R-universe search: animals

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.

animation statistical-computing statistical-graphics statistics

83.7 match 208 stars 12.08 score 2.5k scripts 29 dependents

hughjonesd

anim.plots:Simple Animated Plots for R

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

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

animation graphics plot

114.9 match 8 stars 5.00 score 25 scripts

kcf-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.

animation d3js javascript

83.5 match 30 stars 6.88 score 84 scripts

thomasp85

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.

animation data-visualization ggplot-extension ggplot2 transition

28.1 match 2.0k stars 15.87 score 13k scripts 25 dependents

ggobi

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 dependents

camhowitt

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.

lottie shiny

37.2 match 2 stars 5.52 score 37 scripts

bupaverse

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.

animation bupar business-process event-logs htmlwidgets process-map processmining svg-animations

27.0 match 66 stars 7.54 score 106 scripts

thomasp85

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.

animation plotting transition tweening cpp

15.7 match 399 stars 12.80 score 440 scripts 319 dependents

calbertsen

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.

animal animal-behavior argos-data c-plus-plus gps-data movement movement-ecology solar-geolocator tracking cpp

47.3 match 12 stars 3.92 score 14 scripts

kenaho1

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 dependents

statnet

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 dependents

aschleg

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-shelter animal-welfare-organizations animals api-wrapper petfinder petfinder-api petfinder-database

37.9 match 6 stars 4.48 score 6 scripts

ianjonsen

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-movement animal-tracking random-effects-model state-space-models tmb cpp

21.9 match 39 stars 7.16 score 59 scripts

r-forge

surveillance:Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena

Statistical methods for the modeling and monitoring of time series of counts, proportions and categorical data, as well as for the modeling of continuous-time point processes of epidemic phenomena. The monitoring methods focus on aberration detection in count data time series from public health surveillance of communicable diseases, but applications could just as well originate from environmetrics, reliability engineering, econometrics, or social sciences. The package implements many typical outbreak detection procedures such as the (improved) Farrington algorithm, or the negative binomial GLR-CUSUM method of Hoehle and Paul (2008) <doi:10.1016/j.csda.2008.02.015>. A novel CUSUM approach combining logistic and multinomial logistic modeling is also included. The package contains several real-world data sets, the ability to simulate outbreak data, and to visualize the results of the monitoring in a temporal, spatial or spatio-temporal fashion. A recent overview of the available monitoring procedures is given by Salmon et al. (2016) <doi:10.18637/jss.v070.i10>. For the retrospective analysis of epidemic spread, the package provides three endemic-epidemic modeling frameworks with tools for visualization, likelihood inference, and simulation. hhh4() estimates models for (multivariate) count time series following Paul and Held (2011) <doi:10.1002/sim.4177> and Meyer and Held (2014) <doi:10.1214/14-AOAS743>. twinSIR() models the susceptible-infectious-recovered (SIR) event history of a fixed population, e.g, epidemics across farms or networks, as a multivariate point process as proposed by Hoehle (2009) <doi:10.1002/bimj.200900050>. twinstim() estimates self-exciting point process models for a spatio-temporal point pattern of infective events, e.g., time-stamped geo-referenced surveillance data, as proposed by Meyer et al. (2012) <doi:10.1111/j.1541-0420.2011.01684.x>. A recent overview of the implemented space-time modeling frameworks for epidemic phenomena is given by Meyer et al. (2017) <doi:10.18637/jss.v077.i11>.

Maintained by Sebastian Meyer. Last updated 2 days ago.

cpp

14.3 match 2 stars 10.68 score 446 scripts 3 dependents

trinker

qdap:Bridging the Gap Between Qualitative Data and Quantitative Analysis

Automates many of the tasks associated with quantitative discourse analysis of transcripts containing discourse including frequency counts of sentence types, words, sentences, turns of talk, syllables and other assorted analysis tasks. The package provides parsing tools for preparing transcript data. Many functions enable the user to aggregate data by any number of grouping variables, providing analysis and seamless integration with other R packages that undertake higher level analysis and visualization of text. This affords the user a more efficient and targeted analysis. 'qdap' is designed for transcript analysis, however, many functions are applicable to other areas of Text Mining/ Natural Language Processing.

Maintained by Tyler Rinker. Last updated 4 years ago.

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

14.0 match 176 stars 9.61 score 1.3k scripts 3 dependents

ropensci

spatsoc:Group Animal Relocation Data by Spatial and Temporal Relationship

Detects spatial and temporal groups in GPS relocations (Robitaille et al. (2019) <doi:10.1111/2041-210X.13215>). It can be used to convert GPS relocations to gambit-of-the-group format to build proximity-based social networks In addition, the randomizations function provides data-stream randomization methods suitable for GPS data.

Maintained by Alec L. Robitaille. Last updated 1 months ago.

animal gps network social spatial

12.9 match 24 stars 9.97 score 145 scripts 3 dependents

dmurdoch

rgl:3D Visualization Using OpenGL

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

Maintained by Duncan Murdoch. Last updated 2 months ago.

graphics opengl rgl webgl libglu libglvnd libpng libx11 freetype cpp

6.8 match 91 stars 17.49 score 7.3k scripts 300 dependents

rich-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.

easy-to-use svg

25.9 match 51 stars 4.55 score 14 scripts

sckott

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.

ascii-art

11.5 match 320 stars 10.23 score 239 scripts

dreamrs

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.

shiny

6.8 match 849 stars 17.05 score 8.1k scripts 218 dependents

biodiverse

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.

openblas cpp openmp

8.3 match 4 stars 13.03 score 652 scripts 12 dependents

ropensci

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-manipulation image-processing imagemagick cpp

6.0 match 468 stars 17.31 score 9.0k scripts 256 dependents

thomasp85

transformr:Polygon and Path Transformations

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

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

animation data-visualization interpolation matching-shapes tweening cpp

10.5 match 116 stars 9.82 score 772 scripts 26 dependents

marce10

warbleR:Streamline Bioacoustic Analysis

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

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

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

9.2 match 54 stars 11.01 score 270 scripts 4 dependents

inbo

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-movement animal-tracking biologging data-access fish lifewatch oscibio

22.6 match 8 stars 4.15 score 14 scripts

ropensci

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-signals animal behavior bioacoustics

13.9 match 7 stars 6.72 score 18 scripts

nspyrison

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.

dimension reduction tours visualization

14.9 match 3 stars 6.28 score 105 scripts 1 dependents

rspatial

terra:Spatial Data Analysis

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

Maintained by Robert J. Hijmans. Last updated 1 days ago.

geospatial raster spatial vector onetbb proj gdal geos cpp

5.3 match 559 stars 17.64 score 17k scripts 851 dependents

swarm-lab

swaRm:Processing Collective Movement Data

Function library for processing collective movement data (e.g. fish schools, ungulate herds, baboon troops) collected from GPS trackers or computer vision tracking software.

Maintained by Simon Garnier. Last updated 1 years ago.

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

16.8 match 21 stars 5.50 score 8 scripts 1 dependents

covaruber

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-information mixed-models rcpparmadillo openblas cpp openmp

7.2 match 43 stars 12.70 score 300 scripts 9 dependents

wilkox

ggfittext:Fit Text Inside a Box in 'ggplot2'

A 'ggplot2' extension to fit text into a box by growing, shrinking or wrapping the text.

Maintained by David Wilkins. Last updated 1 years ago.

ggplot2

8.3 match 306 stars 11.08 score 234 scripts 33 dependents

ocean-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 scripts

roaldarbol

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

An R toolbox for analysing animal movement across space and time.

Maintained by Mikkel Roald-Arbøl. Last updated 2 months ago.

animal-behaviour animal-movement neuroethology neuroscience

18.4 match 10 stars 4.81 score 8 scripts

bwlewis

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-visualization graph-animation igraph threejs webgl

7.5 match 304 stars 11.67 score 522 scripts 28 dependents

jmsigner

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 scripts

rspatial

raster:Geographic Data Analysis and Modeling

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

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

cpp

4.9 match 164 stars 17.05 score 58k scripts 555 dependents

yang-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.

jquery-ui shiny

7.7 match 276 stars 10.72 score 464 scripts 16 dependents

swarm-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-behavior animal-behaviour gps gps-data

15.0 match 4 stars 5.42 score 11 scripts 1 dependents

bart1

move:Visualizing and Analyzing Animal Track Data

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

Maintained by Bart Kranstauber. Last updated 4 months ago.

cpp

9.1 match 8.74 score 690 scripts 3 dependents

mikejohnson51

climateR:climateR

Find, subset, and retrive geospatial data by AOI.

Maintained by Mike Johnson. Last updated 3 months ago.

aoi climate dataset geospatial gridded-climate-data weather

9.0 match 187 stars 8.74 score 156 scripts 1 dependents

otoliths

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.

animals biodiversity catalogue-of-life-china catalogue-of-life-global-checklist catalogue-of-life-taiwan-checklist china china-animal-scientific-database fungi microorganisms plants redlist-of-chinese-biodiversity species2000

20.4 match 13 stars 3.81 score 3 scripts

clementcalenge

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 dependents

phuse-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 scripts

lgnbhl

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.

animation aos shiny

15.9 match 7 stars 4.50 score 15 scripts

ropensci

pathviewr:Wrangle, Analyze, and Visualize Animal Movement Data

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

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

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

10.4 match 8 stars 6.56 score 102 scripts

trinker

wakefield:Generate Random Data Sets

Generates random data sets including: data.frames, lists, and vectors.

Maintained by Tyler Rinker. Last updated 5 years ago.

data-generation wakefield

9.4 match 256 stars 7.13 score 209 scripts

clementcalenge

adehabitatHR:Home Range Estimation

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

Maintained by Clement Calenge. Last updated 6 months ago.

7.4 match 6 stars 8.73 score 752 scripts 9 dependents

animint

animint2:Animated Interactive Grammar of Graphics

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

Maintained by Toby Hocking. Last updated 27 days ago.

7.2 match 64 stars 8.87 score 173 scripts

alanarnholt

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 dependents

symbolixau

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.

deckgl geospatial mapbox mapbox-gl mapbox-gl-js maps cpp

6.0 match 363 stars 10.30 score 368 scripts 1 dependents

ctmm-initiative

ctmm:Continuous-Time Movement Modeling

Functions for identifying, fitting, and applying continuous-space, continuous-time stochastic-process movement models to animal tracking data. The package is described in Calabrese et al (2016) <doi:10.1111/2041-210X.12559>, with models and methods based on those introduced and detailed in Fleming & Calabrese et al (2014) <doi:10.1086/675504>, Fleming et al (2014) <doi:10.1111/2041-210X.12176>, Fleming et al (2015) <doi:10.1103/PhysRevE.91.032107>, Fleming et al (2015) <doi:10.1890/14-2010.1>, Fleming et al (2016) <doi:10.1890/15-1607>, Péron & Fleming et al (2016) <doi:10.1186/s40462-016-0084-7>, Fleming & Calabrese (2017) <doi:10.1111/2041-210X.12673>, Péron et al (2017) <doi:10.1002/ecm.1260>, Fleming et al (2017) <doi:10.1016/j.ecoinf.2017.04.008>, Fleming et al (2018) <doi:10.1002/eap.1704>, Winner & Noonan et al (2018) <doi:10.1111/2041-210X.13027>, Fleming et al (2019) <doi:10.1111/2041-210X.13270>, Noonan & Fleming et al (2019) <doi:10.1186/s40462-019-0177-1>, Fleming et al (2020) <doi:10.1101/2020.06.12.130195>, Noonan et al (2021) <doi:10.1111/2041-210X.13597>, Fleming et al (2022) <doi:10.1111/2041-210X.13815>, Silva et al (2022) <doi:10.1111/2041-210X.13786>, Alston & Fleming et al (2023) <doi:10.1111/2041-210X.14025>.

Maintained by Christen H. Fleming. Last updated 2 months ago.

5.8 match 49 stars 10.57 score 534 scripts 4 dependents

marce10

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.

animal raven sounds

10.0 match 10 stars 6.00 score 50 scripts

marcusrowcliffe

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 dependents

henryrscharf

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 scripts

helgasoft

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.

3d animation boxplot charts crosstalk echarts echarty geojson globe graphs heatmap hierarchical-data leaflet maps morphing shapefiles shiny visualization webr

10.0 match 90 stars 5.95 score 20 scripts

bioc

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.

genetics comparativegenomics preprocessing phylogenetics transcriptomics geneexpression animal-models bioconductor bioconductor-package bioinformatics biomedicine comparative-genomics evolutionary-biology genes genomics ontologies translational-research

7.5 match 42 stars 7.85 score 31 scripts 2 dependents

chaoranhu

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-movement brownian-motion hidden-markov-model hidden-states measurement-error telegraph-process gsl cpp

12.9 match 3 stars 4.52 score 11 scripts

swechhya

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.

hacktoberfest shiny

11.8 match 39 stars 4.85 score 36 scripts

tylerlittlefield

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.

css css-animations shiny vov-css

11.2 match 24 stars 4.96 score 76 scripts

gadenbuie

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.

remarkjs rmarkdown slides tabs xaringan xaringan-slides

6.4 match 450 stars 8.41 score 1.9k scripts 1 dependents

mmaechler

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 dependents

jimmcl

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 scripts

davidgohel

ggiraph:Make 'ggplot2' Graphics Interactive

Create interactive 'ggplot2' graphics using 'htmlwidgets'.

Maintained by David Gohel. Last updated 3 months ago.

libpng cpp

3.6 match 819 stars 14.39 score 4.1k scripts 34 dependents

bedapub

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-experiments randomization

7.1 match 8 stars 7.28 score 24 scripts

r4fun

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.

css shiny

12.4 match 16 stars 4.16 score 18 scripts

dsjohnson

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.

openblas cpp

8.2 match 19 stars 6.29 score 63 scripts 3 dependents

miguel-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-movement heterogeneous-landscapes movement-ecology river-networks simulation

8.4 match 15 stars 6.08 score 27 scripts 1 dependents

spluque

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-behavior behavioural-ecology biology diving science

7.5 match 6 stars 6.75 score 55 scripts

liamrevell

phytools:Phylogenetic Tools for Comparative Biology (and Other Things)

A wide range of methods for phylogenetic analysis - concentrated in phylogenetic comparative biology, but also including numerous techniques for visualizing, analyzing, manipulating, reading or writing, and even inferring phylogenetic trees. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, and simulation of phylogenies and trait data. A broad range of plotting methods for phylogenies and comparative data include (but are not restricted to) methods for mapping trait evolution on trees, for projecting trees into phenotype space or a onto a geographic map, and for visualizing correlated speciation between trees. Lastly, numerous functions are designed for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data. For instance, there are functions for computing consensus phylogenies from a set, for simulating phylogenetic trees and data under a range of models, for randomly or non-randomly attaching species or clades to a tree, as well as for a wide range of other manipulations and analyses that phylogenetic biologists might find useful in their research.

Maintained by Liam J. Revell. Last updated 27 days ago.

3.6 match 218 stars 13.85 score 4.8k scripts 76 dependents

cran

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.

openblas

7.8 match 1 stars 6.35 score 36 dependents

robitalec

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.

animal distance-to ecology resource-selection rsf spatial

10.0 match 5 stars 4.88 score 10 scripts 1 dependents

sachaepskamp

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.

cpp

4.3 match 69 stars 11.43 score 1.2k scripts 63 dependents

tylermorganwall

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.

libx11 cpp

4.5 match 630 stars 10.78 score 188 scripts 8 dependents

tidymodels

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 dependents

rethomics

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-analysis parsing

9.8 match 6 stars 4.92 score 31 scripts 1 dependents

daattali

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.

shiny shiny-r

3.4 match 409 stars 13.71 score 4.3k scripts 119 dependents

dtharvey

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 scripts

alexchristensen

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.

dictionaries semantic-network-analysis

9.0 match 4 stars 5.08 score 3 scripts 2 dependents

r-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.

fortran openblas

3.4 match 13.33 score 1.7k scripts 480 dependents

richardgeveritt

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 scripts

frbcesab

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.

animal bayesian counts population precision temporal-trend jags cpp

10.5 match 1 stars 4.30 score

gtatters

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-physiology heat-exchange heat-flux image-frames temperature thermal-biology thermal-images

7.5 match 169 stars 5.85 score 83 scripts

reside-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 dependents

helgasoft

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.

3d amap animation flyover gaode geojson interactive-visualizations layers maps shiny wms

10.0 match 3 stars 4.35 score 15 scripts

inlabru-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 dependents

animaltags

tagtools:Work with Data from High-Resolution Biologging Tags

High-resolution movement-sensor tags typically include accelerometers to measure body posture and sudden movements or changes in speed, magnetometers to measure direction of travel, and pressure sensors to measure dive depth in aquatic or marine animals. The sensors in these tags usually sample many times per second. Some tags include sensors for speed, turning rate (gyroscopes), and sound. This package provides software tools to facilitate calibration, processing, and analysis of such data. Tools are provided for: data import/export; calibration (from raw data to calibrated data in scientific units); visualization (for example, multi-panel time-series plots); data processing (such as event detection, calculation of derived metrics like jerk and dynamic acceleration, dive detection, and dive parameter calculation); and statistical analysis (for example, track reconstruction, a rotation test, and Mahalanobis distance analysis).

Maintained by Stacy DeRuiter. Last updated 9 months ago.

9.4 match 8 stars 4.62 score 26 scripts

inbo

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.

camera-traps oscibio

6.8 match 12 stars 6.27 score 16 scripts

smbc-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.

jags cpp

6.3 match 8 stars 6.77 score 41 scripts

talgalili

dendextend:Extending 'dendrogram' Functionality in R

Offers a set of functions for extending 'dendrogram' objects in R, letting you visualize and compare trees of 'hierarchical clusterings'. You can (1) Adjust a tree's graphical parameters - the color, size, type, etc of its branches, nodes and labels. (2) Visually and statistically compare different 'dendrograms' to one another.

Maintained by Tal Galili. Last updated 2 months ago.

2.5 match 154 stars 17.02 score 6.0k scripts 164 dependents

feddelegrand7

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.

css rmarkdown rmarkdown-document shiny

12.0 match 7 stars 3.54 score 3 scripts

yihui

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-documents knitr literate-programming rmarkdown sweave

1.8 match 2.4k stars 23.62 score 116k scripts 4.2k dependents

bart1

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 dependents

jbengler

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 scripts

andburch

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-behavior collective-behavior

11.2 match 3.70 score 7 scripts

coolbutuseless

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 scripts

matthewwolak

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.

cpp

5.8 match 20 stars 7.13 score 151 scripts 3 dependents

marce10

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-sounds bioacoustics spectrogram

7.5 match 23 stars 5.50 score 34 scripts

trevorld

ggpattern:'ggplot2' Pattern Geoms

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

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

3.3 match 368 stars 12.33 score 1.7k scripts 3 dependents

opengeos

whitebox:'WhiteboxTools' R Frontend

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

Maintained by Andrew Brown. Last updated 5 months ago.

geomorphometry geoprocessing geospatial gis hydrology remote-sensing rstudio

4.3 match 173 stars 9.65 score 203 scripts 2 dependents

floschuberth

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 dependents

johncoene

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

Easily create interactive charts by leveraging the 'Echarts Javascript' library which includes 36 chart types, themes, 'Shiny' proxies and animations.

Maintained by David Munoz Tord. Last updated 3 days ago.

echarts hacktoberfest htmlwidget htmlwidgets visualization

3.5 match 603 stars 11.45 score 1.3k scripts 11 dependents

appelmar

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-sensing satellite-imagery spatial-analysis gdal netcdf cpp

4.8 match 124 stars 8.39 score 356 scripts

gitboosting

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.

cpp

7.3 match 5.38 score 12 scripts

plotly

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.

d3js data-visualization ggplot2 javascript plotly shiny webgl

2.0 match 2.6k stars 19.43 score 93k scripts 797 dependents

johncoene

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.

htmlwidgets network-visualization sigmajs

6.5 match 72 stars 5.92 score 77 scripts

r-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.

cli

2.0 match 664 stars 19.33 score 1.4k scripts 14k dependents

dfsp-spirit

fsbrain:Managing and Visualizing Brain Surface Data

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

Maintained by Tim Schäfer. Last updated 4 months ago.

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

5.9 match 66 stars 6.47 score 15 scripts

jonesor

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 dependents

graemediack

ISO11784Tools:ISO11784 PIT Tag ID Format Converters

Some tools to assist with converting International Organization for Standardization (ISO) standard 11784 (ISO11784) animal ID codes between 4 recognised formats commonly displayed on Passive Integrated Transponder (PIT) tag readers. The most common formats are 15 digit decimal, e.g., 999123456789012, and 13 character hexadecimal 'dot' format, e.g., 3E7.1CBE991A14. These are referred to in this package as isodecimal and isodothex. The other two formats are the raw hexadecimal representation of the ISO11784 binary structure (see <https://en.wikipedia.org/wiki/ISO_11784_and_ISO_11785>). There are two 'flavours' of this format, a left and a right variation. Which flavour a reader happens to output depends on if the developers decided to reverse the binary number or not before converting to hexadecimal, a decision based on the fact that the PIT tags will transmit their binary code Least Significant Bit (LSB) first, or backwards basically.

Maintained by Graeme Diack. Last updated 20 days ago.

10.3 match 1 stars 3.70 score 6 scripts

sanchezi

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 scripts

mhahsler

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-clustering datastream stream-mining cpp

3.8 match 39 stars 10.05 score 132 scripts 3 dependents

r-tmap

tmap:Thematic Maps

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

Maintained by Martijn Tennekes. Last updated 5 days ago.

choropleth-maps maps spatial thematic-maps visualisation

2.3 match 880 stars 16.73 score 13k scripts 24 dependents

covaruber

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 scripts

devopifex

g2r:Interactive Grammar of Graphics

Interactive grammar of graphics.

Maintained by John Coene. Last updated 3 years ago.

visualization

8.3 match 119 stars 4.53 score 57 scripts

mhpob

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-tracking biotelemetry fish fisheries visualization

7.5 match 4 stars 4.92 score 6 scripts 1 dependents

ianjonsen

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.

cran-downloads jags cpp

6.8 match 17 stars 5.42 score 31 scripts

joshcullen

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.

cpp

8.8 match 9 stars 4.18 score 34 scripts

gobbios

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.

cpp

5.3 match 4 stars 6.86 score 61 scripts 1 dependents

adrian-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 dependents

lz100

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 dependents

brry

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 dependents

lewisajones

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 scripts

mayur1009

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 scripts

r-forge

copula:Multivariate Dependence with Copulas

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

Maintained by Martin Maechler. Last updated 11 days ago.

3.0 match 11.83 score 1.2k scripts 86 dependents

swsoyee

r3dmol:Create Interactive 3D Visualizations of Molecular Data

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

Maintained by Wei Su. Last updated 1 years ago.

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

5.5 match 90 stars 6.35 score 166 scripts 1 dependents

famuvie

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 scripts

kjhealy

gssrdoc:Document General Social Survey Variable

The General Social Survey (GSS) is a long-running, mostly annual survey of US households. It is administered by the National Opinion Research Center (NORC). This package contains the a tibble with information on the survey variables, together with every variable documented as an R help page. For more information on the GSS see \url{http://gss.norc.org}.

Maintained by Kieran Healy. Last updated 11 months ago.

14.7 match 2.28 score 38 scripts

birdlifeinternational

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 scripts

scarpino

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 scripts

mikemeredith

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 dependents

mucollective

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 scripts

julianfaraway

faraway:Datasets and Functions for Books by Julian Faraway

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

Maintained by Julian Faraway. Last updated 1 months ago.

data

3.5 match 29 stars 9.43 score 1.7k scripts 1 dependents

feddelegrand7

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.

javascript shiny

6.6 match 21 stars 5.02 score 8 scripts

cran

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 dependents

mhpob

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-tracking api api-wrapper biotelemetry fish fisheries fisheries-research

7.5 match 3 stars 4.35 score 9 scripts

robitalec

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.

animal animal-movement gps targets

18.1 match 1.70 score

marce10

NatureSounds:Animal Sounds for Bioacustic Analysis

Collection of example animal sounds for bioacoustic analysis.

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

bioacoustic-analysis sound

5.5 match 2 stars 5.52 score 22 scripts 5 dependents

great-northern-diver

loon:Interactive Statistical Data Visualization

An extendable toolkit for interactive data visualization and exploration.

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

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

3.4 match 48 stars 9.00 score 93 scripts 5 dependents

rinterface

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 scripts

roaldarbol

anibehavr:Analyse Animal Behaviours

What the package does (one paragraph).

Maintained by Mikkel Roald-Arbøl. Last updated 10 months ago.

animal-behavior behavioural-states data-analysis

10.8 match 3 stars 2.78 score 2 scripts

zankrut20

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.

agriculture animal-science plant-breeding rstudio selection-index selection-indices smith-selection-index

7.5 match 2 stars 4.00 score 5 scripts

krisanata

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 scripts

pilaboratory

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 dependents

oswaldosantos

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 scripts

theomichelot

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.

openblas cpp

3.4 match 38 stars 8.63 score 112 scripts

thebioengineer

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 scripts

sportsdataverse

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.

football ggplot2 playing-surfaces sport sports-analytics sports-data sports-tracking-data sportsdataverse visualization

3.3 match 104 stars 8.08 score 97 scripts

coolbutuseless

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 scripts

trackage

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 dependents

biodiverse

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-sampling hierarchical-models n-mixture-model occupancy stan openblas cpp

3.4 match 35 stars 7.88 score 73 scripts

shanpengli

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 scripts

r-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 scripts

alexchristensen

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.

semantic-network-analysis

5.8 match 23 stars 4.51 score 28 scripts

friendly

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.

diagrams linear-equations matrix matrix-functions matrix-visualizer vector vignette

2.0 match 65 stars 12.89 score 900 scripts 11 dependents

krystian8207

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 dependents

lozalojo

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.

influenza mem

4.0 match 14 stars 6.24 score 82 scripts 1 dependents

cran

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 score

eldarrak

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-ecology solar-geolocation-loggers solar-geolocator

3.4 match 22 stars 7.26 score 111 scripts

trenchproject

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 scripts

cran

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 dependents

murrayefford

secr:Spatially Explicit Capture-Recapture

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

Maintained by Murray Efford. Last updated 3 days ago.

cpp

2.3 match 3 stars 10.18 score 410 scripts 5 dependents

nasserdr

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 scripts

bmcclintock

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.

openblas cpp

2.7 match 43 stars 8.47 score 162 scripts

prabhleenkaur19

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.

cpp

7.2 match 3.18 score

clementcalenge

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 scripts

wavx

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.

fftw3 cpp

2.9 match 47 stars 7.71 score 72 scripts 5 dependents

feddelegrand7

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.

d3 d3js dataviz javascript

3.9 match 44 stars 5.64 score 7 scripts

tylermorganwall

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

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

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

cpp

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

bioinformatics-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.

cpp

3.3 match 9 stars 6.50 score 35 scripts

cran

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.

fortran

6.7 match 2 stars 3.21 score 27 scripts 1 dependents

taylor-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.

ggplot2-geom image-analysis

3.8 match 53 stars 5.70 score 19 scripts

fernandosm

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 scripts

birdscanada

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 scripts

svmiller

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 scripts

eddelbuettel

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.

beamer beamer-presentation beamer-theme markdown pdf rmarkdown rmarkdown-beamer

2.5 match 189 stars 8.31 score 2 scripts 2 dependents

mcandocia

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 scripts

eligurarie

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.

cpp

3.8 match 3 stars 5.26 score 30 scripts

epimodel

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-modeling epidemics epidemiology infectious-diseases network-graph cpp

1.7 match 250 stars 11.57 score 315 scripts

brianbattaile

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 scripts

djnavarro

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 scripts

trafficonese

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-visualization geospatial geospatial-visualization leaflet leaflet-plugins

2.0 match 87 stars 9.70 score 432 scripts 1 dependents

joelkilty

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 scripts

lgnbhl

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.

aniview shiny

5.8 match 2 stars 3.30 score 3 scripts

simondedman

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-bridge home-range home-range-analysis migration residency space-use tracking

3.4 match 17 stars 5.63 score 4 scripts

sizespectrum

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-model fish-population-dynamics fisheries fisheries-management marine-ecosystem population-dynamics simulation size-structure species-interactions transport-equation cpp

2.0 match 38 stars 9.43 score 207 scripts

svmiller

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.

codename reproducibility wu-tang

4.0 match 17 stars 4.62 score 49 scripts

sciurus365

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.

research-tool

2.9 match 6 stars 6.41 score 12 scripts 2 dependents

emilhvitfeldt

emoji:Data and Function to Work with Emojis

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

Maintained by Emil Hvitfeldt. Last updated 5 months ago.

2.3 match 28 stars 7.97 score 304 scripts 3 dependents

ddalthorp

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.

cpp

2.3 match 7 stars 7.81 score 55 scripts 2 dependents

paulnorthrop

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.

anscombe anscombes-quartet anscombesquartet

3.8 match 11 stars 4.74 score 9 scripts

casperhart

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 scripts

cbracis

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.

cpp

2.8 match 10 stars 6.24 score 43 scripts

robindenz1

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

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

Maintained by Robin Denz. Last updated 1 years ago.

causal-inference continuous g-computation survival-analysis visualization

3.2 match 12 stars 5.53 score 56 scripts

sborstein

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 scripts

bodkan

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.

popgen population-genetics simulations spatial-statistics

1.9 match 56 stars 9.15 score 88 scripts

ebeneditos

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.

r-telegram-bot telegram-bot

2.0 match 109 stars 8.57 score 126 scripts 1 dependents

bblonder

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.

openblas cpp

1.7 match 23 stars 9.75 score 211 scripts 7 dependents

egpivo

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.

admm covariance-estimation eigenfunctions lasso matrix-factorization pca rcpparmadillo rcppparallel regularization spatial spatial-data-analysis splines openblas cpp openmp

3.0 match 20 stars 5.53 score 17 scripts

rjknell

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 scripts

bioc

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.

immunooncology proteomics massspectrometry classification clustering qualitycontrol bioconductor proteomics-data spatial-proteomics visualisation openblas cpp

1.9 match 15 stars 8.71 score 101 scripts 2 dependents