Showing 75 of total 75 results (show query)
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 10 days ago.
data-visualisationvisualisation
6.1 match 6.6k stars 25.10 score 645k scripts 7.5k dependents
r4ss
r4ss:R Code for Stock Synthesis
A collection of R functions for use with Stock Synthesis, a fisheries stock assessment modeling platform written in ADMB by Dr. Richard D. Methot at the NOAA Northwest Fisheries Science Center. The functions include tools for summarizing and plotting results, manipulating files, visualizing model parameterizations, and various other common stock assessment tasks. This version of '{r4ss}' is compatible with Stock Synthesis versions 3.24 through 3.30 (specifically version 3.30.23.1, from December 2024). Support for 3.24 models is only through the core functions for reading output and plotting.
Maintained by Ian G. Taylor. Last updated 5 days ago.
fisheriesfisheries-stock-assessmentstock-synthesis
11.8 match 43 stars 11.38 score 1.0k scripts 2 dependents
wilkelab
ggridges:Ridgeline Plots in 'ggplot2'
Ridgeline plots provide a convenient way of visualizing changes in distributions over time or space. This package enables the creation of such plots in 'ggplot2'.
Maintained by Claus O. Wilke. Last updated 3 months ago.
5.0 match 418 stars 16.71 score 14k scripts 285 dependents
elvanceyhan
pcds:Proximity Catch Digraphs and Their Applications
Contains the functions for construction and visualization of various families of the proximity catch digraphs (PCDs) (see (Ceyhan (2005) ISBN:978-3-639-19063-2), for computing the graph invariants for testing the patterns of segregation and association against complete spatial randomness (CSR) or uniformity in one, two and three dimensional cases. The package also has tools for generating points from these spatial patterns. The graph invariants used in testing spatial point data are the domination number (Ceyhan (2011) <doi:10.1080/03610921003597211>) and arc density (Ceyhan et al. (2006) <doi:10.1016/j.csda.2005.03.002>; Ceyhan et al. (2007) <doi:10.1002/cjs.5550350106>). The PCD families considered are Arc-Slice PCDs, Proportional-Edge PCDs, and Central Similarity PCDs.
Maintained by Elvan Ceyhan. Last updated 2 years ago.
12.7 match 5.80 score 21 scripts 2 dependents
tylermorganwall
spacefillr:Space-Filling Random and Quasi-Random Sequences
Generates random and quasi-random space-filling sequences. Supports the following sequences: 'Halton', 'Sobol', 'Owen'-scrambled 'Sobol', 'Owen'-scrambled 'Sobol' with errors distributed as blue noise, progressive jittered, progressive multi-jittered ('PMJ'), 'PMJ' with blue noise, 'PMJ02', and 'PMJ02' with blue noise. Includes a 'C++' 'API'. Methods derived from "Constructing Sobol sequences with better two-dimensional projections" (2012) <doi:10.1137/070709359> S. Joe and F. Y. Kuo, "Progressive Multi-Jittered Sample Sequences" (2018) <https://graphics.pixar.com/library/ProgressiveMultiJitteredSampling/paper.pdf> Christensen, P., Kensler, A. and Kilpatrick, C., and "A Low-Discrepancy Sampler that Distributes Monte Carlo Errors as a Blue Noise in Screen Space" (2019) E. Heitz, B. Laurent, O. Victor, C. David and I. Jean-Claude, <doi:10.1145/3306307.3328191>.
Maintained by Tyler Morgan-Wall. Last updated 21 days ago.
halton-sequencequasi-random-generatorsobol-sequencecpp
9.5 match 7 stars 7.07 score 3 scripts 45 dependents
bioc
ggtreeExtra:An R Package To Add Geometric Layers On Circular Or Other Layout Tree Of "ggtree"
'ggtreeExtra' extends the method for mapping and visualizing associated data on phylogenetic tree using 'ggtree'. These associated data can be presented on the external panels to circular layout, fan layout, or other rectangular layout tree built by 'ggtree' with the grammar of 'ggplot2'.
Maintained by Shuangbin Xu. Last updated 5 months ago.
softwarevisualizationphylogeneticsannotation
6.7 match 90 stars 9.72 score 426 scripts 3 dependents
vpetukhov
ggrastr:Rasterize Layers for 'ggplot2'
Rasterize only specific layers of a 'ggplot2' plot while simultaneously keeping all labels and text in vector format. This allows users to keep plots within the reasonable size limit without loosing vector properties of the scale-sensitive information.
Maintained by Evan Biederstedt. Last updated 2 years ago.
4.8 match 220 stars 13.37 score 1.9k scripts 53 dependents
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 1 years ago.
ggplot-extensionggplot2visualizationcpp
3.6 match 920 stars 15.83 score 9.3k scripts 293 dependents
sidiropoulos
sinaplot:An Enhanced Chart for Simple and Truthful Representation of Single Observations over Multiple Classes
The sinaplot is a data visualization chart suitable for plotting any single variable in a multiclass data set. It is an enhanced jitter strip chart, where the width of the jitter is controlled by the density distribution of the data within each class.
Maintained by Nikos Sidiropoulos. Last updated 8 years ago.
11.8 match 2 stars 4.76 score 57 scripts
eclarke
ggbeeswarm:Categorical Scatter (Violin Point) Plots
Provides two methods of plotting categorical scatter plots such that the arrangement of points within a category reflects the density of data at that region, and avoids over-plotting.
Maintained by Erik Clarke. Last updated 4 months ago.
3.4 match 550 stars 15.45 score 7.6k scripts 84 dependents
dcousin3
superb:Summary Plots with Adjusted Error Bars
Computes standard error and confidence interval of various descriptive statistics under various designs and sampling schemes. The main function, superb(), return a plot. It can also be used to obtain a dataframe with the statistics and their precision intervals so that other plotting environments (e.g., Excel) can be used. See Cousineau and colleagues (2021) <doi:10.1177/25152459211035109> or Cousineau (2017) <doi:10.5709/acp-0214-z> for a review as well as Cousineau (2005) <doi:10.20982/tqmp.01.1.p042>, Morey (2008) <doi:10.20982/tqmp.04.2.p061>, Baguley (2012) <doi:10.3758/s13428-011-0123-7>, Cousineau & Laurencelle (2016) <doi:10.1037/met0000055>, Cousineau & O'Brien (2014) <doi:10.3758/s13428-013-0441-z>, Calderini & Harding <doi:10.20982/tqmp.15.1.p001> for specific references.
Maintained by Denis Cousineau. Last updated 2 months ago.
error-barsplottingstatisticssummary-plotssummary-statisticsvisualization
5.3 match 19 stars 9.55 score 155 scripts 2 dependents
r-spatial
sf:Simple Features for R
Support for simple feature access, a standardized way to encode and analyze spatial vector data. Binds to 'GDAL' <doi: 10.5281/zenodo.5884351> for reading and writing data, to 'GEOS' <doi: 10.5281/zenodo.11396894> for geometrical operations, and to 'PROJ' <doi: 10.5281/zenodo.5884394> for projection conversions and datum transformations. Uses by default the 's2' package for geometry operations on geodetic (long/lat degree) coordinates.
Maintained by Edzer Pebesma. Last updated 17 days ago.
2.3 match 1.4k stars 22.42 score 117k scripts 1.2k dependents
animint
animint2:Animated Interactive Grammar of Graphics
Functions are provided for defining animated, interactive data visualizations in R code, and rendering on a web page. The 2018 Journal of Computational and Graphical Statistics paper, <doi:10.1080/10618600.2018.1513367> describes the concepts implemented.
Maintained by Toby Hocking. Last updated 28 days ago.
5.5 match 64 stars 8.87 score 173 scripts
tdhock
directlabels:Direct Labels for Multicolor Plots
An extensible framework for automatically placing direct labels onto multicolor 'lattice' or 'ggplot2' plots. Label positions are described using Positioning Methods which can be re-used across several different plots. There are heuristics for examining "trellis" and "ggplot" objects and inferring an appropriate Positioning Method.
Maintained by Toby Dylan Hocking. Last updated 11 months ago.
4.5 match 83 stars 10.62 score 1.8k scripts 16 dependents
smin95
smplot2:Create Standalone and Composite Plots in 'ggplot2' for Publications
Provides functions for creating and annotating a composite plot in 'ggplot2'. Offers background themes and shortcut plotting functions that produce figures that are appropriate for the format of scientific journals. Some methods are described in Min and Zhou (2021) <doi:10.3389/fgene.2021.802894>.
Maintained by Seung Hyun Min. Last updated 1 months ago.
easy-to-useggplot2scientific-visualizationvisualization
5.5 match 24 stars 7.08 score 288 scripts 1 dependents
erocoar
gghalves:Compose Half-Half Plots Using Your Favourite Geoms
A 'ggplot2' extension for easy plotting of half-half geom combinations. Think half boxplot and half jitterplot, or half violinplot and half dotplot.
Maintained by Frederik Tiedemann. Last updated 2 years ago.
datavizggplot-extensionggplot2visualization
3.5 match 243 stars 10.78 score 872 scripts 7 dependents
edwbaker
sonicscrewdriver:Bioacoustic Analysis and Publication Tools
Provides tools for manipulating sound files for bioacoustic analysis, and preparing analyses these for publication. The package validates that values are physically possible wherever feasible.
Maintained by Ed Baker. Last updated 1 months ago.
5.2 match 6 stars 7.12 score 26 scripts
momx
Momocs:Morphometrics using R
The goal of 'Momocs' is to provide a complete, convenient, reproducible and open-source toolkit for 2D morphometrics. It includes most common 2D morphometrics approaches on outlines, open outlines, configurations of landmarks, traditional morphometrics, and facilities for data preparation, manipulation and visualization with a consistent grammar throughout. It allows reproducible, complex morphometrics analyses and other morphometrics approaches should be easy to plug in, or develop from, on top of this canvas.
Maintained by Vincent Bonhomme. Last updated 1 years ago.
4.1 match 51 stars 7.42 score 346 scripts
statistikat
VIM:Visualization and Imputation of Missing Values
New tools for the visualization of missing and/or imputed values are introduced, which can be used for exploring the data and the structure of the missing and/or imputed values. Depending on this structure of the missing values, the corresponding methods may help to identify the mechanism generating the missing values and allows to explore the data including missing values. In addition, the quality of imputation can be visually explored using various univariate, bivariate, multiple and multivariate plot methods. A graphical user interface available in the separate package VIMGUI allows an easy handling of the implemented plot methods.
Maintained by Matthias Templ. Last updated 7 months ago.
hotdeckimputation-methodsmodel-predictionsvisualizationcpp
2.0 match 85 stars 14.44 score 2.6k scripts 19 dependents
great-northern-diver
zenplots:Zigzag Expanded Navigation Plots
Graphical tools for visualizing high-dimensional data along a path of alternating one- and two-dimensional plots. Note that this includes interactive graphics plots based on 'loon' in turn based on 'tcltk' (included as part of the standard R distribution). It also requires 'graph' from Bioconductor. For more detail on use and algorithms, see <doi:10.18637/jss.v095.i04>.
Maintained by Wayne Oldford. Last updated 1 years ago.
dimensional-datadimensional-plotsgraphical-systemspairszigzag
5.1 match 3 stars 5.33 score 12 scripts 1 dependents
davidgohel
ggiraph:Make 'ggplot2' Graphics Interactive
Create interactive 'ggplot2' graphics using 'htmlwidgets'.
Maintained by David Gohel. Last updated 3 months ago.
1.9 match 819 stars 14.39 score 4.1k scripts 34 dependents
robinhankin
evitaicossa:Antiassociative Algebra
Methods to deal with the free antiassociative algebra over the reals with an arbitrary number of indeterminates. Antiassociativity means that (xy)z = -x(yz). Antiassociative algebras are nilpotent with nilindex four (Remm, 2022, <doi:10.48550/arXiv.2202.10812>) and this drives the design and philosophy of the package. Methods are defined to create and manipulate arbitrary elements of the antiassociative algebra, and to extract and replace coefficients. A vignette is provided.
Maintained by Robin K. S. Hankin. Last updated 6 days ago.
5.3 match 4.90 score
microsoft
wpa:Tools for Analysing and Visualising Viva Insights Data
Opinionated functions that enable easier and faster analysis of Viva Insights data. There are three main types of functions in 'wpa': (i) Standard functions create a 'ggplot' visual or a summary table based on a specific Viva Insights metric; (2) Report Generation functions generate HTML reports on a specific analysis area, e.g. Collaboration; (3) Other miscellaneous functions cover more specific applications (e.g. Subject Line text mining) of Viva Insights data. This package adheres to 'tidyverse' principles and works well with the pipe syntax. 'wpa' is built with the beginner-to-intermediate R users in mind, and is optimised for simplicity.
Maintained by Martin Chan. Last updated 4 months ago.
3.6 match 30 stars 6.69 score 39 scripts 1 dependentsbioc
iSEE:Interactive SummarizedExperiment Explorer
Create an interactive Shiny-based graphical user interface for exploring data stored in SummarizedExperiment objects, including row- and column-level metadata. The interface supports transmission of selections between plots and tables, code tracking, interactive tours, interactive or programmatic initialization, preservation of app state, and extensibility to new panel types via S4 classes. Special attention is given to single-cell data in a SingleCellExperiment object with visualization of dimensionality reduction results.
Maintained by Kevin Rue-Albrecht. Last updated 11 days ago.
cellbasedassaysclusteringdimensionreductionfeatureextractiongeneexpressionguiimmunooncologyshinyappssinglecelltranscriptiontranscriptomicsvisualizationdimension-reductionfeature-extractiongene-expressionhacktoberfesthuman-cell-atlasshinysingle-cell
1.9 match 225 stars 12.86 score 380 scripts 9 dependents
doi-usgs
EGRET:Exploration and Graphics for RivEr Trends
Statistics and graphics for streamflow history, water quality trends, and the statistical modeling algorithm: Weighted Regressions on Time, Discharge, and Season (WRTDS).
Maintained by Laura DeCicco. Last updated 4 months ago.
usgswater-qualitywater-quality-data
2.3 match 90 stars 10.72 score 362 scripts 1 dependents
aphalo
ggpp:Grammar Extensions to 'ggplot2'
Extensions to 'ggplot2' respecting the grammar of graphics paradigm. Geometries: geom_table(), geom_plot() and geom_grob() add insets to plots using native data coordinates, while geom_table_npc(), geom_plot_npc() and geom_grob_npc() do the same using "npc" coordinates through new aesthetics "npcx" and "npcy". Statistics: select observations based on 2D density. Positions: radial nudging away from a center point and nudging away from a line or curve; combined stacking and nudging; combined dodging and nudging.
Maintained by Pedro J. Aphalo. Last updated 21 days ago.
data-labelsdatavizggplot2-enhancementsggplot2-geomsggplot2-insetsggplot2-positions
1.9 match 130 stars 12.49 score 582 scripts 24 dependents
kbroman
qtl:Tools for Analyzing QTL Experiments
Analysis of experimental crosses to identify genes (called quantitative trait loci, QTLs) contributing to variation in quantitative traits. Broman et al. (2003) <doi:10.1093/bioinformatics/btg112>.
Maintained by Karl W Broman. Last updated 7 months ago.
1.8 match 80 stars 12.79 score 2.4k scripts 29 dependentsmicrosoft
vivainsights:Analyze and Visualize Data from 'Microsoft Viva Insights'
Provides a versatile range of functions, including exploratory data analysis, time-series analysis, organizational network analysis, and data validation, whilst at the same time implements a set of best practices in analyzing and visualizing data specific to 'Microsoft Viva Insights'.
Maintained by Martin Chan. Last updated 24 days ago.
3.6 match 11 stars 6.12 score 68 scripts
haleyjeppson
ggmosaic:Mosaic Plots in the 'ggplot2' Framework
Mosaic plots in the 'ggplot2' framework. Mosaic plot functionality is provided in a single 'ggplot2' layer by calling the geom 'mosaic'.
Maintained by Haley Jeppson. Last updated 6 months ago.
1.9 match 167 stars 11.63 score 1.8k scripts 4 dependentsrobinhankin
disordR:Non-Ordered Vectors
Functionality for manipulating values of associative maps. The package is a dependency for mvp-type packages that use the STL map class: it traps plausible idiom that is ill-defined (implementation-specific) and returns an informative error, rather than returning a possibly incorrect result. To cite the package in publications please use Hankin (2022) <doi:10.48550/ARXIV.2210.03856>.
Maintained by Robin K. S. Hankin. Last updated 4 months ago.
3.3 match 1 stars 6.59 score 20 dependentsbioc
DAPAR:Tools for the Differential Analysis of Proteins Abundance with R
The package DAPAR is a Bioconductor distributed R package which provides all the necessary functions to analyze quantitative data from label-free proteomics experiments. Contrarily to most other similar R packages, it is endowed with rich and user-friendly graphical interfaces, so that no programming skill is required (see `Prostar` package).
Maintained by Samuel Wieczorek. Last updated 5 months ago.
proteomicsnormalizationpreprocessingmassspectrometryqualitycontrolgodataimportprostar1
3.9 match 2 stars 5.42 score 22 scripts 1 dependents
aidangildea
duke:Creating a Color-Blind Friendly Duke Color Package
Generates visualizations with Duke’s official suite of colors in a color blind friendly way.
Maintained by Aidan Gildea. Last updated 1 years ago.
4.3 match 2 stars 4.88 score 15 scripts
davidhodge931
ggblanket:Simplify 'ggplot2' Visualisation
Simplify 'ggplot2' visualisation with 'ggblanket' wrapper functions.
Maintained by David Hodge. Last updated 6 days ago.
data-visualisationdata-visualizationggplotggplot-extensionggplot2ggplot2-enhancementsvisualisationvisualization
2.3 match 170 stars 8.43 score 45 scripts
jonathanlees
RSEIS:Seismic Time Series Analysis Tools
Multiple interactive codes to view and analyze seismic data, via spectrum analysis, wavelet transforms, particle motion, hodograms. Includes general time-series tools, plotting, filtering, interactive display.
Maintained by Jonathan M. Lees. Last updated 6 months ago.
4.3 match 3 stars 4.27 score 262 scripts 4 dependents
grantmcdermott
tinyplot:Lightweight Extension of the Base R Graphics System
Lightweight extension of the base R graphics system, with support for automatic legends, facets, themes, and various other enhancements.
Maintained by Grant McDermott. Last updated 9 hours ago.
1.9 match 313 stars 9.66 score 51 scripts 3 dependentsgreat-northern-diver
loon:Interactive Statistical Data Visualization
An extendable toolkit for interactive data visualization and exploration.
Maintained by R. Wayne Oldford. Last updated 2 years ago.
data-analysisdata-sciencedata-visualizationexploratory-analysisexploratory-data-analysishigh-dimensional-datainteractive-graphicsinteractive-visualizationsloonpythonstatistical-analysisstatistical-graphicsstatisticstcl-extensiontk
2.0 match 48 stars 9.00 score 93 scripts 5 dependents
fishfollower
stockassessment:State-Space Assessment Model
Fitting SAM...
Maintained by Anders Nielsen. Last updated 14 days ago.
2.3 match 49 stars 7.76 score 324 scripts 2 dependents
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.
1.9 match 11 stars 9.25 score 2.6k scripts 70 dependents
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 1 months ago.
convenience-functionsggplot2psychologystatisticsvisualization
1.5 match 43 stars 10.68 score 214 scripts 2 dependents
mlr-org
mlr3torch:Deep Learning with 'mlr3'
Deep Learning library that extends the mlr3 framework by building upon the 'torch' package. It allows to conveniently build, train, and evaluate deep learning models without having to worry about low level details. Custom architectures can be created using the graph language defined in 'mlr3pipelines'.
Maintained by Sebastian Fischer. Last updated 1 months ago.
data-sciencedeep-learningmachine-learningmlr3torch
2.0 match 42 stars 7.63 score 78 scriptsbioc
monocle:Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
Monocle performs differential expression and time-series analysis for single-cell expression experiments. It orders individual cells according to progress through a biological process, without knowing ahead of time which genes define progress through that process. Monocle also performs differential expression analysis, clustering, visualization, and other useful tasks on single cell expression data. It is designed to work with RNA-Seq and qPCR data, but could be used with other types as well.
Maintained by Cole Trapnell. Last updated 5 months ago.
immunooncologysequencingrnaseqgeneexpressiondifferentialexpressioninfrastructuredataimportdatarepresentationvisualizationclusteringmultiplecomparisonqualitycontrolcpp
1.7 match 8.89 score 1.6k scripts 2 dependents
paulojus
geoR:Analysis of Geostatistical Data
Geostatistical analysis including variogram-based, likelihood-based and Bayesian methods. Software companion for Diggle and Ribeiro (2007) <doi:10.1007/978-0-387-48536-2>.
Maintained by Paulo Justiniano Ribeiro Jr. Last updated 1 years ago.
2.0 match 10 stars 7.57 score 1.8k scripts 12 dependents
itsleeds
od:Manipulate and Map Origin-Destination Data
The aim of 'od' is to provide tools and example datasets for working with origin-destination ('OD') datasets of the type used to describe aggregate urban mobility patterns (Carey et al. 1981) <doi:10.1287/trsc.15.1.32>. The package builds on functions for working with 'OD' data in the package 'stplanr', (Lovelace and Ellison 2018) <doi:10.32614/RJ-2018-053> with a focus on computational efficiency and support for the 'sf' class system (Pebesma 2018) <doi:10.32614/RJ-2018-009>. With few dependencies and a simple class system based on data frames, the package is intended to facilitate efficient analysis of 'OD' datasets and to provide a place for developing new functions. The package enables the creation and analysis of geographic entities representing large scale mobility patterns, from daily travel between zones in cities to migration between countries.
Maintained by Robin Lovelace. Last updated 5 months ago.
1.8 match 33 stars 8.50 score 96 scripts 6 dependents
branchlab
metasnf:Meta Clustering with Similarity Network Fusion
Framework to facilitate patient subtyping with similarity network fusion and meta clustering. The similarity network fusion (SNF) algorithm was introduced by Wang et al. (2014) in <doi:10.1038/nmeth.2810>. SNF is a data integration approach that can transform high-dimensional and diverse data types into a single similarity network suitable for clustering with minimal loss of information from each initial data source. The meta clustering approach was introduced by Caruana et al. (2006) in <doi:10.1109/ICDM.2006.103>. Meta clustering involves generating a wide range of cluster solutions by adjusting clustering hyperparameters, then clustering the solutions themselves into a manageable number of qualitatively similar solutions, and finally characterizing representative solutions to find ones that are best for the user's specific context. This package provides a framework to easily transform multi-modal data into a wide range of similarity network fusion-derived cluster solutions as well as to visualize, characterize, and validate those solutions. Core package functionality includes easy customization of distance metrics, clustering algorithms, and SNF hyperparameters to generate diverse clustering solutions; calculation and plotting of associations between features, between patients, and between cluster solutions; and standard cluster validation approaches including resampled measures of cluster stability, standard metrics of cluster quality, and label propagation to evaluate generalizability in unseen data. Associated vignettes guide the user through using the package to identify patient subtypes while adhering to best practices for unsupervised learning.
Maintained by Prashanth S Velayudhan. Last updated 5 days ago.
bioinformaticsclusteringmetaclusteringsnf
1.8 match 8 stars 8.21 score 30 scripts
flr
FLSRTMB:FLSR in TMB
Estimates FLR spawner recruitment relationships in TMB
Maintained by Henning Winker. Last updated 15 days ago.
stock-recruitfisheriesflrtmbadcpp
3.9 match 3.67 score 26 scripts 1 dependents
cran
ggtern:An Extension to 'ggplot2', for the Creation of Ternary Diagrams
Extends the functionality of 'ggplot2', providing the capability to plot ternary diagrams for (subset of) the 'ggplot2' geometries. Additionally, 'ggtern' has implemented several NEW geometries which are unavailable to the standard 'ggplot2' release. For further examples and documentation, please proceed to the 'ggtern' website.
Maintained by Nicholas Hamilton. Last updated 12 months ago.
2.0 match 4 stars 7.05 score 1.1k scripts 6 dependents
molson2
JOUSBoost:Implements Under/Oversampling for Probability Estimation
Implements under/oversampling for probability estimation. To be used with machine learning methods such as AdaBoost, random forests, etc.
Maintained by Matthew Olson. Last updated 8 years ago.
4.0 match 3.33 score 43 scriptsbioc
trackViewer:A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data
Visualize mapped reads along with annotation as track layers for NGS dataset such as ChIP-seq, RNA-seq, miRNA-seq, DNA-seq, SNPs and methylation data.
Maintained by Jianhong Ou. Last updated 2 months ago.
1.5 match 8.71 score 145 scripts 2 dependents
tnagler
kde1d:Univariate Kernel Density Estimation
Provides an efficient implementation of univariate local polynomial kernel density estimators that can handle bounded and discrete data. See Geenens (2014) <doi:10.48550/arXiv.1303.4121>, Geenens and Wang (2018) <doi:10.48550/arXiv.1602.04862>, Nagler (2018a) <doi:10.48550/arXiv.1704.07457>, Nagler (2018b) <doi:10.48550/arXiv.1705.05431>.
Maintained by Thomas Nagler. Last updated 2 months ago.
2.0 match 13 stars 6.39 score 55 scripts 16 dependentsbioc
genefu:Computation of Gene Expression-Based Signatures in Breast Cancer
This package contains functions implementing various tasks usually required by gene expression analysis, especially in breast cancer studies: gene mapping between different microarray platforms, identification of molecular subtypes, implementation of published gene signatures, gene selection, and survival analysis.
Maintained by Benjamin Haibe-Kains. Last updated 4 months ago.
differentialexpressiongeneexpressionvisualizationclusteringclassification
1.7 match 7.42 score 193 scripts 3 dependents
dreamrs
vchartr:Interactive Charts with the 'JavaScript' 'VChart' Library
Provides an 'htmlwidgets' interface to 'VChart.js'. 'VChart', more than just a cross-platform charting library, but also an expressive data storyteller. 'VChart' examples and documentation are available here: <https://www.visactor.io/vchart>.
Maintained by Victor Perrier. Last updated 2 months ago.
1.8 match 9 stars 6.89 score 96 scripts
openanalytics
clinDataReview:Clinical Data Review Tool
Creation of interactive tables, listings and figures ('TLFs') and associated report for exploratory analysis of data in a clinical trial, e.g. for clinical oversight activities. Interactive figures include sunburst, treemap, scatterplot, line plot and barplot of counts data. Interactive tables include table of summary statistics (as counts of adverse events, enrollment table) and listings. Possibility to compare data (summary table or listing) across two data batches/sets. A clinical data review report is created via study-specific configuration files and template 'R Markdown' reports contained in the package.
Maintained by Laure Cougnaud. Last updated 9 months ago.
1.7 match 11 stars 7.10 score 36 scripts
kestrel99
pmxTools:Pharmacometric and Pharmacokinetic Toolkit
Pharmacometric tools for common data analytical tasks; closed-form solutions for calculating concentrations at given times after dosing based on compartmental PK models (1-compartment, 2-compartment and 3-compartment, covering infusions, zero- and first-order absorption, and lag times, after single doses and at steady state, per Bertrand & Mentre (2008) <http://lixoft.com/wp-content/uploads/2016/03/PKPDlibrary.pdf>); parametric simulation from NONMEM-generated parameter estimates and other output; and parsing, tabulating and plotting results generated by Perl-speaks-NONMEM (PsN).
Maintained by Justin Wilkins. Last updated 7 months ago.
nonmempharmacokineticssimulation
1.7 match 32 stars 6.43 score 84 scripts
cmstatr
cmstatr:Statistical Methods for Composite Material Data
An implementation of the statistical methods commonly used for advanced composite materials in aerospace applications. This package focuses on calculating basis values (lower tolerance bounds) for material strength properties, as well as performing the associated diagnostic tests. This package provides functions for calculating basis values assuming several different distributions, as well as providing functions for non-parametric methods of computing basis values. Functions are also provided for testing the hypothesis that there is no difference between strength and modulus data from an alternate sample and that from a "qualification" or "baseline" sample. For a discussion of these statistical methods and their use, see the Composite Materials Handbook, Volume 1 (2012, ISBN: 978-0-7680-7811-4). Additional details about this package are available in the paper by Kloppenborg (2020, <doi:10.21105/joss.02265>).
Maintained by Stefan Kloppenborg. Last updated 4 months ago.
composite-material-datadatamaterials-sciencestatistical-analysisstatistics
1.7 match 4 stars 6.26 score 23 scripts
theropod1
paleoDiv:Extracting and Visualizing Paleobiodiversity
Contains various tools for conveniently downloading and editing taxon-specific datasets from the Paleobiology Database <https://paleobiodb.org>, extracting information on abundance, temporal distribution of subtaxa and taxonomic diversity through deep time, and visualizing these data in relation to phylogeny and stratigraphy.
Maintained by Darius Nau. Last updated 5 months ago.
3.5 match 2 stars 2.78 score
lbb220
GISTools:Further Capabilities in Geographic Information Science
Mapping and spatial data manipulation tools - in particular drawing thematic maps with nice looking legends, and aggregation of point data to polygons.
Maintained by Binbin Lu. Last updated 6 months ago.
2.3 match 4.07 score 584 scripts
mspeekenbrink
sdamr:Statistics: Data Analysis and Modelling
Data sets and functions to support the books "Statistics: Data analysis and modelling" by Speekenbrink, M. (2021) <https://mspeekenbrink.github.io/sdam-book/> and "An R companion to Statistics: data analysis and modelling" by Speekenbrink, M. (2021) <https://mspeekenbrink.github.io/sdam-r-companion/>. All datasets analysed in these books are provided in this package. In addition, the package provides functions to compute sample statistics (variance, standard deviation, mode), create raincloud and enhanced Q-Q plots, and expand Anova results into omnibus tests and tests of individual contrasts.
Maintained by Maarten Speekenbrink. Last updated 1 months ago.
2.0 match 5 stars 4.39 score 99 scripts
miriamesteve
eat:Efficiency Analysis Trees
Functions are provided to determine production frontiers and technical efficiency measures through non-parametric techniques based upon regression trees. The package includes code for estimating radial input, output, directional and additive measures, plotting graphical representations of the scores and the production frontiers by means of trees, and determining rankings of importance of input variables in the analysis. Additionally, an adaptation of Random Forest by a set of individual Efficiency Analysis Trees for estimating technical efficiency is also included. More details in: <doi:10.1016/j.eswa.2020.113783>.
Maintained by Miriam Esteve. Last updated 3 years ago.
1.9 match 5 stars 4.68 score 19 scriptsbioc
SGCP:SGCP: A semi-supervised pipeline for gene clustering using self-training approach in gene co-expression networks
SGC is a semi-supervised pipeline for gene clustering in gene co-expression networks. SGC consists of multiple novel steps that enable the computation of highly enriched modules in an unsupervised manner. But unlike all existing frameworks, it further incorporates a novel step that leverages Gene Ontology information in a semi-supervised clustering method that further improves the quality of the computed modules.
Maintained by Niloofar AghaieAbiane. Last updated 5 months ago.
geneexpressiongenesetenrichmentnetworkenrichmentsystemsbiologyclassificationclusteringdimensionreductiongraphandnetworkneuralnetworknetworkmrnamicroarrayrnaseqvisualizationbioinformaticsgenecoexpressionnetworkgraphsnetworkclusteringnetworksself-trainingsemi-supervised-learningunsupervised-learning
1.7 match 2 stars 5.12 score 44 scriptsbioc
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.
guidatarepresentationnetworkmultiplecomparisonpathwaysreactomevisualizationgeneexpressiongenetargetanalysisbiocancer-interfacecancercancer-studiesrmarkdown
1.3 match 20 stars 5.95 score 7 scripts
chemhouse-group
rchemo:Dimension Reduction, Regression and Discrimination for Chemometrics
Data exploration and prediction with focus on high dimensional data and chemometrics. The package was initially designed about partial least squares regression and discrimination models and variants, in particular locally weighted PLS models (LWPLS). Then, it has been expanded to many other methods for analyzing high dimensional data. The name 'rchemo' comes from the fact that the package is orientated to chemometrics, but most of the provided methods are fully generic to other domains. Functions such as transform(), predict(), coef() and summary() are available. Tuning the predictive models is facilitated by generic functions gridscore() (validation dataset) and gridcv() (cross-validation). Faster versions are also available for models based on latent variables (LVs) (gridscorelv() and gridcvlv()) and ridge regularization (gridscorelb() and gridcvlb()).
Maintained by Marion Brandolini-Bunlon. Last updated 6 months ago.
2.3 match 3 stars 3.52 score 11 scriptscran
caroline:A Collection of Database, Data Structure, Visualization, and Utility Functions for R
The caroline R library contains dozens of functions useful for: database migration (dbWriteTable2), database style joins & aggregation (nerge, groupBy, & bestBy), data structure conversion (nv, tab2df), legend table making (sstable & leghead), automatic legend positioning for scatter and box plots (), plot annotation (labsegs & mvlabs), data visualization (pies, sparge, confound.grid & raPlot), character string manipulation (m & pad), file I/O (write.delim), batch scripting, data exploration, and more. The package's greatest contributions lie in the database style merge, aggregation and interface functions as well as in it's extensive use and propagation of row, column and vector names in most functions.
Maintained by David Schruth. Last updated 5 months ago.
2.3 match 3.29 score 108 scripts 3 dependents
syksy
hamlet:Hierarchical Optimal Matching and Machine Learning Toolbox
Various functions and algorithms are provided here for solving optimal matching tasks in the context of preclinical cancer studies. Further, various helper and plotting functions are provided for unsupervised and supervised machine learning as well as longitudinal mixed-effects modeling of tumor growth response patterns.
Maintained by Teemu Daniel Laajala. Last updated 2 years ago.
1.7 match 4.18 score 25 scripts 2 dependents
vavrycuk-zz
PoDBAY:Vaccine Efficacy Estimation Package
Set of functions that implement the PoDBAY method, described in the publication 'A method to estimate probability of disease and vaccine efficacy from clinical trial immunogenicity data' by Julie Dudasova, Regina Laube, Chandni Valiathan, Matthew C. Wiener, Ferdous Gheyas, Pavel Fiser, Justina Ivanauskaite, Frank Liu and Jeffrey R. Sachs (NPJ Vaccines, 2021), <doi:10.1038/s41541-021-00377-6>.
Maintained by Julie Dudasova (MSD). Last updated 3 years ago.
2.0 match 3.30 score 10 scripts
calbertsen
multiStockassessment:Fitting Multiple State-Space Assessment Models
Fitting multiple SAM models.
Maintained by Christoffer Moesgaard Albertsen. Last updated 3 months ago.
fisheriesfisheries-stock-assessmentstock-assessmentstockassessmentcpp
2.3 match 5 stars 2.88 score 5 scripts
dipterix
rutabaga:Simple R Tools for Analysis and Visualizations
Provides functions (R, C++) to speed up array calculations. Includes various tools for prettier visualizations via R base plots.
Maintained by Zhengjia Wang. Last updated 3 years ago.
3.8 match 1.70 score 2 scripts
ropensci
stplanr:Sustainable Transport Planning
Tools for transport planning with an emphasis on spatial transport data and non-motorized modes. The package was originally developed to support the 'Propensity to Cycle Tool', a publicly available strategic cycle network planning tool (Lovelace et al. 2017) <doi:10.5198/jtlu.2016.862>, but has since been extended to support public transport routing and accessibility analysis (Moreno-Monroy et al. 2017) <doi:10.1016/j.jtrangeo.2017.08.012> and routing with locally hosted routing engines such as 'OSRM' (Lowans et al. 2023) <doi:10.1016/j.enconman.2023.117337>. The main functions are for creating and manipulating geographic "desire lines" from origin-destination (OD) data (building on the 'od' package); calculating routes on the transport network locally and via interfaces to routing services such as <https://cyclestreets.net/> (Desjardins et al. 2021) <doi:10.1007/s11116-021-10197-1>; and calculating route segment attributes such as bearing. The package implements the 'travel flow aggregration' method described in Morgan and Lovelace (2020) <doi:10.1177/2399808320942779> and the 'OD jittering' method described in Lovelace et al. (2022) <doi:10.32866/001c.33873>. Further information on the package's aim and scope can be found in the vignettes and in a paper in the R Journal (Lovelace and Ellison 2018) <doi:10.32614/RJ-2018-053>, and in a paper outlining the landscape of open source software for geographic methods in transport planning (Lovelace, 2021) <doi:10.1007/s10109-020-00342-2>.
Maintained by Robin Lovelace. Last updated 7 months ago.
cyclecyclingdesire-linesorigin-destinationpeer-reviewedpubic-transportroute-networkroutesroutingspatialtransporttransport-planningtransportationwalking
0.5 match 427 stars 12.31 score 684 scripts 3 dependentsbioc
lute:Framework for cell size scale factor normalized bulk transcriptomics deconvolution experiments
Provides a framework for adjustment on cell type size when performing bulk transcripomics deconvolution. The main framework function provides a means of reference normalization using cell size scale factors. It allows for marker selection and deconvolution using non-negative least squares (NNLS) by default. The framework is extensible for other marker selection and deconvolution algorithms, and users may reuse the generics, methods, and classes for these when developing new algorithms.
Maintained by Sean K Maden. Last updated 5 months ago.
rnaseqsequencingsinglecellcoveragetranscriptomicsnormalization
1.2 match 2 stars 5.26 score 3 scripts
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.
1.3 match 4.10 score 33 scripts 2 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 2 days ago.
point-processesrandom-generationsimulationspatial-samplingspatial-simulationcpp
0.5 match 5 stars 10.81 score 84 scripts 175 dependentscran
freqparcoord:Novel Methods for Parallel Coordinates
New approaches to parallel coordinates plots for multivariate data visualization, including applications to clustering, outlier hunting and regression diagnostics. Includes general functions for multivariate nonparametric density and regression estimation, using parallel computation.
Maintained by Norm Matloff. Last updated 9 years ago.
2.0 match 1.78 score 2 dependents
yunrochung
varoc:Value Added Receiver Operating Characteristics Curve
A continuous version of the receiver operating characteristics (ROC) curve to visualize and assess the classification and continuity performances of biomarkers, diagnostic tests, or risk prediction models.
Maintained by Yunro Chung. Last updated 1 years ago.
1.9 match 1.00 scorecran
GeoAdjust:Accounting for Random Displacements of True GPS Coordinates of Data
The purpose is to account for the random displacements (jittering) of true survey household cluster center coordinates in geostatistical analyses of Demographic and Health Surveys program (DHS) data. Adjustment for jittering can be implemented either in the spatial random effect, or in the raster/distance based covariates, or in both. Detailed information about the methods behind the package functionality can be found in two preprints. Umut Altay, John Paige, Andrea Riebler, Geir-Arne Fuglstad (2022) <arXiv:2202.11035v2>. Umut Altay, John Paige, Andrea Riebler, Geir-Arne Fuglstad (2022) <arXiv:2211.07442v1>.
Maintained by Umut Altay. Last updated 2 years ago.
0.8 match 1.70 score 1 scripts