R-universe search: contours

collinerickson

ContourFunctions:Create Contour Plots from Data or a Function

Provides functions for making contour plots. The contour plot can be created from grid data, a function, or a data set. If non-grid data is given, then a Gaussian process is fit to the data and used to create the contour plot.

Maintained by Collin Erickson. Last updated 6 months ago.

contour contour-plot ggplot2

41.8 match 8 stars 6.46 score 27 scripts 3 dependents

davidbolin

excursions:Excursion Sets and Contour Credibility Regions for Random Fields

Functions that compute probabilistic excursion sets, contour credibility regions, contour avoiding regions, and simultaneous confidence bands for latent Gaussian random processes and fields. The package also contains functions that calculate these quantities for models estimated with the INLA package. The main references for excursions are Bolin and Lindgren (2015) <doi:10.1111/rssb.12055>, Bolin and Lindgren (2017) <doi:10.1080/10618600.2016.1228537>, and Bolin and Lindgren (2018) <doi:10.18637/jss.v086.i05>. These can be generated by the citation function in R.

Maintained by David Bolin. Last updated 1 days ago.

gsl cpp openmp

28.9 match 3 stars 6.64 score 40 scripts 1 dependents

cran

Directional:A Collection of Functions for Directional Data Analysis

A collection of functions for directional data (including massive data, with millions of observations) analysis. Hypothesis testing, discriminant and regression analysis, MLE of distributions and more are included. The standard textbook for such data is the "Directional Statistics" by Mardia, K. V. and Jupp, P. E. (2000). Other references include: a) Paine J.P., Preston S.P., Tsagris M. and Wood A.T.A. (2018). "An elliptically symmetric angular Gaussian distribution". Statistics and Computing 28(3): 689-697. <doi:10.1007/s11222-017-9756-4>. b) Tsagris M. and Alenazi A. (2019). "Comparison of discriminant analysis methods on the sphere". Communications in Statistics: Case Studies, Data Analysis and Applications 5(4):467--491. <doi:10.1080/23737484.2019.1684854>. c) Paine J.P., Preston S.P., Tsagris M. and Wood A.T.A. (2020). "Spherical regression models with general covariates and anisotropic errors". Statistics and Computing 30(1): 153--165. <doi:10.1007/s11222-019-09872-2>. d) Tsagris M. and Alenazi A. (2024). "An investigation of hypothesis testing procedures for circular and spherical mean vectors". Communications in Statistics-Simulation and Computation, 53(3): 1387--1408. <doi:10.1080/03610918.2022.2045499>. e) Yu Z. and Huang X. (2024). A new parameterization for elliptically symmetric angular Gaussian distributions of arbitrary dimension. Electronic Journal of Statistics, 18(1): 301--334. <doi:10.1214/23-EJS2210>. f) Tsagris M. and Alzeley O. (2024). "Circular and spherical projected Cauchy distributions: A Novel Framework for Circular and Directional Data Modeling". Australian & New Zealand Journal of Statistics (Accepted for publication). <doi:10.1111/anzs.12434>. g) Tsagris M., Papastamoulis P. and Kato S. (2024). "Directional data analysis: spherical Cauchy or Poisson kernel-based distribution". Statistics and Computing (Accepted for publication). <doi:10.48550/arXiv.2409.03292>.

Maintained by Michail Tsagris. Last updated 1 months ago.

45.5 match 3 stars 4.06 score 3 dependents

marce10

warbleR:Streamline Bioacoustic Analysis

Functions aiming to facilitate the analysis of the structure of animal acoustic signals in 'R'. 'warbleR' makes use of the basic sound analysis tools from the packages 'tuneR' and 'seewave', and offers new tools for explore and quantify acoustic signal structure. The package allows to organize and manipulate multiple sound files, create spectrograms of complete recordings or individual signals in different formats, run several measures of acoustic structure, and characterize different structural levels in acoustic signals.

Maintained by Marcelo Araya-Salas. Last updated 2 months ago.

animal-acoustic-signals audio-processing bioacoustics spectrogram streamline-analysis cpp

14.9 match 56 stars 10.86 score 270 scripts 4 dependents

rspatial

raster:Geographic Data Analysis and Modeling

Reading, writing, manipulating, analyzing and modeling of spatial data. This package has been superseded by the "terra" package <https://CRAN.R-project.org/package=terra>.

Maintained by Robert J. Hijmans. Last updated 2 months ago.

cpp

9.4 match 164 stars 17.05 score 58k scripts 555 dependents

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

12.9 match 7 stars 12.10 score 241 scripts 227 dependents

cran

Compositional:Compositional Data Analysis

Regression, classification, contour plots, hypothesis testing and fitting of distributions for compositional data are some of the functions included. We further include functions for percentages (or proportions). The standard textbook for such data is John Aitchison's (1986) "The statistical analysis of compositional data". Relevant papers include: a) Tsagris M.T., Preston S. and Wood A.T.A. (2011). "A data-based power transformation for compositional data". Fourth International International Workshop on Compositional Data Analysis. <doi:10.48550/arXiv.1106.1451> b) Tsagris M. (2014). "The k-NN algorithm for compositional data: a revised approach with and without zero values present". Journal of Data Science, 12(3): 519--534. <doi:10.6339/JDS.201407_12(3).0008>. c) Tsagris M. (2015). "A novel, divergence based, regression for compositional data". Proceedings of the 28th Panhellenic Statistics Conference, 15-18 April 2015, Athens, Greece, 430--444. <doi:10.48550/arXiv.1511.07600>. d) Tsagris M. (2015). "Regression analysis with compositional data containing zero values". Chilean Journal of Statistics, 6(2): 47--57. <https://soche.cl/chjs/volumes/06/02/Tsagris(2015).pdf>. e) Tsagris M., Preston S. and Wood A.T.A. (2016). "Improved supervised classification for compositional data using the alpha-transformation". Journal of Classification, 33(2): 243--261. <doi:10.1007/s00357-016-9207-5>. f) Tsagris M., Preston S. and Wood A.T.A. (2017). "Nonparametric hypothesis testing for equality of means on the simplex". Journal of Statistical Computation and Simulation, 87(2): 406--422. <doi:10.1080/00949655.2016.1216554>. g) Tsagris M. and Stewart C. (2018). "A Dirichlet regression model for compositional data with zeros". Lobachevskii Journal of Mathematics, 39(3): 398--412. <doi:10.1134/S1995080218030198>. h) Alenazi A. (2019). "Regression for compositional data with compositional data as predictor variables with or without zero values". Journal of Data Science, 17(1): 219--238. <doi:10.6339/JDS.201901_17(1).0010>. i) Tsagris M. and Stewart C. (2020). "A folded model for compositional data analysis". Australian and New Zealand Journal of Statistics, 62(2): 249--277. <doi:10.1111/anzs.12289>. j) Alenazi A.A. (2022). "f-divergence regression models for compositional data". Pakistan Journal of Statistics and Operation Research, 18(4): 867--882. <doi:10.18187/pjsor.v18i4.3969>. k) Tsagris M. and Stewart C. (2022). "A Review of Flexible Transformations for Modeling Compositional Data". In Advances and Innovations in Statistics and Data Science, pp. 225--234. <doi:10.1007/978-3-031-08329-7_10>. l) Alenazi A. (2023). "A review of compositional data analysis and recent advances". Communications in Statistics--Theory and Methods, 52(16): 5535--5567. <doi:10.1080/03610926.2021.2014890>. m) Tsagris M., Alenazi A. and Stewart C. (2023). "Flexible non-parametric regression models for compositional response data with zeros". Statistics and Computing, 33(106). <doi:10.1007/s11222-023-10277-5>. n) Tsagris. M. (2025). "Constrained least squares simplicial-simplicial regression". Statistics and Computing, 35(27). <doi:10.1007/s11222-024-10560-z>. o) Sevinc V. and Tsagris. M. (2024). "Energy Based Equality of Distributions Testing for Compositional Data". <doi:10.48550/arXiv.2412.05199>.

Maintained by Michail Tsagris. Last updated 2 months ago.

41.7 match 3 stars 3.64 score 4 dependents

rspatial

terra:Spatial Data Analysis

Methods for spatial data analysis with vector (points, lines, polygons) and raster (grid) data. Methods for vector data include geometric operations such as intersect and buffer. Raster methods include local, focal, global, zonal and geometric operations. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/> to get started. 'terra' replaces the 'raster' package ('terra' can do more, and it is faster and easier to use).

Maintained by Robert J. Hijmans. Last updated 4 hours ago.

geospatial raster spatial vector onetbb proj gdal geos cpp

8.6 match 560 stars 17.63 score 17k scripts 850 dependents

n8thangreen

BCEA:Bayesian Cost Effectiveness Analysis

Produces an economic evaluation of a sample of suitable variables of cost and effectiveness / utility for two or more interventions, e.g. from a Bayesian model in the form of MCMC simulations. This package computes the most cost-effective alternative and produces graphical summaries and probabilistic sensitivity analysis, see Baio et al (2017) <doi:10.1007/978-3-319-55718-2>.

Maintained by Gianluca Baio. Last updated 2 months ago.

bayesian cost-effectiveness

12.5 match 3 stars 9.90 score 243 scripts 3 dependents

cran

contoureR:Contouring of Non-Regular Three-Dimensional Data

Create contour lines for a non regular series of points, potentially from a non-regular canvas.

Maintained by Nicholas Hamilton. Last updated 10 years ago.

cpp

61.7 match 2 stars 2.00 score

eliocamp

metR:Tools for Easier Analysis of Meteorological Fields

Many useful functions and extensions for dealing with meteorological data in the tidy data framework. Extends 'ggplot2' for better plotting of scalar and vector fields and provides commonly used analysis methods in the atmospheric sciences.

Maintained by Elio Campitelli. Last updated 24 days ago.

atmospheric-science ggplot2 visualization

10.1 match 144 stars 12.19 score 1000 scripts 22 dependents

bnosac

image.ContourDetector:Implementation of the Unsupervised Smooth Contour Line Detection for Images

An implementation of the Unsupervised Smooth Contour Detection algorithm for digital images as described in the paper: "Unsupervised Smooth Contour Detection" by Rafael Grompone von Gioi, and Gregory Randall (2016). The algorithm is explained at <doi:10.5201/ipol.2016.175>.

Maintained by Jan Wijffels. Last updated 1 years ago.

canny-edge-detection computer-vision contours darknet dlib f9 harris-corners harris-interest-point-detector hog-features image-algorithms image-recognition openpano otsu surf cpp

18.9 match 279 stars 5.14 score 7 scripts

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 4 days ago.

oceanography fortran cpp

6.1 match 146 stars 15.42 score 4.2k scripts 18 dependents

ms609

Ternary:Create Ternary and Holdridge Plots

Plots ternary diagrams (simplex plots / Gibbs triangles) and Holdridge life zone plots <doi:10.1126/science.105.2727.367> using the standard graphics functions. Allows custom annotation, interpolating, contouring and scaling of plotting region. Includes a 'Shiny' user interface for point-and-click ternary plotting. An alternative to 'ggtern', which uses the 'ggplot2' family of plotting functions.

Maintained by Martin R. Smith. Last updated 5 months ago.

graphics plotting plotting-in-r ternary-plots

9.9 match 33 stars 9.58 score 103 scripts 5 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 12 days ago.

data-visualisation visualisation

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

murrayefford

secr:Spatially Explicit Capture-Recapture

Functions to estimate the density and size of a spatially distributed animal population sampled with an array of passive detectors, such as traps, or by searching polygons or transects. Models incorporating distance-dependent detection are fitted by maximizing the likelihood. Tools are included for data manipulation and model selection.

Maintained by Murray Efford. Last updated 2 days ago.

cpp

8.8 match 3 stars 10.13 score 410 scripts 5 dependents

r-forge

copula:Multivariate Dependence with Copulas

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

Maintained by Martin Maechler. Last updated 14 days ago.

7.4 match 11.83 score 1.2k scripts 86 dependents

spatstat

spatstat.model:Parametric Statistical Modelling and Inference for the 'spatstat' Family

Functionality for parametric statistical modelling and inference for spatial data, mainly spatial point patterns, in the 'spatstat' family of packages. (Excludes analysis of spatial data on a linear network, which is covered by the separate package 'spatstat.linnet'.) Supports parametric modelling, formal statistical inference, and model validation. Parametric models include Poisson point processes, Cox point processes, Neyman-Scott cluster processes, Gibbs point processes and determinantal point processes. Models can be fitted to data using maximum likelihood, maximum pseudolikelihood, maximum composite likelihood and the method of minimum contrast. Fitted models can be simulated and predicted. Formal inference includes hypothesis tests (quadrat counting tests, Cressie-Read tests, Clark-Evans test, Berman test, Diggle-Cressie-Loosmore-Ford test, scan test, studentised permutation test, segregation test, ANOVA tests of fitted models, adjusted composite likelihood ratio test, envelope tests, Dao-Genton test, balanced independent two-stage test), confidence intervals for parameters, and prediction intervals for point counts. Model validation techniques include leverage, influence, partial residuals, added variable plots, diagnostic plots, pseudoscore residual plots, model compensators and Q-Q plots.

Maintained by Adrian Baddeley. Last updated 10 days ago.

analysis-of-variance cluster-process confidence-intervals cox-process determinantal-point-processes gibbs-process influence leverage model-diagnostics neyman-scott parameter-estimation poisson-process spatial-analysis spatial-modelling spatial-point-processes statistical-inference

8.2 match 5 stars 9.09 score 6 scripts 46 dependents

r-spatial

stars:Spatiotemporal Arrays, Raster and Vector Data Cubes

Reading, manipulating, writing and plotting spatiotemporal arrays (raster and vector data cubes) in 'R', using 'GDAL' bindings provided by 'sf', and 'NetCDF' bindings by 'ncmeta' and 'RNetCDF'.

Maintained by Edzer Pebesma. Last updated 1 months ago.

raster satellite-images spatial

3.7 match 571 stars 18.27 score 7.2k scripts 137 dependents

asgr

imager:Image Processing Library Based on 'CImg'

Fast image processing for images in up to 4 dimensions (two spatial dimensions, one time/depth dimension, one colour dimension). Provides most traditional image processing tools (filtering, morphology, transformations, etc.) as well as various functions for easily analysing image data using R. The package wraps 'CImg', <http://cimg.eu>, a simple, modern C++ library for image processing.

Maintained by Aaron Robotham. Last updated 30 days ago.

libx11 fftw3 tiff cpp openmp

4.9 match 17 stars 13.62 score 2.4k scripts 45 dependents

thej022214

OUwie:Analysis of Evolutionary Rates in an OU Framework

Estimates rates for continuous character evolution under Brownian motion and a new set of Ornstein-Uhlenbeck based Hansen models that allow both the strength of the pull and stochastic motion to vary across selective regimes. Beaulieu et al (2012).

Maintained by Jeremy Beaulieu. Last updated 1 days ago.

7.8 match 9 stars 8.42 score 161 scripts

opengeos

whitebox:'WhiteboxTools' R Frontend

An R frontend for the 'WhiteboxTools' library, which is an advanced geospatial data analysis platform developed by Prof. John Lindsay at the University of Guelph's Geomorphometry and Hydrogeomatics Research Group. 'WhiteboxTools' can be used to perform common geographical information systems (GIS) analysis operations, such as cost-distance analysis, distance buffering, and raster reclassification. Remote sensing and image processing tasks include image enhancement (e.g. panchromatic sharpening, contrast adjustments), image mosaicing, numerous filtering operations, simple classification (k-means), and common image transformations. 'WhiteboxTools' also contains advanced tooling for spatial hydrological analysis (e.g. flow-accumulation, watershed delineation, stream network analysis, sink removal), terrain analysis (e.g. common terrain indices such as slope, curvatures, wetness index, hillshading; hypsometric analysis; multi-scale topographic position analysis), and LiDAR data processing. Suggested citation: Lindsay (2016) <doi:10.1016/j.cageo.2016.07.003>.

Maintained by Andrew Brown. Last updated 5 months ago.

geomorphometry geoprocessing geospatial gis hydrology remote-sensing rstudio

6.8 match 173 stars 9.65 score 203 scripts 2 dependents

bart1

move:Visualizing and Analyzing Animal Track Data

Contains functions to access movement data stored in 'movebank.org' as well as tools to visualize and statistically analyze animal movement data, among others functions to calculate dynamic Brownian Bridge Movement Models. Move helps addressing movement ecology questions.

Maintained by Bart Kranstauber. Last updated 4 months ago.

cpp

7.4 match 8.74 score 690 scripts 3 dependents

spatstat

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

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

Maintained by Adrian Baddeley. Last updated 3 days ago.

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

6.2 match 1 stars 10.18 score 67 scripts 149 dependents

urbananalyst

dodgr:Distances on Directed Graphs

Distances on dual-weighted directed graphs using priority-queue shortest paths (Padgham (2019) <doi:10.32866/6945>). Weighted directed graphs have weights from A to B which may differ from those from B to A. Dual-weighted directed graphs have two sets of such weights. A canonical example is a street network to be used for routing in which routes are calculated by weighting distances according to the type of way and mode of transport, yet lengths of routes must be calculated from direct distances.

Maintained by Mark Padgham. Last updated 8 hours ago.

distance openstreetmap router shortest-paths street-networks cpp

5.3 match 129 stars 11.55 score 229 scripts 4 dependents

deepayan

lattice:Trellis Graphics for R

A powerful and elegant high-level data visualization system inspired by Trellis graphics, with an emphasis on multivariate data. Lattice is sufficient for typical graphics needs, and is also flexible enough to handle most nonstandard requirements. See ?Lattice for an introduction.

Maintained by Deepayan Sarkar. Last updated 11 months ago.

3.4 match 68 stars 17.33 score 27k scripts 13k dependents

dmurdoch

rgl:3D Visualization Using OpenGL

Provides medium to high level functions for 3D interactive graphics, including functions modelled on base graphics (plot3d(), etc.) as well as functions for constructing representations of geometric objects (cube3d(), etc.). Output may be on screen using OpenGL, or to various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.

Maintained by Duncan Murdoch. Last updated 2 months ago.

graphics opengl rgl webgl libglu libglvnd libpng libx11 freetype cpp

3.3 match 91 stars 17.35 score 7.3k scripts 303 dependents

taikisan21

PAMpal:Load and Process Passive Acoustic Data

Tools for loading and processing passive acoustic data. Read in data that has been processed in 'Pamguard' (<https://www.pamguard.org/>), apply a suite processing functions, and export data for reports or external modeling tools. Parameter calculations implement methods by Oswald et al (2007) <doi:10.1121/1.2743157>, Griffiths et al (2020) <doi:10.1121/10.0001229> and Baumann-Pickering et al (2010) <doi:10.1121/1.3479549>.

Maintained by Taiki Sakai. Last updated 16 days ago.

9.8 match 9 stars 5.87 score 79 scripts

zzawadz

DepthProc:Statistical Depth Functions for Multivariate Analysis

Data depth concept offers a variety of powerful and user friendly tools for robust exploration and inference for multivariate data. The offered techniques may be successfully used in cases of lack of our knowledge on parametric models generating data due to their nature. The package consist of among others implementations of several data depth techniques involving multivariate quantile-quantile plots, multivariate scatter estimators, multivariate Wilcoxon tests and robust regressions.

Maintained by Zygmunt Zawadzki. Last updated 3 years ago.

depth-functions exploratory-data-analysis statistics openblas cpp openmp

10.8 match 6 stars 5.27 score 104 scripts 2 dependents

bnosac

image.libfacedetection:Convolutional Neural Network for Face Detection

An open source library for face detection in images. Provides a pretrained convolutional neural network based on <https://github.com/ShiqiYu/libfacedetection> which can be used to detect faces which have size greater than 10x10 pixels.

Maintained by Jan Wijffels. Last updated 1 years ago.

canny-edge-detection computer-vision contours darknet dlib f9 harris-corners harris-interest-point-detector hog-features image-algorithms image-recognition openpano otsu surf cpp openmp

10.0 match 279 stars 5.29 score 14 scripts

adeverse

ade4:Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences

Tools for multivariate data analysis. Several methods are provided for the analysis (i.e., ordination) of one-table (e.g., principal component analysis, correspondence analysis), two-table (e.g., coinertia analysis, redundancy analysis), three-table (e.g., RLQ analysis) and K-table (e.g., STATIS, multiple coinertia analysis). The philosophy of the package is described in Dray and Dufour (2007) <doi:10.18637/jss.v022.i04>.

Maintained by Aurélie Siberchicot. Last updated 15 days ago.

openblas cpp

3.5 match 39 stars 14.96 score 2.2k scripts 256 dependents

bnosac

image.LineSegmentDetector:Detect Line Segments in Images

An implementation of the Line Segment Detector on digital images described in the paper: "LSD: A Fast Line Segment Detector with a False Detection Control" by Rafael Grompone von Gioi et al (2012). The algorithm is explained at <doi:10.5201/ipol.2012.gjmr-lsd>.

Maintained by Jan Wijffels. Last updated 1 years ago.

canny-edge-detection computer-vision contours darknet dlib f9 harris-corners harris-interest-point-detector hog-features image-algorithms image-recognition openpano otsu surf cpp

10.0 match 279 stars 5.14 score 7 scripts

bnosac

image.CornerDetectionF9:Find Corners in Digital Images with FAST-9

An implementation of the "FAST-9" corner detection algorithm explained in the paper 'FASTER and better: A machine learning approach to corner detection' by Rosten E., Porter R. and Drummond T. (2008), available at <arXiv:0810.2434>. The package allows to detect corners in digital images.

Maintained by Jan Wijffels. Last updated 1 years ago.

canny-edge-detection computer-vision contours darknet dlib f9 harris-corners harris-interest-point-detector hog-features image-algorithms image-recognition openpano otsu surf cpp

10.0 match 279 stars 5.14 score 7 scripts

bnosac

image.Otsu:Otsu's Image Segmentation Method

An implementation of the Otsu's Image Segmentation Method described in the paper: "A C++ Implementation of Otsu's Image Segmentation Method". The algorithm is explained at <doi:10.5201/ipol.2016.158>.

Maintained by Jan Wijffels. Last updated 1 years ago.

canny-edge-detection computer-vision contours darknet dlib f9 harris-corners harris-interest-point-detector hog-features image-algorithms image-recognition openpano otsu surf cpp

10.0 match 279 stars 5.14 score

bnosac

image.CornerDetectionHarris:Implementation of the Harris Corner Detection for Images

An implementation of the Harris Corner Detection as described in the paper "An Analysis and Implementation of the Harris Corner Detector" by Sánchez J. et al (2018) available at <doi:10.5201/ipol.2018.229>. The package allows to detect relevant points in images which are characteristic to the digital image.

Maintained by Jan Wijffels. Last updated 1 years ago.

canny-edge-detection computer-vision contours darknet dlib f9 harris-corners harris-interest-point-detector hog-features image-algorithms image-recognition openpano otsu surf cpp openmp

10.0 match 279 stars 5.14 score 2 scripts

bnosac

image.CannyEdges:Implementation of the Canny Edge Detector for Images

An implementation of the Canny Edge Detector for detecting edges in images. The package provides an interface to the algorithm available at <https://github.com/Neseb/canny>.

Maintained by Jan Wijffels. Last updated 1 years ago.

canny-edge-detection computer-vision contours darknet dlib f9 harris-corners harris-interest-point-detector hog-features image-algorithms image-recognition openpano otsu surf fftw3 cpp

10.0 match 278 stars 5.14 score 6 scripts

davidgohel

ggiraph:Make 'ggplot2' Graphics Interactive

Create interactive 'ggplot2' graphics using 'htmlwidgets'.

Maintained by David Gohel. Last updated 3 months ago.

libpng cpp

3.5 match 819 stars 14.39 score 4.1k scripts 34 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 27 days ago.

phonetics software tongue-image ultrasound ultrasound-tongue-imaging

8.6 match 5 stars 5.88 score 17 scripts

nepem-ufsc

pliman:Tools for Plant Image Analysis

Tools for both single and batch image manipulation and analysis (Olivoto, 2022 <doi:10.1111/2041-210X.13803>) and phytopathometry (Olivoto et al., 2022 <doi:10.1007/S40858-021-00487-5>). The tools can be used for the quantification of leaf area, object counting, extraction of image indexes, shape measurement, object landmark identification, and Elliptical Fourier Analysis of object outlines (Claude (2008) <doi:10.1007/978-0-387-77789-4>). The package also provides a comprehensive pipeline for generating shapefiles with complex layouts and supports high-throughput phenotyping of RGB, multispectral, and hyperspectral orthomosaics. This functionality facilitates field phenotyping using UAV- or satellite-based imagery.

Maintained by Tiago Olivoto. Last updated 3 days ago.

openblas fftw3 cpp openmp

7.5 match 10 stars 6.70 score 476 scripts

allenzhuaz

PPQplan:Process Performance Qualification (PPQ) Plans in Chemistry, Manufacturing and Controls (CMC) Statistical Analysis

Assessment for statistically-based PPQ sampling plan, including calculating the passing probability, optimizing the baseline and high performance cutoff points, visualizing the PPQ plan and power dynamically. The analytical idea is based on the simulation methods from the textbook Burdick, R. K., LeBlond, D. J., Pfahler, L. B., Quiroz, J., Sidor, L., Vukovinsky, K., & Zhang, L. (2017). Statistical Methods for CMC Applications. In Statistical Applications for Chemistry, Manufacturing and Controls (CMC) in the Pharmaceutical Industry (pp. 227-250). Springer, Cham.

Maintained by Yalin Zhu. Last updated 3 years ago.

biostatistics pharmaceuticals sampling-methods

12.1 match 1 stars 4.11 score 13 scripts

tylermorganwall

rayshader:Create Maps and Visualize Data in 2D and 3D

Uses a combination of raytracing and multiple hill shading methods to produce 2D and 3D data visualizations and maps. Includes water detection and layering functions, programmable color palette generation, several built-in textures for hill shading, 2D and 3D plotting options, a built-in path tracer, 'Wavefront' OBJ file export, and the ability to save 3D visualizations to a 3D printable format.

Maintained by Tyler Morgan-Wall. Last updated 2 months ago.

cpp

4.3 match 2.1k stars 11.51 score 1.5k scripts 5 dependents

shwilks

rmarchingcubes:Calculate 3D Contour Meshes Using the Marching Cubes Algorithm

A port of the C++ routine for applying the marching cubes algorithm written by Thomas Lewiner et al. (2012) <doi:10.1080/10867651.2003.10487582> into an R package. The package supplies the contour3d() function, which takes a 3-dimensional array of voxel data and calculates the vertices, vertex normals, and faces for a 3d mesh representing the contour(s) at a given level.

Maintained by S. H. Wilks. Last updated 4 years ago.

openblas cpp

8.5 match 8 stars 5.73 score 45 scripts 1 dependents

dieghernan

tidyterra:'tidyverse' Methods and 'ggplot2' Helpers for 'terra' Objects

Extension of the 'tidyverse' for 'SpatRaster' and 'SpatVector' objects of the 'terra' package. It includes also new 'geom_' functions that provide a convenient way of visualizing 'terra' objects with 'ggplot2'.

Maintained by Diego Hernangómez. Last updated 1 hours ago.

terra ggplot-extension r-spatial rspatial

3.5 match 191 stars 13.61 score 1.9k scripts 25 dependents

dnychka

fields:Tools for Spatial Data

For curve, surface and function fitting with an emphasis on splines, spatial data, geostatistics, and spatial statistics. The major methods include cubic, and thin plate splines, Kriging, and compactly supported covariance functions for large data sets. The splines and Kriging methods are supported by functions that can determine the smoothing parameter (nugget and sill variance) and other covariance function parameters by cross validation and also by restricted maximum likelihood. For Kriging there is an easy to use function that also estimates the correlation scale (range parameter). A major feature is that any covariance function implemented in R and following a simple format can be used for spatial prediction. There are also many useful functions for plotting and working with spatial data as images. This package also contains an implementation of sparse matrix methods for large spatial data sets and currently requires the sparse matrix (spam) package. Use help(fields) to get started and for an overview. The fields source code is deliberately commented and provides useful explanations of numerical details as a companion to the manual pages. The commented source code can be viewed by expanding the source code version and looking in the R subdirectory. The reference for fields can be generated by the citation function in R and has DOI <doi:10.5065/D6W957CT>. Development of this package was supported in part by the National Science Foundation Grant 1417857, the National Center for Atmospheric Research, and Colorado School of Mines. See the Fields URL for a vignette on using this package and some background on spatial statistics.

Maintained by Douglas Nychka. Last updated 9 months ago.

fortran

3.6 match 15 stars 12.60 score 7.7k scripts 295 dependents

calbertsen

otoclass:Otolith Classification and Proportion Estimation

Methods for classification and analysis of otoliths along with methods for estimating species proportions in samples.

Maintained by Christoffer Moesgaard Albertsen. Last updated 11 months ago.

contour-detection otolith-classification otolith-shape otoliths cpp

20.5 match 3 stars 2.18 score

carloscinelli

sensemakr:Sensitivity Analysis Tools for Regression Models

Implements a suite of sensitivity analysis tools that extends the traditional omitted variable bias framework and makes it easier to understand the impact of omitted variables in regression models, as discussed in Cinelli, C. and Hazlett, C. (2020), "Making Sense of Sensitivity: Extending Omitted Variable Bias." Journal of the Royal Statistical Society, Series B (Statistical Methodology) <doi:10.1111/rssb.12348>.

Maintained by Carlos Cinelli. Last updated 4 months ago.

4.7 match 92 stars 9.43 score 139 scripts 2 dependents

tilmandavies

sparr:Spatial and Spatiotemporal Relative Risk

Provides functions to estimate kernel-smoothed spatial and spatio-temporal densities and relative risk functions, and perform subsequent inference. Methodological details can be found in the accompanying tutorial: Davies et al. (2018) <DOI:10.1002/sim.7577>.

Maintained by Tilman M. Davies. Last updated 9 months ago.

6.0 match 8 stars 7.11 score 112 scripts 8 dependents

riatelab

tanaka:Design Shaded Contour Lines (or Tanaka) Maps

The Tanaka method enhances the representation of topography on a map using shaded contour lines. In this simplified implementation of the method, north-west white contours represent illuminated topography and south-east black contours represent shaded topography. See Tanaka (1950) <doi:10.2307/211219>.

Maintained by Timothée Giraud. Last updated 1 years ago.

map spatial tanaka

7.9 match 79 stars 5.40 score 21 scripts 1 dependents

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.

3.5 match 631 stars 12.04 score 960 scripts 5 dependents

hypertidy

vapour:Access to the 'Geospatial Data Abstraction Library' ('GDAL')

Provides low-level access to 'GDAL' functionality. 'GDAL' is the 'Geospatial Data Abstraction Library' a translator for raster and vector geospatial data formats that presents a single raster abstract data model and single vector abstract data model to the calling application for all supported formats <https://gdal.org/>. This package is focussed on providing exactly and only what GDAL does, to enable developing further tools.

Maintained by Michael Sumner. Last updated 9 months ago.

cpp gdal gdal-api cpp

4.5 match 86 stars 9.31 score 63 scripts 5 dependents

pokotylo

ddalpha:Depth-Based Classification and Calculation of Data Depth

Contains procedures for depth-based supervised learning, which are entirely non-parametric, in particular the DDalpha-procedure (Lange, Mosler and Mozharovskyi, 2014 <doi:10.1007/s00362-012-0488-4>). The training data sample is transformed by a statistical depth function to a compact low-dimensional space, where the final classification is done. It also offers an extension to functional data and routines for calculating certain notions of statistical depth functions. 50 multivariate and 5 functional classification problems are included. (Pokotylo, Mozharovskyi and Dyckerhoff, 2019 <doi:10.18637/jss.v091.i05>).

Maintained by Oleksii Pokotylo. Last updated 6 months ago.

fortran cpp

8.8 match 2 stars 4.45 score 211 scripts 7 dependents

bioc

flowViz:Visualization for flow cytometry

Provides visualization tools for flow cytometry data.

Maintained by Mike Jiang. Last updated 5 months ago.

immunooncology infrastructure flowcytometry cellbasedassays visualization

5.2 match 7.44 score 231 scripts 12 dependents

adamlilith

fasterRaster:Faster Raster and Spatial Vector Processing Using 'GRASS GIS'

Processing of large-in-memory/large-on disk rasters and spatial vectors using 'GRASS GIS' <https://grass.osgeo.org/>. Most functions in the 'terra' package are recreated. Processing of medium-sized and smaller spatial objects will nearly always be faster using 'terra' or 'sf', but for large-in-memory/large-on-disk objects, 'fasterRaster' may be faster. To use most of the functions, you must have the stand-alone version (not the 'OSGeoW4' installer version) of 'GRASS GIS' 8.0 or higher.

Maintained by Adam B. Smith. Last updated 22 days ago.

aspect distance fragmentation fragmentation-indices gis grass grass-gis raster raster-projection rasterize slope topography vectorization

5.0 match 58 stars 7.69 score 8 scripts

rvlenth

rsm:Response-Surface Analysis

Provides functions to generate response-surface designs, fit first- and second-order response-surface models, make surface plots, obtain the path of steepest ascent, and do canonical analysis. A good reference on these methods is Chapter 10 of Wu, C-F J and Hamada, M (2009) "Experiments: Planning, Analysis, and Parameter Design Optimization" ISBN 978-0-471-69946-0. An early version of the package is documented in Journal of Statistical Software <doi:10.18637/jss.v032.i07>.

Maintained by Russell Lenth. Last updated 9 months ago.

3.8 match 18 stars 10.16 score 192 scripts 8 dependents

bioc

scider:Spatial cell-type inter-correlation by density in R

scider is a user-friendly R package providing functions to model the global density of cells in a slide of spatial transcriptomics data. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. After modelling density, the package allows for serveral downstream analysis, including colocalization analysis, boundary detection analysis and differential density analysis.

Maintained by Yunshun Chen. Last updated 5 months ago.

spatial transcriptomics

7.5 match 3 stars 5.08 score 3 scripts

r-spatial

RSAGA:SAGA Geoprocessing and Terrain Analysis

Provides access to geocomputing and terrain analysis functions of the geographical information system (GIS) 'SAGA' (System for Automated Geoscientific Analyses) from within R by running the command line version of SAGA. This package furthermore provides several R functions for handling ASCII grids, including a flexible framework for applying local functions (including predict methods of fitted models) and focal functions to multiple grids. SAGA GIS is available under GPL-2 / LGPL-2 licences from <https://sourceforge.net/projects/saga-gis/>.

Maintained by Alexander Brenning. Last updated 1 months ago.

4.3 match 23 stars 8.72 score 275 scripts

lindbrook

cholera:Amend, Augment and Aid Analysis of John Snow's Cholera Map

Amends errors, augments data and aids analysis of John Snow's map of the 1854 London cholera outbreak.

Maintained by lindbrook. Last updated 3 hours ago.

cholera data-visualization datasets epidemiology john-snow public-health triangulation-delaunay voronoi voronoi-polygons

3.8 match 136 stars 9.34 score 95 scripts

doi-usgs

EGRET:Exploration and Graphics for RivEr Trends

Statistics and graphics for streamflow history, water quality trends, and the statistical modeling algorithm: Weighted Regressions on Time, Discharge, and Season (WRTDS).

Maintained by Laura DeCicco. Last updated 4 months ago.

usgs water-quality water-quality-data

3.3 match 90 stars 10.72 score 362 scripts 1 dependents

mfasiolo

mgcViz:Visualisations for Generalized Additive Models

Extension of the 'mgcv' package, providing visual tools for Generalized Additive Models that exploit the additive structure of such models, scale to large data sets and can be used in conjunction with a wide range of response distributions. The focus is providing visual methods for better understanding the model output and for aiding model checking and development beyond simple exponential family regression. The graphical framework is based on the layering system provided by 'ggplot2'.

Maintained by Matteo Fasiolo. Last updated 1 days ago.

3.7 match 78 stars 9.42 score 1000 scripts

hypertidy

anglr:Mesh Topology and Visualization for Spatial Data

Gives direct access to generic 3D tools and provides a full suite of mesh-creation and 3D plotting functions. By extending the 'rgl' package conversion and visualization functions for the 'mesh3d' class a wide variety of complex spatial data can be brought into 3D scenes. These tools allow for spatial raster, polygons, and lines that are common in 'GIS' contexts to be converted into mesh forms with high flexibility and the ability to integrate disparate data types. Vector and raster data can be seamlessly combined as meshes, and surfaces can be set to have material properties based on data values or with image textures. Textures and other data combinations use projection transformations to map between coordinate systems, and objects can be easily visualized in an interactive scene at any stage. This package relies on the 'RTriangle' package for high-quality triangular meshing which is licensed restrictively under 'CC BY-NC-SA 4.0'.

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

6.8 match 83 stars 5.09 score 99 scripts

hughjonesd

anim.plots:Simple Animated Plots for R

Simple animated versions of basic R plots, using the 'animation' package. Includes animated versions of plot, barplot, persp, contour, filled.contour, hist, curve, points, lines, text, symbols, segments, and arrows.

Maintained by David Hugh-Jones. Last updated 4 years ago.

animation graphics plot

6.8 match 8 stars 5.00 score 25 scripts

karlines

plot3D:Plotting Multi-Dimensional Data

Functions for viewing 2-D and 3-D data, including perspective plots, slice plots, surface plots, scatter plots, etc. Includes data sets from oceanography.

Maintained by Karline Soetaert. Last updated 1 years ago.

3.5 match 3 stars 9.59 score 2.1k scripts 78 dependents

jeromeecoac

seewave:Sound Analysis and Synthesis

Functions for analysing, manipulating, displaying, editing and synthesizing time waves (particularly sound). This package processes time analysis (oscillograms and envelopes), spectral content, resonance quality factor, entropy, cross correlation and autocorrelation, zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D and 3D spectrograms and many other analyses. See Sueur et al. (2008) <doi:10.1080/09524622.2008.9753600> and Sueur (2018) <doi:10.1007/978-3-319-77647-7>.

Maintained by Jerome Sueur. Last updated 1 years ago.

3.8 match 18 stars 8.88 score 880 scripts 23 dependents

rfastofficial

Rfast2:A Collection of Efficient and Extremely Fast R Functions II

A collection of fast statistical and utility functions for data analysis. Functions for regression, maximum likelihood, column-wise statistics and many more have been included. C++ has been utilized to speed up the functions. References: Tsagris M., Papadakis M. (2018). Taking R to its limits: 70+ tips. PeerJ Preprints 6:e26605v1 <doi:10.7287/peerj.preprints.26605v1>.

Maintained by Manos Papadakis. Last updated 1 years ago.

openblas cpp openmp

4.1 match 38 stars 8.09 score 75 scripts 26 dependents

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 30 days ago.

3.7 match 64 stars 8.84 score 173 scripts

riatelab

mapiso:Create Contour Polygons from Regular Grids

Regularly spaced grids containing continuous data are transformed to contour polygons. A grid can be defined by a data.frame (x, y, value), an 'sf' object or a raster from 'terra'.

Maintained by Timothée Giraud. Last updated 2 years ago.

map rspatial

5.3 match 36 stars 6.03 score 3 scripts 4 dependents

openanalytics

BIGL:Biochemically Intuitive Generalized Loewe Model

Response surface methods for drug synergy analysis. Available methods include generalized and classical Loewe formulations as well as Highest Single Agent methodology. Response surfaces can be plotted in an interactive 3-D plot and formal statistical tests for presence of synergistic effects are available. Implemented methods and tests are described in the article "BIGL: Biochemically Intuitive Generalized Loewe null model for prediction of the expected combined effect compatible with partial agonism and antagonism" by Koen Van der Borght, Annelies Tourny, Rytis Bagdziunas, Olivier Thas, Maxim Nazarov, Heather Turner, Bie Verbist & Hugo Ceulemans (2017) <doi:10.1038/s41598-017-18068-5>.

Maintained by Maxim Nazarov. Last updated 2 years ago.

5.3 match 7 stars 6.02 score 37 scripts

cran

agricolae:Statistical Procedures for Agricultural Research

Original idea was presented in the thesis "A statistical analysis tool for agricultural research" to obtain the degree of Master on science, National Engineering University (UNI), Lima-Peru. Some experimental data for the examples come from the CIP and others research. Agricolae offers extensive functionality on experimental design especially for agricultural and plant breeding experiments, which can also be useful for other purposes. It supports planning of lattice, Alpha, Cyclic, Complete Block, Latin Square, Graeco-Latin Squares, augmented block, factorial, split and strip plot designs. There are also various analysis facilities for experimental data, e.g. treatment comparison procedures and several non-parametric tests comparison, biodiversity indexes and consensus cluster.

Maintained by Felipe de Mendiburu. Last updated 1 years ago.

4.5 match 7 stars 7.01 score 15 dependents

constantino-garcia

nonlinearTseries:Nonlinear Time Series Analysis

Functions for nonlinear time series analysis. This package permits the computation of the most-used nonlinear statistics/algorithms including generalized correlation dimension, information dimension, largest Lyapunov exponent, sample entropy and Recurrence Quantification Analysis (RQA), among others. Basic routines for surrogate data testing are also included. Part of this work was based on the book "Nonlinear time series analysis" by Holger Kantz and Thomas Schreiber (ISBN: 9780521529020).

Maintained by Constantino A. Garcia. Last updated 6 months ago.

chaos chaotic-systems nonlinear-dynamics nonlinear-time-series time-series openblas cpp

3.5 match 35 stars 8.98 score 123 scripts 7 dependents

r-tmap

tmap:Thematic Maps

Thematic maps are geographical maps in which spatial data distributions are visualized. This package offers a flexible, layer-based, and easy to use approach to create thematic maps, such as choropleths and bubble maps.

Maintained by Martijn Tennekes. Last updated 7 days ago.

choropleth-maps maps spatial thematic-maps visualisation

1.9 match 880 stars 16.73 score 13k scripts 24 dependents

brockk

trialr:Clinical Trial Designs in 'rstan'

A collection of clinical trial designs and methods, implemented in 'rstan' and R, including: the Continual Reassessment Method by O'Quigley et al. (1990) <doi:10.2307/2531628>; EffTox by Thall & Cook (2004) <doi:10.1111/j.0006-341X.2004.00218.x>; the two-parameter logistic method of Neuenschwander, Branson & Sponer (2008) <doi:10.1002/sim.3230>; and the Augmented Binary method by Wason & Seaman (2013) <doi:10.1002/sim.5867>; and more. We provide functions to aid model-fitting and analysis. The 'rstan' implementations may also serve as a cookbook to anyone looking to extend or embellish these models. We hope that this package encourages the use of Bayesian methods in clinical trials. There is a preponderance of early phase trial designs because this is where Bayesian methods are used most. If there is a method you would like implemented, please get in touch.

Maintained by Kristian Brock. Last updated 1 years ago.

cpp

3.6 match 41 stars 8.55 score 106 scripts 3 dependents

edzer

sp:Classes and Methods for Spatial Data

Classes and methods for spatial data; the classes document where the spatial location information resides, for 2D or 3D data. Utility functions are provided, e.g. for plotting data as maps, spatial selection, as well as methods for retrieving coordinates, for subsetting, print, summary, etc. From this version, 'rgdal', 'maptools', and 'rgeos' are no longer used at all, see <https://r-spatial.org/r/2023/05/15/evolution4.html> for details.

Maintained by Edzer Pebesma. Last updated 2 months ago.

1.7 match 127 stars 18.63 score 35k scripts 1.3k dependents

cran

soundgen:Sound Synthesis and Acoustic Analysis

Performs parametric synthesis of sounds with harmonic and noise components such as animal vocalizations or human voice. Also offers tools for audio manipulation and acoustic analysis, including pitch tracking, spectral analysis, audio segmentation, pitch and formant shifting, etc. Includes four interactive web apps for synthesizing and annotating audio, manually correcting pitch contours, and measuring formant frequencies. Reference: Anikin (2019) <doi:10.3758/s13428-018-1095-7>.

Maintained by Andrey Anikin. Last updated 2 months ago.

6.0 match 1 stars 4.86 score 110 scripts 2 dependents

corybrunson

ordr:A Tidyverse Extension for Ordinations and Biplots

Ordination comprises several multivariate exploratory and explanatory techniques with theoretical foundations in geometric data analysis; see Podani (2000, ISBN:90-5782-067-6) for techniques and applications and Le Roux & Rouanet (2005) <doi:10.1007/1-4020-2236-0> for foundations. Greenacre (2010, ISBN:978-84-923846) shows how the most established of these, including principal components analysis, correspondence analysis, multidimensional scaling, factor analysis, and discriminant analysis, rely on eigen-decompositions or singular value decompositions of pre-processed numeric matrix data. These decompositions give rise to a set of shared coordinates along which the row and column elements can be measured. The overlay of their scatterplots on these axes, introduced by Gabriel (1971) <doi:10.1093/biomet/58.3.453>, is called a biplot. 'ordr' provides inspection, extraction, manipulation, and visualization tools for several popular ordination classes supported by a set of recovery methods. It is inspired by and designed to integrate into 'tidyverse' workflows provided by Wickham et al (2019) <doi:10.21105/joss.01686>.

Maintained by Jason Cory Brunson. Last updated 16 days ago.

biplot data-visualization dimension-reduction geometric-data-analysis grammar-of-graphics log-ratio-analysis multivariate-analysis multivariate-statistics ordination tidymodels tidyverse

4.0 match 24 stars 7.26 score 28 scripts

bryanhanson

ChemoSpec2D:Exploratory Chemometrics for 2D Spectroscopy

A collection of functions for exploratory chemometrics of 2D spectroscopic data sets such as COSY (correlated spectroscopy) and HSQC (heteronuclear single quantum coherence) 2D NMR (nuclear magnetic resonance) spectra. 'ChemoSpec2D' deploys methods aimed primarily at classification of samples and the identification of spectral features which are important in distinguishing samples from each other. Each 2D spectrum (a matrix) is treated as the unit of observation, and thus the physical sample in the spectrometer corresponds to the sample from a statistical perspective. In addition to chemometric tools, a few tools are provided for plotting 2D spectra, but these are not intended to replace the functionality typically available on the spectrometer. 'ChemoSpec2D' takes many of its cues from 'ChemoSpec' and tries to create consistent graphical output and to be very user friendly.

Maintained by Bryan A. Hanson. Last updated 3 years ago.

2d-spectra nmr spectroscopy

7.2 match 2 stars 4.04 score 11 scripts

bioc

EBImage:Image processing and analysis toolbox for R

EBImage provides general purpose functionality for image processing and analysis. In the context of (high-throughput) microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors. This allows the automation of such tasks using the R programming language and facilitates the use of other tools in the R environment for signal processing, statistical modeling, machine learning and visualization with image data.

Maintained by Andrzej Oleś. Last updated 5 months ago.

visualization bioinformatics image-analysis image-processing cpp

2.3 match 71 stars 12.77 score 1.5k scripts 33 dependents

julienmoeys

soiltexture:Functions for Soil Texture Plot, Classification and Transformation

"The Soil Texture Wizard" is a set of R functions designed to produce texture triangles (also called texture plots, texture diagrams, texture ternary plots), classify and transform soil textures data. These functions virtually allows to plot any soil texture triangle (classification) into any triangle geometry (isosceles, right-angled triangles, etc.). This set of function is expected to be useful to people using soil textures data from different soil texture classification or different particle size systems. Many (> 15) texture triangles from all around the world are predefined in the package. A simple text based graphical user interface is provided: soiltexture_gui().

Maintained by Julien Moeys. Last updated 1 years ago.

4.0 match 28 stars 7.11 score 136 scripts 1 dependents

tkonopka

Rcssplot:Styling of Graphics using Cascading Style Sheets

Provides a means to style plots through cascading style sheets. This separates the aesthetics from the data crunching in plots and charts.

Maintained by Tomasz Konopka. Last updated 4 months ago.

css data-science visualization

5.3 match 10 stars 5.35 score 15 scripts

dfsp-spirit

fsbrain:Managing and Visualizing Brain Surface Data

Provides high-level access to neuroimaging data from standard software packages like 'FreeSurfer' <http://freesurfer.net/> on the level of subjects and groups. Load morphometry data, surfaces and brain parcellations based on atlases. Mask data using labels, load data for specific atlas regions only, and visualize data and statistical results directly in 'R'.

Maintained by Tim Schäfer. Last updated 4 months ago.

3d brain dti freesurfer mesh mri neuroimaging research surface visualization voxel

4.3 match 66 stars 6.47 score 15 scripts

cneyens

raem:Analytic Element Modeling of Steady Single-Layer Groundwater Flow

A model of single-layer groundwater flow in steady-state under the Dupuit-Forchheimer assumption can be created by placing elements such as wells, area-sinks and line-sinks at arbitrary locations in the flow field. Output variables include hydraulic head and the discharge vector. Particle traces can be computed numerically in three dimensions. The underlying theory is described in Haitjema (1995) <doi:10.1016/B978-0-12-316550-3.X5000-4> and references therein.

Maintained by Cas Neyens. Last updated 7 months ago.

analytic-element-model groundwater groundwater-modelling hydrogeology hydrology

4.7 match 8 stars 5.81 score 6 scripts

ltierney

misc3d:Miscellaneous 3D Plots

A collection of miscellaneous 3d plots, including isosurfaces.

Maintained by Luke Tierney. Last updated 3 years ago.

3.5 match 7.65 score 195 scripts 118 dependents

mbinois

hetGP:Heteroskedastic Gaussian Process Modeling and Design under Replication

Performs Gaussian process regression with heteroskedastic noise following the model by Binois, M., Gramacy, R., Ludkovski, M. (2016) <doi:10.48550/arXiv.1611.05902>, with implementation details in Binois, M. & Gramacy, R. B. (2021) <doi:10.18637/jss.v098.i13>. The input dependent noise is modeled as another Gaussian process. Replicated observations are encouraged as they yield computational savings. Sequential design procedures based on the integrated mean square prediction error and lookahead heuristics are provided, and notably fast update functions when adding new observations.

Maintained by Mickael Binois. Last updated 7 months ago.

cpp

5.5 match 5 stars 4.89 score 260 scripts 2 dependents

ailich

MultiscaleDTM:Multi-Scale Geomorphometric Terrain Attributes

Calculates multi-scale geomorphometric terrain attributes from regularly gridded digital terrain models using a variable focal windows size (Ilich et al. (2023) <doi:10.1111/tgis.13067>).

Maintained by Alexander Ilich. Last updated 13 days ago.

openblas cpp

3.8 match 25 stars 7.05 score 30 scripts 2 dependents

cran

sn:The Skew-Normal and Related Distributions Such as the Skew-t and the SUN

Build and manipulate probability distributions of the skew-normal family and some related ones, notably the skew-t and the SUN families. For the skew-normal and the skew-t distributions, statistical methods are provided for data fitting and model diagnostics, in the univariate and the multivariate case.

Maintained by Adelchi Azzalini. Last updated 2 years ago.

3.5 match 3 stars 7.44 score 92 dependents

triadsou

RcmdrPlugin.KMggplot2:R Commander Plug-in for Data Visualization with 'ggplot2'

A GUI front-end for 'ggplot2' supports Kaplan-Meier plot, histogram, Q-Q plot, box plot, errorbar plot, scatter plot, line chart, pie chart, bar chart, contour plot, and distribution plot.

Maintained by Triad sou.. Last updated 6 years ago.

8.1 match 3.18 score 8 scripts

jto888

WeibullR:Weibull Analysis for Reliability Engineering

Life data analysis in the graphical tradition of Waloddi Weibull. Methods derived from Robert B. Abernethy (2008, ISBN 0-965306-3-2), Wayne Nelson (1982, ISBN: 9780471094586), William Q. Meeker and Lois A. Escobar (1998, ISBN: 1-471-14328-6), John I. McCool, (2012, ISBN: 9781118217986).

Maintained by Jacob Ormerod. Last updated 3 years ago.

openblas cpp

7.4 match 3.42 score 44 scripts 4 dependents

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 23 days ago.

3.3 match 174 stars 7.55 score 34 scripts

husson

FactoMineR:Multivariate Exploratory Data Analysis and Data Mining

Exploratory data analysis methods to summarize, visualize and describe datasets. The main principal component methods are available, those with the largest potential in terms of applications: principal component analysis (PCA) when variables are quantitative, correspondence analysis (CA) and multiple correspondence analysis (MCA) when variables are categorical, Multiple Factor Analysis when variables are structured in groups, etc. and hierarchical cluster analysis. F. Husson, S. Le and J. Pages (2017).

Maintained by Francois Husson. Last updated 3 months ago.

1.7 match 47 stars 14.71 score 5.6k scripts 112 dependents

mkossmeier

metaviz:Forest Plots, Funnel Plots, and Visual Funnel Plot Inference for Meta-Analysis

A compilation of functions to create visually appealing and information-rich plots of meta-analytic data using 'ggplot2'. Currently allows to create forest plots, funnel plots, and many of their variants, such as rainforest plots, thick forest plots, additional evidence contour funnel plots, and sunset funnel plots. In addition, functionalities for visual inference with the funnel plot in the context of meta-analysis are provided.

Maintained by Michael Kossmeier. Last updated 5 years ago.

funnel-plots rainforest-plots

3.3 match 17 stars 7.32 score 135 scripts

bryanhanson

exCon:Interactive Exploration of Contour Data

Interactive tools to explore topographic-like data sets. Such data sets take the form of a matrix in which the rows and columns provide location/frequency information, and the matrix elements contain altitude/response information. Such data is found in cartography, 2D spectroscopy and chemometrics. The functions in this package create interactive web pages showing the contoured data, possibly with slices from the original matrix parallel to each dimension. The interactive behavior is created using the 'D3.js' 'JavaScript' library by Mike Bostock.

Maintained by Bryan A. Hanson. Last updated 8 years ago.

7.4 match 4 stars 3.30 score 1 scripts

cran

gaston:Genetic Data Handling (QC, GRM, LD, PCA) & Linear Mixed Models

Manipulation of genetic data (SNPs). Computation of GRM and dominance matrix, LD, heritability with efficient algorithms for linear mixed model (AIREML). Dandine et al <doi:10.1159/000488519>.

Maintained by Hervé Perdry. Last updated 1 years ago.

zlib cpp

4.0 match 5 stars 6.02 score 12 dependents

chengvt

EEM:Read and Preprocess Fluorescence Excitation-Emission Matrix (EEM) Data

Read raw EEM data and prepares them for further analysis.

Maintained by Vipavee Trivittayasil. Last updated 8 years ago.

3.6 match 8 stars 6.72 score 66 scripts

crazycapivara

deckgl:An R Interface to 'deck.gl'

Makes 'deck.gl' <https://deck.gl/>, a WebGL-powered open-source JavaScript framework for visual exploratory data analysis of large datasets, available within R via the 'htmlwidgets' package. Furthermore, it supports basemaps from 'mapbox' <https://www.mapbox.com/> via 'mapbox-gl-js' <https://github.com/mapbox/mapbox-gl-js>.

Maintained by Stefan Kuethe. Last updated 2 years ago.

deck-gl htmlwidgets mapbox-gl maps rspatial spatial webgl

3.8 match 94 stars 6.40 score 54 scripts

hrbrmstr

ggalt:Extra Coordinate Systems, 'Geoms', Statistical Transformations, Scales and Fonts for 'ggplot2'

A compendium of new geometries, coordinate systems, statistical transformations, scales and fonts for 'ggplot2', including splines, 1d and 2d densities, univariate average shifted histograms, a new map coordinate system based on the 'PROJ.4'-library along with geom_cartogram() that mimics the original functionality of geom_map(), formatters for "bytes", a stat_stepribbon() function, increased 'plotly' compatibility and the 'StateFace' open source font 'ProPublica'. Further new functionality includes lollipop charts, dumbbell charts, the ability to encircle points and coordinate-system-based text annotations.

Maintained by Bob Rudis. Last updated 2 years ago.

geom ggplot-extension ggplot2 ggplot2-geom ggplot2-scales

1.9 match 674 stars 12.59 score 2.3k scripts 7 dependents

projectmosaic

mosaic:Project MOSAIC Statistics and Mathematics Teaching Utilities

Data sets and utilities from Project MOSAIC (<http://www.mosaic-web.org>) used to teach mathematics, statistics, computation and modeling. Funded by the NSF, Project MOSAIC is a community of educators working to tie together aspects of quantitative work that students in science, technology, engineering and mathematics will need in their professional lives, but which are usually taught in isolation, if at all.

Maintained by Randall Pruim. Last updated 1 years ago.

1.8 match 93 stars 13.32 score 7.2k scripts 7 dependents

hwborchers

pracma:Practical Numerical Math Functions

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

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

1.9 match 29 stars 12.34 score 6.6k scripts 931 dependents

tarnduong

ks:Kernel Smoothing

Kernel smoothers for univariate and multivariate data, with comprehensive visualisation and bandwidth selection capabilities, including for densities, density derivatives, cumulative distributions, clustering, classification, density ridges, significant modal regions, and two-sample hypothesis tests. Chacon & Duong (2018) <doi:10.1201/9780429485572>.

Maintained by Tarn Duong. Last updated 6 months ago.

2.3 match 6 stars 10.14 score 920 scripts 262 dependents

ghuiber

BTYD:Implementing BTYD Models with the Log Sum Exp Patch

Functions for data preparation, parameter estimation, scoring, and plotting for the BG/BB (Fader, Hardie, and Shang 2010 <doi:10.1287/mksc.1100.0580>), BG/NBD (Fader, Hardie, and Lee 2005 <doi:10.1287/mksc.1040.0098>) and Pareto/NBD and Gamma/Gamma (Fader, Hardie, and Lee 2005 <doi:10.1509/jmkr.2005.42.4.415>) models.

Maintained by Gabi Huiber. Last updated 3 years ago.

3.8 match 7 stars 6.03 score 103 scripts 1 dependents

irsn

DiceView:Methods for Visualization of Computer Experiments Design and Surrogate

View 2D/3D sections, contour plots, mesh of excursion sets for computer experiments designs, surrogates or test functions.

Maintained by Yann Richet. Last updated 3 months ago.

5.5 match 1 stars 4.06 score 33 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

3.8 match 4 stars 5.62 score 8 scripts

oscarperpinan

rasterVis:Visualization Methods for Raster Data

Methods for enhanced visualization and interaction with raster data. It implements visualization methods for quantitative data and categorical data, both for univariate and multivariate rasters. It also provides methods to display spatiotemporal rasters, and vector fields. See the website for examples.

Maintained by Oscar Perpinan Lamigueiro. Last updated 12 months ago.

1.8 match 85 stars 11.74 score 4.2k scripts 13 dependents

robinhankin

elliptic:Weierstrass and Jacobi Elliptic Functions

A suite of elliptic and related functions including Weierstrass and Jacobi forms. Also includes various tools for manipulating and visualizing complex functions.

Maintained by Robin K. S. Hankin. Last updated 14 days ago.

2.3 match 3 stars 9.31 score 54 scripts 79 dependents

robindenz1

contsurvplot:Visualize the Effect of a Continuous Variable on a Time-to-Event Outcome

Graphically display the (causal) effect of a continuous variable on a time-to-event outcome using multiple different types of plots based on g-computation. Those functions include, among others, survival area plots, survival contour plots, survival quantile plots and 3D surface plots. Due to the use of g-computation, all plot allow confounder-adjustment naturally. For details, see Robin Denz, Nina Timmesfeld (2023) <doi:10.1097/EDE.0000000000001630>.

Maintained by Robin Denz. Last updated 1 years ago.

causal-inference continuous g-computation survival-analysis visualization

3.7 match 12 stars 5.53 score 56 scripts

bayesball

LearnBayes:Learning Bayesian Inference

Contains functions for summarizing basic one and two parameter posterior distributions and predictive distributions. It contains MCMC algorithms for summarizing posterior distributions defined by the user. It also contains functions for regression models, hierarchical models, Bayesian tests, and illustrations of Gibbs sampling.

Maintained by Jim Albert. Last updated 7 years ago.

1.8 match 38 stars 11.34 score 690 scripts 31 dependents

cran

visualpred:Visualization 2D of Binary Classification Models

Visual contour and 2D point and contour plots for binary classification modeling under algorithms such as 'glm', 'rf', 'gbm', 'nnet' and 'svm', presented over two dimensions generated by 'famd' and 'mca' methods. Package 'FactoMineR' for multivariate reduction functions and package 'MBA' for interpolation functions are used. The package can be used to visualize the discriminant power of input variables and algorithmic modeling, explore outliers, compare algorithm behaviour, etc. It has been created initially for teaching purposes, but it has also many practical uses under the 'XAI' paradigm.

Maintained by Javier Portela. Last updated 4 months ago.

7.7 match 2.60 score

ips-lmu

wrassp:Interface to the 'ASSP' Library

A wrapper around Michel Scheffers's 'libassp' (<https://libassp.sourceforge.net/>). The 'libassp' (Advanced Speech Signal Processor) library aims at providing functionality for handling speech signal files in most common audio formats and for performing analyses common in phonetic science/speech science. This includes the calculation of formants, fundamental frequency, root mean square, auto correlation, a variety of spectral analyses, zero crossing rate, filtering etc. This wrapper provides R with a large subset of 'libassp's signal processing functions and provides them to the user in a (hopefully) user-friendly manner.

Maintained by Markus Jochim. Last updated 1 years ago.

2.7 match 24 stars 7.43 score 62 scripts 3 dependents

tnagler

VineCopula:Statistical Inference of Vine Copulas

Provides tools for the statistical analysis of regular vine copula models, see Aas et al. (2009) <doi:10.1016/j.insmatheco.2007.02.001> and Dissman et al. (2013) <doi:10.1016/j.csda.2012.08.010>. The package includes tools for parameter estimation, model selection, simulation, goodness-of-fit tests, and visualization. Tools for estimation, selection and exploratory data analysis of bivariate copula models are also provided.

Maintained by Thomas Nagler. Last updated 27 days ago.

copula estimation statistics vine

1.8 match 91 stars 10.99 score 362 scripts 23 dependents

pbs-software

PBSmapping:Mapping Fisheries Data and Spatial Analysis Tools

This software has evolved from fisheries research conducted at the Pacific Biological Station (PBS) in 'Nanaimo', British Columbia, Canada. It extends the R language to include two-dimensional plotting features similar to those commonly available in a Geographic Information System (GIS). Embedded C code speeds algorithms from computational geometry, such as finding polygons that contain specified point events or converting between longitude-latitude and Universal Transverse Mercator (UTM) coordinates. Additionally, we include 'C++' code developed by Angus Johnson for the 'Clipper' library, data for a global shoreline, and other data sets in the public domain. Under the user's R library directory '.libPaths()', specifically in './PBSmapping/doc', a complete user's guide is offered and should be consulted to use package functions effectively.

Maintained by Rowan Haigh. Last updated 6 months ago.

cpp

1.9 match 11 stars 10.29 score 652 scripts 9 dependents

davidhodge931

ggblanket:Simplify 'ggplot2' Visualisation

Simplify 'ggplot2' visualisation with 'ggblanket' wrapper functions.

Maintained by David Hodge. Last updated 19 hours ago.

data-visualisation data-visualization ggplot ggplot-extension ggplot2 ggplot2-enhancements visualisation visualization

2.3 match 173 stars 8.42 score 45 scripts

lbbe-software

nlstools:Tools for Nonlinear Regression Analysis

Several tools for assessing the quality of fit of a gaussian nonlinear model are provided.

Maintained by Aurelie Siberchicot. Last updated 15 days ago.

2.0 match 6 stars 9.42 score 528 scripts 7 dependents

arturstat

TPmsm:Estimation of Transition Probabilities in Multistate Models

Estimation of transition probabilities for the illness-death model and or the three-state progressive model.

Maintained by Artur Araujo. Last updated 1 years ago.

illness-death-model kaplan-meier monte-carlo-simulation multi-state-models openmp-parallelization survival-analysis transition-probabilities openblas openmp

4.1 match 1 stars 4.52 score 22 scripts 1 dependents

jfrench

SpatialTools:Tools for Spatial Data Analysis

Tools for spatial data analysis. Emphasis on kriging. Provides functions for prediction and simulation. Intended to be relatively straightforward, fast, and flexible.

Maintained by Joshua French. Last updated 2 years ago.

openblas cpp

4.3 match 2 stars 4.38 score 100 scripts 4 dependents

r-forge

distrEllipse:S4 Classes for Elliptically Contoured Distributions

Distribution (S4-)classes for elliptically contoured distributions (based on package 'distr').

Maintained by Peter Ruckdeschel. Last updated 2 months ago.

5.3 match 3.46 score 18 scripts

psegaert

mrfDepth:Depth Measures in Multivariate, Regression and Functional Settings

Tools to compute depth measures and implementations of related tasks such as outlier detection, data exploration and classification of multivariate, regression and functional data.

Maintained by Jakob Raymaekers. Last updated 6 years ago.

fortran openblas cpp

3.7 match 3 stars 4.99 score 72 scripts 3 dependents

f-rousset

spaMM:Mixed-Effect Models, with or without Spatial Random Effects

Inference based on models with or without spatially-correlated random effects, multivariate responses, or non-Gaussian random effects (e.g., Beta). Variation in residual variance (heteroscedasticity) can itself be represented by a mixed-effect model. Both classical geostatistical models (Rousset and Ferdy 2014 <doi:10.1111/ecog.00566>), and Markov random field models on irregular grids (as considered in the 'INLA' package, <https://www.r-inla.org>), can be fitted, with distinct computational procedures exploiting the sparse matrix representations for the latter case and other autoregressive models. Laplace approximations are used for likelihood or restricted likelihood. Penalized quasi-likelihood and other variants discussed in the h-likelihood literature (Lee and Nelder 2001 <doi:10.1093/biomet/88.4.987>) are also implemented.

Maintained by François Rousset. Last updated 9 months ago.

gsl cpp openmp

3.7 match 4.94 score 208 scripts 5 dependents

great-northern-diver

loon:Interactive Statistical Data Visualization

An extendable toolkit for interactive data visualization and exploration.

Maintained by R. Wayne Oldford. Last updated 2 years ago.

data-analysis data-science data-visualization exploratory-analysis exploratory-data-analysis high-dimensional-data interactive-graphics interactive-visualizations loon python statistical-analysis statistical-graphics statistics tcl-extension tk

2.0 match 48 stars 9.00 score 93 scripts 5 dependents

bbolker

margins:Marginal Effects for Model Objects

An R port of the margins command from 'Stata', which can be used to calculate marginal (or partial) effects from model objects.

Maintained by Ben Bolker. Last updated 8 months ago.

1.8 match 2 stars 9.85 score 956 scripts 1 dependents

bioc

scDataviz:scDataviz: single cell dataviz and downstream analyses

In the single cell World, which includes flow cytometry, mass cytometry, single-cell RNA-seq (scRNA-seq), and others, there is a need to improve data visualisation and to bring analysis capabilities to researchers even from non-technical backgrounds. scDataviz attempts to fit into this space, while also catering for advanced users. Additonally, due to the way that scDataviz is designed, which is based on SingleCellExperiment, it has a 'plug and play' feel, and immediately lends itself as flexibile and compatibile with studies that go beyond scDataviz. Finally, the graphics in scDataviz are generated via the ggplot engine, which means that users can 'add on' features to these with ease.

Maintained by Kevin Blighe. Last updated 5 months ago.

singlecell immunooncology rnaseq geneexpression transcription flowcytometry massspectrometry dataimport

2.8 match 63 stars 6.30 score 16 scripts

snoweye

EMCluster:EM Algorithm for Model-Based Clustering of Finite Mixture Gaussian Distribution

EM algorithms and several efficient initialization methods for model-based clustering of finite mixture Gaussian distribution with unstructured dispersion in both of unsupervised and semi-supervised learning.

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

openblas

2.3 match 18 stars 7.53 score 123 scripts 2 dependents

jacolien

plotfunctions:Various Functions to Facilitate Visualization of Data and Analysis

When analyzing data, plots are a helpful tool for visualizing data and interpreting statistical models. This package provides a set of simple tools for building plots incrementally, starting with an empty plot region, and adding bars, data points, regression lines, error bars, gradient legends, density distributions in the margins, and even pictures. The package builds further on R graphics by simply combining functions and settings in order to reduce the amount of code to produce for the user. As a result, the package does not use formula input or special syntax, but can be used in combination with default R plot functions. Note: Most of the functions were part of the package 'itsadug', which is now split in two packages: 1. the package 'itsadug', which contains the core functions for visualizing and evaluating nonlinear regression models, and 2. the package 'plotfunctions', which contains more general plot functions.

Maintained by Jacolien van Rij. Last updated 5 years ago.

3.6 match 4.70 score 94 scripts 7 dependents

nathanieltwarog

braidReports:Visualize Combined Action Response Surfaces and Report BRAID Analyses

Provides functions to visualize combined action data in 'ggplot2'. Also provides functions for producing full BRAID analysis reports with custom layouts and aesthetics, using the BRAID method originally described in Twarog et al. (2016) <doi:10.1038/srep25523>.

Maintained by Nathaniel R. Twarog. Last updated 6 months ago.

3.2 match 1 stars 5.13 score 15 scripts

cran

espadon:Easy Study of Patient DICOM Data in Oncology

Exploitation, processing and 2D-3D visualization of DICOM-RT files (structures, dosimetry, imagery) for medical physics and clinical research, in a patient-oriented perspective.

Maintained by Cathy Fontbonne. Last updated 1 months ago.

cpp

5.8 match 2.85 score

arbrazzale

nlreg:Higher Order Inference for Nonlinear Heteroscedastic Models

Likelihood inference based on higher order approximations for nonlinear models with possibly non constant variance.

Maintained by Alessandra R. Brazzale. Last updated 6 years ago.

9.7 match 1.67 score 47 scripts

projectmosaic

mosaicCalc:R-Language Based Calculus Operations for Teaching

Software to support the introductory *MOSAIC Calculus* textbook <https://www.mosaic-web.org/MOSAIC-Calculus/>), one of many data- and modeling-oriented educational resources developed by Project MOSAIC (<https://www.mosaic-web.org/>). Provides symbolic and numerical differentiation and integration, as well as support for applied linear algebra (for data science), and differential equations/dynamics. Includes grammar-of-graphics-based functions for drawing vector fields, trajectories, etc. The software is suitable for general use, but intended mainly for teaching calculus.

Maintained by Daniel Kaplan. Last updated 23 days ago.

1.8 match 13 stars 8.68 score 546 scripts

mthrun

DataVisualizations:Visualizations of High-Dimensional Data

Gives access to data visualisation methods that are relevant from the data scientist's point of view. The flagship idea of 'DataVisualizations' is the mirrored density plot (MD-plot) for either classified or non-classified multivariate data published in Thrun, M.C. et al.: "Analyzing the Fine Structure of Distributions" (2020), PLoS ONE, <DOI:10.1371/journal.pone.0238835>. The MD-plot outperforms the box-and-whisker diagram (box plot), violin plot and bean plot and geom_violin plot of ggplot2. Furthermore, a collection of various visualization methods for univariate data is provided. In the case of exploratory data analysis, 'DataVisualizations' makes it possible to inspect the distribution of each feature of a dataset visually through a combination of four methods. One of these methods is the Pareto density estimation (PDE) of the probability density function (pdf). Additionally, visualizations of the distribution of distances using PDE, the scatter-density plot using PDE for two variables as well as the Shepard density plot and the Bland-Altman plot are presented here. Pertaining to classified high-dimensional data, a number of visualizations are described, such as f.ex. the heat map and silhouette plot. A political map of the world or Germany can be visualized with the additional information defined by a classification of countries or regions. By extending the political map further, an uncomplicated function for a Choropleth map can be used which is useful for measurements across a geographic area. For categorical features, the Pie charts, slope charts and fan plots, improved by the ABC analysis, become usable. More detailed explanations are found in the book by 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 2 months ago.

cpp

2.0 match 7 stars 7.72 score 118 scripts 7 dependents

osimon81

SqueakR:An Experiment Interface for 'DeepSqueak' Bioacoustics Research

Data processing and visualizations for rodent vocalizations exported from 'DeepSqueak'. These functions are compatible with the 'SqueakR' Shiny Dashboard, which can be used to visualize experimental results and analyses.

Maintained by Simon Ogundare. Last updated 3 years ago.

bioacoustics deepsqueak

3.3 match 8 stars 4.60 score 5 scripts

ncss-tech

soilReports:R Markdown Reports and Convenience Functions for Soil Survey

R package container and convenience functions for soil data summary, comparison, and evaluation reports used mainly by NRCS staff.

Maintained by Andrew Brown. Last updated 7 days ago.

nasis nrcs soil soil-survey usda

3.0 match 15 stars 5.11 score 41 scripts

bioc

synergyfinder:Calculate and Visualize Synergy Scores for Drug Combinations

Efficient implementations for analyzing pre-clinical multiple drug combination datasets. It provides efficient implementations for 1.the popular synergy scoring models, including HSA, Loewe, Bliss, and ZIP to quantify the degree of drug combination synergy; 2. higher order drug combination data analysis and synergy landscape visualization for unlimited number of drugs in a combination; 3. statistical analysis of drug combination synergy and sensitivity with confidence intervals and p-values; 4. synergy barometer for harmonizing multiple synergy scoring methods to provide a consensus metric of synergy; 5. evaluation of synergy and sensitivity simultaneously to provide an unbiased interpretation of the clinical potential of the drug combinations. Based on this package, we also provide a web application (http://www.synergyfinder.org) for users who prefer graphical user interface.

Maintained by Shuyu Zheng. Last updated 5 months ago.

software statisticalmethod

2.8 match 5.42 score 44 scripts

simularia

simulariatools:Simularia Tools for the Analysis of Air Pollution Data

A set of tools developed at Simularia for Simularia, to help preprocessing and post-processing of meteorological and air quality data.

Maintained by Giuseppe Carlino. Last updated 7 months ago.

air-quality atmospheric-modelling pollution-prediction visualization

3.6 match 5 stars 4.18 score 4 scripts

songyanyu

dycdtools:Calibration Assistant and Post-Processing Tool for Aquatic Ecosystem Model DYRESM-CAEDYM

Dynamic Reservoir Simulation Model (DYRESM) and Computational Aquatic Ecosystem Dynamics Model (CAEDYM) model development, including assisting with calibrating selected model parameters and visualising model output through time series plot, profile plot, contour plot, and scatter plot. For more details, see Yu et al. (2023) <https://journal.r-project.org/articles/RJ-2023-008/>.

Maintained by Songyan Yu. Last updated 6 months ago.

4.8 match 1 stars 3.18 score 9 scripts

swihart

growth:Multivariate Normal and Elliptically-Contoured Repeated Measurements Models

Functions for fitting various normal theory (growth curve) and elliptically-contoured repeated measurements models with ARMA and random effects dependence.

Maintained by Bruce Swihart. Last updated 6 years ago.

fortran

5.0 match 3.00 score 6 scripts

clementcalenge

adehabitatHR:Home Range Estimation

A collection of tools for the estimation of animals home range.

Maintained by Clement Calenge. Last updated 6 months ago.

1.7 match 6 stars 8.73 score 752 scripts 9 dependents

devopifex

g2r:Interactive Grammar of Graphics

Interactive grammar of graphics.

Maintained by John Coene. Last updated 3 years ago.

visualization

3.3 match 119 stars 4.53 score 57 scripts

american-institutes-for-research

EdSurvey:Analysis of NCES Education Survey and Assessment Data

Read in and analyze functions for education survey and assessment data from the National Center for Education Statistics (NCES) <https://nces.ed.gov/>, including National Assessment of Educational Progress (NAEP) data <https://nces.ed.gov/nationsreportcard/> and data from the International Assessment Database: Organisation for Economic Co-operation and Development (OECD) <https://www.oecd.org/en/about/directorates/directorate-for-education-and-skills.html>, including Programme for International Student Assessment (PISA), Teaching and Learning International Survey (TALIS), Programme for the International Assessment of Adult Competencies (PIAAC), and International Association for the Evaluation of Educational Achievement (IEA) <https://www.iea.nl/>, including Trends in International Mathematics and Science Study (TIMSS), TIMSS Advanced, Progress in International Reading Literacy Study (PIRLS), International Civic and Citizenship Study (ICCS), International Computer and Information Literacy Study (ICILS), and Civic Education Study (CivEd).

Maintained by Paul Bailey. Last updated 19 days ago.

1.9 match 10 stars 7.86 score 139 scripts 1 dependents

bbolker

emdbook:Support Functions and Data for "Ecological Models and Data"

Auxiliary functions and data sets for "Ecological Models and Data", a book presenting maximum likelihood estimation and related topics for ecologists (ISBN 978-0-691-12522-0).

Maintained by Ben Bolker. Last updated 8 months ago.

1.8 match 4 stars 8.04 score 656 scripts 21 dependents

ms609

Quartet:Comparison of Phylogenetic Trees Using Quartet and Split Measures

Calculates the number of four-taxon subtrees consistent with a pair of cladograms, calculating the symmetric quartet distance of Bandelt & Dress (1986), Reconstructing the shape of a tree from observed dissimilarity data, Advances in Applied Mathematics, 7, 309-343 <doi:10.1016/0196-8858(86)90038-2>, and using the tqDist algorithm of Sand et al. (2014), tqDist: a library for computing the quartet and triplet distances between binary or general trees, Bioinformatics, 30, 2079–2080 <doi:10.1093/bioinformatics/btu157> for pairs of binary trees.

Maintained by Martin R. Smith. Last updated 2 months ago.

bioinformatics comparison phylogenetic-trees phylogenetics quartet quartet-distance research-tool tree cpp

1.7 match 14 stars 7.95 score 40 scripts

r-lidar

lasR:Fast and Pipeable Airborne LiDAR Data Tools

Fast and pipeable airborne lidar processing tools. Read/write 'las' and 'laz' files, computation of metrics in area based approach, point filtering, normalization, individual tree segmentation and other manipulations in a powerful and versatile processing chain.

Maintained by Jean-Romain Roussel. Last updated 24 days ago.

gdal cpp openmp

2.0 match 17 stars 6.76 score 26 scripts

tarnduong

eks:Tidy and Geospatial Kernel Smoothing

Extensions of the kernel smoothing functions from the 'ks' package for compatibility with the tidyverse and geospatial ecosystems <doi:10.1007/s00180-024-01543-9>.

Maintained by Tarn Duong. Last updated 2 months ago.

4.6 match 1 stars 2.88 score 25 scripts

bioc

flowClust:Clustering for Flow Cytometry

Robust model-based clustering using a t-mixture model with Box-Cox transformation. Note: users should have GSL installed. Windows users: 'consult the README file available in the inst directory of the source distribution for necessary configuration instructions'.

Maintained by Greg Finak. Last updated 5 months ago.

immunooncology clustering visualization flowcytometry

1.8 match 7.30 score 83 scripts 6 dependents

crparedes

labsimplex:Simplex Optimization Algorithms for Laboratory and Manufacturing Processes

Simplex optimization algorithms as firstly proposed by Spendley et al. (1962) <doi:10.1080/00401706.1962.10490033> and later modified by Nelder and Mead (1965) <doi:10.1093/comjnl/7.4.308> for laboratory and manufacturing processes. The package also provides tools for graphical representation of the simplexes and some example response surfaces that are useful in illustrating the optimization process.

Maintained by Cristhian Paredes. Last updated 3 years ago.

laboratory optimization simplex

3.5 match 1 stars 3.70 score 4 scripts

momx

Momocs:Morphometrics using R

The goal of 'Momocs' is to provide a complete, convenient, reproducible and open-source toolkit for 2D morphometrics. It includes most common 2D morphometrics approaches on outlines, open outlines, configurations of landmarks, traditional morphometrics, and facilities for data preparation, manipulation and visualization with a consistent grammar throughout. It allows reproducible, complex morphometrics analyses and other morphometrics approaches should be easy to plug in, or develop from, on top of this canvas.

Maintained by Vincent Bonhomme. Last updated 1 years ago.

morphometrics

1.8 match 51 stars 7.42 score 346 scripts

vincentporretta

VWPre:Tools for Preprocessing Visual World Data

Gaze data from the Visual World Paradigm requires significant preprocessing prior to plotting and analyzing the data. This package provides functions for preparing visual world eye-tracking data for statistical analysis and plotting. It can prepare data for linear analyses (e.g., ANOVA, Gaussian-family LMER, Gaussian-family GAMM) as well as logistic analyses (e.g., binomial-family LMER and binomial-family GAMM). Additionally, it contains various plotting functions for creating grand average and conditional average plots. See the vignette for samples of the functionality. Currently, the functions in this package are designed for handling data collected with SR Research Eyelink eye trackers using Sample Reports created in SR Research Data Viewer. While we would like to add functionality for data collected with other systems in the future, the current package is considered to be feature-complete; further updates will mainly entail maintenance and the addition of minor functionality.

Maintained by Vincent Porretta. Last updated 4 years ago.

3.0 match 4.28 score 80 scripts 1 dependents

asgr

magicaxis:Pretty Scientific Plotting with Minor-Tick and Log Minor-Tick Support

Functions to make useful (and pretty) plots for scientific plotting. Additional plotting features are added for base plotting, with particular emphasis on making attractive log axis plots.

Maintained by Aaron Robotham. Last updated 5 months ago.

1.9 match 9 stars 6.84 score 184 scripts 7 dependents

paulojus

geoR:Analysis of Geostatistical Data

Geostatistical analysis including variogram-based, likelihood-based and Bayesian methods. Software companion for Diggle and Ribeiro (2007) <doi:10.1007/978-0-387-48536-2>.

Maintained by Paulo Justiniano Ribeiro Jr. Last updated 1 years ago.

1.7 match 10 stars 7.57 score 1.8k scripts 12 dependents

mmm-uca

orloca:Operations Research LOCational Analysis Models

Objects and methods to handle and solve the min-sum location problem, also known as Fermat-Weber problem. The min-sum location problem search for a point such that the weighted sum of the distances to the demand points are minimized. See "The Fermat-Weber location problem revisited" by Brimberg, Mathematical Programming, 1, pg. 71-76, 1995. <DOI:10.1007/BF01592245>. General global optimization algorithms are used to solve the problem, along with the adhoc Weiszfeld method, see "Sur le point pour lequel la Somme des distances de n points donnes est minimum", by Weiszfeld, Tohoku Mathematical Journal, First Series, 43, pg. 355-386, 1937 or "On the point for which the sum of the distances to n given points is minimum", by E. Weiszfeld and F. Plastria, Annals of Operations Research, 167, pg. 7-41, 2009. <DOI:10.1007/s10479-008-0352-z>.

Maintained by Manuel Munoz-Marquez. Last updated 1 years ago.

3.5 match 3.64 score 24 scripts 2 dependents

r-lib

isoband:Generate Isolines and Isobands from Regularly Spaced Elevation Grids

A fast C++ implementation to generate contour lines (isolines) and contour polygons (isobands) from regularly spaced grids containing elevation data.

Maintained by Hadley Wickham. Last updated 2 years ago.

cpp

0.8 match 132 stars 15.01 score 75 scripts 7.6k dependents

lisalibungan

shapeR:Collection and Analysis of Otolith Shape Data

Studies otolith shape variation among fish populations. Otoliths are calcified structures found in the inner ear of teleost fish and their shape has been known to vary among several fish populations and stocks, making them very useful in taxonomy, species identification and to study geographic variations. The package extends previously described software used for otolith shape analysis by allowing the user to automatically extract closed contour outlines from a large number of images, perform smoothing to eliminate pixel noise, choose from conducting either a Fourier or wavelet transform to the outlines and visualize the mean shape. The output of the package are independent Fourier or wavelet coefficients which can be directly imported into a wide range of statistical packages in R. The package might prove useful in studies of any two dimensional objects.

Maintained by Lisa Anne Libungan. Last updated 7 years ago.

2.8 match 9 stars 4.45 score 21 scripts

ccamlr

CCAMLRGIS:Antarctic Spatial Data Manipulation

Loads and creates spatial data, including layers and tools that are relevant to the activities of the Commission for the Conservation of Antarctic Marine Living Resources. Provides two categories of functions: load functions and create functions. Load functions are used to import existing spatial layers from the online CCAMLR GIS such as the ASD boundaries. Create functions are used to create layers from user data such as polygons and grids.

Maintained by Stephane Thanassekos. Last updated 1 months ago.

1.9 match 7 stars 6.34 score 38 scripts

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.

2.3 match 4 stars 5.26 score 23 scripts

drwolf85

spMC:Continuous-Lag Spatial Markov Chains

A set of functions is provided for 1) the stratum lengths analysis along a chosen direction, 2) fast estimation of continuous lag spatial Markov chains model parameters and probability computing (also for large data sets), 3) transition probability maps and transiograms drawing, 4) simulation methods for categorical random fields. More details on the methodology are discussed in Sartore (2013) <doi:10.32614/RJ-2013-022> and Sartore et al. (2016) <doi:10.1016/j.cageo.2016.06.001>.

Maintained by Luca Sartore. Last updated 2 years ago.

openblas openmp

4.0 match 3 stars 2.92 score 55 scripts

obreschkow

cooltools:Practical Tools for Scientific Computations and Visualizations

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

Maintained by Danail Obreschkow. Last updated 3 months ago.

cpp

3.7 match 1 stars 3.17 score 21 scripts

barryrowlingson

spatialkernel:Non-Parametric Estimation of Spatial Segregation in a Multivariate Point Process

Edge-corrected kernel density estimation and binary kernel regression estimation for multivariate spatial point process data. For details, see Diggle, P.J., Zheng, P. and Durr, P. A. (2005) <doi:10.1111/j.1467-9876.2005.05373.x>.

Maintained by Virgilio Gómez-Rubio. Last updated 4 years ago.

fortran

4.5 match 2.54 score 23 scripts

clementcalenge

adehabitatMA:Tools to Deal with Raster Maps

A collection of tools to deal with raster maps.

Maintained by Clement Calenge. Last updated 6 months ago.

1.8 match 1 stars 6.34 score 43 scripts 15 dependents

danlwarren

ENMTools:Analysis of Niche Evolution using Niche and Distribution Models

Constructing niche models and analyzing patterns of niche evolution. Acts as an interface for many popular modeling algorithms, and allows users to conduct Monte Carlo tests to address basic questions in evolutionary ecology and biogeography. Warren, D.L., R.E. Glor, and M. Turelli (2008) <doi:10.1111/j.1558-5646.2008.00482.x> Glor, R.E., and D.L. Warren (2011) <doi:10.1111/j.1558-5646.2010.01177.x> Warren, D.L., R.E. Glor, and M. Turelli (2010) <doi:10.1111/j.1600-0587.2009.06142.x> Cardillo, M., and D.L. Warren (2016) <doi:10.1111/geb.12455> D.L. Warren, L.J. Beaumont, R. Dinnage, and J.B. Baumgartner (2019) <doi:10.1111/ecog.03900>.

Maintained by Dan Warren. Last updated 2 months ago.

1.6 match 105 stars 6.91 score 126 scripts

apguthrie

BRcal:Boldness-Recalibration of Binary Events

Boldness-recalibration maximally spreads out probability predictions while maintaining a user specified level of calibration, facilitated the brcal() function. Supporting functions to assess calibration via Bayesian and Frequentist approaches, Maximum Likelihood Estimator (MLE) recalibration, Linear in Log Odds (LLO)-adjust via any specified parameters, and visualize results are also provided. Methodological details can be found in Guthrie & Franck (2024) <doi:10.1080/00031305.2024.2339266>.

Maintained by Adeline P. Guthrie. Last updated 4 months ago.

2.3 match 4.81 score 5 scripts

arpapiemonte

OpeNoise:Environmental Noise Pollution Data Analysis

Provides analyse, interpret and understand noise pollution data. Data are typically regular time series measured with sound meter. The package is partially described in Fogola, Grasso, Masera and Scordino (2023, <DOI:10.61782/fa.2023.0063>).

Maintained by Pasquale Scordino. Last updated 4 months ago.

3.2 match 2 stars 3.48 score 5 scripts

salbeke

rKIN:(Kernel) Isotope Niche Estimation

Applies methods used to estimate animal homerange, but instead of geospatial coordinates, we use isotopic coordinates. The estimation methods include: 1) 2-dimensional bivariate normal kernel utilization density estimator, 2) bivariate normal ellipse estimator, and 3) minimum convex polygon estimator, all applied to stable isotope data. Additionally, functions to determine niche area, polygon overlap between groups and levels (confidence contours) and plotting capabilities.

Maintained by Shannon E Albeke. Last updated 16 days ago.

2.2 match 4 stars 5.13 score 34 scripts

bozenne

LMMstar:Repeated Measurement Models for Discrete Times

Companion R package for the course "Statistical analysis of correlated and repeated measurements for health science researchers" taught by the section of Biostatistics of the University of Copenhagen. It implements linear mixed models where the model for the variance-covariance of the residuals is specified via patterns (compound symmetry, toeplitz, unstructured, ...). Statistical inference for mean, variance, and correlation parameters is performed based on the observed information and a Satterthwaite approximation of the degrees of freedom. Normalized residuals are provided to assess model misspecification. Statistical inference can be performed for arbitrary linear or non-linear combination(s) of model coefficients. Predictions can be computed conditional to covariates only or also to outcome values.

Maintained by Brice Ozenne. Last updated 5 months ago.

1.8 match 4 stars 6.20 score 141 scripts

jsl5-code

mixexp:Design and Analysis of Mixture Experiments

Functions for creating designs for mixture experiments, making ternary contour plots, and making mixture effect plots.

Maintained by John Lawson. Last updated 5 months ago.

fortran

3.9 match 1 stars 2.76 score 31 scripts 2 dependents

taikisan21

PamBinaries:Read and Process 'Pamguard' Binary Data

Functions for easily reading and processing binary data files created by 'Pamguard' (<https://www.pamguard.org/>). All functions for directly reading the binary data files are based on 'MATLAB' code written by Michael Oswald.

Maintained by Taiki Sakai. Last updated 2 months ago.

2.0 match 10 stars 5.39 score 18 scripts 3 dependents

eikeluedeling

chillR:Statistical Methods for Phenology Analysis in Temperate Fruit Trees

The phenology of plants (i.e. the timing of their annual life phases) depends on climatic cues. For temperate trees and many other plants, spring phases, such as leaf emergence and flowering, have been found to result from the effects of both cool (chilling) conditions and heat. Fruit tree scientists (pomologists) have developed some metrics to quantify chilling and heat (e.g. see Luedeling (2012) <doi:10.1016/j.scienta.2012.07.011>). 'chillR' contains functions for processing temperature records into chilling (Chilling Hours, Utah Chill Units and Chill Portions) and heat units (Growing Degree Hours). Regarding chilling metrics, Chill Portions are often considered the most promising, but they are difficult to calculate. This package makes it easy. 'chillR' also contains procedures for conducting a PLS analysis relating phenological dates (e.g. bloom dates) to either mean temperatures or mean chill and heat accumulation rates, based on long-term weather and phenology records (Luedeling and Gassner (2012) <doi:10.1016/j.agrformet.2011.10.020>). As of version 0.65, it also includes functions for generating weather scenarios with a weather generator, for conducting climate change analyses for temperature-based climatic metrics and for plotting results from such analyses. Since version 0.70, 'chillR' contains a function for interpolating hourly temperature records.

Maintained by Eike Luedeling. Last updated 4 months ago.

cpp

1.7 match 3 stars 6.13 score 346 scripts 1 dependents

baddstats

spatstat.local:Extension to 'spatstat' for Local Composite Likelihood

Extension to the 'spatstat' package, enabling the user to fit point process models to point pattern data by local composite likelihood ('geographically weighted regression').

Maintained by Adrian Baddeley. Last updated 8 months ago.

spatial-analysis spatial-data spatstat

2.3 match 4.66 score 23 scripts

craddm

eegUtils:Utilities for Electroencephalographic (EEG) Analysis

Electroencephalography data processing and visualization tools. Includes import functions for 'BioSemi' (.BDF), 'Neuroscan' (.CNT), 'Brain Vision Analyzer' (.VHDR), 'EEGLAB' (.set) and 'Fieldtrip' (.mat). Many preprocessing functions such as referencing, epoching, filtering, and ICA are available. There are a variety of visualizations possible, including timecourse and topographical plotting.

Maintained by Matt Craddock. Last updated 5 months ago.

eeg eeg-analysis eeg-data eeg-signals eeg-signals-processing openblas cpp openmp

1.6 match 106 stars 6.54 score 82 scripts

bhushan0510

PlotBivInvGaus:Density Contour Plot for Bivariate Inverse Gaussian Distribution

Create the density contour plot for bivariate inverse Gaussian distribution for given non negative random variables.

Maintained by Bhushan Saswade. Last updated 2 years ago.

5.1 match 2.00 score 2 scripts

pakillo

FloraIberica:Taxonomic and distribution data for all the vascular plants present in the Iberian Peninsula and Balearic Islands

Check which plant taxa are present and/or endemic, and get detailed (10x10 km) distribution maps for all the vascular plants present in the Iberian Peninsula and Balearic Islands, from genus to subspecies level, based on the AFLIBER database (<doi:10.1111/geb.13363>).

Maintained by Francisco Rodríguez-Sánchez. Last updated 2 years ago.

biogeography plants

4.0 match 7 stars 2.54 score 4 scripts

eogrady21

vprr:Processing and Visualization of Video Plankton Recorder Data

An oceanographic data processing package for analyzing and visualizing Video Plankton Recorder data. This package was developed at 'Bedford Institute of Oceanography'. Functions are designed to process automated image classification output and create organized and easily portable data products.

Maintained by Emily OGrady. Last updated 1 months ago.

1.8 match 2 stars 5.61 score 17 scripts

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.

1.9 match 5.34 score 139 scripts 5 dependents

seananderson

metafolio:Metapopulation Simulations for Conserving Salmon Through Portfolio Optimization

A tool to simulate salmon metapopulations and apply financial portfolio optimization concepts. The package accompanies the paper Anderson et al. (2015) <doi:10.1101/2022.03.24.485545>.

Maintained by Sean C. Anderson. Last updated 1 years ago.

openblas cpp

2.0 match 2 stars 4.89 score 77 scripts

bioc

bandle:An R package for the Bayesian analysis of differential subcellular localisation experiments

The Bandle package enables the analysis and visualisation of differential localisation experiments using mass-spectrometry data. Experimental methods supported include dynamic LOPIT-DC, hyperLOPIT, Dynamic Organellar Maps, Dynamic PCP. It provides Bioconductor infrastructure to analyse these data.

Maintained by Oliver M. Crook. Last updated 2 months ago.

bayesian classification clustering immunooncology qualitycontrol dataimport proteomics massspectrometry openblas cpp openmp

1.8 match 4 stars 5.56 score 3 scripts

friendly

genridge:Generalized Ridge Trace Plots for Ridge Regression

The genridge package introduces generalizations of the standard univariate ridge trace plot used in ridge regression and related methods. These graphical methods show both bias (actually, shrinkage) and precision, by plotting the covariance ellipsoids of the estimated coefficients, rather than just the estimates themselves. 2D and 3D plotting methods are provided, both in the space of the predictor variables and in the transformed space of the PCA/SVD of the predictors.

Maintained by Michael Friendly. Last updated 4 months ago.

bias-variance graphics principal-component-analysis regression-models ridge-regression singular-value-decomposition

2.0 match 4 stars 4.84 score 69 scripts

ellessenne

rsimsum:Analysis of Simulation Studies Including Monte Carlo Error

Summarise results from simulation studies and compute Monte Carlo standard errors of commonly used summary statistics. This package is modelled on the 'simsum' user-written command in 'Stata' (White I.R., 2010 <https://www.stata-journal.com/article.html?article=st0200>), further extending it with additional performance measures and functionality.

Maintained by Alessandro Gasparini. Last updated 10 months ago.

biostatistics monte-carlo-error simulation simulation-study simulations statistics

1.3 match 28 stars 7.70 score 148 scripts

robustsource

ALTopt:Optimal Experimental Designs for Accelerated Life Testing

Creates the optimal (D, U and I) designs for the accelerated life testing with right censoring or interval censoring. It uses generalized linear model (GLM) approach to derive the asymptotic variance-covariance matrix of regression coefficients. The failure time distribution is assumed to follow Weibull distribution with a known shape parameter and log-linear link functions are used to model the relationship between failure time parameters and stress variables. The acceleration model may have multiple stress factors, although most ALTs involve only two or less stress factors. ALTopt package also provides several plotting functions including contour plot, Fraction of Use Space (FUS) plot and Variance Dispersion graphs of Use Space (VDUS) plot. For more details, see Seo and Pan (2015) <doi:10.32614/RJ-2015-029>.

Maintained by Kangwon Seo. Last updated 5 years ago.

7.9 match 1.20 score 16 scripts

gamlss-dev

gamlss.add:Extra Additive Terms for Generalized Additive Models for Location Scale and Shape

Interface for extra smooth functions including tensor products, neural networks and decision trees.

Maintained by Mikis Stasinopoulos. Last updated 1 years ago.

1.9 match 4.98 score 64 scripts 1 dependents

iohprofiler

IOHanalyzer:Data Analysis Part of 'IOHprofiler'

The data analysis module for the Iterative Optimization Heuristics Profiler ('IOHprofiler'). This module provides statistical analysis methods for the benchmark data generated by optimization heuristics, which can be visualized through a web-based interface. The benchmark data is usually generated by the experimentation module, called 'IOHexperimenter'. 'IOHanalyzer' also supports the widely used 'COCO' (Comparing Continuous Optimisers) data format for benchmarking.

Maintained by Diederick Vermetten. Last updated 10 months ago.

cpp

1.8 match 24 stars 5.10 score 13 scripts

staffanbetner

rethinking:Statistical Rethinking book package

Utilities for fitting and comparing models

Maintained by Richard McElreath. Last updated 4 months ago.

1.7 match 5.42 score 4.4k scripts

bioc

DepecheR:Determination of essential phenotypic elements of clusters in high-dimensional entities

The purpose of this package is to identify traits in a dataset that can separate groups. This is done on two levels. First, clustering is performed, using an implementation of sparse K-means. Secondly, the generated clusters are used to predict outcomes of groups of individuals based on their distribution of observations in the different clusters. As certain clusters with separating information will be identified, and these clusters are defined by a sparse number of variables, this method can reduce the complexity of data, to only emphasize the data that actually matters.

Maintained by Jakob Theorell. Last updated 5 months ago.

software cellbasedassays transcription differentialexpression datarepresentation immunooncology transcriptomics classification clustering dimensionreduction featureextraction flowcytometry rnaseq singlecell visualization cpp

1.8 match 5.18 score 15 scripts

steve-the-bayesian

Boom:Bayesian Object Oriented Modeling

A C++ library for Bayesian modeling, with an emphasis on Markov chain Monte Carlo. Although boom contains a few R utilities (mainly plotting functions), its primary purpose is to install the BOOM C++ library on your system so that other packages can link against it.

Maintained by Steven L. Scott. Last updated 1 years ago.

1.9 match 9 stars 4.82 score 57 scripts 6 dependents

toledo60

ggDoE:Modern Graphs for Design of Experiments with 'ggplot2'

Generate commonly used plots in the field of design of experiments using 'ggplot2'. 'ggDoE' currently supports the following plots: alias matrix, box cox transformation, boxplots, lambda plot, regression diagnostic plots, half normal plots, main and interaction effect plots for factorial designs, contour plots for response surface methodology, Pareto plot, and two dimensional projections of a latin hypercube design.

Maintained by Jose Toledo Luna. Last updated 9 months ago.

2.2 match 11 stars 4.04 score 3 scripts

mmm-uca

RcmdrPlugin.orloca:A GUI for Planar Location Problems

A GUI for the orloca package is provided as a Rcmdr plug-in. The package deals with continuos planar location problems.

Maintained by Manuel Munoz-Marquez. Last updated 4 years ago.

3.8 match 2.30 score 8 scripts

akkyro

PupilPre:Preprocessing Pupil Size Data

Pupillometric data collected using SR Research Eyelink eye trackers requires significant preprocessing. This package contains functions for preparing pupil dilation data for visualization and statistical analysis. Specifically, it provides a pipeline of functions which aid in data validation, the removal of blinks/artifacts, downsampling, and baselining, among others. Additionally, plotting functions for creating grand average and conditional average plots are provided. See the vignette for samples of the functionality. The package is designed for handling data collected with SR Research Eyelink eye trackers using Sample Reports created in SR Research Data Viewer.

Maintained by Aki-Juhani Kyröläinen. Last updated 5 years ago.

3.1 match 2.81 score 13 scripts

jonathanlees

RSEIS:Seismic Time Series Analysis Tools

Multiple interactive codes to view and analyze seismic data, via spectrum analysis, wavelet transforms, particle motion, hodograms. Includes general time-series tools, plotting, filtering, interactive display.

Maintained by Jonathan M. Lees. Last updated 6 months ago.

2.0 match 3 stars 4.27 score 262 scripts 4 dependents

paulgovan

WeibullR.plotly:Interactive Weibull Probability Plots

Build interactive Weibull Probability Plots with 'WeibullR' by David Silkworth and Jurgen Symynck (2022) <https://CRAN.R-project.org/package=WeibullR>, an R package for Weibull analysis, and 'plotly' by Carson Sievert (2020) <https://plotly-r.com>, an interactive web-based graphing library.

Maintained by Paul Govan. Last updated 4 months ago.

life-data-analysis plotly weibull-analysis

2.0 match 4.26 score 12 scripts 1 dependents

c7rishi

BAMBI:Bivariate Angular Mixture Models

Fit (using Bayesian methods) and simulate mixtures of univariate and bivariate angular distributions. Chakraborty and Wong (2021) <doi:10.18637/jss.v099.i11>.

Maintained by Saptarshi Chakraborty. Last updated 5 months ago.

cpp

1.8 match 3 stars 4.83 score 65 scripts 1 dependents

cran

bivpois:Bivariate Poisson Distribution

Maximum likelihood estimation, random values generation, density computation and other functions for the bivariate Poisson distribution. References include: Kawamura K. (1984). "Direct calculation of maximum likelihood estimator for the bivariate Poisson distribution". Kodai Mathematical Journal, 7(2): 211--221. <doi:10.2996/kmj/1138036908>. Kocherlakota S. and Kocherlakota K. (1992). "Bivariate discrete distributions". CRC Press. <doi:10.1201/9781315138480>. Karlis D. and Ntzoufras I. (2003). "Analysis of sports data by using bivariate Poisson models". Journal of the Royal Statistical Society: Series D (The Statistician), 52(3): 381--393. <doi:10.1111/1467-9884.00366>.

Maintained by Michail Tsagris. Last updated 2 months ago.

4.0 match 4 stars 2.08 score 1 dependents

theussl

fMultivar:Rmetrics - Modeling of Multivariate Financial Return Distributions

A collection of functions inspired by Venables and Ripley (2002) <doi:10.1007/978-0-387-21706-2> and Azzalini and Capitanio (1999) <arXiv:0911.2093> to manage, investigate and analyze bivariate and multivariate data sets of financial returns.

Maintained by Stefan Theussl. Last updated 2 years ago.

2.3 match 3.69 score 99 scripts 7 dependents

jongheepark

NetworkChange:Bayesian Package for Network Changepoint Analysis

Network changepoint analysis for undirected network data. The package implements a hidden Markov network change point model (Park and Sohn (2020)). Functions for break number detection using the approximate marginal likelihood and WAIC are also provided.

Maintained by Jong Hee Park. Last updated 3 years ago.

bayesian changepoint latent-space network

1.8 match 5 stars 4.60 score 16 scripts

giorgilancs

PrevMap:Geostatistical Modelling of Spatially Referenced Prevalence Data

Provides functions for both likelihood-based and Bayesian analysis of spatially referenced prevalence data. For a tutorial on the use of the R package, see Giorgi and Diggle (2017) <doi:10.18637/jss.v078.i08>.

Maintained by Emanuele Giorgi. Last updated 2 years ago.

1.9 match 4.36 score 46 scripts

surajitstat

Modalclust:Hierarchical Modal Clustering

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

Maintained by Surajit Ray. Last updated 6 years ago.

3.9 match 2.08 score 12 scripts

brauckhoff

biopixR:Extracting Insights from Biological Images

Combines the 'magick' and 'imager' packages to streamline image analysis, focusing on feature extraction and quantification from biological images, especially microparticles. By providing high throughput pipelines and clustering capabilities, 'biopixR' facilitates efficient insight generation for researchers (Schneider J. et al. (2019) <doi:10.21037/jlpm.2019.04.05>).

Maintained by Tim Brauckhoff. Last updated 4 months ago.

1.3 match 5 stars 6.36 score 23 scripts

jatanrt

eprscope:Processing and Analysis of Electron Paramagnetic Resonance Data and Spectra in Chemistry

Processing, analysis and plottting of Electron Paramagnetic Resonance (EPR) spectra in chemistry. Even though the package is mainly focused on continuous wave (CW) EPR/ENDOR, many functions may be also used for the integrated forms of 1D PULSED EPR spectra. It is able to find the most important spectral characteristics like g-factor, linewidth, maximum of derivative or integral intensities and single/double integrals. This is especially important in spectral (time) series consisting of many EPR spectra like during variable temperature experiments, electrochemical or photochemical radical generation and/or decay. Package also enables processing of data/spectra for the analytical (quantitative) purposes. Namely, how many radicals or paramagnetic centers can be found in the analyte/sample. The goal is to evaluate rate constants, considering different kinetic models, to describe the radical reactions. The key feature of the package resides in processing of the universal ASCII text formats (such as '.txt', '.csv' or '.asc') from scratch. No proprietary formats are used (except the MATLAB EasySpin outputs) and in such respect the package is in accordance with the FAIR data principles. Upon 'reading' (also providing automatic procedures for the most common EPR spectrometers) the spectral data are transformed into the universal R 'data frame' format. Subsequently, the EPR spectra can be visualized and are fully consistent either with the 'ggplot2' package or with the interactive formats based on 'plotly'. Additionally, simulations and fitting of the isotropic EPR spectra are also included in the package. Advanced simulation parameters provided by the MATLAB-EasySpin toolbox and results from the quantum chemical calculations like g-factor and hyperfine splitting/coupling constants (a/A) can be compared and summarized in table-format in order to analyze the EPR spectra by the most effective way.

Maintained by Ján Tarábek. Last updated 1 days ago.

openjdk

1.7 match 4.74 score 7 scripts

swihart

mvpd:Multivariate Product Distributions for Elliptically Contoured Distributions

Estimates multivariate subgaussian stable densities and probabilities as well as generates random variates using product distribution theory. A function for estimating the parameters from data to fit a distribution to data is also provided, using the method from Nolan (2013) <doi:10.1007/s00180-013-0396-7>.

Maintained by Bruce Swihart. Last updated 1 years ago.

2.9 match 2.70 score 8 scripts

tnagler

kdevine:Multivariate Kernel Density Estimation with Vine Copulas

Implements the vine copula based kernel density estimator of Nagler and Czado (2016) <doi:10.1016/j.jmva.2016.07.003>. The estimator does not suffer from the curse of dimensionality and is therefore well suited for high-dimensional applications.

Maintained by Thomas Nagler. Last updated 9 months ago.

cpp

1.8 match 17 stars 4.43 score 32 scripts

cran

MVN:Multivariate Normality Tests

Performs multivariate normality tests and graphical approaches and implements multivariate outlier detection and univariate normality of marginal distributions through plots and tests, and performs multivariate Box-Cox transformation (Korkmaz et al, (2014), <https://journal.r-project.org/archive/2014-2/korkmaz-goksuluk-zararsiz.pdf>).

Maintained by Selcuk Korkmaz. Last updated 4 years ago.

1.3 match 1 stars 5.61 score 4 dependents

chenlaboratory

hexDensity:Fast Kernel Density Estimation with Hexagonal Grid

Kernel density estimation with hexagonal grid for bivariate data. Hexagonal grid has many beneficial properties like equidistant neighbours and less edge bias, making it better for spatial analyses than the more commonly used rectangular grid. Carr, D. B. et al. (1987) <doi:10.2307/2289444>. Diggle, P. J. (2010) <doi:10.1201/9781420072884>. Hill, B. (2017) <https://blog.bruce-hill.com/meandering-triangles>. Jones, M. C. (1993) <doi:10.1007/BF00147776>.

Maintained by Quoc Hoang Nguyen. Last updated 1 months ago.

fortran cpp

1.9 match 3.93 score

cran

GRIDCOPULA:Bivariate Copula Functions Based on Regular Grid

Estimates grid type bivariate copula functions, calculates some association measures and provides several copula graphics.

Maintained by Rogelio Salinas Gutiérrez. Last updated 12 months ago.

3.4 match 2.18 score 1 dependents

hypertidy

ximage:Draw Images of Raster Data and Related Adornments

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

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

2.3 match 8 stars 3.25 score 22 scripts

angelacar

TwoTimeScales:Analysis of Event Data with Two Time Scales

Analyse time to event data with two time scales by estimating a smooth hazard that varies over two time scales. If covariates are available, estimate a proportional hazards model with such a two-dimensional baseline hazard. Functions are provided to prepare the raw data for estimation, to estimate and to plot the two-dimensional smooth hazard. Extension to a competing risks model are implemented. For details about the method please refer to Carollo et al. (2024) <doi:10.1002/sim.10297>.

Maintained by Angela Carollo. Last updated 1 months ago.

1.2 match 9 stars 6.26 score 5 scripts

freezenik

R2BayesX:Estimate Structured Additive Regression Models with 'BayesX'

An R interface to estimate structured additive regression (STAR) models with 'BayesX'.

Maintained by Nikolaus Umlauf. Last updated 1 years ago.

2.0 match 1 stars 3.55 score 118 scripts 1 dependents

haddonm

MQMF:Modelling and Quantitative Methods in Fisheries

Complements the book "Using R for Modelling and Quantitative Methods in Fisheries" ISBN 9780367469894, published in 2021 by Chapman & Hall in their "Using R series". There are numerous functions and data-sets that are used in the book's many practical examples.

Maintained by Malcolm Haddon. Last updated 2 years ago.

ecology fisheries haddon quantitative-methods uncertainty

1.7 match 11 stars 4.14 score 25 scripts

fabianenc

r6qualitytools:R6-Based Statistical Methods for Quality Science

A comprehensive suite of statistical tools for Quality Management, designed around the Define, Measure, Analyze, Improve, and Control (DMAIC) cycle used in Six Sigma methodology. Based on the discontinued CRAN package 'qualitytools', this package refactors its original design by incorporating 'R6' object-oriented programming for increased flexibility and performance. It replaces traditional graphics with modern, interactive visualizations using 'ggplot2' and 'plotly'. Built on 'tidyverse' principles, it simplifies data manipulation and visualization, offering an intuitive approach to quality science.

Maintained by Fabian Encarnacion. Last updated 6 months ago.

2.0 match 2 stars 3.48 score 3 scripts