R-universe search: polarity

rpolars

polars:Lightning-Fast 'DataFrame' Library

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

Maintained by Soren Welling. Last updated 3 days ago.

arrow polars rust

151.3 match 499 stars 12.01 score 1.0k scripts 2 dependents

trinker

lexicon:Lexicons for Text Analysis

A collection of lexical hash tables, dictionaries, and word lists.

Maintained by Tyler Rinker. Last updated 3 years ago.

hash lexicon lookup names-frequent stopwords text-dictionaries text-mining

35.1 match 111 stars 8.80 score 224 scripts 25 dependents

adokter

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.

aeroecology enram eumetnet-opera lifewatch movement-ecology nexrad oscibio radar weather-radar wsr-88d

30.3 match 29 stars 8.65 score 56 scripts

eitsupi

neopolars:R Bindings for the 'polars' Rust Library

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

Maintained by Tatsuya Shima. Last updated 1 days ago.

rust cargo

45.5 match 40 stars 4.86 score 1 scripts

trinker

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.

amplifier polarity sentiment sentiment-analysis valence-shifter

21.2 match 432 stars 9.43 score 680 scripts 2 dependents

trinker

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.

qdap quantitative-discourse-analysis text-analysis text-mining text-plotting openjdk

19.4 match 176 stars 9.61 score 1.3k scripts 3 dependents

bioc

Spectra:Spectra Infrastructure for Mass Spectrometry Data

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

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

infrastructure proteomics massspectrometry metabolomics bioconductor hacktoberfest mass-spectrometry

10.0 match 41 stars 13.01 score 254 scripts 35 dependents

etiennebacher

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 scripts

polar-fhir

fhircrackr:Handling HL7 FHIR® Resources in R

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

Maintained by Julia Palm. Last updated 11 days ago.

fhir fhir-client

15.0 match 33 stars 7.63 score 46 scripts

katrionagoldmann

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.

bioinformatics differential-expression differential-expression-analysis gene-expression interactive omics plotly rna-seq transcriptomics volcanoplots

15.1 match 36 stars 5.90 score 37 scripts

hwborchers

pracma:Practical Numerical Math Functions

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

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

7.1 match 29 stars 12.34 score 6.6k scripts 931 dependents

bioc

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.

immunooncology massspectrometry metabolomics bioconductor feature-detection mass-spectrometry peak-detection cpp

6.0 match 196 stars 14.31 score 984 scripts 11 dependents

openair-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.

openair

12.9 match 21 stars 6.04 score 47 scripts

revelle

psych:Procedures for Psychological, Psychometric, and Personality Research

A general purpose toolbox developed originally for personality, psychometric theory and experimental psychology. Functions are primarily for multivariate analysis and scale construction using factor analysis, principal component analysis, cluster analysis and reliability analysis, although others provide basic descriptive statistics. Item Response Theory is done using factor analysis of tetrachoric and polychoric correlations. Functions for analyzing data at multiple levels include within and between group statistics, including correlations and factor analysis. Validation and cross validation of scales developed using basic machine learning algorithms are provided, as are functions for simulating and testing particular item and test structures. Several functions serve as a useful front end for structural equation modeling. Graphical displays of path diagrams, including mediation models, factor analysis and structural equation models are created using basic graphics. Some of the functions are written to support a book on psychometric theory as well as publications in personality research. For more information, see the <https://personality-project.org/r/> web page.

Maintained by William Revelle. Last updated 3 months ago.

5.1 match 52 stars 13.94 score 29k scripts 317 dependents

stefanocoretta

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.

phonetics software tongue-image ultrasound ultrasound-tongue-imaging

11.9 match 5 stars 5.88 score 17 scripts

openair-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-quality air-quality-data meteorology openair cpp

5.2 match 311 stars 12.91 score 1.2k scripts 12 dependents

mlverse

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-science dplyr llm polars python

10.0 match 86 stars 6.61 score 94 scripts

davidcsterratt

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 score

allancameron

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 dependents

andrisignorell

DescTools:Tools for Descriptive Statistics

A collection of miscellaneous basic statistic functions and convenience wrappers for efficiently describing data. The author's intention was to create a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. The package contains furthermore functions to produce documents using MS Word (or PowerPoint) and functions to import data from Excel. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in absence of convincing alternatives). The 'BigCamelCase' style was consequently applied to functions borrowed from contributed R packages as well.

Maintained by Andri Signorell. Last updated 7 hours ago.

fortran cpp

3.6 match 87 stars 16.70 score 7.7k scripts 99 dependents

bioc

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.

infrastructure proteomics massspectrometry bioconductor mass-spectrometry metabolomics

6.0 match 8 stars 9.43 score 4 scripts 188 dependents

tidyverse

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-visualisation visualisation

2.3 match 6.6k stars 25.10 score 645k scripts 7.5k dependents

bioc

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.

geneexpression differentialexpression genesetenrichment pathways cpp

3.4 match 387 stars 16.25 score 3.9k scripts 101 dependents

mlverse

torch:Tensors and Neural Networks with 'GPU' Acceleration

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

Maintained by Daniel Falbel. Last updated 6 days ago.

autograd deep-learning torch cpp

3.3 match 520 stars 16.52 score 1.4k scripts 38 dependents

dankelley

oce:Analysis of Oceanographic Data

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

Maintained by Dan Kelley. Last updated 1 days ago.

oceanography fortran cpp

3.5 match 146 stars 15.42 score 4.2k scripts 18 dependents

kjhealy

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 scripts

rpolars

polarssql:A 'polars' backend for 'DBI'.

DBI-compliant interface to 'polars'.

Maintained by Tatsuya Shima. Last updated 7 months ago.

dplyr dplyr-sql-backends polars

14.0 match 26 stars 3.41 score 3 scripts

dcgerard

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 dependents

davidcsterratt

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.

cpp

3.5 match 16 stars 12.98 score 776 scripts 139 dependents

bioc

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.

immunooncology massspectrometry metabolomics lipidomics dataimport adduct algae bioconductor hplc-esi-ms lipid mass-spectrometry oxidative-stress-biomarkers oxidized-lipids oxylipins plankton

6.0 match 8 stars 6.56 score 9 scripts

shixiangwang

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.

ggplot2-enhancements

8.3 match 9 stars 4.65 score 7 scripts

bioc

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.

immunooncology infrastructure proteomics massspectrometry qualitycontrol dataimport bioconductor bioinformatics mass-spectrometry proteomics-data visualisation cpp

3.0 match 130 stars 12.81 score 772 scripts 36 dependents

johncoene

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.

echarts hacktoberfest htmlwidget htmlwidgets visualization

3.3 match 603 stars 11.45 score 1.3k scripts 11 dependents

willgearty

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.

geology ggplot2 paleontology visualization

3.5 match 92 stars 10.61 score 207 scripts 3 dependents

fchen365

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-detection exploratory-data-analysis matrix-decompositions pca principal-component-analysis sparse-matrix

7.6 match 11 stars 4.74 score 8 scripts

quanteda

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.

openblas cpp

3.5 match 42 stars 9.56 score 432 scripts

koheiw

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.

lsa quanteda sentiment-analysis text-analysis

5.5 match 55 stars 6.09 score 14 scripts

tyy20

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 score

ouhscbbmc

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-analysis oklahoma-city-bombing publication seasonal time-series

5.3 match 7 stars 6.14 score 44 scripts

sfeuerriegel

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 dependents

ssnn-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.

software annotationdata cpp

3.3 match 9.09 score 424 scripts 7 dependents

ropensci

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.

animal gps network social spatial

3.0 match 24 stars 9.97 score 145 scripts 3 dependents

nmartinkova

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 scripts

geobosh

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-matrix complex-numbers plotting-functions s4 s4class simulation

4.0 match 1 stars 7.32 score 29 scripts 56 dependents

adokter

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.

proj hdf5 zlib gsl cpp

4.4 match 6 stars 6.61 score 19 scripts

jokergoo

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 dependents

mthrun

DatabionicSwarm:Swarm Intelligence for Self-Organized Clustering

Algorithms implementing populations of agents that interact with one another and sense their environment may exhibit emergent behavior such as self-organization and swarm intelligence. Here, a swarm system called Databionic swarm (DBS) is introduced which was published in Thrun, M.C., Ultsch A.: "Swarm Intelligence for Self-Organized Clustering" (2020), Artificial Intelligence, <DOI:10.1016/j.artint.2020.103237>. DBS is able to adapt itself to structures of high-dimensional data such as natural clusters characterized by distance and/or density based structures in the data space. The first module is the parameter-free projection method called Pswarm (Pswarm()), which exploits the concepts of self-organization and emergence, game theory, swarm intelligence and symmetry considerations. The second module is the parameter-free high-dimensional data visualization technique, which generates projected points on the topographic map with hypsometric tints defined by the generalized U-matrix (GeneratePswarmVisualization()). The third module is the clustering method itself with non-critical parameters (DBSclustering()). Clustering can be verified by the visualization and vice versa. The term DBS refers to the method as a whole. It enables even a non-professional in the field of data mining to apply its algorithms for visualization and/or clustering to data sets with completely different structures drawn from diverse research fields. The comparison to common projection methods can be found in the book of Thrun, M.C.: "Projection Based Clustering through Self-Organization and Swarm Intelligence" (2018) <DOI:10.1007/978-3-658-20540-9>.

Maintained by Michael Thrun. Last updated 1 years ago.

openblas cpp

4.7 match 12 stars 6.16 score 27 scripts 1 dependents

ropensci

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 scripts

rmendels

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 scripts

svmiller

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.

eugene peace-science

5.1 match 29 stars 5.49 score 211 scripts

andrewljackson

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-ecology ecology niche-modelling stable-isotopes jags cpp

3.0 match 36 stars 9.13 score 187 scripts 1 dependents

iainmstott

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 dependents

r-forge

agrmt:Calculate Concentration and Dispersion in Ordered Rating Scales

Calculates concentration and dispersion in ordered rating scales. It implements various measures of concentration and dispersion to describe what researchers variably call agreement, concentration, consensus, dispersion, or polarization among respondents in ordered data. It also implements other related measures to classify distributions. In addition to a generic city-block based concentration measure and a generic dispersion measure, the package implements various measures, including van der Eijk's (2001) <DOI: 10.1023/A:1010374114305> measure of agreement A, measures of concentration by Leik, Tatsle and Wierman, Blair and Lacy, Kvalseth, Berry and Mielke, Reardon, and Garcia-Montalvo and Reynal-Querol. Furthermore, the package provides an implementation of Galtungs AJUS-system to classify distributions, as well as a function to identify the position of multiple modes.

Maintained by Didier Ruedin. Last updated 29 days ago.

7.6 match 3.58 score 38 scripts

yunuuuu

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-heatmaps dendrogram dendrogram-heatmap ggplot ggplot-extension ggplot2 heatmap heatmap-visualization heatmaps marginal-plots oncoplot oncoprint tanglegram upset upsetplot

3.8 match 267 stars 7.08 score 27 scripts

great-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-analysis ggplot ggplot-features graphics interactive-plots loon visualizations

3.7 match 24 stars 7.11 score 9 scripts 3 dependents

bioc

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.

software dataimport datarepresentation featureextraction cheminformatics biomedicalinformatics proteomics go systemsbiology bioconductor bioinformatics drug-discovery feature-extraction fingerprint molecular-descriptors protein-sequences

3.4 match 37 stars 7.81 score 29 scripts

nilsmechtel

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 scripts

dmurdoch

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 dependents

gaboraszabo

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 scripts

glenndavis52

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 dependents

trinker

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 dependents

emanuelhuber

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.

conics ellipse elliptic geometry intersection

5.6 match 4.20 score 53 scripts 2 dependents

bioc

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.

metabolomics preprocessing clustering

3.9 match 10 stars 6.04 score 22 scripts

spatstat

spatstat.geom:Geometrical Functionality of the 'spatstat' Family

Defines spatial data types and supports geometrical operations on them. Data types include point patterns, windows (domains), pixel images, line segment patterns, tessellations and hyperframes. Capabilities include creation and manipulation of data (using command line or graphical interaction), plotting, geometrical operations (rotation, shift, rescale, affine transformation), convex hull, discretisation and pixellation, Dirichlet tessellation, Delaunay triangulation, pairwise distances, nearest-neighbour distances, distance transform, morphological operations (erosion, dilation, closing, opening), quadrat counting, geometrical measurement, geometrical covariance, colour maps, calculus on spatial domains, Gaussian blur, level sets of images, transects of images, intersections between objects, minimum distance matching. (Excludes spatial data on a network, which are supported by the package 'spatstat.linnet'.)

Maintained by Adrian Baddeley. Last updated 2 days ago.

classes-and-objects distance-calculation geometry geometry-processing images mensuration plotting point-patterns spatial-data spatial-data-analysis

1.9 match 7 stars 12.11 score 241 scripts 227 dependents

mpru

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 scripts

talgalili

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 dependents

bioc

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.

visualization shinyapps gui

3.9 match 3 stars 5.26 score 3 scripts

bioc

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.

software visualization cellbiology classification infrastructure gui shinyapps bioconductor fluorescence microscopy particles tracking

3.6 match 4 stars 5.62 score 8 scripts

animint

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 scripts

icosa-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.

grid cpp

3.5 match 4 stars 5.41 score 65 scripts

imehlhaff

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 scripts

bioc

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.

microarray preprocessing qualitycontrol differentialexpression visualization geneexpression genesetenrichment pathways bioconductor bioconductor-package bioinformatics gene-set-enrichment transcriptomics

2.3 match 13 stars 8.30 score 183 scripts 7 dependents

ms609

TreeTools:Create, Modify and Analyse Phylogenetic Trees

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

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

evolutionary-biology phylogenetic-trees phylogenetics cpp

1.9 match 21 stars 9.92 score 124 scripts 10 dependents

karlines

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.

fortran

4.0 match 6 stars 4.57 score 52 scripts

roaldarbol

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-behaviour animal-movement neuroethology neuroscience

3.8 match 10 stars 4.81 score 8 scripts

reneschulenberg

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 dependents

emilhvitfeldt

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.

text-datasets

1.8 match 75 stars 9.66 score 1.4k scripts 1 dependents

mrc-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.

cpp openmp

2.2 match 18 stars 7.84 score 60 scripts 3 dependents

cran

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 score

shulele

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 scripts

f-silva-archaeo

skyscapeR:Data Analysis and Visualization for Skyscape Archaeology

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

Maintained by Silva Fabio. Last updated 6 months ago.

3.1 match 5 stars 5.31 score 41 scripts

shikokuchuo

mirai:Minimalist Async Evaluation Framework for R

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

Maintained by Charlie Gao. Last updated 2 days ago.

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

1.3 match 217 stars 11.94 score 130 scripts 7 dependents

cardiomoon

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 dependents

adelmofilho

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.

cryptography r-programming

5.4 match 2.70 score 3 scripts

mmaechler

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.

openblas

3.4 match 2 stars 4.15 score 28 scripts

sssydysss

TransProR:Analysis and Visualization of Multi-Omics Data

A tool for comprehensive transcriptomic data analysis, with a focus on transcript-level data preprocessing, expression profiling, differential expression analysis, and functional enrichment. It enables researchers to identify key biological processes, disease biomarkers, and gene regulatory mechanisms. 'TransProR' is aimed at researchers and bioinformaticians working with RNA-Seq data, providing an intuitive framework for in-depth analysis and visualization of transcriptomic datasets. The package includes comprehensive documentation and usage examples to guide users through the entire analysis pipeline. The differential expression analysis methods incorporated in the package include 'limma' (Ritchie et al., 2015, <doi:10.1093/nar/gkv007>; Smyth, 2005, <doi:10.1007/0-387-29362-0_23>), 'edgeR' (Robinson et al., 2010, <doi:10.1093/bioinformatics/btp616>), 'DESeq2' (Love et al., 2014, <doi:10.1186/s13059-014-0550-8>), and Wilcoxon tests (Li et al., 2022, <doi:10.1186/s13059-022-02648-4>), providing flexible and robust approaches to RNA-Seq data analysis. For more information, refer to the package vignettes and related publications.

Maintained by Dongyue Yu. Last updated 20 days ago.

1.9 match 174 stars 7.55 score 34 scripts

pwarncke77

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 scripts

trackage

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

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

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

3.3 match 4 stars 4.19 score 13 scripts

christopherkenny

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.

cpp

1.7 match 14 stars 7.81 score 191 scripts 1 dependents

wilkox

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.

ggplot2

1.2 match 306 stars 11.08 score 234 scripts 33 dependents

munterfi

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.

3d birds conditional-empirical-random-walk gliding-and-soaring machine-learning movement-ecology random-trajectory-generator random-walk simulation trajectory-generation

2.3 match 6 stars 5.71 score 19 scripts

kylecaudle

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 dependents

dreamrs

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.

data-visualization htmlwidgets

1.5 match 144 stars 8.51 score 247 scripts

kybak90

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 scripts

markheckmann

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.

repertory-grid repgrid

1.9 match 19 stars 6.69 score 156 scripts

r-forge

colorspace:A Toolbox for Manipulating and Assessing Colors and Palettes

Carries out mapping between assorted color spaces including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB, and polar CIELAB. Qualitative, sequential, and diverging color palettes based on HCL colors are provided along with corresponding ggplot2 color scales. Color palette choice is aided by an interactive app (with either a Tcl/Tk or a shiny graphical user interface) and shiny apps with an HCL color picker and a color vision deficiency emulator. Plotting functions for displaying and assessing palettes include color swatches, visualizations of the HCL space, and trajectories in HCL and/or RGB spectrum. Color manipulation functions include: desaturation, lightening/darkening, mixing, and simulation of color vision deficiencies (deutanomaly, protanomaly, tritanomaly). Details can be found on the project web page at <https://colorspace.R-Forge.R-project.org/> and in the accompanying scientific paper: Zeileis et al. (2020, Journal of Statistical Software, <doi:10.18637/jss.v096.i01>).

Maintained by Achim Zeileis. Last updated 4 months ago.

0.8 match 16.23 score 8.2k scripts 8.1k dependents

r-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 dependents

cran

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 dependents

bioc

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.

shinyapps metabolomics massspectrometry visualization

3.5 match 3.48 score 3 scripts

jpnolan

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 dependents

mcrucifix

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.

insolation milankovitch

2.4 match 13 stars 4.88 score 13 scripts 3 dependents

mfacevedol

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 scripts

egarpor

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-statistics directional-statistics uniformity uniformity-tests openblas cpp

1.9 match 8 stars 6.11 score 18 scripts 2 dependents

obreschkow

cooltools:Practical Tools for Scientific Computations and Visualizations

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

Maintained by Danail Obreschkow. Last updated 3 months ago.

cpp

3.6 match 1 stars 3.17 score 21 scripts

imehlhaff

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 scripts

clozanoruiz

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.

bng grid-reference ngr osgb36 ostn15 spatial

3.4 match 4 stars 3.30 score 7 scripts

swarm-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-behavior animal-behaviour collective-behavior collective-behaviour

2.0 match 21 stars 5.50 score 8 scripts 1 dependents

lzumeta

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.

sports sports-injuries

1.7 match 5 stars 6.37 score 27 scripts

mthrun

ProjectionBasedClustering:Projection Based Clustering

A clustering approach applicable to every projection method is proposed here. The two-dimensional scatter plot of any projection method can construct a topographic map which displays unapparent data structures by using distance and density information of the data. The generalized U*-matrix renders this visualization in the form of a topographic map, which can be used to automatically define the clusters of high-dimensional data. The whole system is based on Thrun and Ultsch, "Using Projection based Clustering to Find Distance and Density based Clusters in High-Dimensional Data" <DOI:10.1007/s00357-020-09373-2>. Selecting the correct projection method will result in a visualization in which mountains surround each cluster. The number of clusters can be determined by counting valleys on the topographic map. Most projection methods are wrappers for already available methods in R. By contrast, the neighbor retrieval visualizer (NeRV) is based on C++ source code of the 'dredviz' software package, and the Curvilinear Component Analysis (CCA) is translated from 'MATLAB' ('SOM Toolbox' 2.0) to R.

Maintained by Michael Thrun. Last updated 3 years ago.

cpp

2.0 match 7 stars 5.33 score 34 scripts 3 dependents

xiangpin

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 dependents

pacificclimate

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 dependents

kylecaudle

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 score

cshs-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 scripts

chgrl

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 scripts

r-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 dependents

wasquith

copBasic:General Bivariate Copula Theory and Many Utility Functions

Extensive functions for bivariate copula (bicopula) computations and related operations for bicopula theory. The lower, upper, product, and select other bicopula are implemented along with operations including the diagonal, survival copula, dual of a copula, co-copula, and numerical bicopula density. Level sets, horizontal and vertical sections are supported. Numerical derivatives and inverses of a bicopula are provided through which simulation is implemented. Bicopula composition, convex combination, asymmetry extension, and products also are provided. Support extends to the Kendall Function as well as the Lmoments thereof. Kendall Tau, Spearman Rho and Footrule, Gini Gamma, Blomqvist Beta, Hoeffding Phi, Schweizer- Wolff Sigma, tail dependency, tail order, skewness, and bivariate Lmoments are implemented, and positive/negative quadrant dependency, left (right) increasing (decreasing) are available. Other features include Kullback-Leibler Divergence, Vuong Procedure, spectral measure, and Lcomoments for inference, maximum likelihood, and AIC, BIC, and RMSE for goodness-of-fit.

Maintained by William Asquith. Last updated 1 months ago.

1.8 match 5.34 score 139 scripts 5 dependents

surmann

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 dependents

functionaldata

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 scripts

hypertidy

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 scripts

insileco

graphicsutils:Collection of graphics utilities

A collection of functions to easily customize graphics-based plots.

Maintained by Kevin Cazelles. Last updated 3 years ago.

graphics plot cpp

2.3 match 4 stars 3.90 score 20 scripts

jarioksa

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 scripts

xliaosdsu

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.

openblas cpp

1.9 match 2 stars 4.64 score 21 scripts 21 dependents

cran

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 scripts

thk686

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 scripts

pyanglab

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 dependents

pabrod

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.

biology ethology kinematics

2.0 match 1 stars 4.00 score 9 scripts

aidangildea

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 scripts

sysbiolab

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.

bioinformatics biological-networks graph

1.5 match 2 stars 4.85 score 5 scripts

cran

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 scripts

gastonmaurodiaz

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 scripts

fvidoli

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 scripts

peterbiber

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.

cpp

1.2 match 4 stars 4.75 score 14 scripts

rachel-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 scripts

cran

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 scripts

nepem-ufsc

metan:Multi Environment Trials Analysis

Performs stability analysis of multi-environment trial data using parametric and non-parametric methods. Parametric methods includes Additive Main Effects and Multiplicative Interaction (AMMI) analysis by Gauch (2013) <doi:10.2135/cropsci2013.04.0241>, Ecovalence by Wricke (1965), Genotype plus Genotype-Environment (GGE) biplot analysis by Yan & Kang (2003) <doi:10.1201/9781420040371>, geometric adaptability index by Mohammadi & Amri (2008) <doi:10.1007/s10681-007-9600-6>, joint regression analysis by Eberhart & Russel (1966) <doi:10.2135/cropsci1966.0011183X000600010011x>, genotypic confidence index by Annicchiarico (1992), Murakami & Cruz's (2004) method, power law residuals (POLAR) statistics by Doring et al. (2015) <doi:10.1016/j.fcr.2015.08.005>, scale-adjusted coefficient of variation by Doring & Reckling (2018) <doi:10.1016/j.eja.2018.06.007>, stability variance by Shukla (1972) <doi:10.1038/hdy.1972.87>, weighted average of absolute scores by Olivoto et al. (2019a) <doi:10.2134/agronj2019.03.0220>, and multi-trait stability index by Olivoto et al. (2019b) <doi:10.2134/agronj2019.03.0221>. Non-parametric methods includes superiority index by Lin & Binns (1988) <doi:10.4141/cjps88-018>, nonparametric measures of phenotypic stability by Huehn (1990) <doi:10.1007/BF00024241>, TOP third statistic by Fox et al. (1990) <doi:10.1007/BF00040364>. Functions for computing biometrical analysis such as path analysis, canonical correlation, partial correlation, clustering analysis, and tools for inspecting, manipulating, summarizing and plotting typical multi-environment trial data are also provided.

Maintained by Tiago Olivoto. Last updated 9 days ago.

0.5 match 2 stars 9.48 score 1.3k scripts 2 dependents

stla

cyclotomic:The Field of Cyclotomic Numbers

The cyclotomic numbers are complex numbers that can be thought of as the rational numbers extended with the roots of unity. They are represented exactly, enabling exact computations. They contain the Gaussian rationals (complex numbers with rational real and imaginary parts) as well as the square roots of all rational numbers. They also contain the sine and cosine of all rational multiples of pi. The algorithms implemented in this package are taken from the 'Haskell' package 'cyclotomic', whose algorithms are adapted from code by Martin Schoenert and Thomas Breuer in the 'GAP' project (<https://www.gap-system.org/>). Cyclotomic numbers have applications in number theory, algebraic geometry, algebraic number theory, coding theory, and in the theory of graphs and combinatorics. They have connections to the theory of modular functions and modular curves.

Maintained by Stéphane Laurent. Last updated 1 years ago.

arithmetic cyclotomic-numbers

1.8 match 1 stars 2.70 score 9 scripts

cran

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 score

cran

biogeom:Biological Geometries

Is used to simulate and fit biological geometries. 'biogeom' incorporates several novel universal parametric equations that can generate the profiles of bird eggs, flowers, linear and lanceolate leaves, seeds, starfish, and tree-rings (Gielis (2003) <doi:10.3732/ajb.90.3.333>; Shi et al. (2020) <doi:10.3390/sym12040645>), three growth-rate curves representing the ontogenetic growth trajectories of animals and plants against time, and the axially symmetrical and integral forms of all these functions (Shi et al. (2017) <doi:10.1016/j.ecolmodel.2017.01.012>; Shi et al. (2021) <doi:10.3390/sym13081524>). The optimization method proposed by Nelder and Mead (1965) <doi:10.1093/comjnl/7.4.308> was used to estimate model parameters. 'biogeom' includes several real data sets of the boundary coordinates of natural shapes, including avian eggs, fruit, lanceolate and ovate leaves, tree rings, seeds, and sea stars,and can be potentially applied to other natural shapes. 'biogeom' can quantify the conspecific or interspecific similarity of natural outlines, and provides information with important ecological and evolutionary implications for the growth and form of living organisms. Please see Shi et al. (2022) <doi:10.1111/nyas.14862> for details.

Maintained by Peijian Shi. Last updated 12 months ago.

3.5 match 1 stars 1.30 score 1 scripts

miguelro

Relectoral:Electoral Analysis

Functions to obtain an important number of electoral indicators described in the package, which can be divided into two large sections: The first would be the one containing the indicators of electoral disproportionality, such as, Rae index, Loosemore–Hanby index, etc. The second group is intended to study the dimensions of the party system vote, through the indicators of electoral fragmentation, polarization, volatility, etc. Moreover, multiple seat allocation simulations can also be performed based on different allocation systems, such as the D'Hondt method, Sainte-Laguë, etc. Finally, some of these functions have been built so that, if the user wishes, the data provided by the Spanish Ministry of Home Office for different electoral processes held in Spain can be obtained automatically. All the above will allow the users to carry out deep studies on the results obtained in any type of electoral process. The methods are described in: Oñate, Pablo and Ocaña, Francisco A. (1999, ISBN:9788474762815); Ruiz Rodríguez, Leticia M. and Otero Felipe, Patricia (2011, ISBN:9788474766226).

Maintained by Miguel Rodríguez Asensio. Last updated 5 years ago.

openjdk

2.3 match 2.00 score

cran

ultrapolaRplot:Plotting Ultrasound Tongue Traces

Plots traced ultrasound tongue imaging data according to a polar coordinate system. There is currently support for plotting means and standard deviations of each category's trace; Smoothing Splines Analysis of Variance (SSANOVA) could be implemented as well. The origin of the polar coordinates may be defined manually or automatically determined based on different algorithms. Currently 'ultrapolaRplot' supports ultrasound tongue imaging trace data from 'UltraTrace' (<https://github.com/SwatPhonLab/UltraTrace>). 'UltraTrace' is capable of importing data from Articulate Instruments AAA. 'read_textgrid.R' is required for opening TextGrids to determine category and alignment information of ultrasound traces.

Maintained by Yana Outkin. Last updated 9 months ago.

4.6 match 1.00 score

eguidotti

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.

calculus coordinate-systems curl divergence einstein finite-difference gradient hermite hessian jacobian laplacian numerical-derivation numerical-derivatives numerical-differentiation symbolic-computation symbolic-differentiation taylor cpp

0.5 match 47 stars 8.92 score 66 scripts 7 dependents

sciviews

aurelhy:Hydrometeorological Interpolation

Hydrometeorological interpolation using the AURELHY method.

Maintained by Philippe Grosjean. Last updated 1 years ago.

interpolation spatial-data-analysis

2.3 match 2 stars 2.00 score 5 scripts

glenndavis52

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.

cpp

1.5 match 3.00 score 8 scripts

theropod1

gdi:Volumetric Analysis using Graphic Double Integration

Tools implementing an automated version of the graphic double integration technique (GDI) for volume implementation, and some other related utilities for paleontological image-analysis. GDI was first employed by Jerison (1973) <ISBN:9780323141086> and Hurlburt (1999) <doi:10.1080/02724634.1999.10011145> and is primarily used for volume or mass estimation of (extinct) animals. The package 'gdi' aims to make this technique as convenient and versatile as possible. The core functions of 'gdi' provide utilities for automatically measuring diameters from digital silhouettes provided as image files and calculating volume via graphic double integration with simple elliptical, superelliptical (following Motani 2001 <doi:10.1666/0094-8373(2001)027%3C0735:EBMFST%3E2.0.CO;2>) or complex cross-sectional models. Additionally, the package provides functions for estimating the center of mass position (COM), the moment of inertia (I) for 3D shapes and the second moment of area (Ix, Iy, Iz) of 2D cross-sections, as well as for visualization of results.

Maintained by Darius Nau. Last updated 11 months ago.

1.6 match 2.68 score 16 scripts

wanglabcsu

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 score

jmmonnet

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 score

bioc

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.

annotation visualization

1.8 match 2.30 score 1 scripts

jpnolan

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 dependents

cran

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 dependents

dkibalnikov

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 scripts

monicacalsan

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 scripts

leilamarvian

WeatherSentiment:Comprehensive Analysis of Tweet Sentiments and Weather Data

A comprehensive suite of functions for processing, analyzing, and visualizing textual data from tweets is offered. Users can clean tweets, analyze their sentiments, visualize data, and examine the correlation between sentiments and environmental data such as weather conditions. Main features include text processing, sentiment analysis, data visualization, correlation analysis, and synthetic data generation. Text processing involves cleaning and preparing tweets by removing textual noise and irrelevant words. Sentiment analysis extracts and accurately analyzes sentiments from tweet texts using advanced algorithms. Data visualization creates various charts like word clouds and sentiment polarity graphs for visual representation of data. Correlation analysis examines and calculates the correlation between tweet sentiments and environmental variables such as weather conditions. Additionally, random tweets can be generated for testing and evaluating the performance of analyses, empowering users to effectively analyze and interpret 'Twitter' data for research and commercial purposes.

Maintained by Leila Marvian Mashhad. Last updated 7 months ago.

2.4 match 1.00 score

philshea

binfunest:Estimates Parameters of Functions Driving Binomial Random Variables

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

Maintained by Philip Shea. Last updated 2 years ago.

0.5 match 4.18 score 1 scripts

kurthornik

NLPutils:Natural Language Processing Utilities

Utilities for Natural Language Processing.

Maintained by Kurt Hornik. Last updated 2 years ago.

openjdk

2.0 match 1.00 score 4 scripts

abdoulma

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.

data-visualization

0.5 match 8 stars 3.60 score 8 scripts

patterninstitute

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 dependents

cran

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

polars:Lightning-Fast 'DataFrame' Library

lexicon:Lexicons for Text Analysis

bioRad:Biological Analysis and Visualization of Weather Radar Data

neopolars:R Bindings for the 'polars' Rust Library

sentimentr:Calculate Text Polarity Sentiment

qdap:Bridging the Gap Between Qualitative Data and Quantitative Analysis

Spectra:Spectra Infrastructure for Mass Spectrometry Data

tidypolars:Get the Power of Polars with the Syntax of the Tidyverse

fhircrackr:Handling HL7 FHIR® Resources in R

volcano3D:3D Volcano Plots and Polar Plots for Three-Class Data

pracma:Practical Numerical Math Functions

xcms:LC-MS and GC-MS Data Analysis

openairmaps:Create Maps of Air Pollution Data

psych:Procedures for Psychological, Psychometric, and Personality Research

rticulate:Articulatory Data Processing in R

openair:Tools for the Analysis of Air Pollution Data

mall:Run Multiple Large Language Model Predictions Against a Table, or Vectors

retistruct:Retinal Reconstruction Program

geomtextpath:Curved Text in 'ggplot2'

DescTools:Tools for Descriptive Statistics

ProtGenerics:Generic infrastructure for Bioconductor mass spectrometry packages

ggplot2:Create Elegant Data Visualisations Using the Grammar of Graphics

fgsea:Fast Gene Set Enrichment Analysis

torch:Tensors and Neural Networks with 'GPU' Acceleration

oce:Analysis of Oceanographic Data

gssrdoc:Document General Social Survey Variable

polarssql:A 'polars' backend for 'DBI'.

tensr:Covariance Inference and Decompositions for Tensor Datasets

geometry:Mesh Generation and Surface Tessellation

LOBSTAHS:Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences

ggpolar:Dots and Their Connections in Polar Coordinate System

MSnbase:Base Functions and Classes for Mass Spectrometry and Proteomics

echarts4r:Create Interactive Graphs with 'Echarts JavaScript' Version 5

deeptime:Plotting Tools for Anyone Working in Deep Time

epca:Exploratory Principal Component Analysis

quanteda.textmodels:Scaling Models and Classifiers for Textual Data

LSX:Semi-Supervised Algorithm for Document Scaling

KEPTED:Kernel-Embedding-of-Probability Test for Elliptical Distribution

Wats:Wrap Around Time Series Graphics

SentimentAnalysis:Dictionary-Based Sentiment Analysis

alakazam:Immunoglobulin Clonal Lineage and Diversity Analysis

spatsoc:Group Animal Relocation Data by Spatial and Temporal Relationship

diemr:Diagnostic Index Expectation Maximisation in R

gbutils:Utilities for Simulation, Plots, Quantile Functions and Programming

vol2birdR:Vertical Profiles of Biological Signals in Weather Radar Data

circlize:Circular Visualization

DatabionicSwarm:Swarm Intelligence for Self-Organized Clustering

GLMMcosinor:Fit a Cosinor Model Using a Generalized Mixed Modeling Framework

rerddapXtracto:Extracts Environmental Data from 'ERDDAP™' Web Services

peacesciencer:Tools and Data for Quantitative Peace Science Research

SIBER:Stable Isotope Bayesian Ellipses in R

popdemo:Demographic Modelling Using Projection Matrices

agrmt:Calculate Concentration and Dispersion in Ordered Rating Scales

ggalign:A 'ggplot2' Extension for Consistent Axis Alignment

loon.ggplot:A Grammar of Interactive Graphics

Rcpi:Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery

MetAlyzer:Read and Analyze 'MetIDQ&trade;' Software Output Files

plotrix:Various Plotting Functions

sherlock:Graphical Displays for Structured Problem Solving and Diagnosis

spacesXYZ:CIE XYZ and some of Its Derived Color Spaces

qdapDictionaries:Dictionaries and Word Lists for the 'qdap' Package

RConics:Computations on Conics

CluMSID:Clustering of MS2 Spectra for Metabolite Identification

spatstat.geom:Geometrical Functionality of the 'spatstat' Family

ggcleveland:Implementation of Plots from Cleveland's Visualizing Data Book

dendextend:Extending 'dendrogram' Functionality in R

bettr:A Better Way To Explore What Is Best

flowcatchR:Tools to analyze in vivo microscopy imaging data focused on tracking flowing blood cells

animint2:Animated Interactive Grammar of Graphics

icosa:Global Triangular and Penta-Hexagonal Grids Based on Tessellated Icosahedra

CPC:Implementation of Cluster-Polarization Coefficient

piano:Platform for integrative analysis of omics data

TreeTools:Create, Modify and Analyse Phylogenetic Trees

ReacTran:Reactive Transport Modelling in 1d, 2d and 3d

animovement:An R toolbox for analysing animal movement across space and time

dineq:Decomposition of (Income) Inequality

textdata:Download and Load Various Text Datasets

dust:Iterate Multiple Realisations of Stochastic Models

DER:Income Polarization Index

RoundAndRound:Plot Objects Moving in Orbits

MetAlyzer:Read and Analyze 'MetIDQ™' Software Output Files