, calculates pairwise associations and maps the location of each item response as a node in a force-directed network. Please refer to <https://www.resinmethod.net/> for more details.
Maintained by Philip Warncke. Last updated 5 months ago.
3.1 match 4.48 score 3 scriptstrackage
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.
3.3 match 4 stars 4.19 score 13 scriptschristopherkenny
geomander:Geographic Tools for Studying Gerrymandering
A compilation of tools to complete common tasks for studying gerrymandering. This focuses on the geographic tool side of common problems, such as linking different levels of spatial units or estimating how to break up units. Functions exist for creating redistricting-focused data for the US.
Maintained by Christopher T. Kenny. Last updated 18 days ago.
1.7 match 14 stars 7.81 score 191 scripts 1 dependentswilkox
ggfittext:Fit Text Inside a Box in 'ggplot2'
A 'ggplot2' extension to fit text into a box by growing, shrinking or wrapping the text.
Maintained by David Wilkins. Last updated 1 years ago.
1.2 match 306 stars 11.08 score 234 scripts 33 dependentsmunterfi
eRTG3D:Empirically Informed Random Trajectory Generation in 3-D
Creates realistic random trajectories in a 3-D space between two given fix points, so-called conditional empirical random walks (CERWs). The trajectory generation is based on empirical distribution functions extracted from observed trajectories (training data) and thus reflects the geometrical movement characteristics of the mover. A digital elevation model (DEM), representing the Earth's surface, and a background layer of probabilities (e.g. food sources, uplift potential, waterbodies, etc.) can be used to influence the trajectories. Unterfinger M (2018). "3-D Trajectory Simulation in Movement Ecology: Conditional Empirical Random Walk". Master's thesis, University of Zurich. <https://www.geo.uzh.ch/dam/jcr:6194e41e-055c-4635-9807-53c5a54a3be7/MasterThesis_Unterfinger_2018.pdf>. Technitis G, Weibel R, Kranstauber B, Safi K (2016). "An algorithm for empirically informed random trajectory generation between two endpoints". GIScience 2016: Ninth International Conference on Geographic Information Science, 9, online. <doi:10.5167/uzh-130652>.
Maintained by Merlin Unterfinger. Last updated 3 years ago.
3dbirdsconditional-empirical-random-walkgliding-and-soaringmachine-learningmovement-ecologyrandom-trajectory-generatorrandom-walksimulationtrajectory-generation
2.3 match 6 stars 5.71 score 19 scriptskylecaudle
rTensor2:MultiLinear Algebra
A set of tools for basic tensor operators. A tensor in the context of data analysis in a multidimensional array. The tools in this package rely on using any discrete transformation (e.g. Fast Fourier Transform (FFT)). Standard tools included are the Eigenvalue decomposition of a tensor, the QR decomposition and LU decomposition. Other functionality includes the inverse of a tensor and the transpose of a symmetric tensor. Functionality in the package is outlined in Kernfeld et al. (2015) <https://www.sciencedirect.com/science/article/pii/S0024379515004358>.
Maintained by Kyle Caudle. Last updated 12 months ago.
5.2 match 2.48 score 2 scripts 1 dependentsdreamrs
apexcharter:Create Interactive Chart with the JavaScript 'ApexCharts' Library
Provides an 'htmlwidgets' interface to 'apexcharts.js'. 'Apexcharts' is a modern JavaScript charting library to build interactive charts and visualizations with simple API. 'Apexcharts' examples and documentation are available here: <https://apexcharts.com/>.
Maintained by Victor Perrier. Last updated 25 days ago.
1.5 match 144 stars 8.51 score 247 scriptskybak90
spheresmooth:Piecewise Geodesic Smoothing for Spherical Data
Fitting a smooth path to a given set of noisy spherical data observed at known time points. It implements a piecewise geodesic curve fitting method on the unit sphere based on a velocity-based penalization scheme. The proposed approach is implemented using the Riemannian block coordinate descent algorithm. To understand the method and algorithm, one can refer to Bak, K. Y., Shin, J. K., & Koo, J. Y. (2023) <doi:10.1080/02664763.2022.2054962> for the case of order 1. Additionally, this package includes various functions necessary for handling spherical data.
Maintained by Kwan-Young Bak. Last updated 3 months ago.
4.0 match 3.18 score 2 scriptsmarkheckmann
OpenRepGrid:Tools to Analyze Repertory Grid Data
Analyze repertory grids, a qualitative-quantitative data collection technique devised by George A. Kelly in the 1950s. Today, grids are used across various domains ranging from clinical psychology to marketing. The package contains functions to quantitatively analyze and visualize repertory grid data (e.g. 'Fransella', 'Bell', & 'Bannister', 2004, ISBN: 978-0-470-09080-0). The package is part of the The package is part of the <https://openrepgrid.org/> project.
Maintained by Mark Heckmann. Last updated 14 days ago.
1.9 match 19 stars 6.69 score 156 scriptsr-forge
RHRV:Heart Rate Variability Analysis of ECG Data
Allows users to import data files containing heartbeat positions in the most broadly used formats, to remove outliers or points with unacceptable physiological values present in the time series, to plot HRV data, and to perform time domain, frequency domain and nonlinear HRV analysis. See Garcia et al. (2017) <DOI:10.1007/978-3-319-65355-6>.
Maintained by Leandro Rodriguez-Linares. Last updated 6 months ago.
1.8 match 6.79 score 63 scripts 1 dependentscran
MDSMap:High Density Genetic Linkage Mapping using Multidimensional Scaling
Estimate genetic linkage maps for markers on a single chromosome (or in a single linkage group) from pairwise recombination fractions or intermarker distances using weighted metric multidimensional scaling. The methods are suitable for autotetraploid as well as diploid populations. Options for assessing the fit to a known map are also provided. Methods are discussed in detail in Preedy and Hackett (2016) <doi:10.1007/s00122-016-2761-8>.
Maintained by Bram Boskamp. Last updated 7 years ago.
4.0 match 3.08 score 1 dependentsbioc
MetCirc:Navigating mass spectral similarity in high-resolution MS/MS metabolomics data metabolomics data
MetCirc comprises a workflow to interactively explore high-resolution MS/MS metabolomics data. MetCirc uses the Spectra object infrastructure defined in the package Spectra that stores MS/MS spectra. MetCirc offers functionality to calculate similarity between precursors based on the normalised dot product, neutral losses or user-defined functions and visualise similarities in a circular layout. Within the interactive framework the user can annotate MS/MS features based on their similarity to (known) related MS/MS features.
Maintained by Thomas Naake. Last updated 5 months ago.
shinyappsmetabolomicsmassspectrometryvisualization
3.5 match 3.48 score 3 scriptsjpnolan
SphericalCubature:Numerical Integration over Spheres and Balls in n-Dimensions; Multivariate Polar Coordinates
Provides several methods to integrate functions over the unit sphere and ball in n-dimensional Euclidean space. Routines for converting to/from multivariate polar/spherical coordinates are also provided.
Maintained by John P. Nolan. Last updated 4 years ago.
6.8 match 1.78 score 5 scripts 2 dependentsmcrucifix
palinsol:Insolation for Palaeoclimate Studies
R package to compute Incoming Solar Radiation (insolation) for palaeoclimate studies. Features three solutions: Berger (1978), Berger and Loutre (1991) and Laskar et al. (2004). Computes daily-mean, season-averaged and annual means and for all latitudes, and polar night dates.
Maintained by Michel Crucifix. Last updated 25 days ago.
2.4 match 13 stars 4.88 score 13 scripts 3 dependentsmfacevedol
renpow:Renewable Power Systems and the Environment
Supports calculations and visualization for renewable power systems and the environment. Analysis and graphical tools for DC and AC circuits and their use in electric power systems. Analysis and graphical tools for thermodynamic cycles and heat engines, supporting efficiency calculations in coal-fired power plants, gas-fired power plants. Calculations of carbon emissions and atmospheric CO2 dynamics. Analysis of power flow and demand for the grid, as well as power models for microgrids and off-grid systems. Provides resource and power generation for hydro power, wind power, and solar power.
Maintained by Miguel F. Acevedo. Last updated 7 years ago.
7.8 match 1.48 score 30 scriptsegarpor
sphunif:Uniformity Tests on the Circle, Sphere, and Hypersphere
Implementation of uniformity tests on the circle and (hyper)sphere. The main function of the package is unif_test(), which conveniently collects more than 35 tests for assessing uniformity on S^{p-1} = {x in R^p : ||x|| = 1}, p >= 2. The test statistics are implemented in the unif_stat() function, which allows computing several statistics for different samples within a single call, thus facilitating Monte Carlo experiments. Furthermore, the unif_stat_MC() function allows parallelizing them in a simple way. The asymptotic null distributions of the statistics are available through the function unif_stat_distr(). The core of 'sphunif' is coded in C++ by relying on the 'Rcpp' package. The package also provides several novel datasets and gives the replicability for the data applications/simulations in García-Portugués et al. (2021) <doi:10.1007/978-3-030-69944-4_12>, García-Portugués et al. (2023) <doi:10.3150/21-BEJ1454>, García-Portugués et al. (2024) <doi:10.48550/arXiv.2108.09874>, and Fernández-de-Marcos and García-Portugués (2024) <doi:10.48550/arXiv.2405.13531>.
Maintained by Eduardo García-Portugués. Last updated 10 months ago.
circular-statisticsdirectional-statisticsuniformityuniformity-testsopenblascpp
1.9 match 8 stars 6.11 score 18 scripts 2 dependentsimehlhaff
PolarCAP:Access the Polarization in Comparative Attitudes Project
Distributes data from the Polarization in Comparative Attitudes Project. Helper functions enable data retrieval in wide and tidy formats for user-defined countries and years. Provides support for case-insensitive country names in many languages. Mehlhaff (2022) <https://imehlhaff.net/files/Polarization%20and%20Democracy.pdf>.
Maintained by Isaac Mehlhaff. Last updated 5 months ago.
3.8 match 3.00 score 3 scriptsclozanoruiz
sgo:Simple Geographical Operations (with OSGB36)
Methods focused in performing the OSGB36/ETRS89 transformation (Great Britain and the Isle of Man only) by using the Ordnance Survey's OSTN15/OSGM15 transformation model. Calculation of distances and areas from sets of points defined in any of the supported Coordinated Systems is also available.
Maintained by Carlos Lozano Ruiz. Last updated 2 years ago.
bnggrid-referencengrosgb36ostn15spatial
3.4 match 4 stars 3.30 score 7 scriptsswarm-lab
swaRm:Processing Collective Movement Data
Function library for processing collective movement data (e.g. fish schools, ungulate herds, baboon troops) collected from GPS trackers or computer vision tracking software.
Maintained by Simon Garnier. Last updated 1 years ago.
animal-behavioranimal-behaviourcollective-behaviorcollective-behaviour
2.0 match 21 stars 5.50 score 8 scripts 1 dependentslzumeta
injurytools:A Toolkit for Sports Injury and Illness Data Analysis
Sports Injury Data analysis aims to identify and describe the magnitude of the injury problem, and to gain more insights (e.g. determine potential risk factors) by statistical modelling approaches. The 'injurytools' package provides standardized routines and utilities that simplify such analyses. It offers functions for data preparation, informative visualizations and descriptive and model-based analyses.
Maintained by Lore Zumeta Olaskoaga. Last updated 5 months ago.
1.7 match 5 stars 6.37 score 27 scriptsxiangpin
ggstar:Multiple Geometric Shape Point Layer for 'ggplot2'
To create the multiple polygonal point layer for easily discernible shapes, we developed the package, it is like the 'geom_point' of 'ggplot2'. It can be used to draw the scatter plot.
Maintained by Shuangbin Xu. Last updated 11 months ago.
1.3 match 101 stars 8.22 score 282 scripts 3 dependentspacificclimate
ncdf4.helpers:Helper Functions for Use with the 'ncdf4' Package
Contains a collection of helper functions for dealing with 'NetCDF' files <https://www.unidata.ucar.edu/software/netcdf/> opened using 'ncdf4', particularly 'NetCDF' files that conform to the Climate and Forecast (CF) Metadata Conventions <http://cfconventions.org/Data/cf-conventions/cf-conventions-1.7/cf-conventions.html>.
Maintained by Lee Zeman. Last updated 3 years ago.
1.8 match 5 stars 5.85 score 236 scripts 1 dependentskylecaudle
TensorTools:Multilinear Algebra
A set of tools for basic tensor operators. A tensor in the context of data analysis in a multidimensional array. The tools in this package rely on using any discrete transformation (e.g. Fast Fourier Transform (FFT)). Standard tools included are the Eigenvalue decomposition of a tensor, the QR decomposition and LU decomposition. Other functionality includes the inverse of a tensor and the transpose of a symmetric tensor. Functionality in the package is outlined in Kernfeld, E., Kilmer, M., and Aeron, S. (2015) <doi:10.1016/j.laa.2015.07.021>.
Maintained by Kyle Caudle. Last updated 5 months ago.
5.1 match 2.00 scorecshs-hydrology
CSHShydRology:Canadian Hydrological Analyses
A collection of user submitted functions to aid in the analysis of hydrological data.
Maintained by Kevin Shook. Last updated 3 years ago.
1.9 match 4 stars 5.26 score 23 scriptschgrl
bReeze:Functions for Wind Resource Assessment
A collection of functions to analyse, visualize and interpret wind data and to calculate the potential energy production of wind turbines.
Maintained by Christian Graul. Last updated 1 years ago.
2.3 match 20 stars 4.34 score 22 scriptsr-forge
Rwave:Time-Frequency analysis of 1-D signals
Rwave is a library of R functions which provide an environment for the Time-Frequency analysis of 1-D signals (and especially for the wavelet and Gabor transforms of noisy signals). It was originally written for Splus by Rene Carmona, Bruno Torresani, and Wen L. Hwang, first at the University of California at Irvine and then at Princeton University. Credit should also be given to Andrea Wang whose functions on the dyadic wavelet transform are included. Rwave is based on the book: "Practical Time-Frequency Analysis: Gabor and Wavelet Transforms with an Implementation in S", by Rene Carmona, Wen L. Hwang and Bruno Torresani, Academic Press, 1998. This package is no longer actively maintained. A C++ rewrite of core functionality is in progress. If you'd like to participate, please contact Christian Gunning.
Maintained by Brandon Whitcher. Last updated 13 years ago.
2.0 match 4.82 score 88 scripts 5 dependentssurmann
ODEnetwork:Network of Differential Equations
Simulates a network of ordinary differential equations of order two. The package provides an easy interface to construct networks. In addition you are able to define different external triggers to manipulate the trajectory. The method is described by Surmann, Ligges, and Weihs (2014) <doi:10.1109/ENERGYCON.2014.6850482>.
Maintained by Dirk Surmann. Last updated 5 years ago.
1.9 match 4 stars 5.08 score 20 scripts 1 dependentsfunctionaldata
frechet:Statistical Analysis for Random Objects and Non-Euclidean Data
Provides implementation of statistical methods for random objects lying in various metric spaces, which are not necessarily linear spaces. The core of this package is Fréchet regression for random objects with Euclidean predictors, which allows one to perform regression analysis for non-Euclidean responses under some mild conditions. Examples include distributions in L^2-Wasserstein space, covariance matrices endowed with power metric (with Frobenius metric as a special case), Cholesky and log-Cholesky metrics. References: Petersen, A., & Müller, H.-G. (2019) <doi:10.1214/17-AOS1624>.
Maintained by Yaqing Chen. Last updated 6 months ago.
1.9 match 11 stars 4.82 score 20 scriptshypertidy
graticule:Meridional and Parallel Lines for Maps
Create graticule lines and labels for maps. Control the creation of lines or tiles by setting their placement (at particular meridians and parallels) and extent (along parallels and meridians). Labels are created independently of lines.
Maintained by Michael D. Sumner. Last updated 1 years ago.
1.5 match 18 stars 5.94 score 97 scriptsinsileco
graphicsutils:Collection of graphics utilities
A collection of functions to easily customize graphics-based plots.
Maintained by Kevin Cazelles. Last updated 3 years ago.
2.3 match 4 stars 3.90 score 20 scriptsjarioksa
natto:An Extreme 'vegan' Package of Experimental Code
Random code that is too experimental or too weird to be included in the vegan package.
Maintained by Jari Oksanen. Last updated 28 days ago.
1.9 match 8 stars 4.68 score 1 scriptsxliaosdsu
coneproj:Primal or Dual Cone Projections with Routines for Constrained Regression
Routines doing cone projection and quadratic programming, as well as doing estimation and inference for constrained parametric regression and shape-restricted regression problems. See Mary C. Meyer (2013)<doi:10.1080/03610918.2012.659820> for more details.
Maintained by Xiyue Liao. Last updated 25 days ago.
1.9 match 2 stars 4.64 score 21 scripts 21 dependentscran
circularEV:Extreme Value Analysis for Circular Data
General functions for performing extreme value analysis on a circular domain as part of the statistical methodology in the paper by Konzen, E., Neves, C., and Jonathan, P. (2021). Modeling nonstationary extremes of storm severity: Comparing parametric and semiparametric inference. Environmetrics, 32(4), e2667.
Maintained by Evandro Konzen. Last updated 3 years ago.
3.7 match 2.30 score 8 scriptsthk686
fftab:Tidy Manipulation of Fourier Transformed Data
The 'fftab' package stores Fourier coefficients in a tibble and allows their manipulation in various ways. Functions are available for converting between complex, rectangular ('re', 'im'), and polar ('mod', 'arg') representations, as well as for extracting components as vectors or matrices. Inputs can include vectors, time series, and arrays of arbitrary dimensions, which are restored to their original form when inverting the transform. Since 'fftab' stores Fourier frequencies as columns in the tibble, many standard operations on spectral data can be easily performed using tidy packages like 'dplyr'.
Maintained by Timothy Keitt. Last updated 2 months ago.
2.4 match 3.54 score 3 scriptspyanglab
directPA:Direction Analysis for Pathways and Kinases
Direction analysis is a set of tools designed to identify combinatorial effects of multiple treatments/conditions on pathways and kinases profiled by microarray, RNA-seq, proteomics, or phosphoproteomics data. See Yang P et al (2014) <doi:10.1093/bioinformatics/btt616>; and Yang P et al. (2016) <doi:10.1002/pmic.201600068>.
Maintained by Pengyi Yang. Last updated 1 years ago.
2.0 match 4.14 score 31 scripts 1 dependentspabrod
kinematics:Studying Sampled Trajectories
Allows analyzing time series representing two-dimensional movements. It accepts a data frame with a time (t), horizontal (x) and vertical (y) coordinate as columns, and returns several dynamical properties such as speed, acceleration or curvature.
Maintained by Pablo Rodriguez-Sanchez. Last updated 8 months ago.
2.0 match 1 stars 4.00 score 9 scriptsaidangildea
duke:Creating a Color-Blind Friendly Duke Color Package
Generates visualizations with Duke’s official suite of colors in a color blind friendly way.
Maintained by Aidan Gildea. Last updated 1 years ago.
1.5 match 2 stars 4.88 score 15 scriptssysbiolab
PathwaySpace:Spatial Projection of Network Signals along Geodesic Paths
For a given graph containing vertices, edges, and a signal associated with the vertices, the 'PathwaySpace' package performs a convolution operation, which involves a weighted combination of neighboring vertices and their associated signals. The package then uses a decay function to project these signals, creating geodesic paths on a 2D-image space. 'PathwaySpace' could have various applications, such as visualizing and analyzing network data in a graphical format that highlights the relationships and signal strengths between vertices. It can be particularly useful for understanding the influence of signals through complex networks. By combining graph theory, signal processing, and visualization, the 'PathwaySpace' package provides a novel way of representing and analyzing graph data.
Maintained by Mauro Castro. Last updated 2 months ago.
bioinformaticsbiological-networksgraph
1.5 match 2 stars 4.85 score 5 scriptscran
interfr:Interference Color Charts for Polarized Light Microscopy
Computes interference color tables and plots customized Michel-Levy or Raith-Sorensen charts. Automatic interpretation of polarized-light microscopy images is still under development and will come soon.
Maintained by Olivier Eterradossi. Last updated 8 years ago.
7.0 match 1 stars 1.00 score 4 scriptsgastonmaurodiaz
rcaiman:CAnopy IMage ANalysis
Tools for pre-processing and processing canopy photographs with support for raw data reading. Works with images taken with both regular and fisheye lenses (all types). Includes algorithms specifically designed to mitigate errors caused by direct sunlight.
Maintained by Gastón Mauro Díaz. Last updated 9 days ago.
1.8 match 1 stars 3.54 score 2 scriptsfvidoli
Compind:Composite Indicators Functions
A collection of functions to calculate Composite Indicators methods, focusing, in particular, on the normalisation and weighting-aggregation steps, as described in OECD Handbook on constructing composite indicators: methodology and user guide, 2008, 'Vidoli' and 'Fusco' and 'Mazziotta' <doi:10.1007/s11205-014-0710-y>, 'Mazziotta' and 'Pareto' (2016) <doi:10.1007/s11205-015-0998-2>, 'Van Puyenbroeck and 'Rogge' <doi:10.1016/j.ejor.2016.07.038> and other authors.
Maintained by Francesco Vidoli. Last updated 2 months ago.
2.0 match 1 stars 2.90 score 40 scriptspeterbiber
viscomplexr:Phase Portraits of Functions in the Complex Number Plane
Functionality for creating phase portraits of functions in the complex number plane. Works with R base graphics, whose full functionality is available. Parallel processing is used for optimum performance.
Maintained by Peter Biber. Last updated 4 months ago.
1.2 match 4 stars 4.75 score 14 scriptsrachel-carroll
eiExpand:Utilities for Expanding Functionality of 'eiCompare'
Augments the 'eiCompare' package's Racially Polarized Voting (RPV) functionality to streamline analyses and visualizations used to support voting rights and redistricting litigation. The package implements methods described in Barreto, M., Collingwood, L., Garcia-Rios, S., & Oskooii, K. A. (2022). "Estimating Candidate Support in Voting Rights Act Cases: Comparing Iterative EI and EI-R×C Methods" <doi:10.1177/0049124119852394>.
Maintained by Rachel Carroll. Last updated 2 years ago.
4.0 match 1.23 score 17 scriptscran
affluenceIndex:Affluence (Richness) Indices
Enables to compute the statistical indices of affluence (richness) with bootstrap errors, and inequality and polarization indices. Moreover, gives the possibility of calculation of affluence line. Some simple errors are fixed and it works with new version of Spatial Statistics packaged.
Maintained by Alicja Wolny-Dominiak. Last updated 6 months ago.
4.8 match 1.00 score 9 scriptscran
EnvNicheR:Niche Estimation
A plot overlying the niche of multiple species is obtained: 1) to determine the niche conditions which favor a higher species richness, 2) to create a box plot with the range of environmental variables of the species, 3) to obtain a list of species in an area of the niche selected by the user and, 4) to estimate niche overlap among the species.
Maintained by Castor Guisande Gonzalez. Last updated 1 years ago.
3.6 match 1.30 scoreeguidotti
calculus:High Dimensional Numerical and Symbolic Calculus
Efficient C++ optimized functions for numerical and symbolic calculus as described in Guidotti (2022) <doi:10.18637/jss.v104.i05>. It includes basic arithmetic, tensor calculus, Einstein summing convention, fast computation of the Levi-Civita symbol and generalized Kronecker delta, Taylor series expansion, multivariate Hermite polynomials, high-order derivatives, ordinary differential equations, differential operators (Gradient, Jacobian, Hessian, Divergence, Curl, Laplacian) and numerical integration in arbitrary orthogonal coordinate systems: cartesian, polar, spherical, cylindrical, parabolic or user defined by custom scale factors.
Maintained by Emanuele Guidotti. Last updated 2 years ago.
calculuscoordinate-systemscurldivergenceeinsteinfinite-differencegradienthermitehessianjacobianlaplaciannumerical-derivationnumerical-derivativesnumerical-differentiationsymbolic-computationsymbolic-differentiationtaylorcpp
0.5 match 47 stars 8.92 score 66 scripts 7 dependentssciviews
aurelhy:Hydrometeorological Interpolation
Hydrometeorological interpolation using the AURELHY method.
Maintained by Philippe Grosjean. Last updated 1 years ago.
interpolationspatial-data-analysis
2.3 match 2 stars 2.00 score 5 scriptsglenndavis52
zonohedra:Compute and Plot Zonohedra from Vector Generators
Computes a zonohedron from real vector generators. The package also computes zonogons (2D zonotopes) and zonosegs (1D zonotopes). An elementary S3 class for matroids is included, which supports matroids with rank 3, 2, and 1. Optimization methods are taken from Heckbert (1985) <https://www.cs.cmu.edu/~ph/zono.ps.gz>.
Maintained by Glenn Davis. Last updated 1 months ago.
1.5 match 3.00 score 8 scriptswanglabcsu
regverse:Streamlined Data Modeling and Visualization in Biomedical Regression Analysis
Provides a comprehensive suite of tools to enhance regression analysis and interpretation in the field of computational biology and clinical medicine.
Maintained by Shixiang Wang. Last updated 25 days ago.
1.8 match 2.30 scorejmmonnet
lidaRtRee:Forest Analysis with Airborne Laser Scanning (LiDAR) Data
Provides functions for forest objects detection, structure metrics computation, model calibration and mapping with airborne laser scanning: co-registration of field plots (Monnet and Mermin (2014) <doi:10.3390/f5092307>); tree detection (method 1 in Eysn et al. (2015) <doi:10.3390/f6051721>) and segmentation; forest parameters estimation with the area-based approach: model calibration with ground reference, and maps export (Aussenac et al. (2023) <doi:10.12688/openreseurope.15373.2>); extraction of both physical (gaps, edges, trees) and statistical features useful for e.g. habitat suitability modeling (Glad et al. (2020) <doi:10.1002/rse2.117>) and forest maturity mapping (Fuhr et al. (2022) <doi:10.1002/rse2.274>).
Maintained by Jean-Matthieu Monnet. Last updated 2 months ago.
1.9 match 3 stars 2.18 scorebioc
ecolitk:Meta-data and tools for E. coli
Meta-data and tools to work with E. coli. The tools are mostly plotting functions to work with circular genomes. They can used with other genomes/plasmids.
Maintained by Laurent Gautier. Last updated 5 months ago.
1.8 match 2.30 score 1 scriptsjpnolan
mvmesh:Multivariate Meshes and Histograms in Arbitrary Dimensions
Define, manipulate and plot meshes on simplices, spheres, balls, rectangles and tubes. Directional and other multivariate histograms are provided.
Maintained by John P. Nolan. Last updated 5 years ago.
1.6 match 2.08 score 1 scripts 4 dependentscran
s2dv:A Set of Common Tools for Seasonal to Decadal Verification
The advanced version of package 's2dverification'. It is intended for 'seasonal to decadal' (s2d) climate forecast verification, but it can also be used in other kinds of forecasts or general climate analysis. This package is specially designed for the comparison between the experimental and observational datasets. The functionality of the included functions covers from data retrieval, data post-processing, skill scores against observation, to visualization. Compared to 's2dverification', 's2dv' is more compatible with the package 'startR', able to use multiple cores for computation and handle multi-dimensional arrays with a higher flexibility. The CDO version used in development is 1.9.8.
Maintained by Ariadna Batalla. Last updated 5 months ago.
1.7 match 1.95 score 3 dependentsdkibalnikov
donutsk:Construct Advanced Donut Charts
Build donut/pie charts with 'ggplot2' layer by layer, exploiting the advantages of polar symmetry. Leverage layouts to distribute labels effectively. Connect labels to donut segments using pins. Streamline annotation and highlighting.
Maintained by Dmitry Kibalnikov. Last updated 11 months ago.
0.5 match 6 stars 5.18 score 2 scriptsmonicacalsan
MScombine:Combine Data from Positive and Negative Ionization Mode Finding Common Entities
Find common entities detected in both positive and negative ionization mode, delete this entity in the less sensible mode and combine both matrices.
Maintained by Monica Calderon-Santiago. Last updated 6 years ago.
1.9 match 2 stars 1.30 score 5 scriptskurthornik
NLPutils:Natural Language Processing Utilities
Utilities for Natural Language Processing.
Maintained by Kurt Hornik. Last updated 2 years ago.
2.0 match 1.00 score 4 scriptsabdoulma
ggtricks:Create Sector and Other Charts Easily Using Grammar of Graphics
A collection of several geoms to create graphics, using 'ggplot2' and the Cartesian coordinate system. You use the familiar mapping 'Grammar of Graphics' without the need to do another transformation into polar coordinates.
Maintained by Abdoul ISSA BIDA. Last updated 2 years ago.
0.5 match 8 stars 3.60 score 8 scriptspatterninstitute
grantham:Calculate the 'Grantham' Distance
A minimal set of routines to calculate the 'Grantham' distance <doi:10.1126/science.185.4154.862>. The 'Grantham' distance attempts to provide a proxy for the evolutionary distance between two amino acids based on three key chemical properties: composition, polarity and molecular volume. In turn, evolutionary distance is used as a proxy for the impact of missense mutations. The higher the distance, the more deleterious the substitution is expected to be.
Maintained by Ramiro Magno. Last updated 8 months ago.
0.5 match 4 stars 2.78 score 7 scripts 1 dependentscran
pgnorm:The p-Generalized Normal Distribution
Evaluation of the pdf and the cdf of the univariate, noncentral, p-generalized normal distribution. Sampling from the univariate, noncentral, p-generalized normal distribution using either the p-generalized polar method, the p-generalized rejecting polar method, the Monty Python method, the Ziggurat method or the method of Nardon and Pianca. The package also includes routines for the simulation of the bivariate, p-generalized uniform distribution and the simulation of the corresponding angular distribution.
Maintained by Steve Kalke. Last updated 9 years ago.
0.8 match 1.78 score 2 dependents