Showing 200 of total 413 results (show query)
yihui
animation:A Gallery of Animations in Statistics and Utilities to Create Animations
Provides functions for animations in statistics, covering topics in probability theory, mathematical statistics, multivariate statistics, non-parametric statistics, sampling survey, linear models, time series, computational statistics, data mining and machine learning. These functions may be helpful in teaching statistics and data analysis. Also provided in this package are a series of functions to save animations to various formats, e.g. Flash, 'GIF', HTML pages, 'PDF' and videos. 'PDF' animations can be inserted into 'Sweave' / 'knitr' easily.
Maintained by Yihui Xie. Last updated 2 years ago.
animationstatistical-computingstatistical-graphicsstatistics
83.7 match 208 stars 12.08 score 2.5k scripts 29 dependentshughjonesd
anim.plots:Simple Animated Plots for R
Simple animated versions of basic R plots, using the 'animation' package. Includes animated versions of plot, barplot, persp, contour, filled.contour, hist, curve, points, lines, text, symbols, segments, and arrows.
Maintained by David Hugh-Jones. Last updated 4 years ago.
114.9 match 8 stars 5.00 score 25 scriptskcf-jackson
animate:A Web-Based Graphics Device for Animated Visualisations
Implements a web-based graphics device for animated visualisations. Modelled on the 'base' syntax, it extends the 'base' graphics functions to support frame-by-frame animation and keyframes animation. The target use cases are real-time animated visualisations, including agent-based models, dynamical systems, and animated diagrams. The generated visualisations can be deployed as GIF images / MP4 videos, as 'Shiny' apps (with interactivity) or as HTML documents through embedding into R Markdown documents.
Maintained by Chun Fung Kwok. Last updated 11 months ago.
83.5 match 30 stars 6.88 score 84 scriptsthomasp85
gganimate:A Grammar of Animated Graphics
The grammar of graphics as implemented in the 'ggplot2' package has been successful in providing a powerful API for creating static visualisation. In order to extend the API for animated graphics this package provides a completely new set of grammar, fully compatible with 'ggplot2' for specifying transitions and animations in a flexible and extensible way.
Maintained by Thomas Lin Pedersen. Last updated 1 years ago.
animationdata-visualizationggplot-extensionggplot2transition
28.1 match 2.0k stars 15.87 score 13k scripts 25 dependentsggobi
tourr:Tour Methods for Multivariate Data Visualisation
Implements geodesic interpolation and basis generation functions that allow you to create new tour methods from R.
Maintained by Dianne Cook. Last updated 17 days ago.
27.0 match 65 stars 11.17 score 426 scripts 9 dependentscamhowitt
shinyLottie:Seamlessly Integrate 'Lottie' Animations into 'shiny' Applications
Easily integrate and control 'Lottie' animations within 'shiny' applications', without the need for idiosyncratic expression or use of 'JavaScript'. This includes utilities for generating animation instances, controlling playback, manipulating animation properties, and more. For more information on 'Lottie', see: <https://airbnb.io/lottie/#/>. Additionally, see the official 'Lottie' GitHub repository at <https://github.com/airbnb/lottie>.
Maintained by Cameron Howitt. Last updated 9 months ago.
37.2 match 2 stars 5.52 score 37 scriptsbupaverse
processanimateR:Process Map Token Replay Animation
Provides animated process maps based on the 'procesmapR' package. Cases stored in event logs created with with 'bupaR' S3 class eventlog() are rendered as tokens (SVG shapes) and animated according to their occurrence times on top of the process map. For rendering SVG animations ('SMIL') and the 'htmlwidget' package are used.
Maintained by Felix Mannhardt. Last updated 2 years ago.
animationbuparbusiness-processevent-logshtmlwidgetsprocess-mapprocessminingsvg-animations
27.0 match 66 stars 7.54 score 106 scriptsthomasp85
tweenr:Interpolate Data for Smooth Animations
In order to create smooth animation between states of data, tweening is necessary. This package provides a range of functions for creating tweened data that can be used as basis for animation. Furthermore it adds a number of vectorized interpolaters for common R data types such as numeric, date and colour.
Maintained by Thomas Lin Pedersen. Last updated 1 years ago.
animationplottingtransitiontweeningcpp
15.7 match 399 stars 12.80 score 440 scripts 319 dependentscalbertsen
argosTrack:Fit Movement Models to Argos Data for Marine Animals
Fits various state-space animal movement models to Argos data. Models are fitted by maximum likelihood with the Laplace approximation via 'TMB' and 'nlminb'. Functionality to visualize and simulate the models is available.
Maintained by Christoffer Moesgaard Albertsen. Last updated 4 years ago.
animalanimal-behaviorargos-datac-plus-plusgps-datamovementmovement-ecologysolar-geolocatortrackingcpp
47.3 match 12 stars 3.92 score 14 scriptskenaho1
asbio:A Collection of Statistical Tools for Biologists
Contains functions from: Aho, K. (2014) Foundational and Applied Statistics for Biologists using R. CRC/Taylor and Francis, Boca Raton, FL, ISBN: 978-1-4398-7338-0.
Maintained by Ken Aho. Last updated 2 months ago.
25.0 match 5 stars 7.32 score 310 scripts 3 dependentsstatnet
ndtv:Network Dynamic Temporal Visualizations
Renders dynamic network data from 'networkDynamic' objects as movies, interactive animations, or other representations of changing relational structures and attributes.
Maintained by Skye Bender-deMoll. Last updated 9 months ago.
20.9 match 52 stars 8.36 score 254 scripts 1 dependentsaschleg
PetfindeR:'Petfinder' API Wrapper
Wrapper of the 'Petfinder API' <https://www.petfinder.com/developers/v2/docs/> that implements methods for interacting with and extracting data from the 'Petfinder' database. The 'Petfinder REST API' allows access to the 'Petfinder' database, one of the largest online databases of adoptable animals and animal welfare organizations across North America.
Maintained by Aaron Schlegel. Last updated 5 years ago.
animal-shelteranimal-welfare-organizationsanimalsapi-wrapperpetfinderpetfinder-apipetfinder-database
37.9 match 6 stars 4.48 score 6 scriptsianjonsen
aniMotum:Fit Continuous-Time State-Space and Latent Variable Models for Quality Control of Argos Satellite (and Other) Telemetry Data and for Estimating Changes in Animal Movement
Fits continuous-time random walk, correlated random walk and move persistence state-space models for location estimation and behavioural inference from animal tracking data ('Argos', processed light-level 'geolocation', 'GPS'). Template Model Builder ('TMB') is used for fast random-effects estimation. The 'Argos' data can be: (older) least squares-based locations; (newer) Kalman filter-based locations with error ellipse information; or a mixture of both. The models estimate two sets of location states corresponding to: 1) each observation, which are (usually) irregularly timed; and 2) user-specified time intervals (regular or irregular). A track re-routing function is provided to adjust location estimates for known movement barriers. Track simulation functions are provided. Latent variable models are also provided to estimate move persistence from track data not requiring state-space model filtering.
Maintained by Ian Jonsen. Last updated 10 days ago.
animal-movementanimal-trackingrandom-effects-modelstate-space-modelstmbcpp
21.9 match 39 stars 7.16 score 59 scriptstrinker
qdap:Bridging the Gap Between Qualitative Data and Quantitative Analysis
Automates many of the tasks associated with quantitative discourse analysis of transcripts containing discourse including frequency counts of sentence types, words, sentences, turns of talk, syllables and other assorted analysis tasks. The package provides parsing tools for preparing transcript data. Many functions enable the user to aggregate data by any number of grouping variables, providing analysis and seamless integration with other R packages that undertake higher level analysis and visualization of text. This affords the user a more efficient and targeted analysis. 'qdap' is designed for transcript analysis, however, many functions are applicable to other areas of Text Mining/ Natural Language Processing.
Maintained by Tyler Rinker. Last updated 4 years ago.
qdapquantitative-discourse-analysistext-analysistext-miningtext-plottingopenjdk
14.0 match 176 stars 9.61 score 1.3k scripts 3 dependentsropensci
spatsoc:Group Animal Relocation Data by Spatial and Temporal Relationship
Detects spatial and temporal groups in GPS relocations (Robitaille et al. (2019) <doi:10.1111/2041-210X.13215>). It can be used to convert GPS relocations to gambit-of-the-group format to build proximity-based social networks In addition, the randomizations function provides data-stream randomization methods suitable for GPS data.
Maintained by Alec L. Robitaille. Last updated 1 months ago.
12.9 match 24 stars 9.97 score 145 scripts 3 dependentsdmurdoch
rgl:3D Visualization Using OpenGL
Provides medium to high level functions for 3D interactive graphics, including functions modelled on base graphics (plot3d(), etc.) as well as functions for constructing representations of geometric objects (cube3d(), etc.). Output may be on screen using OpenGL, or to various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Maintained by Duncan Murdoch. Last updated 2 months ago.
graphicsopenglrglwebgllibglulibglvndlibpnglibx11freetypecpp
6.8 match 91 stars 17.49 score 7.3k scripts 300 dependentsrich-iannone
omsvg:Build and Transform 'SVG' Objects
Build 'SVG' components using element-based functions. With an 'svg' object, we can modify its graphical elements with a suite of transform functions.
Maintained by Richard Iannone. Last updated 4 years ago.
25.9 match 51 stars 4.55 score 14 scriptssckott
cowsay:Messages, Warnings, Strings with Ascii Animals
Allows printing of character strings as messages/warnings/etc. with ASCII animals, including cats, cows, frogs, chickens, ghosts, and more.
Maintained by Scott Chamberlain. Last updated 2 months ago.
11.5 match 320 stars 10.23 score 239 scriptsdreamrs
shinyWidgets:Custom Inputs Widgets for Shiny
Collection of custom input controls and user interface components for 'Shiny' applications. Give your applications a unique and colorful style !
Maintained by Victor Perrier. Last updated 12 days ago.
6.8 match 849 stars 17.05 score 8.1k scripts 218 dependentsbiodiverse
unmarked:Models for Data from Unmarked Animals
Fits hierarchical models of animal abundance and occurrence to data collected using survey methods such as point counts, site occupancy sampling, distance sampling, removal sampling, and double observer sampling. Parameters governing the state and observation processes can be modeled as functions of covariates. References: Kellner et al. (2023) <doi:10.1111/2041-210X.14123>, Fiske and Chandler (2011) <doi:10.18637/jss.v043.i10>.
Maintained by Ken Kellner. Last updated 1 days ago.
8.3 match 4 stars 13.03 score 652 scripts 12 dependentsropensci
magick:Advanced Graphics and Image-Processing in R
Bindings to 'ImageMagick': the most comprehensive open-source image processing library available. Supports many common formats (png, jpeg, tiff, pdf, etc) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All operations are vectorized via the Magick++ STL meaning they operate either on a single frame or a series of frames for working with layers, collages, or animation. In RStudio images are automatically previewed when printed to the console, resulting in an interactive editing environment. The latest version of the package includes a native graphics device for creating in-memory graphics or drawing onto images using pixel coordinates.
Maintained by Jeroen Ooms. Last updated 20 days ago.
image-manipulationimage-processingimagemagickcpp
6.0 match 468 stars 17.31 score 9.0k scripts 256 dependentsthomasp85
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.
animationdata-visualizationinterpolationmatching-shapestweeningcpp
10.5 match 116 stars 9.82 score 772 scripts 26 dependentsmarce10
warbleR:Streamline Bioacoustic Analysis
Functions aiming to facilitate the analysis of the structure of animal acoustic signals in 'R'. 'warbleR' makes use of the basic sound analysis tools from the packages 'tuneR' and 'seewave', and offers new tools for explore and quantify acoustic signal structure. The package allows to organize and manipulate multiple sound files, create spectrograms of complete recordings or individual signals in different formats, run several measures of acoustic structure, and characterize different structural levels in acoustic signals.
Maintained by Marcelo Araya-Salas. Last updated 2 months ago.
animal-acoustic-signalsaudio-processingbioacousticsspectrogramstreamline-analysiscpp
9.2 match 54 stars 11.01 score 270 scripts 4 dependentsinbo
etn:Access Data from the European Tracking Network
Package with functions to access and process data from the European Tracking Network hosted by VLIZ.
Maintained by Pieter Huybrechts. Last updated 2 months ago.
animal-movementanimal-trackingbiologgingdata-accessfishlifewatchoscibio
22.6 match 8 stars 4.15 score 14 scriptsropensci
baRulho:Quantifying (Animal) Sound Degradation
Intended to facilitate acoustic analysis of (animal) sound propagation experiments, which typically aim to quantify changes in signal structure when transmitted in a given habitat by broadcasting and re-recording animal sounds at increasing distances. The package offers a workflow with functions to prepare the data set for analysis as well as to calculate and visualize several degradation metrics, including blur ratio, signal-to-noise ratio, excess attenuation and envelope correlation among others (Dabelsteen et al 1993 <doi:10.1121/1.406682>).
Maintained by Marcelo Araya-Salas. Last updated 24 days ago.
acoustic-signalsanimalbehaviorbioacoustics
13.9 match 7 stars 6.72 score 18 scriptsnspyrison
spinifex:Manual Tours, Manual Control of Dynamic Projections of Numeric Multivariate Data
Data visualization tours animates linear projection of multivariate data as its basis (ie. orientation) changes. The 'spinifex' packages generates paths for manual tours by manipulating the contribution of a single variable at a time Cook & Buja (1997) <doi:10.1080/10618600.1997.10474754>. Other types of tours, such as grand (random walk) and guided (optimizing some objective function) are available in the 'tourr' package Wickham et al. <doi:10.18637/jss.v040.i02>. 'spinifex' builds on 'tourr' and can render tours with 'gganimate' and 'plotly' graphics, and allows for exporting as an .html widget and as an .gif, respectively. This work is fully discussed in Spyrison & Cook (2020) <doi:10.32614/RJ-2020-027>.
Maintained by Nicholas Spyrison. Last updated 2 months ago.
dimensionreductiontoursvisualization
14.9 match 3 stars 6.28 score 105 scripts 1 dependentsrspatial
terra:Spatial Data Analysis
Methods for spatial data analysis with vector (points, lines, polygons) and raster (grid) data. Methods for vector data include geometric operations such as intersect and buffer. Raster methods include local, focal, global, zonal and geometric operations. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/> to get started. 'terra' replaces the 'raster' package ('terra' can do more, and it is faster and easier to use).
Maintained by Robert J. Hijmans. Last updated 1 days ago.
geospatialrasterspatialvectoronetbbprojgdalgeoscpp
5.3 match 559 stars 17.64 score 17k scripts 851 dependentsswarm-lab
swaRm:Processing Collective Movement Data
Function library for processing collective movement data (e.g. fish schools, ungulate herds, baboon troops) collected from GPS trackers or computer vision tracking software.
Maintained by Simon Garnier. Last updated 1 years ago.
animal-behavioranimal-behaviourcollective-behaviorcollective-behaviour
16.8 match 21 stars 5.50 score 8 scripts 1 dependentscovaruber
sommer:Solving Mixed Model Equations in R
Structural multivariate-univariate linear mixed model solver for estimation of multiple random effects with unknown variance-covariance structures (e.g., heterogeneous and unstructured) and known covariance among levels of random effects (e.g., pedigree and genomic relationship matrices) (Covarrubias-Pazaran, 2016 <doi:10.1371/journal.pone.0156744>; Maier et al., 2015 <doi:10.1016/j.ajhg.2014.12.006>; Jensen et al., 1997). REML estimates can be obtained using the Direct-Inversion Newton-Raphson and Direct-Inversion Average Information algorithms for the problems r x r (r being the number of records) or using the Henderson-based average information algorithm for the problem c x c (c being the number of coefficients to estimate). Spatial models can also be fitted using the two-dimensional spline functionality available.
Maintained by Giovanny Covarrubias-Pazaran. Last updated 22 days ago.
average-informationmixed-modelsrcpparmadilloopenblascppopenmp
7.2 match 43 stars 12.70 score 300 scripts 9 dependentswilkox
ggfittext:Fit Text Inside a Box in 'ggplot2'
A 'ggplot2' extension to fit text into a box by growing, shrinking or wrapping the text.
Maintained by David Wilkins. Last updated 1 years ago.
8.3 match 306 stars 11.08 score 234 scripts 33 dependentsocean-tracking-network
glatos:A package for the Great Lakes Acoustic Telemetry Observation System
Functions useful to members of the Great Lakes Acoustic Telemetry Observation System https://glatos.glos.us; many more broadly relevant to simulating, processing, analysing, and visualizing acoustic telemetry data.
Maintained by Christopher Holbrook. Last updated 6 months ago.
14.1 match 10 stars 6.38 score 112 scriptsroaldarbol
animovement:An R toolbox for analysing animal movement across space and time
An R toolbox for analysing animal movement across space and time.
Maintained by Mikkel Roald-Arbøl. Last updated 2 months ago.
animal-behaviouranimal-movementneuroethologyneuroscience
18.4 match 10 stars 4.81 score 8 scriptsbwlewis
threejs:Interactive 3D Scatter Plots, Networks and Globes
Create interactive 3D scatter plots, network plots, and globes using the 'three.js' visualization library (<https://threejs.org>).
Maintained by B. W. Lewis. Last updated 3 years ago.
data-visualizationgraph-animationigraphthreejswebgl
7.5 match 304 stars 11.67 score 522 scripts 28 dependentsjmsigner
amt:Animal Movement Tools
Manage and analyze animal movement data. The functionality of 'amt' includes methods to calculate home ranges, track statistics (e.g. step lengths, speed, or turning angles), prepare data for fitting habitat selection analyses, and simulation of space-use from fitted step-selection functions.
Maintained by Johannes Signer. Last updated 4 months ago.
8.2 match 41 stars 10.54 score 418 scriptsrspatial
raster:Geographic Data Analysis and Modeling
Reading, writing, manipulating, analyzing and modeling of spatial data. This package has been superseded by the "terra" package <https://CRAN.R-project.org/package=terra>.
Maintained by Robert J. Hijmans. Last updated 2 months ago.
4.9 match 164 stars 17.05 score 58k scripts 555 dependentsyang-tang
shinyjqui:'jQuery UI' Interactions and Effects for Shiny
An extension to shiny that brings interactions and animation effects from 'jQuery UI' library.
Maintained by Yang Tang. Last updated 1 years ago.
7.7 match 276 stars 10.72 score 464 scripts 16 dependentsswarm-lab
trackdf:Data Frame Class for Tracking Data
Data frame class for storing collective movement data (e.g. fish schools, ungulate herds, baboon troops) collected from GPS trackers or computer vision tracking software.
Maintained by Simon Garnier. Last updated 2 years ago.
animal-behavioranimal-behaviourgpsgps-data
15.0 match 4 stars 5.42 score 11 scripts 1 dependentsbart1
move:Visualizing and Analyzing Animal Track Data
Contains functions to access movement data stored in 'movebank.org' as well as tools to visualize and statistically analyze animal movement data, among others functions to calculate dynamic Brownian Bridge Movement Models. Move helps addressing movement ecology questions.
Maintained by Bart Kranstauber. Last updated 4 months ago.
9.1 match 8.74 score 690 scripts 3 dependentsmikejohnson51
climateR:climateR
Find, subset, and retrive geospatial data by AOI.
Maintained by Mike Johnson. Last updated 3 months ago.
aoiclimatedatasetgeospatialgridded-climate-dataweather
9.0 match 187 stars 8.74 score 156 scripts 1 dependentsotoliths
SP2000:Catalogue of Life Toolkit
A programmatic interface to <http://sp2000.org.cn>, re-written based on an accompanying 'Species 2000' API. Access tables describing catalogue of the Chinese known species of animals, plants, fungi, micro-organisms, and more. This package also supports access to catalogue of life global <http://catalogueoflife.org>, China animal scientific database <http://zoology.especies.cn> and catalogue of life Taiwan <https://taibnet.sinica.edu.tw/home_eng.php>. The development of 'SP2000' package were supported by Biodiversity Survey and Assessment Project of the Ministry of Ecology and Environment, China <2019HJ2096001006>,Yunnan University's "Double First Class" Project <C176240405> and Yunnan University's Research Innovation Fund for Graduate Students <2019227>.
Maintained by Liuyong Ding. Last updated 1 years ago.
animalsbiodiversitycatalogue-of-life-chinacatalogue-of-life-global-checklistcatalogue-of-life-taiwan-checklistchinachina-animal-scientific-databasefungimicroorganismsplantsredlist-of-chinese-biodiversityspecies2000
20.4 match 13 stars 3.81 score 3 scriptsclementcalenge
adehabitatLT:Analysis of Animal Movements
A collection of tools for the analysis of animal movements.
Maintained by Clement Calenge. Last updated 6 months ago.
8.8 match 6 stars 8.60 score 370 scripts 12 dependentsphuse-org
sendigR:Enable Cross-Study Analysis of 'CDISC' 'SEND' Datasets
A system enables cross study Analysis by extracting and filtering study data for control animals from 'CDISC' 'SEND' Study Repository. These data types are supported: Body Weights, Laboratory test results and Microscopic findings. These database types are supported: 'SQLite' and 'Oracle'.
Maintained by Wenxian Wang. Last updated 10 days ago.
12.0 match 12 stars 6.28 score 6 scriptslgnbhl
aos:Animate on Scroll Library for 'shiny'
Trigger animation effects on scroll on any HTML element of 'shiny' and 'rmarkdown', such as any text or plot, thanks to the 'AOS' Animate On Scroll jQuery library <http://michalsnik.github.io/aos/>.
Maintained by Félix Luginbuhl. Last updated 6 months ago.
15.9 match 7 stars 4.50 score 15 scriptsropensci
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-movementflydramotionmovement-dataoptitracktrajectoriestrajectory-analysisvisual-guidancevisual-perception
10.4 match 8 stars 6.56 score 102 scriptstrinker
wakefield:Generate Random Data Sets
Generates random data sets including: data.frames, lists, and vectors.
Maintained by Tyler Rinker. Last updated 5 years ago.
9.4 match 256 stars 7.13 score 209 scriptsclementcalenge
adehabitatHR:Home Range Estimation
A collection of tools for the estimation of animals home range.
Maintained by Clement Calenge. Last updated 6 months ago.
7.4 match 6 stars 8.73 score 752 scripts 9 dependentsanimint
animint2:Animated Interactive Grammar of Graphics
Functions are provided for defining animated, interactive data visualizations in R code, and rendering on a web page. The 2018 Journal of Computational and Graphical Statistics paper, <doi:10.1080/10618600.2018.1513367> describes the concepts implemented.
Maintained by Toby Hocking. Last updated 27 days ago.
7.2 match 64 stars 8.87 score 173 scriptsalanarnholt
BSDA:Basic Statistics and Data Analysis
Data sets for book "Basic Statistics and Data Analysis" by Larry J. Kitchens.
Maintained by Alan T. Arnholt. Last updated 2 years ago.
6.8 match 7 stars 9.11 score 1.3k scripts 6 dependentssymbolixau
mapdeck:Interactive Maps Using 'Mapbox GL JS' and 'Deck.gl'
Provides a mechanism to plot an interactive map using 'Mapbox GL' (<https://docs.mapbox.com/mapbox-gl-js/api/>), a javascript library for interactive maps, and 'Deck.gl' (<https://deck.gl/>), a javascript library which uses 'WebGL' for visualising large data sets.
Maintained by David Cooley. Last updated 3 months ago.
deckglgeospatialmapboxmapbox-glmapbox-gl-jsmapscpp
6.0 match 363 stars 10.30 score 368 scripts 1 dependentsmarce10
Rraven:Connecting R and 'Raven' Sound Analysis Software
A tool to exchange data between R and 'Raven' sound analysis software (Cornell Lab of Ornithology). Functions work on data formats compatible with the R package 'warbleR'.
Maintained by Marcelo Araya-Salas. Last updated 2 months ago.
10.0 match 10 stars 6.00 score 50 scriptsmarcusrowcliffe
activity:Animal Activity Statistics
Provides functions to express clock time data relative to anchor points (typically solar); fit kernel density functions to animal activity time data; plot activity distributions; quantify overall levels of activity; statistically compare activity metrics through bootstrapping; evaluate variation in linear variables with time (or other circular variables).
Maintained by Marcus Rowcliffe. Last updated 1 years ago.
13.4 match 1 stars 4.45 score 190 scripts 1 dependentshenryrscharf
anipaths:Animation of Multiple Trajectories with Uncertainty
Animation of observed trajectories using spline-based interpolation (see for example, Buderman, F. E., Hooten, M. B., Ivan, J. S. and Shenk, T. M. (2016), <doi:10.1111/2041-210X.12465> "A functional model for characterizing long-distance movement behaviour". Methods Ecol Evol). Intended to be used exploratory data analysis, and perhaps for preparation of presentations.
Maintained by Henry Scharf. Last updated 15 days ago.
20.4 match 2.92 score 14 scriptshelgasoft
echarty:Minimal R/Shiny Interface to JavaScript Library 'ECharts'
Deliver the full functionality of 'ECharts' with minimal overhead. 'echarty' users build R lists for 'ECharts' API. Lean set of powerful commands.
Maintained by Larry Helgason. Last updated 2 months ago.
3danimationboxplotchartscrosstalkechartsechartygeojsonglobegraphsheatmaphierarchical-dataleafletmapsmorphingshapefilesshinyvisualizationwebr
10.0 match 90 stars 5.95 score 20 scriptsbioc
orthogene:Interspecies gene mapping
`orthogene` is an R package for easy mapping of orthologous genes across hundreds of species. It pulls up-to-date gene ortholog mappings across **700+ organisms**. It also provides various utility functions to aggregate/expand common objects (e.g. data.frames, gene expression matrices, lists) using **1:1**, **many:1**, **1:many** or **many:many** gene mappings, both within- and between-species.
Maintained by Brian Schilder. Last updated 5 months ago.
geneticscomparativegenomicspreprocessingphylogeneticstranscriptomicsgeneexpressionanimal-modelsbioconductorbioconductor-packagebioinformaticsbiomedicinecomparative-genomicsevolutionary-biologygenesgenomicsontologiestranslational-research
7.5 match 42 stars 7.85 score 31 scripts 2 dependentschaoranhu
smam:Statistical Modeling of Animal Movements
Animal movement models including Moving-Resting Process with Embedded Brownian Motion (Yan et al., 2014, <doi:10.1007/s10144-013-0428-8>; Pozdnyakov et al., 2017, <doi:10.1007/s11009-017-9547-6>), Brownian Motion with Measurement Error (Pozdnyakov et al., 2014, <doi:10.1890/13-0532.1>), Moving-Resting-Handling Process with Embedded Brownian Motion (Pozdnyakov et al., 2020, <doi:10.1007/s11009-020-09774-1>), Moving-Resting Process with Measurement Error (Hu et al., 2021, <doi:10.1111/2041-210X.13694>), Moving-Moving Process with two Embedded Brownian Motions.
Maintained by Chaoran Hu. Last updated 1 years ago.
animal-movementbrownian-motionhidden-markov-modelhidden-statesmeasurement-errortelegraph-processgslcpp
12.9 match 3 stars 4.52 score 11 scriptsswechhya
shinyanimate:Animation for 'shiny' Elements
An extension of 'animate.css' that allows user to easily add animations to any UI element in 'shiny' app using the elements id.
Maintained by Swechhya Bista. Last updated 1 years ago.
11.8 match 39 stars 4.85 score 36 scriptstylerlittlefield
vov:CSS Animations for 'shiny' Elements
A wrapper around a CSS library called 'vov.css', intended for use in 'shiny' applications. Simply wrap a UI element in one of the animation functions to see it move.
Maintained by Tyler Littlefield. Last updated 5 years ago.
11.2 match 24 stars 4.96 score 76 scriptsgadenbuie
xaringanExtra:Extras and Extensions for 'xaringan' Slides
Extras and extensions for 'xaringan' slides. Navigate your slides with tile view. Make your slides editable, live! Announce slide changes with subtle tones. Animate slide transitions with 'animate.css'. Add tabbed panels to slides with 'panelset'. Use the 'Tachyons CSS' utility toolkit for rapid slide development. Scribble on your slides. Add a copy button to your code chunks with 'clipboard'. Add a logo or top or bottom banner to every slide. Broadcast slides to stay in sync with remote viewers. Include yourself in your slides with 'webcam'. Plus a whole lot more!
Maintained by Garrick Aden-Buie. Last updated 10 months ago.
remarkjsrmarkdownslidestabsxaringanxaringan-slides
6.4 match 450 stars 8.41 score 1.9k scripts 1 dependentsmmaechler
cluster:"Finding Groups in Data": Cluster Analysis Extended Rousseeuw et al.
Methods for Cluster analysis. Much extended the original from Peter Rousseeuw, Anja Struyf and Mia Hubert, based on Kaufman and Rousseeuw (1990) "Finding Groups in Data".
Maintained by Martin Maechler. Last updated 4 days ago.
4.5 match 3 stars 11.98 score 14k scripts 2.2k dependentsjimmcl
trajr:Animal Trajectory Analysis
A toolbox to assist with statistical analysis of animal trajectories. It provides simple access to algorithms for calculating and assessing a variety of characteristics such as speed and acceleration, as well as multiple measures of straightness or tortuosity. Some support is provided for 3-dimensional trajectories. McLean & Skowron Volponi (2018) <doi:10.1111/eth.12739>.
Maintained by Jim McLean. Last updated 8 months ago.
7.0 match 27 stars 7.69 score 151 scriptsdavidgohel
ggiraph:Make 'ggplot2' Graphics Interactive
Create interactive 'ggplot2' graphics using 'htmlwidgets'.
Maintained by David Gohel. Last updated 3 months ago.
3.6 match 819 stars 14.39 score 4.1k scripts 34 dependentsbedapub
designit:Blocking and Randomization for Experimental Design
Intelligently assign samples to batches in order to reduce batch effects. Batch effects can have a significant impact on data analysis, especially when the assignment of samples to batches coincides with the contrast groups being studied. By defining a batch container and a scoring function that reflects the contrasts, this package allows users to assign samples in a way that minimizes the potential impact of batch effects on the comparison of interest. Among other functionality, we provide an implementation for OSAT score by Yan et al. (2012, <doi:10.1186/1471-2164-13-689>).
Maintained by Iakov I. Davydov. Last updated 4 months ago.
design-of-experimentsrandomization
7.1 match 8 stars 7.28 score 24 scriptsr4fun
hover:CSS Animations for 'shiny' Button Elements
A wrapper around a CSS library called 'Hover.css', intended for use in 'shiny' applications.
Maintained by Tyler Littlefield. Last updated 4 years ago.
12.4 match 16 stars 4.16 score 18 scriptsdsjohnson
crawl:Fit Continuous-Time Correlated Random Walk Models to Animal Movement Data
Fit continuous-time correlated random walk models with time indexed covariates to animal telemetry data. The model is fit using the Kalman-filter on a state space version of the continuous-time stochastic movement process.
Maintained by Devin S. Johnson. Last updated 5 months ago.
8.2 match 19 stars 6.29 score 63 scripts 3 dependentsmiguel-porto
SiMRiv:Simulating Multistate Movements in River/Heterogeneous Landscapes
Provides functions to generate and analyze spatially-explicit individual-based multistate movements in rivers, heterogeneous and homogeneous spaces. This is done by incorporating landscape bias on local behaviour, based on resistance rasters. Although originally conceived and designed to simulate trajectories of species constrained to linear habitats/dendritic ecological networks (e.g. river networks), the simulation algorithm is built to be highly flexible and can be applied to any (aquatic, semi-aquatic or terrestrial) organism, independently on the landscape in which it moves. Thus, the user will be able to use the package to simulate movements either in homogeneous landscapes, heterogeneous landscapes (e.g. semi-aquatic animal moving mainly along rivers but also using the matrix), or even in highly contrasted landscapes (e.g. fish in a river network). The algorithm and its input parameters are the same for all cases, so that results are comparable. Simulated trajectories can then be used as mechanistic null models (Potts & Lewis 2014, <DOI:10.1098/rspb.2014.0231>) to test a variety of 'Movement Ecology' hypotheses (Nathan et al. 2008, <DOI:10.1073/pnas.0800375105>), including landscape effects (e.g. resources, infrastructures) on animal movement and species site fidelity, or for predictive purposes (e.g. road mortality risk, dispersal/connectivity). The package should be relevant to explore a broad spectrum of ecological phenomena, such as those at the interface of animal behaviour, management, landscape and movement ecology, disease and invasive species spread, and population dynamics.
Maintained by Miguel Porto. Last updated 6 months ago.
animal-movementheterogeneous-landscapesmovement-ecologyriver-networkssimulation
8.4 match 15 stars 6.08 score 27 scripts 1 dependentsspluque
diveMove:Dive Analysis and Calibration
Utilities to represent, visualize, filter, analyse, and summarize time-depth recorder (TDR) data. Miscellaneous functions for handling location data are also provided.
Maintained by Sebastian P. Luque. Last updated 5 months ago.
animal-behaviorbehavioural-ecologybiologydivingscience
7.5 match 6 stars 6.75 score 55 scriptscran
compositions:Compositional Data Analysis
Provides functions for the consistent analysis of compositional data (e.g. portions of substances) and positive numbers (e.g. concentrations) in the way proposed by J. Aitchison and V. Pawlowsky-Glahn.
Maintained by K. Gerald van den Boogaart. Last updated 1 years ago.
7.8 match 1 stars 6.35 score 36 dependentsrobitalec
distanceto:Calculate Distance to Features
Calculates distances from point locations to features. The usual approach for eg. resource selection function analyses is to generate a complete distance to features surface then sample it with your observed and random points. Since these raster based approaches can be pretty costly with large areas, and often lead to memory issues in R, the distanceto package opts to compute these distances using efficient, vector based approaches. As a helper, there's a decidedly low-res raster based approach for visually inspecting your region's distance surface. But the workhorse is distance_to.
Maintained by Alec L. Robitaille. Last updated 2 years ago.
animaldistance-toecologyresource-selectionrsfspatial
10.0 match 5 stars 4.88 score 10 scripts 1 dependentssachaepskamp
qgraph:Graph Plotting Methods, Psychometric Data Visualization and Graphical Model Estimation
Fork of qgraph - Weighted network visualization and analysis, as well as Gaussian graphical model computation. See Epskamp et al. (2012) <doi:10.18637/jss.v048.i04>.
Maintained by Sacha Epskamp. Last updated 1 years ago.
4.3 match 69 stars 11.43 score 1.2k scripts 63 dependentstylermorganwall
rayrender:Build and Raytrace 3D Scenes
Render scenes using pathtracing. Build 3D scenes out of spheres, cubes, planes, disks, triangles, cones, curves, line segments, cylinders, ellipsoids, and 3D models in the 'Wavefront' OBJ file format or the PLY Polygon File Format. Supports several material types, textures, multicore rendering, and tone-mapping. Based on the "Ray Tracing in One Weekend" book series. Peter Shirley (2018) <https://raytracing.github.io>.
Maintained by Tyler Morgan-Wall. Last updated 17 days ago.
4.5 match 630 stars 10.78 score 188 scripts 8 dependentstidymodels
probably:Tools for Post-Processing Predicted Values
Models can be improved by post-processing class probabilities, by: recalibration, conversion to hard probabilities, assessment of equivocal zones, and other activities. 'probably' contains tools for conducting these operations as well as calibration tools and conformal inference techniques for regression models.
Maintained by Max Kuhn. Last updated 5 months ago.
4.0 match 115 stars 12.09 score 21k scripts 1 dependentsrethomics
damr:Interface to Drosophila Activity Monitor System Result Files
Loads behavioural data from the widely used Drosophila Activity Monitor System (DAMS, TriKinetics <https://trikinetics.com/>) into the rethomics framework.
Maintained by Quentin Geissmann. Last updated 11 months ago.
biological-data-analysisparsing
9.8 match 6 stars 4.92 score 31 scripts 1 dependentsdaattali
shinycssloaders:Add Loading Animations to a 'shiny' Output While It's Recalculating
When a 'Shiny' output (such as a plot, table, map, etc.) is recalculating, it remains visible but gets greyed out. Using 'shinycssloaders', you can add a loading animation ("spinner") to outputs instead. By wrapping a 'Shiny' output in 'withSpinner()', a spinner will automatically appear while the output is recalculating. You can also manually show and hide the spinner, or add a full-page spinner to cover the entire page. See the demo online at <https://daattali.com/shiny/shinycssloaders-demo/>.
Maintained by Dean Attali. Last updated 8 months ago.
3.4 match 409 stars 13.71 score 4.3k scripts 119 dependentsdtharvey
eChem:Simulations for Electrochemistry Experiments
Simulates cyclic voltammetry, linear-sweep voltammetry (both with and without stirring of the solution), and single-pulse and double-pulse chronoamperometry and chronocoulometry experiments using the implicit finite difference method outlined in Gosser (1993, ISBN: 9781560810261) and in Brown (2015) <doi:10.1021/acs.jchemed.5b00225>. Additional functions provide ways to display and to examine the results of these simulations. The primary purpose of this package is to provide tools for use in courses in analytical chemistry.
Maintained by David Harvey. Last updated 6 years ago.
7.7 match 6 stars 6.11 score 27 scriptsalexchristensen
SemNetDictionaries:Dictionaries for the 'SemNetCleaner' Package
Implements dictionaries that can be used in the 'SemNetCleaner' package. Also includes several functions aimed at facilitating the text cleaning analysis in the 'SemNetCleaner' package. This package is designed to integrate and update word lists and dictionaries based on each user's individual needs by allowing users to store and save their own dictionaries. Dictionaries can be added to the 'SemNetDictionaries' package by submitting user-defined dictionaries to <https://github.com/AlexChristensen/SemNetDictionaries>.
Maintained by Alexander P. Christensen. Last updated 3 years ago.
dictionariessemantic-network-analysis
9.0 match 4 stars 5.08 score 3 scripts 2 dependentsr-forge
robustbase:Basic Robust Statistics
"Essential" Robust Statistics. Tools allowing to analyze data with robust methods. This includes regression methodology including model selections and multivariate statistics where we strive to cover the book "Robust Statistics, Theory and Methods" by 'Maronna, Martin and Yohai'; Wiley 2006.
Maintained by Martin Maechler. Last updated 4 months ago.
3.4 match 13.33 score 1.7k scripts 480 dependentsrichardgeveritt
ggsmc:Visualising Output from Sequential Monte Carlo and Ensemble-Based Methods
Functions for plotting, and animating, the output of importance samplers, sequential Monte Carlo samplers (SMC) and ensemble-based methods. The package can be used to plot and animate histograms, densities, scatter plots and time series, and to plot the genealogy of an SMC or ensemble-based algorithm. These functions all rely on algorithm output to be supplied in tidy format. A function is provided to transform algorithm output from matrix format (one Monte Carlo point per row) to the tidy format required by the plotting and animating functions.
Maintained by Richard G Everitt. Last updated 2 months ago.
10.1 match 4.48 score 6 scriptsfrbcesab
popbayes:Bayesian Model to Estimate Population Trends from Counts Series
Infers the trends of one or several animal populations over time from series of counts. It does so by accounting for count precision (provided or inferred based on expert knowledge, e.g. guesstimates), smoothing the population rate of increase over time, and accounting for the maximum demographic potential of species. Inference is carried out in a Bayesian framework. This work is part of the FRB-CESAB working group AfroBioDrivers <https://www.fondationbiodiversite.fr/en/the-frb-in-action/programs-and-projects/le-cesab/afrobiodrivers/>.
Maintained by Nicolas Casajus. Last updated 1 years ago.
animalbayesiancountspopulationprecisiontemporal-trendjagscpp
10.5 match 1 stars 4.30 scoregtatters
Thermimage:Thermal Image Analysis
A collection of functions and routines for inputting thermal image video files, plotting and converting binary raw data into estimates of temperature. First published 2015-03-26. Written primarily for research purposes in biological applications of thermal images. v1 included the base calculations for converting thermal image binary values to temperatures. v2 included additional equations for providing heat transfer calculations and an import function for thermal image files (v2.2.3 fixed error importing thermal image to windows OS). v3. Added numerous functions for converting thermal image, videos, rewriting and exporting. v3.1. Added new functions to convert files. v3.2. Fixed the various functions related to finding frame times. v4.0. fixed an error in atmospheric attenuation constants, affecting raw2temp and temp2raw functions. Recommend update for use with long distance calculations. v.4.1.3. changed to frameLocates to reflect change to as.character() to format().
Maintained by Glenn J. Tattersall. Last updated 3 years ago.
animal-physiologyheat-exchangeheat-fluximage-framestemperaturethermal-biologythermal-images
7.5 match 169 stars 5.85 score 83 scriptsreside-ic
ids:Generate Random Identifiers
Generate random or human readable and pronounceable identifiers.
Maintained by Rich FitzJohn. Last updated 3 years ago.
3.3 match 94 stars 13.27 score 175 scripts 165 dependentshelgasoft
amapro:Thin Wrapper for Mapping Library 'AMap'
Build and control interactive 2D and 3D maps with 'R/Shiny'. Lean set of powerful commands wrapping native calls to 'AMap' <https://lbs.amap.com/api/jsapi-v2/summary/>. Deliver rich mapping functionality with minimal overhead.
Maintained by Larry Helgason. Last updated 2 years ago.
3damapanimationflyovergaodegeojsoninteractive-visualizationslayersmapsshinywms
10.0 match 3 stars 4.35 score 15 scriptsinlabru-org
inlabru:Bayesian Latent Gaussian Modelling using INLA and Extensions
Facilitates spatial and general latent Gaussian modeling using integrated nested Laplace approximation via the INLA package (<https://www.r-inla.org>). Additionally, extends the GAM-like model class to more general nonlinear predictor expressions, and implements a log Gaussian Cox process likelihood for modeling univariate and spatial point processes based on ecological survey data. Model components are specified with general inputs and mapping methods to the latent variables, and the predictors are specified via general R expressions, with separate expressions for each observation likelihood model in multi-likelihood models. A prediction method based on fast Monte Carlo sampling allows posterior prediction of general expressions of the latent variables. Ecology-focused introduction in Bachl, Lindgren, Borchers, and Illian (2019) <doi:10.1111/2041-210X.13168>.
Maintained by Finn Lindgren. Last updated 4 days ago.
3.4 match 96 stars 12.62 score 832 scripts 6 dependentsinbo
camtraptor:Read, Explore and Visualize Camera Trap Data Packages
Read, explore and visualize Camera Trap Data Packages (Camtrap DP). 'Camtrap DP' (<https://camtrap-dp.tdwg.org>) is a community developed data exchange format for this type of data. With camtraptor you can read and filter data, create overviews of observed species, relative abundance or effort, and plot these data on a map.
Maintained by Damiano Oldoni. Last updated 28 days ago.
6.8 match 12 stars 6.27 score 16 scriptssmbc-nzp
MigConnectivity:Estimate Migratory Connectivity for Migratory Animals
Allows the user to estimate transition probabilities for migratory animals between any two phases of the annual cycle, using a variety of different data types. Also quantifies the strength of migratory connectivity (MC), a standardized metric to quantify the extent to which populations co-occur between two phases of the annual cycle. Includes functions to estimate MC and the more traditional metric of migratory connectivity strength (Mantel correlation) incorporating uncertainty from multiple sources of sampling error. For cross-species comparisons, methods are provided to estimate differences in migratory connectivity strength, incorporating uncertainty. See Cohen et al. (2018) <doi:10.1111/2041-210X.12916>, Cohen et al. (2019) <doi:10.1111/ecog.03974>, and Roberts et al. (2023) <doi:10.1002/eap.2788> for details on some of these methods.
Maintained by Jeffrey A. Hostetler. Last updated 12 months ago.
6.3 match 8 stars 6.77 score 41 scriptstalgalili
dendextend:Extending 'dendrogram' Functionality in R
Offers a set of functions for extending 'dendrogram' objects in R, letting you visualize and compare trees of 'hierarchical clusterings'. You can (1) Adjust a tree's graphical parameters - the color, size, type, etc of its branches, nodes and labels. (2) Visually and statistically compare different 'dendrograms' to one another.
Maintained by Tal Galili. Last updated 2 months ago.
2.5 match 154 stars 17.02 score 6.0k scripts 164 dependentsfeddelegrand7
GomoGomonoMi:Animate Text using the 'Animate.css' Library
Allows the user to animate text within 'rmarkdown' documents and 'shiny' applications. The animations are activated using the 'Animate.css' library. See <https://animate.style/> for more information.
Maintained by Mohamed El Fodil Ihaddaden. Last updated 4 years ago.
cssrmarkdownrmarkdown-documentshiny
12.0 match 7 stars 3.54 score 3 scriptsyihui
knitr:A General-Purpose Package for Dynamic Report Generation in R
Provides a general-purpose tool for dynamic report generation in R using Literate Programming techniques.
Maintained by Yihui Xie. Last updated 2 days ago.
dynamic-documentsknitrliterate-programmingrmarkdownsweave
1.8 match 2.4k stars 23.62 score 116k scripts 4.2k dependentsbart1
move2:Processing and Analysing Animal Trajectories
Tools to handle, manipulate and explore trajectory data, with an emphasis on data from tracked animals. The package is designed to support large studies with several million location records and keep track of units where possible. Data import directly from 'movebank' <https://www.movebank.org/cms/movebank-main> and files is facilitated.
Maintained by Bart Kranstauber. Last updated 1 months ago.
5.6 match 7.51 score 169 scripts 1 dependentsjbengler
tidyplots:Tidy Plots for Scientific Papers
The goal of 'tidyplots' is to streamline the creation of publication-ready plots for scientific papers. It allows to gradually add, remove and adjust plot components using a consistent and intuitive syntax.
Maintained by Jan Broder Engler. Last updated 4 days ago.
4.5 match 482 stars 9.40 score 85 scriptsandburch
rabi:Generate Codes to Uniquely and Robustly Identify Individuals for Animal Behavior Studies
Facilitates the design and generation of optimal color (or symbol) codes that can be used to mark and identify individual animals. These codes are made such that the IDs are robust to partial erasure: even if sections of the code are lost, the entire identity of the animal can be reconstructed. Thus, animal subjects are not confused and no ambiguity is introduced.
Maintained by Andrew Taylor Burchill. Last updated 3 years ago.
animal-behaviorcollective-behavior
11.2 match 3.70 score 7 scriptscoolbutuseless
emphatic:Exploratory Analysis of Tabular Data using Colour Highlighting
Tools for exploratory analysis of tabular data using colour highlighting. Highlighting is displayed in any console supporting 'ANSI' colours, and can be converted to 'HTML', 'typst', 'latex' and 'SVG'. 'quarto' and 'rmarkdown' rendering are directly supported. It is also possible to add colour to regular expression matches and highlight differences between two arbitrary R objects.
Maintained by Mike Cheng. Last updated 3 months ago.
5.5 match 141 stars 7.55 score 12 scriptsmatthewwolak
nadiv:(Non)Additive Genetic Relatedness Matrices
Constructs (non)additive genetic relationship matrices, and their inverses, from a pedigree to be used in linear mixed effect models (A.K.A. the 'animal model'). Also includes other functions to facilitate the use of animal models. Some functions have been created to be used in conjunction with the R package 'asreml' for the 'ASReml' software, which can be obtained upon purchase from 'VSN' international (<https://vsni.co.uk/software/asreml>).
Maintained by Matthew Wolak. Last updated 10 months ago.
5.8 match 20 stars 7.13 score 151 scripts 3 dependentsmarce10
dynaSpec:Dynamic Spectrogram Visualizations
A set of tools to generate dynamic spectrogram visualizations in video format.
Maintained by Marcelo Araya-Salas. Last updated 16 days ago.
animal-soundsbioacousticsspectrogram
7.5 match 23 stars 5.50 score 34 scriptstrevorld
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.
3.3 match 368 stars 12.33 score 1.7k scripts 3 dependentsopengeos
whitebox:'WhiteboxTools' R Frontend
An R frontend for the 'WhiteboxTools' library, which is an advanced geospatial data analysis platform developed by Prof. John Lindsay at the University of Guelph's Geomorphometry and Hydrogeomatics Research Group. 'WhiteboxTools' can be used to perform common geographical information systems (GIS) analysis operations, such as cost-distance analysis, distance buffering, and raster reclassification. Remote sensing and image processing tasks include image enhancement (e.g. panchromatic sharpening, contrast adjustments), image mosaicing, numerous filtering operations, simple classification (k-means), and common image transformations. 'WhiteboxTools' also contains advanced tooling for spatial hydrological analysis (e.g. flow-accumulation, watershed delineation, stream network analysis, sink removal), terrain analysis (e.g. common terrain indices such as slope, curvatures, wetness index, hillshading; hypsometric analysis; multi-scale topographic position analysis), and LiDAR data processing. Suggested citation: Lindsay (2016) <doi:10.1016/j.cageo.2016.07.003>.
Maintained by Andrew Brown. Last updated 5 months ago.
geomorphometrygeoprocessinggeospatialgishydrologyremote-sensingrstudio
4.3 match 173 stars 9.65 score 203 scripts 2 dependentsfloschuberth
cSEM:Composite-Based Structural Equation Modeling
Estimate, assess, test, and study linear, nonlinear, hierarchical and multigroup structural equation models using composite-based approaches and procedures, including estimation techniques such as partial least squares path modeling (PLS-PM) and its derivatives (PLSc, ordPLSc, robustPLSc), generalized structured component analysis (GSCA), generalized structured component analysis with uniqueness terms (GSCAm), generalized canonical correlation analysis (GCCA), principal component analysis (PCA), factor score regression (FSR) using sum score, regression or Bartlett scores (including bias correction using Croon’s approach), as well as several tests and typical postestimation procedures (e.g., verify admissibility of the estimates, assess the model fit, test the model fit etc.).
Maintained by Florian Schuberth. Last updated 17 days ago.
4.5 match 28 stars 9.11 score 56 scripts 2 dependentsjohncoene
echarts4r:Create Interactive Graphs with 'Echarts JavaScript' Version 5
Easily create interactive charts by leveraging the 'Echarts Javascript' library which includes 36 chart types, themes, 'Shiny' proxies and animations.
Maintained by David Munoz Tord. Last updated 3 days ago.
echartshacktoberfesthtmlwidgethtmlwidgetsvisualization
3.5 match 603 stars 11.45 score 1.3k scripts 11 dependentsappelmar
gdalcubes:Earth Observation Data Cubes from Satellite Image Collections
Processing collections of Earth observation images as on-demand multispectral, multitemporal raster data cubes. Users define cubes by spatiotemporal extent, resolution, and spatial reference system and let 'gdalcubes' automatically apply cropping, reprojection, and resampling using the 'Geospatial Data Abstraction Library' ('GDAL'). Implemented functions on data cubes include reduction over space and time, applying arithmetic expressions on pixel band values, moving window aggregates over time, filtering by space, time, bands, and predicates on pixel values, exporting data cubes as 'netCDF' or 'GeoTIFF' files, plotting, and extraction from spatial and or spatiotemporal features. All computational parts are implemented in C++, linking to the 'GDAL', 'netCDF', 'CURL', and 'SQLite' libraries. See Appel and Pebesma (2019) <doi:10.3390/data4030092> for further details.
Maintained by Marius Appel. Last updated 1 years ago.
remote-sensingsatellite-imageryspatial-analysisgdalnetcdfcpp
4.8 match 124 stars 8.39 score 356 scriptsgitboosting
imuf:Estimate Orientation of an Inertial Measurement Unit
Estimate the orientation of an inertial measurement unit (IMU) with a 3-axis accelerometer and a 3-axis gyroscope using a complementary filter. 'imuf' takes an IMU's accelerometer and gyroscope readings, time duration, its initial orientation, and a gain factor as inputs, and returns an estimate of the IMU's final orientation.
Maintained by Felix Chan. Last updated 17 days ago.
7.3 match 5.38 score 12 scriptsplotly
plotly:Create Interactive Web Graphics via 'plotly.js'
Create interactive web graphics from 'ggplot2' graphs and/or a custom interface to the (MIT-licensed) JavaScript library 'plotly.js' inspired by the grammar of graphics.
Maintained by Carson Sievert. Last updated 3 months ago.
d3jsdata-visualizationggplot2javascriptplotlyshinywebgl
2.0 match 2.6k stars 19.43 score 93k scripts 797 dependentsjohncoene
sigmajs:Interface to 'Sigma.js' Graph Visualization Library
Interface to 'sigma.js' graph visualization library including animations, plugins and shiny proxies.
Maintained by John Coene. Last updated 4 years ago.
htmlwidgetsnetwork-visualizationsigmajs
6.5 match 72 stars 5.92 score 77 scriptsr-lib
cli:Helpers for Developing Command Line Interfaces
A suite of tools to build attractive command line interfaces ('CLIs'), from semantic elements: headings, lists, alerts, paragraphs, etc. Supports custom themes via a 'CSS'-like language. It also contains a number of lower level 'CLI' elements: rules, boxes, trees, and 'Unicode' symbols with 'ASCII' alternatives. It support ANSI colors and text styles as well.
Maintained by Gábor Csárdi. Last updated 2 days ago.
2.0 match 664 stars 19.33 score 1.4k scripts 14k dependentsdfsp-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.
3dbraindtifreesurfermeshmrineuroimagingresearchsurfacevisualizationvoxel
5.9 match 66 stars 6.47 score 15 scriptsjonesor
Rcompadre:Utilities for using the 'COM(P)ADRE' Matrix Model Database
Utility functions for interacting with the 'COMPADRE' and 'COMADRE' databases of matrix population models. Described in Jones et al. (2021) <doi:10.1101/2021.04.26.441330>.
Maintained by Owen Jones. Last updated 5 months ago.
4.9 match 11 stars 7.74 score 55 scripts 2 dependentssanchezi
kfino:Kalman Filter for Impulse Noised Outliers
A method for detecting outliers with a Kalman filter on impulsed noised outliers and prediction on cleaned data. 'kfino' is a robust sequential algorithm allowing to filter data with a large number of outliers. This algorithm is based on simple latent linear Gaussian processes as in the Kalman Filter method and is devoted to detect impulse-noised outliers. These are data points that differ significantly from other observations. 'ML' (Maximization Likelihood) and 'EM' (Expectation-Maximization algorithm) algorithms were implemented in 'kfino'. The method is described in full details in the following arXiv e-Print: <arXiv:2208.00961>.
Maintained by Isabelle Sanchez. Last updated 2 years ago.
12.6 match 3.00 score 6 scriptsmhahsler
stream:Infrastructure for Data Stream Mining
A framework for data stream modeling and associated data mining tasks such as clustering and classification. The development of this package was supported in part by NSF IIS-0948893, NSF CMMI 1728612, and NIH R21HG005912. Hahsler et al (2017) <doi:10.18637/jss.v076.i14>.
Maintained by Michael Hahsler. Last updated 4 days ago.
data-stream-clusteringdatastreamstream-miningcpp
3.8 match 39 stars 10.05 score 132 scripts 3 dependentsr-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 5 days ago.
choropleth-mapsmapsspatialthematic-mapsvisualisation
2.3 match 880 stars 16.73 score 13k scripts 24 dependentscovaruber
lme4breeding:Relationship-Based Mixed-Effects Models
Fit relationship-based and customized mixed-effects models with complex variance-covariance structures using the 'lme4' machinery. The core computational algorithms are implemented using the 'Eigen' 'C++' library for numerical linear algebra and 'RcppEigen' 'glue'.
Maintained by Giovanny Covarrubias-Pazaran. Last updated 22 days ago.
7.2 match 6 stars 5.23 score 7 scriptsdevopifex
g2r:Interactive Grammar of Graphics
Interactive grammar of graphics.
Maintained by John Coene. Last updated 3 years ago.
8.3 match 119 stars 4.53 score 57 scriptsmhpob
otndo:Understand your OTN data
This package provides functions to summarize the various type of OTN-style data.
Maintained by Michael OBrien. Last updated 9 days ago.
animal-trackingbiotelemetryfishfisheriesvisualization
7.5 match 4 stars 4.92 score 6 scripts 1 dependentsianjonsen
bsam:Bayesian State-Space Models for Animal Movement
Tools to fit Bayesian state-space models to animal tracking data. Models are provided for location filtering, location filtering and behavioural state estimation, and their hierarchical versions. The models are primarily intended for fitting to ARGOS satellite tracking data but options exist to fit to other tracking data types. For Global Positioning System data, consider the 'moveHMM' package. Simplified Markov Chain Monte Carlo convergence diagnostic plotting is provided but users are encouraged to explore tools available in packages such as 'coda' and 'boa'.
Maintained by Ian Jonsen. Last updated 9 months ago.
6.8 match 17 stars 5.42 score 31 scriptsjoshcullen
bayesmove:Non-Parametric Bayesian Analyses of Animal Movement
Methods for assessing animal movement from telemetry and biologging data using non-parametric Bayesian methods. This includes features for pre- processing and analysis of data, as well as the visualization of results from the models. This framework does not rely on standard parametric density functions, which provides flexibility during model fitting. Further details regarding part of this framework can be found in Cullen et al. (2022) <doi:10.1111/2041-210X.13745>.
Maintained by Joshua Cullen. Last updated 1 years ago.
8.8 match 9 stars 4.18 score 34 scriptsgobbios
EloRating:Animal Dominance Hierarchies by Elo Rating
Provides functions to quantify animal dominance hierarchies. The major focus is on Elo rating and its ability to deal with temporal dynamics in dominance interaction sequences. For static data, David's score and de Vries' I&SI are also implemented. In addition, the package provides functions to assess transitivity, linearity and stability of dominance networks. See Neumann et al (2011) <doi:10.1016/j.anbehav.2011.07.016> for an introduction.
Maintained by Christof Neumann. Last updated 8 months ago.
5.3 match 4 stars 6.86 score 61 scripts 1 dependentsadrian-bowman
rpanel:Simple Interactive Controls for R using the 'tcltk' Package
A set of functions to build simple GUI controls for R functions. These are built on the 'tcltk' package. Uses could include changing a parameter on a graph by animating it with a slider or a "doublebutton", up to more sophisticated control panels. Some functions for specific graphical tasks, referred to as 'cartoons', are provided.
Maintained by Adrian Bowman. Last updated 2 years ago.
8.4 match 1 stars 4.30 score 157 scripts 9 dependentslz100
spsComps:'systemPipeShiny' UI and Server Components
The systemPipeShiny (SPS) framework comes with many UI and server components. However, installing the whole framework is heavy and takes some time. If you would like to use UI and server components from SPS in your own Shiny apps, do not hesitate to try this package.
Maintained by Le Zhang. Last updated 1 years ago.
5.5 match 31 stars 6.56 score 65 scripts 4 dependentsbrry
berryFunctions:Function Collection Related to Plotting and Hydrology
Draw horizontal histograms, color scattered points by 3rd dimension, enhance date- and log-axis plots, zoom in X11 graphics, trace errors and warnings, use the unit hydrograph in a linear storage cascade, convert lists to data.frames and arrays, fit multiple functions.
Maintained by Berry Boessenkool. Last updated 1 months ago.
3.8 match 13 stars 9.43 score 350 scripts 16 dependentslewisajones
sepkoski:Sepkoski's Fossil Marine Animal Genera Compendium
Stratigraphic ranges of fossil marine animal genera from Sepkoski's (2002) published compendium. No changes have been made to any taxonomic names. However, first and last appearance intervals have been updated to be consistent with stages of the International Geological Timescale. Functionality for generating a plot of Sepkoski's evolutionary fauna is also included. For specific details on the compendium see: Sepkoski, J. J. (2002). A compendium of fossil marine animal genera. Bulletins of American Paleontology, 363, pp. 1–560 (ISBN 0-87710-450-6). Access: <https://www.biodiversitylibrary.org/item/40634#page/5/mode/1up>.
Maintained by Lewis A. Jones. Last updated 6 months ago.
10.8 match 2 stars 3.30 score 3 scriptsmayur1009
cleanTS:Testbench for Univariate Time Series Cleaning
A reliable and efficient tool for cleaning univariate time series data. It implements reliable and efficient procedures for automating the process of cleaning univariate time series data. The package provides integration with already developed and deployed tools for missing value imputation and outlier detection. It also provides a way of visualizing large time-series data in different resolutions.
Maintained by Mayur Shende. Last updated 1 years ago.
9.5 match 11 stars 3.74 score 3 scriptsr-forge
copula:Multivariate Dependence with Copulas
Classes (S4) of commonly used elliptical, Archimedean, extreme-value and other copula families, as well as their rotations, mixtures and asymmetrizations. Nested Archimedean copulas, related tools and special functions. Methods for density, distribution, random number generation, bivariate dependence measures, Rosenblatt transform, Kendall distribution function, perspective and contour plots. Fitting of copula models with potentially partly fixed parameters, including standard errors. Serial independence tests, copula specification tests (independence, exchangeability, radial symmetry, extreme-value dependence, goodness-of-fit) and model selection based on cross-validation. Empirical copula, smoothed versions, and non-parametric estimators of the Pickands dependence function.
Maintained by Martin Maechler. Last updated 11 days ago.
3.0 match 11.83 score 1.2k scripts 86 dependentsswsoyee
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.
3dcomputational-biologycomputational-chemistryhacktoberfesthtmlwidgetsmolecular-graphicsmolecular-modelingproteinprotein-structurevisualization
5.5 match 90 stars 6.35 score 166 scripts 1 dependentsfamuvie
breedR:Statistical Methods for Forest Genetic Resources Analysts
Statistical tools to build predictive models for the breeders community. It aims to assess the genetic value of individuals under a number of situations, including spatial autocorrelation, genetic/environment interaction and competition. It is under active development as part of the Trees4Future project, particularly developed having forest genetic trials in mind. But can be used for animals or other situations as well.
Maintained by Facundo Muñoz. Last updated 8 months ago.
6.2 match 33 stars 5.44 score 24 scriptskjhealy
gssrdoc:Document General Social Survey Variable
The General Social Survey (GSS) is a long-running, mostly annual survey of US households. It is administered by the National Opinion Research Center (NORC). This package contains the a tibble with information on the survey variables, together with every variable documented as an R help page. For more information on the GSS see \url{http://gss.norc.org}.
Maintained by Kieran Healy. Last updated 11 months ago.
14.7 match 2.28 score 38 scriptsbirdlifeinternational
track2KBA:Identifying Important Areas from Animal Tracking Data
Functions for preparing and analyzing animal tracking data, with the intention of identifying areas which are potentially important at the population level and therefore of conservation interest. Areas identified using this package may be checked against global or regionally-defined criteria, such as those set by the Key Biodiversity Area program. The method published herein is described in full in Beal et al. 2021 <doi:10.1111/2041-210X.13713>.
Maintained by Martin Beal. Last updated 9 months ago.
5.1 match 11 stars 6.51 score 59 scriptsscarpino
multiDimBio:Multivariate Analysis and Visualization for Biological Data
Code to support a systems biology research program from inception through publication. The methods focus on dimension reduction approaches to detect patterns in complex, multivariate experimental data and places an emphasis on informative visualizations. The goal for this project is to create a package that will evolve over time, thereby remaining relevant and reflective of current methods and techniques. As a result, we encourage suggested additions to the package, both methodological and graphical.
Maintained by Samuel V. Scarpino. Last updated 5 years ago.
13.7 match 2.41 score 26 scriptsmikemeredith
overlap:Estimates of Coefficient of Overlapping for Animal Activity Patterns
Provides functions to fit kernel density functions to data on temporal activity patterns of animals; estimate coefficients of overlapping of densities for two species; and calculate bootstrap estimates of confidence intervals.
Maintained by Liz Campbell. Last updated 2 years ago.
5.2 match 2 stars 6.42 score 265 scripts 1 dependentsmucollective
multiverse:Create 'multiverse analysis' in R
Implement 'multiverse' style analyses (Steegen S., Tuerlinckx F, Gelman A., Vanpaemal, W., 2016) <doi:10.1177/1745691616658637> to show the robustness of statistical inference. 'Multiverse analysis' is a philosophy of statistical reporting where paper authors report the outcomes of many different statistical analyses in order to show how fragile or robust their findings are. The 'multiverse' package (Sarma A., Kale A., Moon M., Taback N., Chevalier F., Hullman J., Kay M., 2021) <doi:10.31219/osf.io/yfbwm> allows users to concisely and flexibly implement 'multiverse-style' analysis, which involve declaring alternate ways of performing an analysis step, in R and R Notebooks.
Maintained by Abhraneel Sarma. Last updated 4 months ago.
3.9 match 62 stars 8.37 score 42 scriptsjulianfaraway
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 1 months ago.
3.5 match 29 stars 9.43 score 1.7k scripts 1 dependentsfeddelegrand7
scrollrevealR:Animate 'shiny' Elements when They Scroll into View using the 'scrollrevealjs' Library
Allows the user to animate 'shiny' elements when scrolling to view them. The animations are activated using the 'scrollrevealjs' library. See <https://scrollrevealjs.org/> for more information.
Maintained by Mohamed El Fodil Ihaddaden. Last updated 4 years ago.
6.6 match 21 stars 5.02 score 8 scriptscran
boot:Bootstrap Functions (Originally by Angelo Canty for S)
Functions and datasets for bootstrapping from the book "Bootstrap Methods and Their Application" by A. C. Davison and D. V. Hinkley (1997, CUP), originally written by Angelo Canty for S.
Maintained by Alessandra R. Brazzale. Last updated 7 months ago.
4.0 match 2 stars 8.21 score 2.3k dependentsmhpob
matos:Interface with the Mid-Atlantic Acoustic Telemetry Observing System (MATOS)
This package provides HTML-scaping functions to interact with the MATOS website (https://matos.asascience.com/), allowing aggregation of data and the downloading and posting of files.
Maintained by Michael OBrien. Last updated 3 months ago.
animal-trackingapiapi-wrapperbiotelemetryfishfisheriesfisheries-research
7.5 match 3 stars 4.35 score 9 scriptsrobitalec
preparelocs:Prepares Relocations For The WEEL
Prepares animal relocation datasets for the Wildlife Evolutionary Ecology Lab at Memorial University.
Maintained by Alec L. Robitaille. Last updated 1 years ago.
animalanimal-movementgpstargets
18.1 match 1.70 scoremarce10
NatureSounds:Animal Sounds for Bioacustic Analysis
Collection of example animal sounds for bioacoustic analysis.
Maintained by Marcelo Araya-Salas. Last updated 2 years ago.
5.5 match 2 stars 5.52 score 22 scripts 5 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
3.4 match 48 stars 9.00 score 93 scripts 5 dependentsrinterface
shinyEffects:Customize Your Web Apps with Fancy Effects
Add fancy CSS effects to your 'shinydashboards' or 'shiny' apps. 100% compatible with 'shinydashboardPlus' and 'bs4Dash'.
Maintained by David Granjon. Last updated 4 years ago.
5.8 match 50 stars 5.21 score 65 scriptsroaldarbol
anibehavr:Analyse Animal Behaviours
What the package does (one paragraph).
Maintained by Mikkel Roald-Arbøl. Last updated 10 months ago.
animal-behaviorbehavioural-statesdata-analysis
10.8 match 3 stars 2.78 score 2 scriptszankrut20
selection.index:Analysis of Selection Index in Plant Breeding
The aim of most plant breeding programmes is simultaneous improvement of several characters. An objective method involving simultaneous selection for several attributes then becomes necessary. It has been recognised that most rapid improvements in the economic value is expected from selection applied simultaneously to all the characters which determine the economic value of a plant, and appropriate assigned weights to each character according to their economic importance, heritability and correlations between characters. So the selection for economic value is a complex matter. If the component characters are combined together into an index in such a way that when selection is applied to the index, as if index is the character to be improved, most rapid improvement of economic value is expected. Such an index was first proposed by Smith (1937 <doi:10.1111/j.1469-1809.1936.tb02143.x>) based on the Fisher's (1936 <doi:10.1111/j.1469-1809.1936.tb02137.x>) "discriminant function" Dabholkar (1999 <https://books.google.co.in/books?id=mlFtumAXQ0oC&lpg=PA4&ots=Xgxp1qLuxS&dq=elements%20of%20biometrical%20genetics&lr&pg=PP1#v=onepage&q&f=false>). In this package selection index is calculated based on the Smith (1937) selection index method.
Maintained by Zankrut Goyani. Last updated 5 months ago.
agricultureanimal-scienceplant-breedingrstudioselection-indexselection-indicessmith-selection-index
7.5 match 2 stars 4.00 score 5 scriptskrisanata
animbook:Visualizing Changes in Performance Measures and Demographic Affiliations using Animation
Create an interactive visualization to be used for communication purposes. Providing the function for preparing, plotting, and animating the data. Krisanat Anukarnsakulchularp (2023) <https://github.com/KrisanatA/animbook-journal>
Maintained by Krisanat Anukarnsakulchularp. Last updated 11 months ago.
8.1 match 1 stars 3.70 score 10 scriptspilaboratory
sads:Maximum Likelihood Models for Species Abundance Distributions
Maximum likelihood tools to fit and compare models of species abundance distributions and of species rank-abundance distributions.
Maintained by Paulo I. Prado. Last updated 1 years ago.
3.4 match 23 stars 8.66 score 244 scripts 3 dependentsoswaldosantos
capm:Companion Animal Population Management
Quantitative analysis to support companion animal population management. Some functions assist survey sampling tasks (calculate sample size for simple and complex designs, select sampling units and estimate population parameters) while others assist the modelling of population dynamics. For demographic characterizations and population management evaluations see: "Baquero, et al." (2018), <doi:10.1016/j.prevetmed.2018.07.006>. For modelling of population dynamics see: "Baquero et al." (2016), <doi:10.1016/j.prevetmed.2015.11.009>. For sampling methods see: "Levy PS & Lemeshow S" (2013), "ISBN-10: 0470040076"; "Lumley" (2010), "ISBN: 978-0-470-28430-8".
Maintained by Oswaldo Santos Baquero. Last updated 6 years ago.
8.9 match 4 stars 3.30 score 4 scriptstheomichelot
moveHMM:Animal Movement Modelling using Hidden Markov Models
Provides tools for animal movement modelling using hidden Markov models. These include processing of tracking data, fitting hidden Markov models to movement data, visualization of data and fitted model, decoding of the state process, etc. <doi:10.1111/2041-210X.12578>.
Maintained by Theo Michelot. Last updated 1 years ago.
3.4 match 38 stars 8.63 score 112 scriptsthebioengineer
camcorder:Record Your Plot History
Record and generate a 'gif' of your 'R' sessions plots. When creating a visualization, there is inevitably iteration and refinement that occurs. Automatically save the plots made to a specified directory, previewing them as they would be saved. Then combine all plots generated into a 'gif' to show the plot refinement over time.
Maintained by Ellis Hughes. Last updated 1 years ago.
3.1 match 208 stars 9.21 score 980 scriptssportsdataverse
sportyR:Plot Scaled 'ggplot' Representations of Sports Playing Surfaces
Create scaled 'ggplot' representations of playing surfaces. Playing surfaces are drawn pursuant to rule-book specifications. This package should be used as a baseline plot for displaying any type of tracking data.
Maintained by Ross Drucker. Last updated 1 months ago.
footballggplot2playing-surfacessportsports-analyticssports-datasports-tracking-datasportsdataversevisualization
3.3 match 104 stars 8.08 score 97 scriptscoolbutuseless
isocubes:Voxel Rendering with Isometric Cubes
Visualising three-dimensional voxel data.
Maintained by Mike Cheng. Last updated 4 months ago.
5.3 match 67 stars 5.13 score 8 scriptstrackage
trip:Tracking Data
Access and manipulate spatial tracking data, with straightforward coercion from and to other formats. Filter for speed and create time spent maps from tracking data. There are coercion methods to convert between 'trip' and 'ltraj' from 'adehabitatLT', and between 'trip' and 'psp' and 'ppp' from 'spatstat'. Trip objects can be created from raw or grouped data frames, and from types in the 'sp', sf', 'amt', 'trackeR', 'mousetrap', and other packages, Sumner, MD (2011) <https://figshare.utas.edu.au/articles/thesis/The_tag_location_problem/23209538>.
Maintained by Michael D. Sumner. Last updated 8 months ago.
3.4 match 13 stars 7.72 score 137 scripts 1 dependentsbiodiverse
ubms:Bayesian Models for Data from Unmarked Animals using 'Stan'
Fit Bayesian hierarchical models of animal abundance and occurrence via the 'rstan' package, the R interface to the 'Stan' C++ library. Supported models include single-season occupancy, dynamic occupancy, and N-mixture abundance models. Covariates on model parameters are specified using a formula-based interface similar to package 'unmarked', while also allowing for estimation of random slope and intercept terms. References: Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>; Fiske and Chandler (2011) <doi:10.18637/jss.v043.i10>.
Maintained by Ken Kellner. Last updated 18 days ago.
distance-samplinghierarchical-modelsn-mixture-modeloccupancystanopenblascpp
3.4 match 35 stars 7.88 score 73 scriptsshanpengli
PDXpower:Time to Event Outcome in Experimental Designs of Pre-Clinical Studies
Conduct simulation-based customized power calculation for clustered time to event data in a mixed crossed/nested design, where a number of cell lines and a number of mice within each cell line are considered to achieve a desired statistical power, motivated by Eckel-Passow and colleagues (2021) <doi:10.1093/neuonc/noab137> and Li and colleagues (2024) <doi:10.48550/arXiv.2404.08927>. This package provides two commonly used models for powering a design, linear mixed effects and Cox frailty model. Both models account for within-subject (cell line) correlation while holding different distributional assumptions about the outcome. Alternatively, the counterparts of fixed effects model are also available, which produces similar estimates of statistical power.
Maintained by Shanpeng Li. Last updated 2 months ago.
7.2 match 1 stars 3.65 score 2 scriptsr-lib
asciicast:Create 'Ascii' Screen Casts from R Scripts
Record 'asciicast' screen casts from R scripts. Convert them to animated SVG images, to be used in 'README' files, or blog posts. Includes 'asciinema-player' as an 'HTML' widget, and an 'asciicast' 'knitr' engine, to embed 'ascii' screen casts in 'Rmarkdown' documents.
Maintained by Gábor Csárdi. Last updated 5 months ago.
4.1 match 232 stars 6.34 score 8 scriptsalexchristensen
SemNeT:Methods and Measures for Semantic Network Analysis
Implements several functions for the analysis of semantic networks including different network estimation algorithms, partial node bootstrapping (Kenett, Anaki, & Faust, 2014 <doi:10.3389/fnhum.2014.00407>), random walk simulation (Kenett & Austerweil, 2016 <http://alab.psych.wisc.edu/papers/files/Kenett16CreativityRW.pdf>), and a function to compute global network measures. Significance tests and plotting features are also implemented.
Maintained by Alexander P. Christensen. Last updated 2 years ago.
5.8 match 23 stars 4.51 score 28 scriptsfriendly
matlib:Matrix Functions for Teaching and Learning Linear Algebra and Multivariate Statistics
A collection of matrix functions for teaching and learning matrix linear algebra as used in multivariate statistical methods. Many of these functions are designed for tutorial purposes in learning matrix algebra ideas using R. In some cases, functions are provided for concepts available elsewhere in R, but where the function call or name is not obvious. In other cases, functions are provided to show or demonstrate an algorithm. In addition, a collection of functions are provided for drawing vector diagrams in 2D and 3D and for rendering matrix expressions and equations in LaTeX.
Maintained by Michael Friendly. Last updated 2 days ago.
diagramslinear-equationsmatrixmatrix-functionsmatrix-visualizervectorvignette
2.0 match 65 stars 12.89 score 900 scripts 11 dependentskrystian8207
shinyGizmo:Custom Components for Shiny Applications
Provides useful UI components and input widgets for 'Shiny' applications. The offered components allow to apply non-standard operations and view to your 'Shiny' application, but also help to overcome common performance issues.
Maintained by Krystian Igras. Last updated 2 years ago.
8.8 match 3 stars 2.83 score 15 scripts 1 dependentslozalojo
mem:The Moving Epidemic Method
The Moving Epidemic Method, created by T Vega and JE Lozano (2012, 2015) <doi:10.1111/j.1750-2659.2012.00422.x>, <doi:10.1111/irv.12330>, allows the weekly assessment of the epidemic and intensity status to help in routine respiratory infections surveillance in health systems. Allows the comparison of different epidemic indicators, timing and shape with past epidemics and across different regions or countries with different surveillance systems. Also, it gives a measure of the performance of the method in terms of sensitivity and specificity of the alert week.
Maintained by Jose E. Lozano. Last updated 2 years ago.
4.0 match 14 stars 6.24 score 82 scripts 1 dependentscran
socialh:Rank and Social Hierarchy for Gregarious Animals
Tools developed to facilitate the establishment of the rank and social hierarchy for gregarious animals by the Si method developed by Kondo & Hurnik (1990)<doi:10.1016/0168-1591(90)90125-W>. It is also possible to determine the number of agonistic interactions between two individuals, sociometric and dyadics matrix from dataset obtained through electronic bins. In addition, it is possible plotting the results using a bar plot, box plot, and sociogram.
Maintained by Julia de Paula Soares Valente. Last updated 2 years ago.
12.4 match 2.00 scoreeldarrak
FLightR:Reconstruct Animal Paths from Solar Geolocation Loggers Data
Spatio-temporal locations of an animal are computed from annotated data with a hidden Markov model via particle filter algorithm. The package is relatively robust to varying degrees of shading. The hidden Markov model is described in Movement Ecology - Rakhimberdiev et al. (2015) <doi:10.1186/s40462-015-0062-5>, general package description is in the Methods in Ecology and Evolution - Rakhimberdiev et al. (2017) <doi:10.1111/2041-210X.12765> and package accuracy assessed in the Journal of Avian Biology - Rakhimberdiev et al. (2016) <doi:10.1111/jav.00891>.
Maintained by Eldar Rakhimberdiev. Last updated 6 months ago.
movement-ecologysolar-geolocation-loggerssolar-geolocator
3.4 match 22 stars 7.26 score 111 scriptstrenchproject
TrenchR:Tools for Microclimate and Biophysical Ecology
Tools for translating environmental change into organismal response. Microclimate models to vertically scale weather station data to organismal heights. The biophysical modeling tools include both general models for heat flows and specific models to predict body temperatures for a variety of ectothermic taxa. Additional functions model and temporally partition air and soil temperatures and solar radiation. Utility functions estimate the organismal and environmental parameters needed for biophysical ecology. 'TrenchR' focuses on relatively simple and modular functions so users can create transparent and flexible biophysical models. Many functions are derived from Gates (1980) <doi:10.1007/978-1-4612-6024-0> and Campbell and Norman (1988) <isbn:9780387949376>.
Maintained by Lauren Buckley. Last updated 1 years ago.
3.5 match 13 stars 6.89 score 43 scriptscran
asnipe:Animal Social Network Inference and Permutations for Ecologists
Implements several tools that are used in animal social network analysis, as described in Whitehead (2007) Analyzing Animal Societies <University of Chicago Press> and Farine & Whitehead (2015) <doi: 10.1111/1365-2656.12418>. In particular, this package provides the tools to infer groups and generate networks from observation data, perform permutation tests on the data, calculate lagged association rates, and performed multiple regression analysis on social network data.
Maintained by Damien R. Farine. Last updated 2 years ago.
5.4 match 2 stars 4.36 score 173 scripts 2 dependentsmurrayefford
secr:Spatially Explicit Capture-Recapture
Functions to estimate the density and size of a spatially distributed animal population sampled with an array of passive detectors, such as traps, or by searching polygons or transects. Models incorporating distance-dependent detection are fitted by maximizing the likelihood. Tools are included for data manipulation and model selection.
Maintained by Murray Efford. Last updated 3 days ago.
2.3 match 3 stars 10.18 score 410 scripts 5 dependentsnasserdr
digiRhythm:Analyzing Animal's Rhythmicity
Analyze and visualize the rhythmic behavior of animals using the degree of functional coupling (See Scheibe (1999) <doi:10.1076/brhm.30.2.216.1420>), compute and visualize harmonic power, actograms, average activity and diurnality index.
Maintained by Hassan-Roland Nasser. Last updated 6 days ago.
3.9 match 6.06 score 22 scriptsbmcclintock
momentuHMM:Maximum Likelihood Analysis of Animal Movement Behavior Using Multivariate Hidden Markov Models
Extended tools for analyzing telemetry data using generalized hidden Markov models. Features of momentuHMM (pronounced ``momentum'') include data pre-processing and visualization, fitting HMMs to location and auxiliary biotelemetry or environmental data, biased and correlated random walk movement models, discrete- or continuous-time HMMs, continuous- or discrete-space movement models, approximate Langevin diffusion models, hierarchical HMMs, multiple imputation for incorporating location measurement error and missing data, user-specified design matrices and constraints for covariate modelling of parameters, random effects, decoding of the state process, visualization of fitted models, model checking and selection, and simulation. See McClintock and Michelot (2018) <doi:10.1111/2041-210X.12995>.
Maintained by Brett McClintock. Last updated 1 months ago.
2.7 match 43 stars 8.47 score 162 scriptsprabhleenkaur19
aniSNA:Statistical Network Analysis of Animal Social Networks
Obtain network structures from animal GPS telemetry observations and statistically analyse them to assess their adequacy for social network analysis. Methods include pre-network data permutations, bootstrapping techniques to obtain confidence intervals for global and node-level network metrics, and correlation and regression analysis of the local network metrics.
Maintained by Prabhleen Kaur. Last updated 2 months ago.
7.2 match 3.18 scoreclementcalenge
adehabitatHS:Analysis of Habitat Selection by Animals
A collection of tools for the analysis of habitat selection.
Maintained by Clement Calenge. Last updated 6 months ago.
4.8 match 1 stars 4.77 score 51 scriptswavx
bioacoustics:Analyse Audio Recordings and Automatically Extract Animal Vocalizations
Contains all the necessary tools to process audio recordings of various formats (e.g., WAV, WAC, MP3, ZC), filter noisy files, display audio signals, detect and extract automatically acoustic features for further analysis such as classification.
Maintained by Jean Marchal. Last updated 1 years ago.
2.9 match 47 stars 7.71 score 72 scripts 5 dependentsfeddelegrand7
ddplot:Create D3 Based SVG Graphics
Create 'D3' based 'SVG' ('Scalable Vector Graphics') graphics using a simple 'R' API. The package aims to simplify the creation of many 'SVG' plot types using a straightforward 'R' API. The package relies on the 'r2d3' 'R' package and the 'D3' 'JavaScript' library. See <https://rstudio.github.io/r2d3/> and <https://d3js.org/> respectively.
Maintained by Mohamed El Fodil Ihaddaden. Last updated 2 years ago.
3.9 match 44 stars 5.64 score 7 scriptstylermorganwall
rayshader:Create Maps and Visualize Data in 2D and 3D
Uses a combination of raytracing and multiple hill shading methods to produce 2D and 3D data visualizations and maps. Includes water detection and layering functions, programmable color palette generation, several built-in textures for hill shading, 2D and 3D plotting options, a built-in path tracer, 'Wavefront' OBJ file export, and the ability to save 3D visualizations to a 3D printable format.
Maintained by Tyler Morgan-Wall. Last updated 2 months ago.
1.9 match 2.1k stars 11.51 score 1.5k scripts 5 dependentsbioinformatics-ptp
detectRUNS:Detect Runs of Homozygosity and Runs of Heterozygosity in Diploid Genomes
Detection of runs of homozygosity and of heterozygosity in diploid genomes using two methods: sliding windows (Purcell et al (2007) <doi:10.1086/519795>) and consecutive runs (Marras et al (2015) <doi:10.1111/age.12259>).
Maintained by Filippo Biscarini. Last updated 3 years ago.
3.3 match 9 stars 6.50 score 35 scriptscran
stpp:Space-Time Point Pattern Simulation, Visualisation and Analysis
Many of the models encountered in applications of point process methods to the study of spatio-temporal phenomena are covered in 'stpp'. This package provides statistical tools for analyzing the global and local second-order properties of spatio-temporal point processes, including estimators of the space-time inhomogeneous K-function and pair correlation function. It also includes tools to get static and dynamic display of spatio-temporal point patterns. See Gabriel et al (2013) <doi:10.18637/jss.v053.i02>.
Maintained by Edith Gabriel. Last updated 9 months ago.
6.7 match 2 stars 3.21 score 27 scripts 1 dependentstaylor-arnold
ggimg:Graphics Layers for Plotting Image Data with 'ggplot2'
Provides two new layer types for displaying image data as layers within the Grammar of Graphics framework. Displays images using either a rectangle interface, with a fixed bounding box, or a point interface using a central point and general size parameter. Images can be given as local JPEG or PNG files, external resources, or as a list column containing raster image data.
Maintained by Taylor B. Arnold. Last updated 1 years ago.
3.8 match 53 stars 5.70 score 19 scriptsfernandosm
hybridModels:An R Package for the Stochastic Simulation of Disease Spreading in Dynamic Networks
Simulates stochastic hybrid models for transmission of infectious diseases in dynamic networks. It is a metapopulation model in which each node in the network is a sub-population and disease spreads within nodes and among them, combining two approaches: stochastic simulation algorithm (<doi:10.1146/annurev.physchem.58.032806.104637>) and individual-based approach, respectively. Equations that models spread within nodes are customizable and there are two link types among nodes: migration and influence (commuting). More information in Fernando S. Marques, Jose H. H. Grisi-Filho, Marcos Amaku et al. (2020) <doi:10.18637/jss.v094.i06>.
Maintained by Fernando S. Marques. Last updated 5 years ago.
7.1 match 2 stars 3.00 score 4 scriptsbirdscanada
naturecounts:Access and download data on plant and animal populations from NatureCounts
Access and download data on plant and animal populations from various databases through NatureCounts, a service managed by Bird Studies Canada.
Maintained by Denis Lepage. Last updated 6 months ago.
5.1 match 14 stars 4.11 score 46 scriptssvmiller
stevedata:Steve's Toy Data for Teaching About a Variety of Methodological, Social, and Political Topics
This is a collection of various kinds of data with broad uses for teaching. My students, and academics like me who teach the same topics I teach, should find this useful if their teaching workflow is also built around the R programming language. The applications are multiple but mostly cluster on topics of statistical methodology, international relations, and political economy.
Maintained by Steve Miller. Last updated 4 days ago.
3.5 match 8 stars 5.97 score 178 scriptseddelbuettel
binb:'binb' is not 'Beamer'
A collection of 'LaTeX' styles using 'Beamer' customization for pdf-based presentation slides in 'RMarkdown'. At present it contains 'RMarkdown' adaptations of the LaTeX themes 'Metropolis' (formerly 'mtheme') theme by Matthias Vogelgesang and others (now included in 'TeXLive'), the 'IQSS' them by Ista Zahn (which is included here), and the 'Monash' theme by Rob J Hyndman. Additional (free) fonts may be needed: 'Metropolis' prefers 'Fira', and 'IQSS' requires 'Libertinus'.
Maintained by Dirk Eddelbuettel. Last updated 3 months ago.
beamerbeamer-presentationbeamer-thememarkdownpdfrmarkdownrmarkdown-beamer
2.5 match 189 stars 8.31 score 2 scripts 2 dependentsmcandocia
keyToEnglish:Convert Data to Memorable Phrases
Convert keys and other values to memorable phrases. Includes some methods to build lists of words.
Maintained by Max Candocia. Last updated 4 years ago.
7.6 match 1 stars 2.70 score 3 scriptseligurarie
bcpa:Behavioral Change Point Analysis of Animal Movement
The Behavioral Change Point Analysis (BCPA) is a method of identifying hidden shifts in the underlying parameters of a time series, developed specifically to be applied to animal movement data which is irregularly sampled. The method is based on: E. Gurarie, R. Andrews and K. Laidre A novel method for identifying behavioural changes in animal movement data (2009) Ecology Letters 12:5 395-408. A development version is on <https://github.com/EliGurarie/bcpa>. NOTE: the BCPA method may be useful for any univariate, irregularly sampled Gaussian time-series, but animal movement analysts are encouraged to apply correlated velocity change point analysis as implemented in the smoove package, as of this writing on GitHub at <https://github.com/EliGurarie/smoove>. An example of a univariate analysis is provided in the UnivariateBCPA vignette.
Maintained by Eliezer Gurarie. Last updated 3 years ago.
3.8 match 3 stars 5.26 score 30 scriptsepimodel
EpiModel:Mathematical Modeling of Infectious Disease Dynamics
Tools for simulating mathematical models of infectious disease dynamics. Epidemic model classes include deterministic compartmental models, stochastic individual-contact models, and stochastic network models. Network models use the robust statistical methods of exponential-family random graph models (ERGMs) from the Statnet suite of software packages in R. Standard templates for epidemic modeling include SI, SIR, and SIS disease types. EpiModel features an API for extending these templates to address novel scientific research aims. Full methods for EpiModel are detailed in Jenness et al. (2018, <doi:10.18637/jss.v084.i08>).
Maintained by Samuel Jenness. Last updated 2 months ago.
agent-based-modelingepidemicsepidemiologyinfectious-diseasesnetwork-graphcpp
1.7 match 250 stars 11.57 score 315 scriptsbrianbattaile
TrackReconstruction:Reconstruct Animal Tracks from Magnetometer, Accelerometer, Depth and Optional Speed Data
Reconstructs animal tracks from magnetometer, accelerometer, depth and optional speed data. Designed primarily using data from Wildlife Computers Daily Diary tags deployed on northern fur seals.
Maintained by Brian Battaile. Last updated 3 years ago.
6.9 match 2.85 score 35 scriptsdjnavarro
jasmines:Generative Art
It doesn't do much, really.
Maintained by Danielle Navarro. Last updated 4 years ago.
4.0 match 112 stars 4.90 score 141 scriptstrafficonese
leaflet.extras2:Extra Functionality for 'leaflet' Package
Several 'leaflet' plugins are integrated, which are available as extension to the 'leaflet' package.
Maintained by Gatscha Sebastian. Last updated 11 days ago.
data-visualizationgeospatialgeospatial-visualizationleafletleaflet-plugins
2.0 match 87 stars 9.70 score 432 scripts 1 dependentsjoelkilty
MMAC:Data for Mathematical Modeling and Applied Calculus
Contains the data sets for the textbook "Mathematical Modeling and Applied Calculus" by Joel Kilty and Alex M. McAllister. The book will be published by Oxford University Press in 2018 with ISBN-13: 978-019882472.
Maintained by Joel Kilty. Last updated 7 years ago.
7.8 match 2.50 score 63 scriptslgnbhl
aniview:Animate 'shiny' and 'rmarkdown' Content when it Comes into View
Animate 'shiny' and 'rmarkdown' content when it comes into view using 'animate-css' effects <https://daneden.github.io/animate.css/> thanks to 'jQuery AniView' <https://jjcosgrove.github.io/jquery-aniview/>.
Maintained by Félix Luginbuhl. Last updated 6 months ago.
5.8 match 2 stars 3.30 score 3 scriptssimondedman
movegroup:Visualizing and Quantifying Space Use Data for Groups of Animals
Offers an easy and automated way to scale up individual-level space use analysis to that of groups. Contains a function from the 'move' package to calculate a dynamic Brownian bridge movement model from movement data for individual animals, as well as functions to visualize and quantify space use for individuals aggregated in groups. Originally written with passive acoustic telemetry in mind, this package also provides functionality to account for unbalanced acoustic receiver array designs, and satellite tag data.
Maintained by Simon Dedman. Last updated 2 months ago.
brownian-bridgehome-rangehome-range-analysismigrationresidencyspace-usetracking
3.4 match 17 stars 5.63 score 4 scriptssizespectrum
mizer:Dynamic Multi-Species Size Spectrum Modelling
A set of classes and methods to set up and run multi-species, trait based and community size spectrum ecological models, focused on the marine environment.
Maintained by Gustav Delius. Last updated 2 months ago.
ecosystem-modelfish-population-dynamicsfisheriesfisheries-managementmarine-ecosystempopulation-dynamicssimulationsize-structurespecies-interactionstransport-equationcpp
2.0 match 38 stars 9.43 score 207 scriptssvmiller
codename:Generation of Code Names for Organizations, People, Projects, and Whatever Else
This creates code names that a user can consider for their organizations, their projects, themselves, people in their organizations or projects, or whatever else. The user can also supply a numeric seed (and even a character seed) for maximum reproducibility. Use is simple and the code names produced come in various types too, contingent on what the user may be desiring as a code name or nickname.
Maintained by Steve Miller. Last updated 2 years ago.
codenamereproducibilitywu-tang
4.0 match 17 stars 4.62 score 49 scriptssciurus365
simlandr:Simulation-Based Landscape Construction for Dynamical Systems
A toolbox for constructing potential landscapes for dynamical systems using Monte Carlo simulation. The method is based on the potential landscape definition by Wang et al. (2008) <doi:10.1073/pnas.0800579105> (also see Zhou & Li, 2016 <doi:10.1063/1.4943096> for further mathematical discussions) and can be used for a large variety of models.
Maintained by Jingmeng Cui. Last updated 1 months ago.
2.9 match 6 stars 6.41 score 12 scripts 2 dependentsemilhvitfeldt
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.
2.3 match 28 stars 7.97 score 304 scripts 3 dependentsddalthorp
GenEst:Generalized Mortality Estimator
Command-line and 'shiny' GUI implementation of the GenEst models for estimating bird and bat mortality at wind and solar power facilities, following Dalthorp, et al. (2018) <doi:10.3133/tm7A2>.
Maintained by Daniel Dalthorp. Last updated 2 years ago.
2.3 match 7 stars 7.81 score 55 scripts 2 dependentspaulnorthrop
anscombiser:Create Datasets with Identical Summary Statistics
Anscombe's quartet are a set of four two-variable datasets that have several common summary statistics but which have very different joint distributions. This becomes apparent when the data are plotted, which illustrates the importance of using graphical displays in Statistics. This package enables the creation of datasets that have identical marginal sample means and sample variances, sample correlation, least squares regression coefficients and coefficient of determination. The user supplies an initial dataset, which is shifted, scaled and rotated in order to achieve target summary statistics. The general shape of the initial dataset is retained. The target statistics can be supplied directly or calculated based on a user-supplied dataset. The 'datasauRus' package <https://cran.r-project.org/package=datasauRus> provides further examples of datasets that have markedly different scatter plots but share many sample summary statistics.
Maintained by Paul J. Northrop. Last updated 2 years ago.
anscombeanscombes-quartetanscombesquartet
3.8 match 11 stars 4.74 score 9 scriptscasperhart
detourr:Portable and Performant Tour Animations
Provides 2D and 3D tour animations as HTML widgets. The user can interact with the widgets using orbit controls, tooltips, brushing, and timeline controls. Linked brushing is supported using 'crosstalk', and widgets can be embedded in Shiny apps or HTML documents.
Maintained by Casper Hart. Last updated 5 months ago.
3.6 match 7 stars 4.83 score 48 scriptscbracis
recurse:Computes Revisitation Metrics for Trajectory Data
Computes revisitation metrics for trajectory data, such as the number of revisitations for each location as well as the time spent for that visit and the time since the previous visit. Also includes functions to plot data.
Maintained by Chloe Bracis. Last updated 8 months ago.
2.8 match 10 stars 6.24 score 43 scriptsrobindenz1
contsurvplot:Visualize the Effect of a Continuous Variable on a Time-to-Event Outcome
Graphically display the (causal) effect of a continuous variable on a time-to-event outcome using multiple different types of plots based on g-computation. Those functions include, among others, survival area plots, survival contour plots, survival quantile plots and 3D surface plots. Due to the use of g-computation, all plot allow confounder-adjustment naturally. For details, see Robin Denz, Nina Timmesfeld (2023) <doi:10.1097/EDE.0000000000001630>.
Maintained by Robin Denz. Last updated 1 years ago.
causal-inferencecontinuousg-computationsurvival-analysisvisualization
3.2 match 12 stars 5.53 score 56 scriptssborstein
AnnotationBustR:Extract Subsequences from GenBank Annotations
Extraction of subsequences into FASTA files from GenBank annotations where gene names may vary among accessions. Borstein & O'Meara (2018) <doi:10.7717/peerj.5179>.
Maintained by Samuel R. Borstein. Last updated 5 months ago.
3.6 match 5 stars 4.78 score 12 scriptsbodkan
slendr:A Simulation Framework for Spatiotemporal Population Genetics
A framework for simulating spatially explicit genomic data which leverages real cartographic information for programmatic and visual encoding of spatiotemporal population dynamics on real geographic landscapes. Population genetic models are then automatically executed by the 'SLiM' software by Haller et al. (2019) <doi:10.1093/molbev/msy228> behind the scenes, using a custom built-in simulation 'SLiM' script. Additionally, fully abstract spatial models not tied to a specific geographic location are supported, and users can also simulate data from standard, non-spatial, random-mating models. These can be simulated either with the 'SLiM' built-in back-end script, or using an efficient coalescent population genetics simulator 'msprime' by Baumdicker et al. (2022) <doi:10.1093/genetics/iyab229> with a custom-built 'Python' script bundled with the R package. Simulated genomic data is saved in a tree-sequence format and can be loaded, manipulated, and summarised using tree-sequence functionality via an R interface to the 'Python' module 'tskit' by Kelleher et al. (2019) <doi:10.1038/s41588-019-0483-y>. Complete model configuration, simulation and analysis pipelines can be therefore constructed without a need to leave the R environment, eliminating friction between disparate tools for population genetic simulations and data analysis.
Maintained by Martin Petr. Last updated 12 days ago.
popgenpopulation-geneticssimulationsspatial-statistics
1.9 match 56 stars 9.15 score 88 scriptsebeneditos
telegram.bot:Develop a 'Telegram Bot' with R
Provides a pure interface for the 'Telegram Bot API' <http://core.telegram.org/bots/api>. In addition to the pure API implementation, it features a number of tools to make the development of 'Telegram' bots with R easy and straightforward, providing an easy-to-use interface that takes some work off the programmer.
Maintained by Ernest Benedito. Last updated 3 years ago.
2.0 match 109 stars 8.57 score 126 scripts 1 dependentsbblonder
hypervolume:High Dimensional Geometry, Set Operations, Projection, and Inference Using Kernel Density Estimation, Support Vector Machines, and Convex Hulls
Estimates the shape and volume of high-dimensional datasets and performs set operations: intersection / overlap, union, unique components, inclusion test, and hole detection. Uses stochastic geometry approach to high-dimensional kernel density estimation, support vector machine delineation, and convex hull generation. Applications include modeling trait and niche hypervolumes and species distribution modeling.
Maintained by Benjamin Blonder. Last updated 2 months ago.
1.7 match 23 stars 9.75 score 211 scripts 7 dependentsegpivo
SpatPCA:Regularized Principal Component Analysis for Spatial Data
Provide regularized principal component analysis incorporating smoothness, sparseness and orthogonality of eigen-functions by using the alternating direction method of multipliers algorithm (Wang and Huang, 2017, <DOI:10.1080/10618600.2016.1157483>). The method can be applied to either regularly or irregularly spaced data, including 1D, 2D, and 3D.
Maintained by Wen-Ting Wang. Last updated 7 months ago.
admmcovariance-estimationeigenfunctionslassomatrix-factorizationpcarcpparmadillorcppparallelregularizationspatialspatial-data-analysissplinesopenblascppopenmp
3.0 match 20 stars 5.53 score 17 scriptsrjknell
Biostatistics:Statistics Tutorials for Biologists
Tutorials for statistics, aimed at biological scientists. Subjects range from basic descriptive statistics through to complex linear modelling. The tutorials include text, videos, interactive coding exercises and multiple choice quizzes. The package also includes 19 datasets which are used in the tutorials.
Maintained by Rob Knell. Last updated 3 years ago.
3.6 match 4.54 score 5 scriptsbioc
pRoloc:A unifying bioinformatics framework for spatial proteomics
The pRoloc package implements machine learning and visualisation methods for the analysis and interogation of quantitiative mass spectrometry data to reliably infer protein sub-cellular localisation.
Maintained by Lisa Breckels. Last updated 27 days ago.
immunooncologyproteomicsmassspectrometryclassificationclusteringqualitycontrolbioconductorproteomics-dataspatial-proteomicsvisualisationopenblascpp
1.9 match 15 stars 8.71 score 101 scripts 2 dependents