R-universe search: shapes

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

143.8 match 51 stars 7.42 score 346 scripts

karlines

shape:Functions for Plotting Graphical Shapes, Colors

Functions for plotting graphical shapes such as ellipses, circles, cylinders, arrows, ...

Maintained by Karline Soetaert. Last updated 1 years ago.

69.2 match 10.95 score 984 scripts 1.4k dependents

geomorphr

geomorph:Geometric Morphometric Analyses of 2D and 3D Landmark Data

Read, manipulate, and digitize landmark data, generate shape variables via Procrustes analysis for points, curves and surfaces, perform shape analyses, and provide graphical depictions of shapes and patterns of shape variation.

Maintained by Dean Adams. Last updated 2 months ago.

58.3 match 76 stars 12.05 score 700 scripts 6 dependents

iandryden

shapes:Statistical Shape Analysis

Routines for the statistical analysis of landmark shapes, including Procrustes analysis, graphical displays, principal components analysis, permutation and bootstrap tests, thin-plate spline transformation grids and comparing covariance matrices. See Dryden, I.L. and Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd Edition), John Wiley and Sons.

Maintained by Ian Dryden. Last updated 5 days ago.

77.2 match 7 stars 8.61 score 225 scripts 24 dependents

rstudio

keras3:R Interface to 'Keras'

Interface to 'Keras' <https://keras.io>, a high-level neural networks API. 'Keras' was developed with a focus on enabling fast experimentation, supports both convolution based networks and recurrent networks (as well as combinations of the two), and runs seamlessly on both CPU and GPU devices.

Maintained by Tomasz Kalinowski. Last updated 11 days ago.

34.0 match 845 stars 13.63 score 264 scripts 2 dependents

jrnold

ggthemes:Extra Themes, Scales and Geoms for 'ggplot2'

Some extra themes, geoms, and scales for 'ggplot2'. Provides 'ggplot2' themes and scales that replicate the look of plots by Edward Tufte, Stephen Few, 'Fivethirtyeight', 'The Economist', 'Stata', 'Excel', and 'The Wall Street Journal', among others. Provides 'geoms' for Tufte's box plot and range frame.

Maintained by Jeffrey B. Arnold. Last updated 1 years ago.

data-visualisation ggplot2 ggplot2-themes plot plotting theme visualization

28.3 match 1.3k stars 16.17 score 40k scripts 102 dependents

bioc

RCy3:Functions to Access and Control Cytoscape

Vizualize, analyze and explore networks using Cytoscape via R. Anything you can do using the graphical user interface of Cytoscape, you can now do with a single RCy3 function.

Maintained by Alex Pico. Last updated 5 days ago.

visualization graphandnetwork thirdpartyclient network

25.9 match 52 stars 13.47 score 628 scripts 17 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 3 days ago.

graphics opengl rgl webgl libglu libglvnd libpng libx11 freetype cpp

19.9 match 91 stars 17.40 score 7.3k scripts 303 dependents

igraph

igraph:Network Analysis and Visualization

Routines for simple graphs and network analysis. It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.

Maintained by Kirill Müller. Last updated 1 hours ago.

complex-networks graph-algorithms graph-theory mathematics network-analysis network-graph fortran libxml2 glpk openblas cpp

14.7 match 584 stars 21.13 score 31k scripts 1.9k dependents

gaospecial

ggVennDiagram:A 'ggplot2' Implement of Venn Diagram

Easy-to-use functions to generate 2-7 sets Venn or upset plot in publication quality. 'ggVennDiagram' plot Venn or upset using well-defined geometry dataset and 'ggplot2'. The shapes of 2-4 sets Venn use circles and ellipses, while the shapes of 4-7 sets Venn use irregular polygons (4 has both forms), which are developed and imported from another package 'venn', authored by Adrian Dusa. We provided internal functions to integrate shape data with user provided sets data, and calculated the geometry of every regions/intersections of them, then separately plot Venn in four components, set edges/labels, and region edges/labels. From version 1.0, it is possible to customize these components as you demand in ordinary 'ggplot2' grammar. From version 1.4.4, it supports unlimited number of sets, as it can draw a plain upset plot automatically when number of sets is more than 7.

Maintained by Chun-Hui Gao. Last updated 5 months ago.

set-operations upset upsetplot venn-diagram venn-plot

22.6 match 292 stars 12.31 score 1.3k scripts 4 dependents

lbelzile

mev:Modelling of Extreme Values

Various tools for the analysis of univariate, multivariate and functional extremes. Exact simulation from max-stable processes [Dombry, Engelke and Oesting (2016) <doi:10.1093/biomet/asw008>, R-Pareto processes for various parametric models, including Brown-Resnick (Wadsworth and Tawn, 2014, <doi:10.1093/biomet/ast042>) and Extremal Student (Thibaud and Opitz, 2015, <doi:10.1093/biomet/asv045>). Threshold selection methods, including Wadsworth (2016) <doi:10.1080/00401706.2014.998345>, and Northrop and Coleman (2014) <doi:10.1007/s10687-014-0183-z>. Multivariate extreme diagnostics. Estimation and likelihoods for univariate extremes, e.g., Coles (2001) <doi:10.1007/978-1-4471-3675-0>.

Maintained by Leo Belzile. Last updated 5 months ago.

extreme-value-statistics likelihood-functions max-stable simulation threshold-selection openblas cpp openmp

28.6 match 14 stars 8.21 score 94 scripts 4 dependents

t-kalinowski

keras:R Interface to 'Keras'

Interface to 'Keras' <https://keras.io>, a high-level neural networks 'API'. 'Keras' was developed with a focus on enabling fast experimentation, supports both convolution based networks and recurrent networks (as well as combinations of the two), and runs seamlessly on both 'CPU' and 'GPU' devices.

Maintained by Tomasz Kalinowski. Last updated 12 months ago.

20.4 match 10.93 score 10k scripts 55 dependents

mikeblazanin

gcplyr:Wrangle and Analyze Growth Curve Data

Easy wrangling and model-free analysis of microbial growth curve data, as commonly output by plate readers. Tools for reshaping common plate reader outputs into 'tidy' formats and merging them with design information, making data easy to work with using 'gcplyr' and other packages. Also streamlines common growth curve processing steps, like smoothing and calculating derivatives, and facilitates model-free characterization and analysis of growth data. See methods at <https://mikeblazanin.github.io/gcplyr/>.

Maintained by Mike Blazanin. Last updated 2 months ago.

dplyr ggplot2 tidyverse

28.7 match 30 stars 7.53 score 75 scripts

zarquon42b

Morpho:Calculations and Visualisations Related to Geometric Morphometrics

A toolset for Geometric Morphometrics and mesh processing. This includes (among other stuff) mesh deformations based on reference points, permutation tests, detection of outliers, processing of sliding semi-landmarks and semi-automated surface landmark placement.

Maintained by Stefan Schlager. Last updated 5 months ago.

openblas cpp openmp

18.7 match 51 stars 10.01 score 218 scripts 13 dependents

xliaosdsu

cgam:Constrained Generalized Additive Model

A constrained generalized additive model is fitted by the cgam routine. Given a set of predictors, each of which may have a shape or order restrictions, the maximum likelihood estimator for the constrained generalized additive model is found using an iteratively re-weighted cone projection algorithm. The ShapeSelect routine chooses a subset of predictor variables and describes the component relationships with the response. For each predictor, the user needs only specify a set of possible shape or order restrictions. A model selection method chooses the shapes and orderings of the relationships as well as the variables. The cone information criterion (CIC) is used to select the best combination of variables and shapes. A genetic algorithm may be used when the set of possible models is large. In addition, the cgam routine implements a two-dimensional isotonic regression using warped-plane splines without additivity assumptions. It can also fit a convex or concave regression surface with triangle splines without additivity assumptions. See Liao X, Meyer MC (2019)<doi:10.18637/jss.v089.i05> for more details.

Maintained by Xiyue Liao. Last updated 1 months ago.

45.2 match 1 stars 3.52 score 59 scripts 2 dependents

cgoo4

ggfoundry:Shape Foundry & Geom for 'ggplot2'

A 'ggplot2' extension that supports arbitrary hand-crafted colourable & fillable shapes. New shapes may be feature requested via a Github issue.

Maintained by Carl Goodwin. Last updated 9 months ago.

ggplot ggplot-extension ggplot2 ggplot2-geom shapes visualisation visualization

22.4 match 17 stars 6.64 score 64 scripts

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 6 days ago.

data-visualisation visualisation

5.8 match 6.6k stars 25.10 score 645k scripts 7.6k dependents

bioc

DNAshapeR:High-throughput prediction of DNA shape features

DNAhapeR is an R/BioConductor package for ultra-fast, high-throughput predictions of DNA shape features. The package allows to predict, visualize and encode DNA shape features for statistical learning.

Maintained by Tsu-Pei Chiu. Last updated 5 months ago.

structuralprediction dna3dstructure software cpp

25.8 match 5.57 score 37 scripts

a-dudek-ue

clusterSim:Searching for Optimal Clustering Procedure for a Data Set

Distance measures (GDM1, GDM2, Sokal-Michener, Bray-Curtis, for symbolic interval-valued data), cluster quality indices (Calinski-Harabasz, Baker-Hubert, Hubert-Levine, Silhouette, Krzanowski-Lai, Hartigan, Gap, Davies-Bouldin), data normalization formulas (metric data, interval-valued symbolic data), data generation (typical and non-typical data), HINoV method, replication analysis, linear ordering methods, spectral clustering, agreement indices between two partitions, plot functions (for categorical and symbolic interval-valued data). (MILLIGAN, G.W., COOPER, M.C. (1985) <doi:10.1007/BF02294245>, HUBERT, L., ARABIE, P. (1985) <doi:10.1007%2FBF01908075>, RAND, W.M. (1971) <doi:10.1080/01621459.1971.10482356>, JAJUGA, K., WALESIAK, M. (2000) <doi:10.1007/978-3-642-57280-7_11>, MILLIGAN, G.W., COOPER, M.C. (1988) <doi:10.1007/BF01897163>, JAJUGA, K., WALESIAK, M., BAK, A. (2003) <doi:10.1007/978-3-642-55721-7_12>, DAVIES, D.L., BOULDIN, D.W. (1979) <doi:10.1109/TPAMI.1979.4766909>, CALINSKI, T., HARABASZ, J. (1974) <doi:10.1080/03610927408827101>, HUBERT, L. (1974) <doi:10.1080/01621459.1974.10480191>, TIBSHIRANI, R., WALTHER, G., HASTIE, T. (2001) <doi:10.1111/1467-9868.00293>, BRECKENRIDGE, J.N. (2000) <doi:10.1207/S15327906MBR3502_5>, WALESIAK, M., DUDEK, A. (2008) <doi:10.1007/978-3-540-78246-9_11>).

Maintained by Andrzej Dudek. Last updated 7 months ago.

cpp

21.2 match 2 stars 6.35 score 512 scripts 9 dependents

riazakhan94

loadshaper:Producing Load Shape with Target Peak and Load Factor

Modifying a load shape to match specific peak and load factor is a fundamental component for various power system planning and operation studies. This package is an efficient tool to modify a reference load shape while matching the desired peak and load factor. The package offers both linear and non-linear method, described in <https://rpubs.com/riazakhan94/load_shape_match_peak_energy>. The user can control the shape of the final load shape by regulating certain parameters. The package provides validation metrics for assessing the derived load shape in terms of preserving time series properties. It also offers powerful graphics, that allows the user to visually assess the derived load shape.

Maintained by Md Riaz Ahmed Khan. Last updated 3 years ago.

32.6 match 3.70 score 2 scripts

alarm-redist

redist:Simulation Methods for Legislative Redistricting

Enables researchers to sample redistricting plans from a pre-specified target distribution using Sequential Monte Carlo and Markov Chain Monte Carlo algorithms. The package allows for the implementation of various constraints in the redistricting process such as geographic compactness and population parity requirements. Tools for analysis such as computation of various summary statistics and plotting functionality are also included. The package implements the SMC algorithm of McCartan and Imai (2023) <doi:10.1214/23-AOAS1763>, the enumeration algorithm of Fifield, Imai, Kawahara, and Kenny (2020) <doi:10.1080/2330443X.2020.1791773>, the Flip MCMC algorithm of Fifield, Higgins, Imai and Tarr (2020) <doi:10.1080/10618600.2020.1739532>, the Merge-split/Recombination algorithms of Carter et al. (2019) <arXiv:1911.01503> and DeFord et al. (2021) <doi:10.1162/99608f92.eb30390f>, and the Short-burst optimization algorithm of Cannon et al. (2020) <arXiv:2011.02288>.

Maintained by Christopher T. Kenny. Last updated 2 months ago.

geospatial gerrymandering redistricting sampling openblas cpp openmp

12.7 match 69 stars 9.18 score 259 scripts

csdaw

ggprism:A 'ggplot2' Extension Inspired by 'GraphPad Prism'

Provides various themes, palettes, and other functions that are used to customise ggplots to look like they were made in 'GraphPad Prism'. The 'Prism'-look is achieved with theme_prism() and scale_fill|colour_prism(), axes can be changed with custom guides like guide_prism_minor(), and significance indicators added with add_pvalue().

Maintained by Charlotte Dawson. Last updated 1 years ago.

ggplot-extension ggplot2 prism

9.8 match 175 stars 10.56 score 1.1k scripts 5 dependents

amalan-constat

fitODBOD:Modeling Over Dispersed Binomial Outcome Data Using BMD and ABD

Contains Probability Mass Functions, Cumulative Mass Functions, Negative Log Likelihood value, parameter estimation and modeling data using Binomial Mixture Distributions (BMD) (Manoj et al (2013) <doi:10.5539/ijsp.v2n2p24>) and Alternate Binomial Distributions (ABD) (Paul (1985) <doi:10.1080/03610928508828990>), also Journal article to use the package(<doi:10.21105/joss.01505>).

Maintained by Amalan Mahendran. Last updated 4 months ago.

binomial-outcome-data overdispersion

21.5 match 1 stars 4.44 score 139 scripts

r-transit

tidytransit:Read, Validate, Analyze, and Map GTFS Feeds

Read General Transit Feed Specification (GTFS) zipfiles into a list of R dataframes. Perform validation of the data structure against the specification. Analyze the headways and frequencies at routes and stops. Create maps and perform spatial analysis on the routes and stops. Please see the GTFS documentation here for more detail: <https://gtfs.org/>.

Maintained by Flavio Poletti. Last updated 2 months ago.

gtfs public public-transport tidyverse transit transit-data transport transportation

8.8 match 151 stars 10.47 score 272 scripts 1 dependents

r-lib

textshaping:Bindings to the 'HarfBuzz' and 'Fribidi' Libraries for Text Shaping

Provides access to the text shaping functionality in the 'HarfBuzz' library and the bidirectional algorithm in the 'Fribidi' library. 'textshaping' is a low-level utility package mainly for graphic devices that expands upon the font tool-set provided by the 'systemfonts' package.

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

harfbuzz freetype fribidi cpp

6.7 match 19 stars 13.58 score 66 scripts 484 dependents

asardaes

dtwclust:Time Series Clustering Along with Optimizations for the Dynamic Time Warping Distance

Time series clustering along with optimized techniques related to the Dynamic Time Warping distance and its corresponding lower bounds. Implementations of partitional, hierarchical, fuzzy, k-Shape and TADPole clustering are available. Functionality can be easily extended with custom distance measures and centroid definitions. Implementations of DTW barycenter averaging, a distance based on global alignment kernels, and the soft-DTW distance and centroid routines are also provided. All included distance functions have custom loops optimized for the calculation of cross-distance matrices, including parallelization support. Several cluster validity indices are included.

Maintained by Alexis Sarda. Last updated 8 months ago.

clustering dtw time-series openblas cpp

7.1 match 262 stars 12.35 score 406 scripts 14 dependents

bioc

CAGEfightR:Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor

CAGE is a widely used high throughput assay for measuring transcription start site (TSS) activity. CAGEfightR is an R/Bioconductor package for performing a wide range of common data analysis tasks for CAGE and 5'-end data in general. Core functionality includes: import of CAGE TSSs (CTSSs), tag (or unidirectional) clustering for TSS identification, bidirectional clustering for enhancer identification, annotation with transcript and gene models, correlation of TSS and enhancer expression, calculation of TSS shapes, quantification of CAGE expression as expression matrices and genome brower visualization.

Maintained by Malte Thodberg. Last updated 5 months ago.

software transcription coverage geneexpression generegulation peakdetection dataimport datarepresentation transcriptomics sequencing annotation genomebrowsers normalization preprocessing visualization

11.4 match 8 stars 7.46 score 67 scripts 1 dependents

swsoyee

r3dmol:Create Interactive 3D Visualizations of Molecular Data

Create rich and fully interactive 3D visualizations of molecular data. Visualizations can be included in Shiny apps and R markdown documents, or viewed from the R console and 'RStudio' Viewer. 'r3dmol' includes an extensive API to manipulate the visualization after creation, and supports getting data out of the visualization into R. Based on the '3dmol.js' and the 'htmlwidgets' R package.

Maintained by Wei Su. Last updated 1 years ago.

3d computational-biology computational-chemistry hacktoberfest htmlwidgets molecular-graphics molecular-modeling protein protein-structure visualization

13.3 match 90 stars 6.35 score 166 scripts 1 dependents

mlverse

torch:Tensors and Neural Networks with 'GPU' Acceleration

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

Maintained by Daniel Falbel. Last updated 6 days ago.

autograd deep-learning torch cpp

5.0 match 521 stars 16.50 score 1.4k scripts 39 dependents

ms609

TreeTools:Create, Modify and Analyse Phylogenetic Trees

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

Maintained by Martin R. Smith. Last updated 7 days ago.

evolutionary-biology phylogenetic-trees phylogenetics cpp

8.0 match 23 stars 9.83 score 124 scripts 10 dependents

thomasp85

transformr:Polygon and Path Transformations

In order to smoothly animate the transformation of polygons and paths, many aspects needs to be taken into account, such as differing number of control points, changing center of rotation, etc. The 'transformr' package provides an extensive framework for manipulating the shapes of polygons and paths and can be seen as the spatial brother to the 'tweenr' package.

Maintained by Thomas Lin Pedersen. Last updated 1 years ago.

animation data-visualization interpolation matching-shapes tweening cpp

8.0 match 116 stars 9.81 score 772 scripts 26 dependents

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 6 months ago.

geomorphometry geoprocessing geospatial gis hydrology remote-sensing rstudio

8.1 match 173 stars 9.65 score 203 scripts 2 dependents

xliaosdsu

coneproj:Primal or Dual Cone Projections with Routines for Constrained Regression

Routines doing cone projection and quadratic programming, as well as doing estimation and inference for constrained parametric regression and shape-restricted regression problems. See Mary C. Meyer (2013)<doi:10.1080/03610918.2012.659820> for more details.

Maintained by Xiyue Liao. Last updated 1 months ago.

openblas cpp

16.4 match 2 stars 4.75 score 21 scripts 21 dependents

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 1 months ago.

9.0 match 13 stars 8.63 score 546 scripts

gamlss-dev

gamlss:Generalized Additive Models for Location Scale and Shape

Functions for fitting the Generalized Additive Models for Location Scale and Shape introduced by Rigby and Stasinopoulos (2005), <doi:10.1111/j.1467-9876.2005.00510.x>. The models use a distributional regression approach where all the parameters of the conditional distribution of the response variable are modelled using explanatory variables.

Maintained by Mikis Stasinopoulos. Last updated 4 months ago.

6.9 match 18 stars 11.19 score 2.0k scripts 48 dependents

yunuuuu

ggalign:A 'ggplot2' Extension for Consistent Axis Alignment

A 'ggplot2' extension offers various tools the creation of complex, multi-plot visualizations. Built on the familiar grammar of graphics, it provides intuitive tools to align and organize plots, making it ideal for complex visualizations. It excels in multi-omics research—such as genomics and microbiomes—by simplifying the visualization of intricate relationships between datasets, for example, linking genes to pathways. Whether you need to stack plots, arrange them around a central figure, or create a circular layout, 'ggalign' delivers flexibility and accuracy with minimal effort.

Maintained by Yun Peng. Last updated 16 days ago.

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

10.9 match 267 stars 7.08 score 27 scripts

brandmaier

pdc:Permutation Distribution Clustering

Permutation Distribution Clustering is a clustering method for time series. Dissimilarity of time series is formalized as the divergence between their permutation distributions. The permutation distribution was proposed as measure of the complexity of a time series.

Maintained by Andreas M. Brandmaier. Last updated 2 years ago.

13.4 match 6 stars 5.61 score 25 scripts 9 dependents

jfrench

smerc:Statistical Methods for Regional Counts

Implements statistical methods for analyzing the counts of areal data, with a focus on the detection of spatial clusters and clustering. The package has a heavy emphasis on spatial scan methods, which were first introduced by Kulldorff and Nagarwalla (1995) <doi:10.1002/sim.4780140809> and Kulldorff (1997) <doi:10.1080/03610929708831995>.

Maintained by Joshua French. Last updated 5 months ago.

cpp

12.2 match 3 stars 6.08 score 45 scripts 3 dependents

jdtuck

fdasrvf:Elastic Functional Data Analysis

Performs alignment, PCA, and modeling of multidimensional and unidimensional functions using the square-root velocity framework (Srivastava et al., 2011 <doi:10.48550/arXiv.1103.3817> and Tucker et al., 2014 <DOI:10.1016/j.csda.2012.12.001>). This framework allows for elastic analysis of functional data through phase and amplitude separation.

Maintained by J. Derek Tucker. Last updated 1 months ago.

openblas cpp openmp

9.4 match 13 stars 7.79 score 83 scripts 3 dependents

ludvigolsen

rearrr:Rearranging Data

Arrange data by a set of methods. Use rearrangers to reorder data points and mutators to change their values. From basic utilities, to centering the greatest value, to swirling in 3-dimensional space, 'rearrr' enables creativity when plotting and experimenting with data.

Maintained by Ludvig Renbo Olsen. Last updated 25 days ago.

arrange cluster expand forming generate ggplot2 order plotting-in-r roll rotate shaping swirl transformations

10.0 match 24 stars 7.26 score 128 scripts 8 dependents

r-tmap

tmaptools:Thematic Map Tools

Set of tools for reading and processing spatial data. The aim is to supply the workflow to create thematic maps. This package also facilitates 'tmap', the package for visualizing thematic maps.

Maintained by Martijn Tennekes. Last updated 3 months ago.

6.1 match 42 stars 11.67 score 1.8k scripts 26 dependents

r-forge

distr:Object Oriented Implementation of Distributions

S4-classes and methods for distributions.

Maintained by Peter Ruckdeschel. Last updated 2 months ago.

8.1 match 8.77 score 327 scripts 32 dependents

christopherkenny

geomander:Geographic Tools for Studying Gerrymandering

A compilation of tools to complete common tasks for studying gerrymandering. This focuses on the geographic tool side of common problems, such as linking different levels of spatial units or estimating how to break up units. Functions exist for creating redistricting-focused data for the US.

Maintained by Christopher T. Kenny. Last updated 1 months ago.

cpp

9.1 match 14 stars 7.81 score 191 scripts 1 dependents

cran

ICSNP:Tools for Multivariate Nonparametrics

Tools for multivariate nonparametrics, as location tests based on marginal ranks, spatial median and spatial signs computation, Hotelling's T-test, estimates of shape are implemented.

Maintained by Klaus Nordhausen. Last updated 2 years ago.

cpp

16.8 match 3.84 score 14 dependents

thomasp85

ggraph:An Implementation of Grammar of Graphics for Graphs and Networks

The grammar of graphics as implemented in ggplot2 is a poor fit for graph and network visualizations due to its reliance on tabular data input. ggraph is an extension of the ggplot2 API tailored to graph visualizations and provides the same flexible approach to building up plots layer by layer.

Maintained by Thomas Lin Pedersen. Last updated 1 years ago.

ggplot-extension ggplot2 graph-visualization network-visualization visualization cpp

3.8 match 1.1k stars 16.96 score 9.2k scripts 111 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.

14.4 match 9 stars 4.45 score 21 scripts

openanalytics

clinUtils:General Utility Functions for Analysis of Clinical Data

Utility functions to facilitate the import, the reporting and analysis of clinical data. Example datasets in 'SDTM' and 'ADaM' format, containing a subset of patients/domains from the 'CDISC Pilot 01 study' are also available as R datasets to demonstrate the package functionalities.

Maintained by Laure Cougnaud. Last updated 11 months ago.

9.4 match 3 stars 6.78 score 105 scripts 3 dependents

eagerai

fastai:Interface to 'fastai'

The 'fastai' <https://docs.fast.ai/index.html> library simplifies training fast and accurate neural networks using modern best practices. It is based on research in to deep learning best practices undertaken at 'fast.ai', including 'out of the box' support for vision, text, tabular, audio, time series, and collaborative filtering models.

Maintained by Turgut Abdullayev. Last updated 12 months ago.

audio collaborative-filtering darknet darknet-image-classification fastai medical object-detection tabular text vision

6.6 match 118 stars 9.40 score 76 scripts

gmcmacran

LRTesteR:Likelihood Ratio Tests and Confidence Intervals

A collection of hypothesis tests and confidence intervals based on the likelihood ratio <https://en.wikipedia.org/wiki/Likelihood-ratio_test>.

Maintained by Greg McMahan. Last updated 7 months ago.

10.4 match 5.83 score 168 scripts

estfernan

SAFARI:Shape Analysis for AI-Reconstructed Images

Provides functionality for image processing and shape analysis in the context of reconstructed medical images generated by deep learning-based methods or standard image processing algorithms and produced from different medical imaging types, such as X-ray, Computational Tomography (CT), Magnetic Resonance Imaging (MRI), and pathology imaging. Specifically, offers tools to segment regions of interest and to extract quantitative shape descriptors for applications in signal processing, statistical analysis and modeling, and machine learning.

Maintained by Esteban Fernandez. Last updated 3 years ago.

reconstructed-images shape-analysis

15.3 match 2 stars 3.90 score 6 scripts

animint

animint2:Animated Interactive Grammar of Graphics

Functions are provided for defining animated, interactive data visualizations in R code, and rendering on a web page. The 2018 Journal of Computational and Graphical Statistics paper, <doi:10.1080/10618600.2018.1513367> describes the concepts implemented.

Maintained by Toby Hocking. Last updated 1 months ago.

6.6 match 64 stars 8.84 score 173 scripts

cran

scam:Shape Constrained Additive Models

Generalized additive models under shape constraints on the component functions of the linear predictor. Models can include multiple shape-constrained (univariate and bivariate) and unconstrained terms. Routines of the package 'mgcv' are used to set up the model matrix, print, and plot the results. Multiple smoothing parameter estimation by the Generalized Cross Validation or similar. See Pya and Wood (2015) <doi:10.1007/s11222-013-9448-7> for an overview. A broad selection of shape-constrained smoothers, linear functionals of smooths with shape constraints, and Gaussian models with AR1 residuals.

Maintained by Natalya Pya. Last updated 2 months ago.

11.1 match 5 stars 5.24 score 24 dependents

peter-t-ruehr

forceR:Force Measurement Analyses

For cleaning and analysis of graphs, such as animal closing force measurements. 'forceR' was initially written and optimized to deal with insect bite force measurements, but can be used for any time series. Includes a full workflow to load, plot and crop data, correct amplifier and baseline drifts, identify individual peak shapes (bites), rescale (normalize) peak curves, and find best polynomial fits to describe and analyze force curve shapes.

Maintained by Peter T. Rühr. Last updated 1 years ago.

15.5 match 3.70 score 10 scripts

mhahsler

dbscan:Density-Based Spatial Clustering of Applications with Noise (DBSCAN) and Related Algorithms

A fast reimplementation of several density-based algorithms of the DBSCAN family. Includes the clustering algorithms DBSCAN (density-based spatial clustering of applications with noise) and HDBSCAN (hierarchical DBSCAN), the ordering algorithm OPTICS (ordering points to identify the clustering structure), shared nearest neighbor clustering, and the outlier detection algorithms LOF (local outlier factor) and GLOSH (global-local outlier score from hierarchies). The implementations use the kd-tree data structure (from library ANN) for faster k-nearest neighbor search. An R interface to fast kNN and fixed-radius NN search is also provided. Hahsler, Piekenbrock and Doran (2019) <doi:10.18637/jss.v091.i01>.

Maintained by Michael Hahsler. Last updated 2 months ago.

clustering dbscan density-based-clustering hdbscan lof optics cpp

3.6 match 324 stars 15.60 score 1.6k scripts 85 dependents

hzhanghenry

RCircos:Circos 2D Track Plot

A simple and flexible way to generate Circos 2D track plot images for genomic data visualization is implemented in this package. The types of plots include: heatmap, histogram, lines, scatterplot, tiles and plot items for further decorations include connector, link (lines and ribbons), and text (gene) label. All functions require only R graphics package that comes with R base installation.

Maintained by Hongen Zhang. Last updated 3 years ago.

7.5 match 6 stars 7.21 score 298 scripts 3 dependents

gamlss-dev

gamlss.dist:Distributions for Generalized Additive Models for Location Scale and Shape

A set of distributions which can be used for modelling the response variables in Generalized Additive Models for Location Scale and Shape, Rigby and Stasinopoulos (2005), <doi:10.1111/j.1467-9876.2005.00510.x>. The distributions can be continuous, discrete or mixed distributions. Extra distributions can be created, by transforming, any continuous distribution defined on the real line, to a distribution defined on ranges 0 to infinity or 0 to 1, by using a 'log' or a 'logit' transformation respectively.

Maintained by Mikis Stasinopoulos. Last updated 1 months ago.

5.1 match 4 stars 10.51 score 346 scripts 71 dependents

cran

matRiks:Generates Raven-Like Matrices According to Rules

Generates Raven like matrices according to different rules and the response list associated to the matrix. The package can generate matrices composed of 4 or 9 cells, along with a response list of 11 elements (the correct response + 10 incorrect responses). The matrices can be generated according to both logical rules (i.e., the relationships between the elements in the matrix are manipulated to create the matrix) and visual-spatial rules (i.e., the visual or spatial characteristics of the elements are manipulated to generate the matrix). The graphical elements of this package are based on the 'DescTools' package. This package has been developed within the PRIN2020 Project (Prot. 20209WKCLL) titled "Computerized, Adaptive and Personalized Assessment of Executive Functions and Fluid Intelligence" and founded by the Italian Ministry of Education and Research.

Maintained by Andrea Brancaccio. Last updated 1 years ago.

14.8 match 3.60 score

haghish

shapley:Weighted Mean SHAP and CI for Robust Feature Assessment in ML Grid

This R package introduces Weighted Mean SHapley Additive exPlanations (WMSHAP), an innovative method for calculating SHAP values for a grid of fine-tuned base-learner machine learning models as well as stacked ensembles, a method not previously available due to the common reliance on single best-performing models. By integrating the weighted mean SHAP values from individual base-learners comprising the ensemble or individual base-learners in a tuning grid search, the package weights SHAP contributions according to each model's performance, assessed by multiple either R squared (for both regression and classification models). alternatively, this software also offers weighting SHAP values based on the area under the precision-recall curve (AUCPR), the area under the curve (AUC), and F2 measures for binary classifiers. It further extends this framework to implement weighted confidence intervals for weighted mean SHAP values, offering a more comprehensive and robust feature importance evaluation over a grid of machine learning models, instead of solely computing SHAP values for the best model. This methodology is particularly beneficial for addressing the severe class imbalance (class rarity) problem by providing a transparent, generalized measure of feature importance that mitigates the risk of reporting SHAP values for an overfitted or biased model and maintains robustness under severe class imbalance, where there is no universal criteria of identifying the absolute best model. Furthermore, the package implements hypothesis testing to ascertain the statistical significance of SHAP values for individual features, as well as comparative significance testing of SHAP contributions between features. Additionally, it tackles a critical gap in feature selection literature by presenting criteria for the automatic feature selection of the most important features across a grid of models or stacked ensembles, eliminating the need for arbitrary determination of the number of top features to be extracted. This utility is invaluable for researchers analyzing feature significance, particularly within severely imbalanced outcomes where conventional methods fall short. Moreover, it is also expected to report democratic feature importance across a grid of models, resulting in a more comprehensive and generalizable feature selection. The package further implements a novel method for visualizing SHAP values both at subject level and feature level as well as a plot for feature selection based on the weighted mean SHAP ratios.

Maintained by E. F. Haghish. Last updated 13 days ago.

class-imbalance class-imbalance-problem feature-extraction feature-importance feature-selection machine-learning machine-learning-algorithms shap shap-analysis shap-values shapely shapley-additive-explanations shapley-decomposition shapley-value shapley-values shapleyvalue weighted-shap weighted-shap-confidence-interval weighted-shapley weighted-shapley-ci

10.0 match 15 stars 5.25 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 4 days ago.

openblas fftw3 cpp openmp

7.7 match 11 stars 6.76 score 476 scripts

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 8 days ago.

libx11 fftw3 tiff cpp openmp

3.8 match 17 stars 13.53 score 2.4k scripts 44 dependents

rstudio

tensorflow:R Interface to 'TensorFlow'

Interface to 'TensorFlow' <https://www.tensorflow.org/>, an open source software library for numerical computation using data flow graphs. Nodes in the graph represent mathematical operations, while the graph edges represent the multidimensional data arrays (tensors) communicated between them. The flexible architecture allows you to deploy computation to one or more 'CPUs' or 'GPUs' in a desktop, server, or mobile device with a single 'API'. 'TensorFlow' was originally developed by researchers and engineers working on the Google Brain Team within Google's Machine Intelligence research organization for the purposes of conducting machine learning and deep neural networks research, but the system is general enough to be applicable in a wide variety of other domains as well.

Maintained by Tomasz Kalinowski. Last updated 5 days ago.

3.3 match 1.3k stars 15.47 score 3.2k scripts 75 dependents

kassambara

factoextra:Extract and Visualize the Results of Multivariate Data Analyses

Provides some easy-to-use functions to extract and visualize the output of multivariate data analyses, including 'PCA' (Principal Component Analysis), 'CA' (Correspondence Analysis), 'MCA' (Multiple Correspondence Analysis), 'FAMD' (Factor Analysis of Mixed Data), 'MFA' (Multiple Factor Analysis) and 'HMFA' (Hierarchical Multiple Factor Analysis) functions from different R packages. It contains also functions for simplifying some clustering analysis steps and provides 'ggplot2' - based elegant data visualization.

Maintained by Alboukadel Kassambara. Last updated 5 years ago.

3.6 match 363 stars 14.13 score 15k scripts 52 dependents

jmadinlab

habtools:Tools and Metrics for 3D Surfaces and Objects

A collection of functions for sampling and simulating 3D surfaces and objects and estimating metrics like rugosity, fractal dimension, convexity, sphericity, circularity, second moments of area and volume, and more.

Maintained by Nina Schiettekatte. Last updated 26 days ago.

8.3 match 12 stars 6.10 score 9 scripts

rrwen

draw:Wrapper Functions for Producing Graphics

A set of user-friendly wrapper functions for creating consistent graphics and diagrams with lines, common shapes, text, and page settings. Compatible with and based on the R 'grid' package.

Maintained by Richard Wen. Last updated 7 years ago.

box circle curve diagram draw graphics grid line page rectangle reproducible shape square text triangle

11.5 match 2 stars 4.39 score 35 scripts

beatrizpateiro

alphashape3d:Implementation of the 3D Alpha-Shape for the Reconstruction of 3D Sets from a Point Cloud

Implementation in R of the alpha-shape of a finite set of points in the three-dimensional space. The alpha-shape generalizes the convex hull and allows to recover the shape of non-convex and even non-connected sets in 3D, given a random sample of points taken into it. Besides the computation of the alpha-shape, this package provides users with functions to compute the volume of the alpha-shape, identify the connected components and facilitate the three-dimensional graphical visualization of the estimated set.

Maintained by Beatriz Pateiro-Lopez. Last updated 2 years ago.

9.5 match 2 stars 5.34 score 82 scripts 5 dependents

trafficonese

leaflet.extras:Extra Functionality for 'leaflet' Package

The 'leaflet' JavaScript library provides many plugins some of which are available in the core 'leaflet' package, but there are many more. It is not possible to support them all in the core 'leaflet' package. This package serves as an add-on to the 'leaflet' package by providing extra functionality via 'leaflet' plugins.

Maintained by Sebastian Gatscha. Last updated 3 months ago.

data-visualization geospatial leaflet

3.8 match 218 stars 13.27 score 2.5k scripts 25 dependents

rstudio

tfdatasets:Interface to 'TensorFlow' Datasets

Interface to 'TensorFlow' Datasets, a high-level library for building complex input pipelines from simple, re-usable pieces. See <https://www.tensorflow.org/guide> for additional details.

Maintained by Tomasz Kalinowski. Last updated 20 days ago.

5.3 match 34 stars 9.32 score 656 scripts 3 dependents

nschiett

fishualize:Color Palettes Based on Fish Species

Implementation of color palettes based on fish species.

Maintained by Nina M. D. Schiettekatte. Last updated 11 months ago.

5.5 match 154 stars 8.53 score 370 scripts

robinhankin

permutations:The Symmetric Group: Permutations of a Finite Set

Manipulates invertible functions from a finite set to itself. Can transform from word form to cycle form and back. To cite the package in publications please use Hankin (2020) "Introducing the permutations R package", SoftwareX, volume 11 <doi:10.1016/j.softx.2020.100453>.

Maintained by Robin K. S. Hankin. Last updated 2 months ago.

5.6 match 6 stars 8.23 score 49 scripts 2 dependents

dbosak01

procs:Recreates Some 'SAS®' Procedures in 'R'

Contains functions to simulate the most commonly used 'SAS®' procedures. Specifically, the package aims to simulate the functionality of 'proc freq', 'proc means', 'proc ttest', 'proc reg', 'proc transpose', 'proc sort', and 'proc print'. The simulation will include recreating all statistics with the highest fidelity possible.

Maintained by David Bosak. Last updated 10 months ago.

6.0 match 6 stars 7.57 score 37 scripts 2 dependents

martin3141

spant:MR Spectroscopy Analysis Tools

Tools for reading, visualising and processing Magnetic Resonance Spectroscopy data. The package includes methods for spectral fitting: Wilson (2021) <DOI:10.1002/mrm.28385> and spectral alignment: Wilson (2018) <DOI:10.1002/mrm.27605>.

Maintained by Martin Wilson. Last updated 4 days ago.

brain mri mrs mrshub spectroscopy fortran

5.3 match 25 stars 8.52 score 81 scripts

wjbraun

DAAG:Data Analysis and Graphics Data and Functions

Functions and data sets used in examples and exercises in the text Maindonald, J.H. and Braun, W.J. (2003, 2007, 2010) "Data Analysis and Graphics Using R", and in an upcoming Maindonald, Braun, and Andrews text that builds on this earlier text.

Maintained by W. John Braun. Last updated 12 months ago.

5.4 match 8.35 score 1.2k scripts 1 dependents

rstudio

tfprobability:Interface to 'TensorFlow Probability'

Interface to 'TensorFlow Probability', a 'Python' library built on 'TensorFlow' that makes it easy to combine probabilistic models and deep learning on modern hardware ('TPU', 'GPU'). 'TensorFlow Probability' includes a wide selection of probability distributions and bijectors, probabilistic layers, variational inference, Markov chain Monte Carlo, and optimizers such as Nelder-Mead, BFGS, and SGLD.

Maintained by Tomasz Kalinowski. Last updated 3 years ago.

5.2 match 54 stars 8.63 score 221 scripts 3 dependents

xiangpin

ggstar:Multiple Geometric Shape Point Layer for 'ggplot2'

To create the multiple polygonal point layer for easily discernible shapes, we developed the package, it is like the 'geom_point' of 'ggplot2'. It can be used to draw the scatter plot.

Maintained by Shuangbin Xu. Last updated 12 months ago.

5.3 match 101 stars 8.22 score 282 scripts 3 dependents

ashenoy-cmbi

grafify:Easy Graphs for Data Visualisation and Linear Models for ANOVA

Easily explore data by plotting graphs with a few lines of code. Use these ggplot() wrappers to quickly draw graphs of scatter/dots with box-whiskers, violins or SD error bars, data distributions, before-after graphs, factorial ANOVA and more. Customise graphs in many ways, for example, by choosing from colour blind-friendly palettes (12 discreet, 3 continuous and 2 divergent palettes). Use the simple code for ANOVA as ordinary (lm()) or mixed-effects linear models (lmer()), including randomised-block or repeated-measures designs, and fit non-linear outcomes as a generalised additive model (gam) using mgcv(). Obtain estimated marginal means and perform post-hoc comparisons on fitted models (via emmeans()). Also includes small datasets for practising code and teaching basics before users move on to more complex designs. See vignettes for details on usage <https://grafify.shenoylab.com/>. Citation: <doi:10.5281/zenodo.5136508>.

Maintained by Avinash R Shenoy. Last updated 17 days ago.

ggplot2 linear-models post-hoc-comparisons statistics vignettes

8.2 match 48 stars 5.31 score 107 scripts

mrc-ide

EpiEstim:Estimate Time Varying Reproduction Numbers from Epidemic Curves

Tools to quantify transmissibility throughout an epidemic from the analysis of time series of incidence as described in Cori et al. (2013) <doi:10.1093/aje/kwt133> and Wallinga and Teunis (2004) <doi:10.1093/aje/kwh255>.

Maintained by Anne Cori. Last updated 7 months ago.

3.6 match 95 stars 12.06 score 1.0k scripts 7 dependents

alexkowa

EnvStats:Package for Environmental Statistics, Including US EPA Guidance

Graphical and statistical analyses of environmental data, with focus on analyzing chemical concentrations and physical parameters, usually in the context of mandated environmental monitoring. Major environmental statistical methods found in the literature and regulatory guidance documents, with extensive help that explains what these methods do, how to use them, and where to find them in the literature. Numerous built-in data sets from regulatory guidance documents and environmental statistics literature. Includes scripts reproducing analyses presented in the book "EnvStats: An R Package for Environmental Statistics" (Millard, 2013, Springer, ISBN 978-1-4614-8455-4, <doi:10.1007/978-1-4614-8456-1>).

Maintained by Alexander Kowarik. Last updated 22 hours ago.

3.3 match 26 stars 12.85 score 2.4k scripts 47 dependents

flr

FLa4a:A Simple and Robust Statistical Catch at Age Model

A simple and robust statistical Catch at Age model that is specifically designed for stocks with intermediate levels of data quantity and quality.

Maintained by Ernesto Jardim. Last updated 11 days ago.

6.3 match 12 stars 6.71 score 177 scripts 2 dependents

cran

MASS:Support Functions and Datasets for Venables and Ripley's MASS

Functions and datasets to support Venables and Ripley, "Modern Applied Statistics with S" (4th edition, 2002).

Maintained by Brian Ripley. Last updated 1 months ago.

4.0 match 19 stars 10.64 score 11k dependents

ishidamgm

TreeRingShape:Recording Tree-Ring Shapes of Tree Disks with Manual Digitizing and Interpolating Model

Record all tree-ring Shapefile of tree disk with GIS soft ('Qgis'<https://www.qgis.org/en/site/>) and interpolating model from high resolution tree disk image.

Maintained by Megumi ISHIDA. Last updated 5 months ago.

9.4 match 4.48 score

r-forge

distrEx:Extensions of Package 'distr'

Extends package 'distr' by functionals, distances, and conditional distributions.

Maintained by Matthias Kohl. Last updated 2 months ago.

6.3 match 6.64 score 107 scripts 17 dependents

jonesor

Rage:Life History Metrics from Matrix Population Models

Functions for calculating life history metrics using matrix population models ('MPMs'). Described in Jones et al. (2021) <doi:10.1101/2021.04.26.441330>.

Maintained by Owen Jones. Last updated 3 months ago.

5.1 match 12 stars 8.18 score 62 scripts 1 dependents

bioc

sosta:A package for the analysis of anatomical tissue structures in spatial omics data

sosta (Spatial Omics STructure Analysis) is a package for analyzing spatial omics data to explore tissue organization at the anatomical structure level. It reconstructs morphologically relevant structures based on molecular features or cell types. It further calculates a range of structural and shape metrics to quantitatively describe tissue architecture. The package is designed to integrate with other packages for the analysis of spatial (omics) data.

Maintained by Samuel Gunz. Last updated 11 days ago.

software spatial transcriptomics visualization

7.3 match 1 stars 5.68 score 2 scripts 1 dependents

spatstat

spatstat.data:Datasets for 'spatstat' Family

Contains all the datasets for the 'spatstat' family of packages.

Maintained by Adrian Baddeley. Last updated 15 days ago.

kernel-density point-process spatial-analysis spatial-data spatial-data-analysis spatstat statistical-analysis statistical-methods statistical-tests statistics

3.8 match 6 stars 11.07 score 186 scripts 228 dependents

kurthornik

mlbench:Machine Learning Benchmark Problems

A collection of artificial and real-world machine learning benchmark problems, including, e.g., several data sets from the UCI repository.

Maintained by Kurt Hornik. Last updated 3 months ago.

4.5 match 2 stars 8.98 score 5.0k scripts 54 dependents

jfmunozrosas

giniVarCI:Gini Indices, Variances and Confidence Intervals for Finite and Infinite Populations

Estimates the Gini index and computes variances and confidence intervals for finite and infinite populations, using different methods; also computes Gini index for continuous probability distributions, draws samples from continuous probability distributions with Gini indices set by the user; uses 'Rcpp'. References: Muñoz et al. (2023) <doi:10.1177/00491241231176847>. Álvarez et al. (2021) <doi:10.3390/math9243252>. Giorgi and Gigliarano (2017) <doi:10.1111/joes.12185>. Langel and Tillé (2013) <doi:10.1111/j.1467-985X.2012.01048.x>.

Maintained by Juan Francisco Muñoz. Last updated 1 years ago.

cpp

20.0 match 2.00 score

r-lib

scales:Scale Functions for Visualization

Graphical scales map data to aesthetics, and provide methods for automatically determining breaks and labels for axes and legends.

Maintained by Thomas Lin Pedersen. Last updated 5 months ago.

ggplot2

2.0 match 418 stars 19.90 score 88k scripts 8.0k dependents

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

6.1 match 68 stars 6.49 score 15 scripts

cran

ashapesampler:Generating Alpha Shapes

Understanding morphological variation is an important task in many applications. Recent studies in computational biology have focused on developing computational tools for the task of sub-image selection which aims at identifying structural features that best describe the variation between classes of shapes. A major part in assessing the utility of these approaches is to demonstrate their performance on both simulated and real datasets. However, when creating a model for shape statistics, real data can be difficult to access and the sample sizes for these data are often small due to them being expensive to collect. Meanwhile, the landscape of current shape simulation methods has been mostly limited to approaches that use black-box inference---making it difficult to systematically assess the power and calibration of sub-image models. In this R package, we introduce the alpha-shape sampler: a probabilistic framework for simulating realistic 2D and 3D shapes based on probability distributions which can be learned from real data or explicitly stated by the user. The 'ashapesampler' package supports two mechanisms for sampling shapes in two and three dimensions. The first, empirically sampling based on an existing data set, was highlighted in the original main text of the paper. The second, probabilistic sampling from a known distribution, is the computational implementation of the theory derived in that paper. Work based on Winn-Nunez et al. (2024) <doi:10.1101/2024.01.09.574919>.

Maintained by Emily Winn-Nunez. Last updated 1 years ago.

11.9 match 3.30 score

freezenik

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

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

Maintained by Nikolaus Umlauf. Last updated 6 months ago.

openblas

6.8 match 1 stars 5.76 score 239 scripts 5 dependents

corradolanera

CrossClustering:A Partial Clustering Algorithm

Provide the 'CrossClustering' algorithm (Tellaroli et al. (2016) <doi:10.1371/journal.pone.0152333>), which is a partial clustering algorithm that combines the Ward's minimum variance and Complete Linkage algorithms, providing automatic estimation of a suitable number of clusters and identification of outlier elements.

Maintained by Paola Tellaroli. Last updated 11 months ago.

10.6 match 1 stars 3.59 score 39 scripts

ropensci

pathviewr:Wrangle, Analyze, and Visualize Animal Movement Data

Tools to import, clean, and visualize movement data, particularly from motion capture systems such as Optitrack's 'Motive', the Straw Lab's 'Flydra', or from other sources. We provide functions to remove artifacts, standardize tunnel position and tunnel axes, select a region of interest, isolate specific trajectories, fill gaps in trajectory data, and calculate 3D and per-axis velocity. For experiments of visual guidance, we also provide functions that use subject position to estimate perception of visual stimuli.

Maintained by Vikram B. Baliga. Last updated 2 years ago.

animal-movement flydra motion movement-data optitrack trajectories trajectory-analysis visual-guidance visual-perception

5.8 match 8 stars 6.56 score 102 scripts

bioc

Rgraphviz:Provides plotting capabilities for R graph objects

Interfaces R with the AT and T graphviz library for plotting R graph objects from the graph package.

Maintained by Kasper Daniel Hansen. Last updated 6 days ago.

graphandnetwork visualization zlib

3.3 match 11.51 score 1.2k scripts 107 dependents

beatrizpateiro

alphahull:Generalization of the Convex Hull of a Sample of Points in the Plane

Computation of the alpha-shape and alpha-convex hull of a given sample of points in the plane. The concepts of alpha-shape and alpha-convex hull generalize the definition of the convex hull of a finite set of points. The programming is based on the duality between the Voronoi diagram and Delaunay triangulation. The package also includes a function that returns the Delaunay mesh of a given sample of points and its dual Voronoi diagram in one single object.

Maintained by Beatriz Pateiro-Lopez. Last updated 2 years ago.

4.8 match 1 stars 7.90 score 251 scripts 12 dependents

stla

syt:Young Tableaux

Deals with Young tableaux (field of combinatorics). For standard Young tabeaux, performs enumeration, counting, random generation, the Robinson-Schensted correspondence, and conversion to and from paths on the Young lattice. Also performs enumeration and counting of semistandard Young tableaux, enumeration of skew semistandard Young tableaux, enumeration of Gelfand-Tsetlin patterns, and computation of Kostka numbers.

Maintained by Stéphane Laurent. Last updated 8 months ago.

combinatorics young-tableaux

7.6 match 3 stars 4.94 score 24 scripts 1 dependents

kgoldfeld

simstudy:Simulation of Study Data

Simulates data sets in order to explore modeling techniques or better understand data generating processes. The user specifies a set of relationships between covariates, and generates data based on these specifications. The final data sets can represent data from randomized control trials, repeated measure (longitudinal) designs, and cluster randomized trials. Missingness can be generated using various mechanisms (MCAR, MAR, NMAR).

Maintained by Keith Goldfeld. Last updated 8 months ago.

data-generation data-simulation simulation statistical-models cpp

3.4 match 82 stars 10.90 score 972 scripts 1 dependents

lbbe-software

fitdistrplus:Help to Fit of a Parametric Distribution to Non-Censored or Censored Data

Extends the fitdistr() function (of the MASS package) with several functions to help the fit of a parametric distribution to non-censored or censored data. Censored data may contain left censored, right censored and interval censored values, with several lower and upper bounds. In addition to maximum likelihood estimation (MLE), the package provides moment matching (MME), quantile matching (QME), maximum goodness-of-fit estimation (MGE) and maximum spacing estimation (MSE) methods (available only for non-censored data). Weighted versions of MLE, MME, QME and MSE are available. See e.g. Casella & Berger (2002), Statistical inference, Pacific Grove, for a general introduction to parametric estimation.

Maintained by Aurélie Siberchicot. Last updated 28 days ago.

2.3 match 54 stars 16.15 score 4.5k scripts 153 dependents

signaturescience

rplanes:Plausibility Analysis of Epidemiological Signals

Provides functionality to prepare data and analyze plausibility of both forecasted and reported epidemiological signals. The functions implement a set of plausibility algorithms that are agnostic to geographic and time resolutions and are calculated independently then presented as a combined score.

Maintained by VP Nagraj. Last updated 9 months ago.

6.0 match 9 stars 6.03 score 7 scripts

cran

Anthropometry:Statistical Methods for Anthropometric Data

Statistical methodologies especially developed to analyze anthropometric data. These methods are aimed at providing effective solutions to some commons problems related to Ergonomics and Anthropometry. They are based on clustering, the statistical concept of data depth, statistical shape analysis and archetypal analysis. Please see Vinue (2017) <doi:10.18637/jss.v077.i06>.

Maintained by Guillermo Vinue. Last updated 2 years ago.

13.0 match 1 stars 2.78 score 2 dependents

kwstat

agridat:Agricultural Datasets

Datasets from books, papers, and websites related to agriculture. Example graphics and analyses are included. Data come from small-plot trials, multi-environment trials, uniformity trials, yield monitors, and more.

Maintained by Kevin Wright. Last updated 1 months ago.

data

3.3 match 126 stars 10.78 score 1.7k scripts 1 dependents

biogeomacro

GIFT:Access to the Global Inventory of Floras and Traits (GIFT)

Retrieving regional plant checklists, species traits and distributions, and environmental data from the Global Inventory of Floras and Traits (GIFT). More information about the GIFT database can be found at <https://gift.uni-goettingen.de/about> and the map of available floras can be visualized at <https://gift.uni-goettingen.de/map>. The API and associated queries can be accessed according the following scheme: <https://gift.uni-goettingen.de/api/extended/index2.0.php?query=env_raster>.

Maintained by Pierre Denelle. Last updated 15 days ago.

biodiversity biodiversity-informatics plants-database plants-distribution

5.5 match 18 stars 6.54 score 24 scripts

psolymos

EDMAinR:Euclidean Distance Matrix Analysis in R

A coordinate-free approach for comparing biological shapes using landmark data based on Lele and Richtsmeier (1991) <doi:10.1002/ajpa.1330860307>.

Maintained by Peter Solymos. Last updated 2 years ago.

comparing-biological-shapes coordinate-free landmark-data morphometrics multivariate-statistics

9.4 match 3 stars 3.78 score 9 scripts

davidgohel

officer:Manipulation of Microsoft Word and PowerPoint Documents

Access and manipulate 'Microsoft Word', 'RTF' and 'Microsoft PowerPoint' documents from R. The package focuses on tabular and graphical reporting from R; it also provides two functions that let users get document content into data objects. A set of functions lets add and remove images, tables and paragraphs of text in new or existing documents. The package does not require any installation of Microsoft products to be able to write Microsoft files.

Maintained by David Gohel. Last updated 9 days ago.

ms-office-documents powerpoint word

2.3 match 629 stars 15.85 score 4.1k scripts 142 dependents

green-striped-gecko

dartR:Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Functions are provided that facilitate the import and analysis of 'SNP' (single nucleotide polymorphism) and 'silicodart' (presence/absence) data. The main focus is on data generated by 'DarT' (Diversity Arrays Technology), however, data from other sequencing platforms can be used once 'SNP' or related fragment presence/absence data from any source is imported. Genetic datasets are stored in a derived 'genlight' format (package 'adegenet'), that allows for a very compact storage of data and metadata. Functions are available for importing and exporting of 'SNP' and 'silicodart' data, for reporting on and filtering on various criteria (e.g. 'CallRate', heterozygosity, reproducibility, maximum allele frequency). Additional functions are available for visualization (e.g. Principle Coordinate Analysis) and creating a spatial representation using maps. 'dartR' supports also the analysis of 3rd party software package such as 'newhybrid', 'structure', 'NeEstimator' and 'blast'. Since version 2.0.3 we also implemented simulation functions, that allow to forward simulate 'SNP' dynamics under different population and evolutionary dynamics. Comprehensive tutorials and support can be found at our 'github' repository: github.com/green-striped-gecko/dartR/. If you want to cite 'dartR', you find the information by typing citation('dartR') in the console.

Maintained by Bernd Gruber. Last updated 4 days ago.

4.8 match 34 stars 7.41 score

chrhennig

fpc:Flexible Procedures for Clustering

Various methods for clustering and cluster validation. Fixed point clustering. Linear regression clustering. Clustering by merging Gaussian mixture components. Symmetric and asymmetric discriminant projections for visualisation of the separation of groupings. Cluster validation statistics for distance based clustering including corrected Rand index. Standardisation of cluster validation statistics by random clusterings and comparison between many clustering methods and numbers of clusters based on this. Cluster-wise cluster stability assessment. Methods for estimation of the number of clusters: Calinski-Harabasz, Tibshirani and Walther's prediction strength, Fang and Wang's bootstrap stability. Gaussian/multinomial mixture fitting for mixed continuous/categorical variables. Variable-wise statistics for cluster interpretation. DBSCAN clustering. Interface functions for many clustering methods implemented in R, including estimating the number of clusters with kmeans, pam and clara. Modality diagnosis for Gaussian mixtures. For an overview see package?fpc.

Maintained by Christian Hennig. Last updated 6 months ago.

3.8 match 11 stars 9.32 score 2.6k scripts 69 dependents

bioc

EnhancedVolcano:Publication-ready volcano plots with enhanced colouring and labeling

Volcano plots represent a useful way to visualise the results of differential expression analyses. Here, we present a highly-configurable function that produces publication-ready volcano plots. EnhancedVolcano will attempt to fit as many point labels in the plot window as possible, thus avoiding 'clogging' up the plot with labels that could not otherwise have been read. Other functionality allows the user to identify up to 4 different types of attributes in the same plot space via colour, shape, size, and shade parameter configurations.

Maintained by Kevin Blighe. Last updated 5 months ago.

rnaseq geneexpression transcription differentialexpression immunooncology

2.9 match 427 stars 12.16 score 2.7k scripts 1 dependents

karlines

diagram:Functions for Visualising Simple Graphs (Networks), Plotting Flow Diagrams

Visualises simple graphs (networks) based on a transition matrix, utilities to plot flow diagrams, visualising webs, electrical networks, etc. Support for the book "A practical guide to ecological modelling - using R as a simulation platform" by Karline Soetaert and Peter M.J. Herman (2009), Springer. and the book "Solving Differential Equations in R" by Karline Soetaert, Jeff Cash and Francesca Mazzia (2012), Springer. Includes demo(flowchart), demo(plotmat), demo(plotweb).

Maintained by Karline Soetaert. Last updated 5 years ago.

3.4 match 10.06 score 598 scripts 487 dependents

swarm-lab

CEC:Cross-Entropy Clustering

Splits data into Gaussian type clusters using the Cross-Entropy Clustering ('CEC') method. This method allows for the simultaneous use of various types of Gaussian mixture models, for performing the reduction of unnecessary clusters, and for discovering new clusters by splitting them. 'CEC' is based on the work of Spurek, P. and Tabor, J. (2014) <doi:10.1016/j.patcog.2014.03.006>.

Maintained by Simon Garnier. Last updated 6 months ago.

clustering cross-entropy openblas cpp

8.0 match 10 stars 4.26 score 18 scripts

usaid-oha-si

themask:Masks and houses the PEPFAR MSD-style training dataset for testing and training

This package creates and hosts a masked, dummy dataset that should be used for testing, training, and demoing instead of using actual PEPFAR data.

Maintained by Aaron Chafetz. Last updated 10 months ago.

11.3 match 1 stars 3.00 score 8 scripts

zrmacc

Temporal:Parametric Time to Event Analysis

Performs maximum likelihood based estimation and inference on time to event data, possibly subject to non-informative right censoring. FitParaSurv() provides maximum likelihood estimates of model parameters and distributional characteristics, including the mean, median, variance, and restricted mean. CompParaSurv() compares the mean, median, and restricted mean survival experiences of two treatment groups. Candidate distributions include the exponential, gamma, generalized gamma, log-normal, and Weibull.

Maintained by Zachary McCaw. Last updated 2 years ago.

5.6 match 3 stars 5.96 score 34 scripts 1 dependents

bioc

bioCancer:Interactive Multi-Omics Cancers Data Visualization and Analysis

This package is a Shiny App to visualize and analyse interactively Multi-Assays of Cancer Genomic Data.

Maintained by Karim Mezhoud. Last updated 5 months ago.

gui datarepresentation network multiplecomparison pathways reactome visualization geneexpression genetarget analysis biocancer-interface cancer cancer-studies rmarkdown

5.8 match 20 stars 5.78 score 7 scripts

jdench

rSHAPE:Simulated Haploid Asexual Population Evolution

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

Maintained by Jonathan Dench. Last updated 6 years ago.

33.5 match 1.00 score

holans

stcos:Space-Time Change of Support

Spatio-temporal change of support (STCOS) methods are designed for statistical inference on geographic and time domains which differ from those on which the data were observed. In particular, a parsimonious class of STCOS models supporting Gaussian outcomes was introduced by Bradley, Wikle, and Holan <doi:10.1002/sta4.94>. The 'stcos' package contains tools which facilitate use of STCOS models.

Maintained by Andrew M. Raim. Last updated 2 years ago.

openblas cpp

10.5 match 3 stars 3.18 score 4 scripts

f0nzie

rTorch:R Bindings to 'PyTorch'

'R' implementation and interface of the Machine Learning platform 'PyTorch' <https://pytorch.org/> developed in 'Python'. It requires a 'conda' environment with 'torch' and 'torchvision' Python packages to provide 'PyTorch' functions, methods and classes. The key object in 'PyTorch' is the tensor which is in essence a multidimensional array. These tensors are fairly flexible in performing calculations in CPUs as well as 'GPUs' to accelerate tensor operations.

Maintained by Alfonso R. Reyes. Last updated 3 years ago.

5.6 match 6 stars 5.97 score 157 scripts

julianfaraway

faraway:Datasets and Functions for Books by Julian Faraway

Books are "Linear Models with R" published 1st Ed. August 2004, 2nd Ed. July 2014, 3rd Ed. February 2025 by CRC press, ISBN 9781439887332, and "Extending the Linear Model with R" published by CRC press in 1st Ed. December 2005 and 2nd Ed. March 2016, ISBN 9781584884248 and "Practical Regression and ANOVA in R" contributed documentation on CRAN (now very dated).

Maintained by Julian Faraway. Last updated 2 months ago.

data

3.5 match 29 stars 9.43 score 1.7k scripts 1 dependents

femiguez

nlraa:Nonlinear Regression for Agricultural Applications

Additional nonlinear regression functions using self-start (SS) algorithms. One of the functions is the Beta growth function proposed by Yin et al. (2003) <doi:10.1093/aob/mcg029>. There are several other functions with breakpoints (e.g. linear-plateau, plateau-linear, exponential-plateau, plateau-exponential, quadratic-plateau, plateau-quadratic and bilinear), a non-rectangular hyperbola and a bell-shaped curve. Twenty eight (28) new self-start (SS) functions in total. This package also supports the publication 'Nonlinear regression Models and applications in agricultural research' by Archontoulis and Miguez (2015) <doi:10.2134/agronj2012.0506>, a book chapter with similar material <doi:10.2134/appliedstatistics.2016.0003.c15> and a publication by Oddi et. al. (2019) in Ecology and Evolution <doi:10.1002/ece3.5543>. The function 'nlsLMList' uses 'nlsLM' for fitting, but it is otherwise almost identical to 'nlme::nlsList'.In addition, this release of the package provides functions for conducting simulations for 'nlme' and 'gnls' objects as well as bootstrapping. These functions are intended to work with the modeling framework of the 'nlme' package. It also provides four vignettes with extended examples.

Maintained by Fernando Miguez. Last updated 11 months ago.

agricultural ecology nonlinear-mixed-models nonlinear-regression

4.0 match 23 stars 8.19 score 112 scripts 2 dependents

ipeagit

gtfstools:General Transit Feed Specification (GTFS) Editing and Analysing Tools

Utility functions to read, manipulate, analyse and write transit feeds in the General Transit Feed Specification (GTFS) data format.

Maintained by Daniel Herszenhut. Last updated 2 months ago.

gtfs public-transport publictransport cpp

3.5 match 40 stars 9.31 score 126 scripts 3 dependents

ucl

rmcmc:Robust Markov Chain Monte Carlo Methods

Functions for simulating Markov chains using the Barker proposal to compute Markov chain Monte Carlo (MCMC) estimates of expectations with respect to a target distribution on a real-valued vector space. The Barker proposal, described in Livingstone and Zanella (2022) <doi:10.1111/rssb.12482>, is a gradient-based MCMC algorithm inspired by the Barker accept-reject rule. It combines the robustness of simpler MCMC schemes, such as random-walk Metropolis, with the efficiency of gradient-based methods, such as the Metropolis adjusted Langevin algorithm. The key function provided by the package is sample_chain(), which allows sampling a Markov chain with a specified target distribution as its stationary distribution. The chain is sampled by generating proposals and accepting or rejecting them using a Metropolis-Hasting acceptance rule. During an initial warm-up stage, the parameters of the proposal distribution can be adapted, with adapters available to both: tune the scale of the proposals by coercing the average acceptance rate to a target value; tune the shape of the proposals to match covariance estimates under the target distribution. As well as the default Barker proposal, the package also provides implementations of alternative proposal distributions, such as (Gaussian) random walk and Langevin proposals. Optionally, if 'BridgeStan's R interface <https://roualdes.github.io/bridgestan/latest/languages/r.html>, available on GitHub <https://github.com/roualdes/bridgestan>, is installed, then 'BridgeStan' can be used to specify the target distribution to sample from.

Maintained by Matthew M. Graham. Last updated 29 days ago.

approximate-inference mcmc

5.6 match 5 stars 5.85 score 8 scripts

neilstats

ckbplotr:Create CKB Plots

ckbplotr provides functions to help create and style plots in R. It is being developed by, and primarily for, China Kadoorie Biobank researchers.

Maintained by Neil Wright. Last updated 2 months ago.

5.6 match 10 stars 5.77 score 37 scripts

cran

GSM:Gamma Shape Mixture

Implementation of a Bayesian approach for estimating a mixture of gamma distributions in which the mixing occurs over the shape parameter. This family provides a flexible and novel approach for modeling heavy-tailed distributions, it is computationally efficient, and it only requires to specify a prior distribution for a single parameter.

Maintained by Sergio Venturini. Last updated 10 years ago.

16.2 match 2.00 score

haakoneidemhaakstad

betafunctions:Functions for Working with Two- And Four-Parameter Beta Probability Distributions and Psychometric Analysis of Classifications

Package providing a number of functions for working with Two- and Four-parameter Beta and closely related distributions (i.e., the Gamma- Binomial-, and Beta-Binomial distributions). Includes, among other things: - d/p/q/r functions for Four-Parameter Beta distributions and Generalized "Binomial" (continuous) distributions, and d/p/r- functions for Beta- Binomial distributions. - d/p/q/r functions for Two- and Four-Parameter Beta distributions parameterized in terms of their means and variances rather than their shape-parameters. - Moment generating functions for Binomial distributions, Beta-Binomial distributions, and observed value distributions. - Functions for estimating classification accuracy and consistency, making use of the Classical Test-Theory based 'Livingston and Lewis' (L&L) and 'Hanson and Brennan' approaches. A shiny app is available, providing a GUI for the L&L approach when used for binary classifications. For url to the app, see documentation for the LL.CA() function. Livingston and Lewis (1995) <doi:10.1111/j.1745-3984.1995.tb00462.x>. Lord (1965) <doi:10.1007/BF02289490>. Hanson (1991) <https://files.eric.ed.gov/fulltext/ED344945.pdf>.

Maintained by Haakon Eidem Haakstad. Last updated 5 months ago.

10.2 match 3.18 score 8 scripts 1 dependents

dicook

mulgar:Functions for Pre-Processing Data for Multivariate Data Visualisation using Tours

This is a companion to the book Cook, D. and Laa, U. (2023) <https://dicook.github.io/mulgar_book/> "Interactively exploring high-dimensional data and models in R". by Cook and Laa. It contains useful functions for processing data in preparation for visualising with a tour. There are also several sample data sets.

Maintained by Dianne Cook. Last updated 2 months ago.

7.1 match 4 stars 4.50 score 79 scripts

bioc

ComplexHeatmap:Make Complex Heatmaps

Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential patterns. Here the ComplexHeatmap package provides a highly flexible way to arrange multiple heatmaps and supports various annotation graphics.

Maintained by Zuguang Gu. Last updated 5 months ago.

software visualization sequencing clustering complex-heatmaps heatmap

1.9 match 1.4k stars 16.94 score 16k scripts 155 dependents

revelle

psych:Procedures for Psychological, Psychometric, and Personality Research

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

Maintained by William Revelle. Last updated 10 days ago.

2.3 match 52 stars 14.12 score 29k scripts 317 dependents

mrcieu

gwasglue2:GWAS summary data sources connected to analytical tools

Description: Many tools exist that use GWAS summary data for colocalisation, fine mapping, Mendelian randomization, visualisation, etc. This package is a conduit that connects R packages that can retrieve GWAS summary data to various tools for analysing those data.

Maintained by Rita Rasteiro. Last updated 1 years ago.

5.5 match 21 stars 5.69 score 11 scripts 2 dependents

kassambara

ggpubr:'ggplot2' Based Publication Ready Plots

The 'ggplot2' package is excellent and flexible for elegant data visualization in R. However the default generated plots requires some formatting before we can send them for publication. Furthermore, to customize a 'ggplot', the syntax is opaque and this raises the level of difficulty for researchers with no advanced R programming skills. 'ggpubr' provides some easy-to-use functions for creating and customizing 'ggplot2'- based publication ready plots.

Maintained by Alboukadel Kassambara. Last updated 2 years ago.

1.9 match 1.2k stars 16.68 score 65k scripts 409 dependents

jclavel

mvMORPH:Multivariate Comparative Tools for Fitting Evolutionary Models to Morphometric Data

Fits multivariate (Brownian Motion, Early Burst, ACDC, Ornstein-Uhlenbeck and Shifts) models of continuous traits evolution on trees and time series. 'mvMORPH' also proposes high-dimensional multivariate comparative tools (linear models using Generalized Least Squares and multivariate tests) based on penalized likelihood. See Clavel et al. (2015) <DOI:10.1111/2041-210X.12420>, Clavel et al. (2019) <DOI:10.1093/sysbio/syy045>, and Clavel & Morlon (2020) <DOI:10.1093/sysbio/syaa010>.

Maintained by Julien Clavel. Last updated 2 months ago.

openblas

3.3 match 17 stars 9.46 score 189 scripts 3 dependents

kristyrobledo

VarReg:Semi-Parametric Variance Regression

Methods for fitting semi-parametric mean and variance models, with normal or censored data. Extended to allow a regression in the location, scale and shape parameters, and further for multiple regression in each.

Maintained by Kristy Robledo. Last updated 2 years ago.

7.0 match 1 stars 4.46 score 29 scripts

klauschn

ICtest:Estimating and Testing the Number of Interesting Components in Linear Dimension Reduction

For different linear dimension reduction methods like principal components analysis (PCA), independent components analysis (ICA) and supervised linear dimension reduction tests and estimates for the number of interesting components (ICs) are provided.

Maintained by Klaus Nordhausen. Last updated 4 days ago.

openblas cpp

5.1 match 6.05 score 63 scripts 4 dependents

symbolixau

googleway:Accesses Google Maps APIs to Retrieve Data and Plot Maps

Provides a mechanism to plot a 'Google Map' from 'R' and overlay it with shapes and markers. Also provides access to 'Google Maps' APIs, including places, directions, roads, distances, geocoding, elevation and timezone.

Maintained by David Cooley. Last updated 7 months ago.

google-map google-maps google-maps-api google-maps-javascript-api spatial spatial-analysis

3.2 match 236 stars 9.67 score 536 scripts 2 dependents

bpfaff

evir:Extreme Values in R

Functions for extreme value theory, which may be divided into the following groups; exploratory data analysis, block maxima, peaks over thresholds (univariate and bivariate), point processes, gev/gpd distributions.

Maintained by Bernhard Pfaff. Last updated 9 years ago.

5.2 match 2 stars 5.94 score 211 scripts 6 dependents

ropensci

rdhs:API Client and Dataset Management for the Demographic and Health Survey (DHS) Data

Provides a client for (1) querying the DHS API for survey indicators and metadata (<https://api.dhsprogram.com/#/index.html>), (2) identifying surveys and datasets for analysis, (3) downloading survey datasets from the DHS website, (4) loading datasets and associate metadata into R, and (5) extracting variables and combining datasets for pooled analysis.

Maintained by OJ Watson. Last updated 1 months ago.

dataset dhs dhs-api extract peer-reviewed survey-data

3.0 match 37 stars 10.16 score 286 scripts 4 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 3 days ago.

choropleth-maps maps spatial thematic-maps visualisation

1.9 match 879 stars 16.25 score 13k scripts 24 dependents

wjschne

ggdiagram:Object-Oriented Diagram Plots with ggplot2

The ggdiagram package creates path diagrams with an object-oriented approach and plots diagrams with ggplot2.

Maintained by W. Joel Schneider. Last updated 8 days ago.

diagrams factor-analysis ggplot2 path-analysis s7 structural-equation-modeling

5.6 match 32 stars 5.43 score

ipeagit

gtfs2gps:Converting Transport Data from GTFS Format to GPS-Like Records

Convert general transit feed specification (GTFS) data to global positioning system (GPS) records in 'data.table' format. It also has some functions to subset GTFS data in time and space and to convert both representations to simple feature format.

Maintained by Pedro R. Andrade. Last updated 2 months ago.

gps-format gtfs gtfs-format public-transport rspatial transport cpp

3.6 match 73 stars 8.22 score 101 scripts 1 dependents

r-forge

RobExtremes:Optimally Robust Estimation for Extreme Value Distributions

Optimally robust estimation for extreme value distributions using S4 classes and methods (based on packages 'distr', 'distrEx', 'distrMod', 'RobAStBase', and 'ROptEst'); the underlying theoretic results can be found in Ruckdeschel and Horbenko, (2013 and 2012), \doi{10.1080/02331888.2011.628022} and \doi{10.1007/s00184-011-0366-4}.

Maintained by Peter Ruckdeschel. Last updated 2 months ago.

8.1 match 3.67 score 39 scripts

lgnbhl

xlcharts:Create Native 'Excel' Charts and Work with Microsoft 'Excel' Files

An R interface to the 'OpenPyXL' 'Python' library to create native 'Excel' charts and work with Microsoft 'Excel' files.

Maintained by Felix Luginbuhl. Last updated 27 days ago.

excel

6.6 match 12 stars 4.48 score 4 scripts

paulnorthrop

revdbayes:Ratio-of-Uniforms Sampling for Bayesian Extreme Value Analysis

Provides functions for the Bayesian analysis of extreme value models. The 'rust' package <https://cran.r-project.org/package=rust> is used to simulate a random sample from the required posterior distribution. The functionality of 'revdbayes' is similar to the 'evdbayes' package <https://cran.r-project.org/package=evdbayes>, which uses Markov Chain Monte Carlo ('MCMC') methods for posterior simulation. In addition, there are functions for making inferences about the extremal index, using the models for threshold inter-exceedance times of Suveges and Davison (2010) <doi:10.1214/09-AOAS292> and Holesovsky and Fusek (2020) <doi:10.1007/s10687-020-00374-3>. Also provided are d,p,q,r functions for the Generalised Extreme Value ('GEV') and Generalised Pareto ('GP') distributions that deal appropriately with cases where the shape parameter is very close to zero.

Maintained by Paul J. Northrop. Last updated 7 months ago.

analysis bayesian extreme extreme-value-statistics extremes generalized-pareto-distribution gev inference nhpp point-process posterior predictive rcpp value openblas cpp

3.9 match 4 stars 7.41 score 58 scripts 4 dependents

malaria-atlas-project

malariaAtlas:An R Interface to Open-Access Malaria Data, Hosted by the 'Malaria Atlas Project'

A suite of tools to allow you to download all publicly available parasite rate survey points, mosquito occurrence points and raster surfaces from the 'Malaria Atlas Project' <https://malariaatlas.org/> servers as well as utility functions for plotting the downloaded data.

Maintained by Mauricio van den Berg. Last updated 9 months ago.

database malaria opendata raster

3.2 match 44 stars 9.10 score 118 scripts 3 dependents

daya6489

SmartEDA:Summarize and Explore the Data

Exploratory analysis on any input data describing the structure and the relationships present in the data. The package automatically select the variable and does related descriptive statistics. Analyzing information value, weight of evidence, custom tables, summary statistics, graphical techniques will be performed for both numeric and categorical predictors.

Maintained by Dayanand Ubrangala. Last updated 1 years ago.

analysis exploratory-data-analysis

4.0 match 42 stars 7.25 score 214 scripts

thomasp85

ggforce:Accelerating 'ggplot2'

The aim of 'ggplot2' is to aid in visual data investigations. This focus has led to a lack of facilities for composing specialised plots. 'ggforce' aims to be a collection of mainly new stats and geoms that fills this gap. All additional functionality is aimed to come through the official extension system so using 'ggforce' should be a stable experience.

Maintained by Thomas Lin Pedersen. Last updated 7 days ago.

ggplot-extension ggplot2 visualization cpp

1.8 match 929 stars 15.98 score 9.3k scripts 298 dependents

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

andrisignorell

DescTools:Tools for Descriptive Statistics

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

Maintained by Andri Signorell. Last updated 4 days ago.

fortran cpp

1.7 match 86 stars 16.73 score 7.7k scripts 101 dependents

rdinnager

phyf:Phylogenetic Flow Objects for Easy Manipulation and Modelling of Data on Phylogenetic Trees and Graphs

The {phyf} package implements a tibble and vctrs based object for storing phylogenetic trees along with data. It is fast and flexible and directly produces data structures useful for phylogenetic modelling in the {fibre} package.

Maintained by Russell Dinnage. Last updated 7 months ago.

6.8 match 1 stars 4.20 score 53 scripts 1 dependents

terminological

arear:Geospatial Convenience Functions and a Supply Demand Catchment Area Generator

Geospatial function collection from the COVID-19 pandemic. The main focus of this was integrating geospatial demographic, hospital capacity and COVID data from England, Scotland, Wales and Northern Ireland, all of which were available on different sites and methods. The UK has a wide range of administrative geographic boundaries for different purposes and moving from different scales and resolutions proved necessary. As the geospatial operations are quite time consuming but don't need to be repeated the ability to cache results of geospatial transformations is useful and embedded into these functions.

Maintained by Robert Challen. Last updated 11 months ago.

8.6 match 4 stars 3.30 score 4 scripts

msuzen

Julia:Fractal Image Data Generator

Generates image data for fractals (Julia and Mandelbrot sets) on the complex plane in the given region and resolution. Benoit B Mandelbrot (1982).

Maintained by Mehmet Suzen. Last updated 8 months ago.

fractals julia julia-fractal julia-sets mandelbrot-fractal mandelbrot-renderer mandelbrot-set r-programming shape-analysis

7.5 match 1 stars 3.74 score 11 scripts

gamlss-dev

gamlss.ggplots:Plotting Functions for Generalized Additive Model for Location Scale and Shape

Functions for plotting Generalized Additive Models for Location Scale and Shape from the 'gamlss' package, Stasinopoulos and Rigby (2007) <doi:10.18637/jss.v023.i07>, using the graphical methods from 'ggplot2'.

Maintained by Mikis Stasinopoulos. Last updated 4 months ago.

5.0 match 2 stars 5.56 score 24 scripts

opatp

GTFSwizard:Exploring and Manipulating 'GTFS' Files

Exploring, analyzing, and manipulating General Transit Feed Specification (GTFS) files, which represent public transportation schedules and geographic data. The package allows users to filter data by routes, trips, stops, and time, generate spatial visualizations, and perform detailed analyses of transit networks, including headway, dwell times, and route frequencies. Designed for transit planners, researchers, and data analysts, 'GTFSwizard' integrates functionalities from popular packages to enable efficient GTFS data manipulation and visualization.

Maintained by Nelson de O. Quesado Filho. Last updated 3 months ago.

gtfs transit

6.3 match 1 stars 4.41 score

rstudio

tfestimators:Interface to 'TensorFlow' Estimators

Interface to 'TensorFlow' Estimators <https://www.tensorflow.org/guide/estimator>, a high-level API that provides implementations of many different model types including linear models and deep neural networks.

Maintained by Tomasz Kalinowski. Last updated 3 years ago.

3.3 match 57 stars 8.42 score 170 scripts

janmarvin

openxlsx2:Read, Write and Edit 'xlsx' Files

Simplifies the creation of 'xlsx' files by providing a high level interface to writing, styling and editing worksheets.

Maintained by Jan Marvin Garbuszus. Last updated 1 days ago.

xlsx cpp

2.0 match 139 stars 13.62 score 194 scripts 11 dependents

bioc

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

A molecular informatics toolkit with an integration of bioinformatics and chemoinformatics tools for drug discovery.

Maintained by Nan Xiao. Last updated 5 months ago.

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

3.5 match 37 stars 7.81 score 29 scripts

ropensci

iheatmapr:Interactive, Complex Heatmaps

Make complex, interactive heatmaps. 'iheatmapr' includes a modular system for iteratively building up complex heatmaps, as well as the iheatmap() function for making relatively standard heatmaps.

Maintained by Alan OCallaghan. Last updated 8 months ago.

heatmap plotly interactive-visualizations data-visualization htmlwidgets peer-reviewed

3.0 match 267 stars 9.08 score 99 scripts 1 dependents

davidgohel

ggiraph:Make 'ggplot2' Graphics Interactive

Create interactive 'ggplot2' graphics using 'htmlwidgets'.

Maintained by David Gohel. Last updated 4 days ago.

libpng cpp

1.9 match 822 stars 14.37 score 4.1k scripts 35 dependents

bbuchsbaum

multivarious:Extensible Data Structures for Multivariate Analysis

Provides a set of basic and extensible data structures and functions for multivariate analysis, including dimensionality reduction techniques, projection methods, and preprocessing functions. The aim of this package is to offer a flexible and user-friendly framework for multivariate analysis that can be easily extended for custom requirements and specific data analysis tasks.

Maintained by Bradley Buchsbaum. Last updated 3 months ago.

7.6 match 3.53 score 17 scripts

jkim82133

TDA:Statistical Tools for Topological Data Analysis

Tools for Topological Data Analysis. The package focuses on statistical analysis of persistent homology and density clustering. For that, this package provides an R interface for the efficient algorithms of the C++ libraries 'GUDHI' <https://project.inria.fr/gudhi/software/>, 'Dionysus' <https://www.mrzv.org/software/dionysus/>, and 'PHAT' <https://bitbucket.org/phat-code/phat/>. This package also implements methods from Fasy et al. (2014) <doi:10.1214/14-AOS1252> and Chazal et al. (2015) <doi:10.20382/jocg.v6i2a8> for analyzing the statistical significance of persistent homology features.

Maintained by Jisu Kim. Last updated 2 months ago.

gmp cpp

3.7 match 9 stars 7.18 score 204 scripts 5 dependents

neurodata

mgc:Multiscale Graph Correlation

Multiscale Graph Correlation (MGC) is a framework developed by Vogelstein et al. (2019) <DOI:10.7554/eLife.41690> that extends global correlation procedures to be multiscale; consequently, MGC tests typically require far fewer samples than existing methods for a wide variety of dependence structures and dimensionalities, while maintaining computational efficiency. Moreover, MGC provides a simple and elegant multiscale characterization of the potentially complex latent geometry underlying the relationship.

Maintained by Eric Bridgeford. Last updated 4 years ago.

3.5 match 9 stars 7.50 score 59 scripts 2 dependents

emilhvitfeldt

emoji:Data and Function to Work with Emojis

Contains data about emojis with relevant metadata, and functions to work with emojis when they are in strings.

Maintained by Emil Hvitfeldt. Last updated 5 months ago.

3.3 match 28 stars 7.93 score 304 scripts 3 dependents

myles-lewis

locuszoomr:Gene Locus Plot with Gene Annotations

Publication-ready regional gene locus plots similar to those produced by the web interface 'LocusZoom' <https://my.locuszoom.org>, but running locally in R. Genetic or genomic data with gene annotation tracks are plotted via R base graphics, 'ggplot2' or 'plotly', allowing flexibility and easy customisation including laying out multiple locus plots on the same page. It uses the 'LDlink' API <https://ldlink.nih.gov/?tab=apiaccess> to query linkage disequilibrium data from the 1000 Genomes Project and can overlay this on plots <doi:10.1093/bioadv/vbaf006>.

Maintained by Myles Lewis. Last updated 29 days ago.

3.5 match 40 stars 7.43 score 50 scripts

otsegun

fdaoutlier:Outlier Detection Tools for Functional Data Analysis

A collection of functions for outlier detection in functional data analysis. Methods implemented include directional outlyingness by Dai and Genton (2019) <doi:10.1016/j.csda.2018.03.017>, MS-plot by Dai and Genton (2018) <doi:10.1080/10618600.2018.1473781>, total variation depth and modified shape similarity index by Huang and Sun (2019) <doi:10.1080/00401706.2019.1574241>, and sequential transformations by Dai et al. (2020) <doi:10.1016/j.csda.2020.106960 among others. Additional outlier detection tools and depths for functional data like functional boxplot, (modified) band depth etc., are also available.

Maintained by Oluwasegun Taiwo Ojo. Last updated 1 years ago.

outlier-detection cpp

5.5 match 5 stars 4.70 score 20 scripts

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

5.8 match 2 stars 4.45 score 211 scripts 7 dependents

aphalo

ggpmisc:Miscellaneous Extensions to 'ggplot2'

Extensions to 'ggplot2' respecting the grammar of graphics paradigm. Statistics: locate and tag peaks and valleys; label plot with the equation of a fitted polynomial or other types of models; labels with P-value, R^2 or adjusted R^2 or information criteria for fitted models; label with ANOVA table for fitted models; label with summary for fitted models. Model fit classes for which suitable methods are provided by package 'broom' and 'broom.mixed' are supported. Scales and stats to build volcano and quadrant plots based on outcomes, fold changes, p-values and false discovery rates.

Maintained by Pedro J. Aphalo. Last updated 2 days ago.

data-analysis dataviz ggplot2-annotations ggplot2-stats statistics

1.9 match 107 stars 13.64 score 4.4k scripts 14 dependents

tidyverse

googlesheets4:Access Google Sheets using the Sheets API V4

Interact with Google Sheets through the Sheets API v4 <https://developers.google.com/sheets/api>. "API" is an acronym for "application programming interface"; the Sheets API allows users to interact with Google Sheets programmatically, instead of via a web browser. The "v4" refers to the fact that the Sheets API is currently at version 4. This package can read and write both the metadata and the cell data in a Sheet.

Maintained by Jennifer Bryan. Last updated 8 months ago.

google-drive google-sheets spreadsheet

1.8 match 363 stars 14.55 score 7.0k scripts 142 dependents

mikkovihtakari

ggOceanMaps:Plot Data on Oceanographic Maps using 'ggplot2'

Allows plotting data on bathymetric maps using 'ggplot2'. Plotting oceanographic spatial data is made as simple as feasible, but also flexible for custom modifications. Data that contain geographic information from anywhere around the globe can be plotted on maps generated by the basemap() or qmap() functions using 'ggplot2' layers separated by the '+' operator. The package uses spatial shape- ('sf') and raster ('stars') files, geospatial packages for R to manipulate, and the 'ggplot2' package to plot these files. The package ships with low-resolution spatial data files and higher resolution files for detailed maps are stored in the 'ggOceanMapsLargeData' repository on GitHub and downloaded automatically when needed.

Maintained by Mikko Vihtakari. Last updated 5 months ago.

4.3 match 48 stars 5.97 score 193 scripts

r-lidar

lidR:Airborne LiDAR Data Manipulation and Visualization for Forestry Applications

Airborne LiDAR (Light Detection and Ranging) interface for data manipulation and visualization. Read/write 'las' and 'laz' files, computation of metrics in area based approach, point filtering, artificial point reduction, classification from geographic data, normalization, individual tree segmentation and other manipulations.

Maintained by Jean-Romain Roussel. Last updated 2 months ago.

als forestry las laz lidar point-cloud remote-sensing openblas cpp openmp

1.8 match 623 stars 14.47 score 844 scripts 8 dependents

edzer

hexbin:Hexagonal Binning Routines

Binning and plotting functions for hexagonal bins.

Maintained by Edzer Pebesma. Last updated 5 months ago.

fortran

1.8 match 37 stars 14.00 score 2.4k scripts 114 dependents

sem-in-r

seminr:Building and Estimating Structural Equation Models

A powerful, easy to syntax for specifying and estimating complex Structural Equation Models. Models can be estimated using Partial Least Squares Path Modeling or Covariance-Based Structural Equation Modeling or covariance based Confirmatory Factor Analysis. Methods described in Ray, Danks, and Valdez (2021).

Maintained by Nicholas Patrick Danks. Last updated 3 years ago.

common-factors composites construct pls-models

3.4 match 62 stars 7.46 score 284 scripts

giocomai

latlon2map:Facilitates matching lat/lon data with administrative units and other geographic shapes

Facilitates matching lat/lon data with administrative units and other geographic shapes

Maintained by Giorgio Comai. Last updated 6 months ago.

rspatial shiny

6.8 match 10 stars 3.70 score

blakedickson

Morphoscape:Computation and Visualization of Adaptive Landscapes

Implements adaptive landscape methods first described by Polly et al. (2016) <doi:10.1080/02724634.2016.1111225> for the integration, analysis and visualization of biological trait data on a phenotypic morphospace - typically defined by shape metrics.

Maintained by Blake Dickson. Last updated 10 months ago.

4.5 match 4 stars 5.56 score 8 scripts

r-spatialecology

landscapemetrics:Landscape Metrics for Categorical Map Patterns

Calculates landscape metrics for categorical landscape patterns in a tidy workflow. 'landscapemetrics' reimplements the most common metrics from 'FRAGSTATS' (<https://www.fragstats.org/>) and new ones from the current literature on landscape metrics. This package supports 'terra' SpatRaster objects as input arguments. It further provides utility functions to visualize patches, select metrics and building blocks to develop new metrics.

Maintained by Maximilian H.K. Hesselbarth. Last updated 2 months ago.

landscape-ecology landscape-metrics raster spatial cpp

2.0 match 240 stars 12.47 score 584 scripts 4 dependents

xliaosdsu

ShapeSelectForest:Shape Selection for Landsat Time Series of Forest Dynamics

Landsat satellites collect important data about global forest conditions. Documentation about Landsat's role in forest disturbance estimation is available at the site <https://landsat.gsfc.nasa.gov/>. By constrained quadratic B-splines, this package delivers an optimal shape-restricted trajectory to a time series of Landsat imagery for the purpose of modeling annual forest disturbance dynamics to behave in an ecologically sensible manner assuming one of seven possible "shapes", namely, flat, decreasing, one-jump (decreasing, jump up, decreasing), inverted vee (increasing then decreasing), vee (decreasing then increasing), linear increasing, and double-jump (decreasing, jump up, decreasing, jump up, decreasing). The main routine selects the best shape according to the minimum Bayes information criterion (BIC) or the cone information criterion (CIC), which is defined as the log of the estimated predictive squared error. The package also provides parameters summarizing the temporal pattern including year(s) of inflection, magnitude of change, pre- and post-inflection rates of growth or recovery. In addition, it contains routines for converting a flat map of disturbance agents to time-series disturbance maps and a graphical routine displaying the fitted trajectory of Landsat imagery.

Maintained by Xiyue Liao. Last updated 2 years ago.

16.9 match 1.48 score 9 scripts

gertvv

hitandrun:"Hit and Run" and "Shake and Bake" for Sampling Uniformly from Convex Shapes

The "Hit and Run" Markov Chain Monte Carlo method for sampling uniformly from convex shapes defined by linear constraints, and the "Shake and Bake" method for sampling from the boundary of such shapes. Includes specialized functions for sampling normalized weights with arbitrary linear constraints. Tervonen, T., van Valkenhoef, G., Basturk, N., and Postmus, D. (2012) <doi:10.1016/j.ejor.2012.08.026>. van Valkenhoef, G., Tervonen, T., and Postmus, D. (2014) <doi:10.1016/j.ejor.2014.06.036>.

Maintained by Gert van Valkenhoef. Last updated 3 years ago.

openblas

3.6 match 16 stars 6.92 score 121 scripts 9 dependents

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.

5.7 match 4.36 score 46 scripts

rstudio

tfhub:Interface to 'TensorFlow' Hub

'TensorFlow' Hub is a library for the publication, discovery, and consumption of reusable parts of machine learning models. A module is a self-contained piece of a 'TensorFlow' graph, along with its weights and assets, that can be reused across different tasks in a process known as transfer learning. Transfer learning train a model with a smaller dataset, improve generalization, and speed up training.

Maintained by Tomasz Kalinowski. Last updated 3 years ago.

3.3 match 29 stars 7.46 score 73 scripts 1 dependents

lchiffon

wordcloud2:Create Word Cloud by htmlWidget

A fast visualization tool for creating wordcloud by using wordcloud2.js.

Maintained by Dawei Lang. Last updated 7 years ago.

1.9 match 402 stars 13.10 score 2.8k scripts 11 dependents

winvector

sigr:Succinct and Correct Statistical Summaries for Reports

Succinctly and correctly format statistical summaries of various models and tests (F-test, Chi-Sq-test, Fisher-test, T-test, and rank-significance). This package also includes empirical tests, such as Monte Carlo and bootstrap distribution estimates.

Maintained by John Mount. Last updated 2 years ago.

3.4 match 28 stars 7.18 score 97 scripts 1 dependents

dsalfran

ImputeRobust:Robust Multiple Imputation with Generalized Additive Models for Location Scale and Shape

Provides new imputation methods for the 'mice' package based on generalized additive models for location, scale, and shape (GAMLSS) as described in de Jong, van Buuren and Spiess <doi:10.1080/03610918.2014.911894>.

Maintained by Daniel Salfran. Last updated 6 years ago.

imputation missing-data multiple-imputation

6.7 match 9 stars 3.65 score 4 scripts

rempsyc

rempsyc:Convenience Functions for Psychology

Make your workflow faster and easier. Easily customizable plots (via 'ggplot2'), nice APA tables (following the style of the *American Psychological Association*) exportable to Word (via 'flextable'), easily run statistical tests or check assumptions, and automatize various other tasks.

Maintained by Rémi Thériault. Last updated 2 months ago.

convenience-functions ggplot2 psychology statistics visualization

2.2 match 43 stars 10.68 score 214 scripts 2 dependents

mstasinopoulos

gamlss.data:Data for Generalised Additive Models for Location Scale and Shape

Data used as examples in the current two books on Generalised Additive Models for Location Scale and Shape introduced by Rigby and Stasinopoulos (2005), <doi:10.1111/j.1467-9876.2005.00510.x>.

Maintained by Mikis Stasinopoulos. Last updated 1 years ago.

3.4 match 7.04 score 108 scripts 49 dependents

r-lib

systemfonts:System Native Font Finding

Provides system native access to the font catalogue. As font handling varies between systems it is difficult to correctly locate installed fonts across different operating systems. The 'systemfonts' package provides bindings to the native libraries on Windows, macOS and Linux for finding font files that can then be used further by e.g. graphic devices. The main use is intended to be from compiled code but 'systemfonts' also provides access from R.

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

fonts fontconfig freetype cpp

1.5 match 95 stars 15.62 score 384 scripts 990 dependents

mjockers

syuzhet:Extracts Sentiment and Sentiment-Derived Plot Arcs from Text

Extracts sentiment and sentiment-derived plot arcs from text using a variety of sentiment dictionaries conveniently packaged for consumption by R users. Implemented dictionaries include "syuzhet" (default) developed in the Nebraska Literary Lab "afinn" developed by Finn Årup Nielsen, "bing" developed by Minqing Hu and Bing Liu, and "nrc" developed by Mohammad, Saif M. and Turney, Peter D. Applicable references are available in README.md and in the documentation for the "get_sentiment" function. The package also provides a hack for implementing Stanford's coreNLP sentiment parser. The package provides several methods for plot arc normalization.

Maintained by Matthew Jockers. Last updated 2 years ago.

1.8 match 336 stars 12.92 score 1.4k scripts 31 dependents

trevorld

ggpattern:'ggplot2' Pattern Geoms

Provides 'ggplot2' geoms filled with various patterns. Includes a patterned version of every 'ggplot2' geom that has a region that can be filled with a pattern. Provides a suite of 'ggplot2' aesthetics and scales for controlling pattern appearances. Supports over a dozen builtin patterns (every pattern implemented by 'gridpattern') as well as allowing custom user-defined patterns.

Maintained by Trevor L. Davis. Last updated 2 months ago.

1.9 match 370 stars 12.36 score 1.7k scripts 3 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

projectmosaic

ggformula:Formula Interface to the Grammar of Graphics

Provides a formula interface to 'ggplot2' graphics.

Maintained by Randall Pruim. Last updated 1 years ago.

2.0 match 38 stars 11.55 score 1.7k scripts 25 dependents

marco-geraci

Qtools:Utilities for Quantiles

Functions for unconditional and conditional quantiles. These include methods for transformation-based quantile regression, quantile-based measures of location, scale and shape, methods for quantiles of discrete variables, quantile-based multiple imputation, restricted quantile regression, directional quantile classification, and quantile ratio regression. A vignette is given in Geraci (2016, The R Journal) <doi:10.32614/RJ-2016-037> and included in the package.

Maintained by Marco Geraci. Last updated 1 years ago.

cpp

5.6 match 4.10 score 33 scripts 2 dependents

walkerke

tidycensus:Load US Census Boundary and Attribute Data as 'tidyverse' and 'sf'-Ready Data Frames

An integrated R interface to several United States Census Bureau APIs (<https://www.census.gov/data/developers/data-sets.html>) and the US Census Bureau's geographic boundary files. Allows R users to return Census and ACS data as tidyverse-ready data frames, and optionally returns a list-column with feature geometry for mapping and spatial analysis.

Maintained by Kyle Walker. Last updated 2 months ago.

1.6 match 648 stars 14.02 score 7.5k scripts 10 dependents

feddelegrand7

fabricerin:Create Easily Canvas in 'shiny' and 'RMarkdown' Documents

Allows the user to implement easily canvas elements within a 'shiny' app or an 'RMarkdown' document. The user can create shapes, images and text elements within the canvas which can also be used as a drawing tool for taking notes. The package relies on the 'fabricjs' 'JavaScript' library. See <http://fabricjs.com/>.

Maintained by Mohamed El Fodil Ihaddaden. Last updated 4 years ago.

canvas javascript rmarkdown rmarkdown-document shiny

4.1 match 54 stars 5.40 score 31 scripts

asheshrambachan

HonestDiD:Robust Inference in Difference-in-Differences and Event Study Designs

Provides functions to conduct robust inference in difference-in-differences and event study designs by implementing the methods developed in Rambachan & Roth (2023) <doi:10.1093/restud/rdad018>, "A More Credible Approach to Parallel Trends" [Previously titled "An Honest Approach..."]. Inference is conducted under a weaker version of the parallel trends assumption. Uniformly valid confidence sets are constructed based upon conditional confidence sets, fixed-length confidence sets and hybridized confidence sets.

Maintained by Ashesh Rambachan. Last updated 1 months ago.

difference-in-differences event-studies robust-inference

3.2 match 197 stars 7.05 score 63 scripts

bioc

peakPantheR:Peak Picking and Annotation of High Resolution Experiments

An automated pipeline for the detection, integration and reporting of predefined features across a large number of mass spectrometry data files. It enables the real time annotation of multiple compounds in a single file, or the parallel annotation of multiple compounds in multiple files. A graphical user interface as well as command line functions will assist in assessing the quality of annotation and update fitting parameters until a satisfactory result is obtained.

Maintained by Arnaud Wolfer. Last updated 5 months ago.

massspectrometry metabolomics peakdetection feature-detection mass-spectrometry

3.3 match 12 stars 6.65 score 23 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.

4.4 match 4.98 score 64 scripts 1 dependents

winvector

cdata:Fluid Data Transformations

Supplies higher-order coordinatized data specification and fluid transform operators that include pivot and anti-pivot as special cases. The methodology is describe in 'Zumel', 2018, "Fluid data reshaping with 'cdata'", <https://winvector.github.io/FluidData/FluidDataReshapingWithCdata.html> , <DOI:10.5281/zenodo.1173299> . This package introduces the idea of explicit control table specification of data transforms. Works on in-memory data or on remote data using 'rquery' and 'SQL' database interfaces.

Maintained by John Mount. Last updated 6 months ago.

2.8 match 45 stars 7.82 score 71 scripts 1 dependents

cbmc-gcmp

dafishr:Download, Wrangle, and Analyse Vessel Monitoring System Data

Allows to download, clean and analyse raw Vessel Monitoring System, VMS, data from Mexican government. You can use the vms_download() function to download raw data, or you can use the sample_dataset provided within the package. You can follow the tutorial in the vignette available at <https://cbmc-gcmp.github.io/dafishr/index.html>.

Maintained by Fabio Favoretto. Last updated 9 months ago.

4.5 match 7 stars 4.85 score 5 scripts

cran

mgcv:Mixed GAM Computation Vehicle with Automatic Smoothness Estimation

Generalized additive (mixed) models, some of their extensions and other generalized ridge regression with multiple smoothing parameter estimation by (Restricted) Marginal Likelihood, Generalized Cross Validation and similar, or using iterated nested Laplace approximation for fully Bayesian inference. See Wood (2017) <doi:10.1201/9781315370279> for an overview. Includes a gam() function, a wide variety of smoothers, 'JAGS' support and distributions beyond the exponential family.

Maintained by Simon Wood. Last updated 1 years ago.

openblas openmp

1.7 match 32 stars 12.71 score 17k scripts 7.8k dependents

spatstat

spatstat.random:Random Generation Functionality for the 'spatstat' Family

Functionality for random generation of spatial data in the 'spatstat' family of packages. Generates random spatial patterns of points according to many simple rules (complete spatial randomness, Poisson, binomial, random grid, systematic, cell), randomised alteration of patterns (thinning, random shift, jittering), simulated realisations of random point processes including simple sequential inhibition, Matern inhibition models, Neyman-Scott cluster processes (using direct, Brix-Kendall, or hybrid algorithms), log-Gaussian Cox processes, product shot noise cluster processes and Gibbs point processes (using Metropolis-Hastings birth-death-shift algorithm, alternating Gibbs sampler, or coupling-from-the-past perfect simulation). Also generates random spatial patterns of line segments, random tessellations, and random images (random noise, random mosaics). Excludes random generation on a linear network, which is covered by the separate package 'spatstat.linnet'.

Maintained by Adrian Baddeley. Last updated 13 days ago.

point-processes random-generation simulation spatial-sampling spatial-simulation cpp

2.0 match 5 stars 10.85 score 84 scripts 175 dependents

jeffreyracine

np:Nonparametric Kernel Smoothing Methods for Mixed Data Types

Nonparametric (and semiparametric) kernel methods that seamlessly handle a mix of continuous, unordered, and ordered factor data types. We would like to gratefully acknowledge support from the Natural Sciences and Engineering Research Council of Canada (NSERC, <https://www.nserc-crsng.gc.ca/>), the Social Sciences and Humanities Research Council of Canada (SSHRC, <https://www.sshrc-crsh.gc.ca/>), and the Shared Hierarchical Academic Research Computing Network (SHARCNET, <https://sharcnet.ca/>). We would also like to acknowledge the contributions of the GNU GSL authors. In particular, we adapt the GNU GSL B-spline routine gsl_bspline.c adding automated support for quantile knots (in addition to uniform knots), providing missing functionality for derivatives, and for extending the splines beyond their endpoints.

Maintained by Jeffrey S. Racine. Last updated 2 months ago.

1.7 match 49 stars 12.64 score 672 scripts 44 dependents

flavjack

huito:Reproducible and Flexible Label Design

An open-source R package to deploys reproducible and flexible labels using layers. The 'huito' package is part of the 'inkaverse' project for developing different procedures and tools used in plant science and experimental designs. Learn more about the 'inkaverse' project at <https://inkaverse.com/>.

Maintained by Flavio Lozano-Isla. Last updated 7 months ago.

inkaverse labels stickers

4.5 match 1 stars 4.79 score 31 scripts

process-analytics

bpmnVisualizationR:Visualize Process Execution Data on 'BPMN' Diagrams

To visualize the execution data of the processes on 'BPMN' (Business Process Model and Notation) diagrams, using overlays, style customization and interactions, with the 'bpmn-visualization' 'TypeScript' library.

Maintained by Celine Souchet. Last updated 2 months ago.

bpmn bpmn-visualization hacktoberfest process-analytics visualization

3.9 match 16 stars 5.51 score 3 scripts

cran

MNM:Multivariate Nonparametric Methods. An Approach Based on Spatial Signs and Ranks

Multivariate tests, estimates and methods based on the identity score, spatial sign score and spatial rank score are provided. The methods include one and c-sample problems, shape estimation and testing, linear regression and principal components. The methodology is described in Oja (2010) <doi:10.1007/978-1-4419-0468-3> and Nordhausen and Oja (2011) <doi:10.18637/jss.v043.i05>.

Maintained by Klaus Nordhausen. Last updated 1 years ago.

8.6 match 2.48 score 1 dependents

cran

forge:Casting Values into Shape

Helper functions with a consistent interface to coerce and verify the types and shapes of values for input checking.

Maintained by Kevin Kuo. Last updated 6 years ago.

5.9 match 3.60 score 4 dependents

ateucher

rmapshaper:Client for 'mapshaper' for 'Geospatial' Operations

Edit and simplify 'geojson', 'Spatial', and 'sf' objects. This is wrapper around the 'mapshaper' 'JavaScript' library by Matthew Bloch <https://github.com/mbloch/mapshaper/> to perform topologically-aware polygon simplification, as well as other operations such as clipping, erasing, dissolving, and converting 'multi-part' to 'single-part' geometries.

Maintained by Andy Teucher. Last updated 9 months ago.

rlang

1.8 match 204 stars 11.64 score 2.1k scripts 18 dependents

lbenitesanchez

ssmsn:Scale-Shape Mixtures of Skew-Normal Distributions

It provides the density and random number generator for the Scale-Shape Mixtures of Skew-Normal Distributions proposed by Jamalizadeh and Lin (2016) <doi:10.1007/s00180-016-0691-1>.

Maintained by Luis Benites. Last updated 8 years ago.

6.9 match 2 stars 3.00 score 2 scripts