R-universe search: open street map

adeckmyn

maps:Draw Geographical Maps

Display of maps. Projection code and larger maps are in separate packages ('mapproj' and 'mapdata').

Maintained by Alex Deckmyn. Last updated 2 months ago.

152.7 match 24 stars 14.70 score 19k scripts 490 dependents

r-tmap

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

79.2 match 880 stars 16.73 score 13k scripts 24 dependents

bioc

RCy3:Functions to Access and Control Cytoscape

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

Maintained by Alex Pico. Last updated 5 months ago.

visualization graphandnetwork thirdpartyclient network

91.4 match 52 stars 13.39 score 628 scripts 15 dependents

kbroman

qtl:Tools for Analyzing QTL Experiments

Analysis of experimental crosses to identify genes (called quantitative trait loci, QTLs) contributing to variation in quantitative traits. Broman et al. (2003) <doi:10.1093/bioinformatics/btg112>.

Maintained by Karl W Broman. Last updated 7 months ago.

openblas

80.8 match 80 stars 12.79 score 2.4k scripts 29 dependents

acorg

Racmacs:Antigenic Cartography Macros

A toolkit for making antigenic maps from immunological assay data, in order to quantify and visualize antigenic differences between different pathogen strains as described in Smith et al. (2004) <doi:10.1126/science.1097211> and used in the World Health Organization influenza vaccine strain selection process. Additional functions allow for the diagnostic evaluation of antigenic maps and an interactive viewer is provided to explore antigenic relationships amongst several strains and incorporate the visualization of associated genetic information.

Maintained by Sam Wilks. Last updated 9 months ago.

openblas cpp openmp

108.4 match 21 stars 8.06 score 362 scripts

walkerke

mapgl:Interactive Maps with 'Mapbox GL JS' and 'MapLibre GL JS'

Provides an interface to the 'Mapbox GL JS' (<https://docs.mapbox.com/mapbox-gl-js/guides>) and the 'MapLibre GL JS' (<https://maplibre.org/maplibre-gl-js/docs/>) interactive mapping libraries to help users create custom interactive maps in R. Users can create interactive globe visualizations; layer 'sf' objects to create filled maps, circle maps, 'heatmaps', and three-dimensional graphics; and customize map styles and views. The package also includes utilities to use 'Mapbox' and 'MapLibre' maps in 'Shiny' web applications.

Maintained by Kyle Walker. Last updated 1 days ago.

101.6 match 114 stars 8.06 score 138 scripts

rstudio

leaflet:Create Interactive Web Maps with the JavaScript 'Leaflet' Library

Create and customize interactive maps using the 'Leaflet' JavaScript library and the 'htmlwidgets' package. These maps can be used directly from the R console, from 'RStudio', in Shiny applications and R Markdown documents.

Maintained by Joe Cheng. Last updated 13 days ago.

gis leaflet-map spatial

47.4 match 821 stars 17.20 score 39k scripts 178 dependents

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.

56.1 match 218 stars 13.85 score 4.8k scripts 76 dependents

andysouth

rworldmap:Mapping Global Data

Enables mapping of country level and gridded user datasets.

Maintained by Andy South. Last updated 2 years ago.

64.3 match 30 stars 11.83 score 3.2k scripts 14 dependents

spatstat

spatstat.geom:Geometrical Functionality of the 'spatstat' Family

Defines spatial data types and supports geometrical operations on them. Data types include point patterns, windows (domains), pixel images, line segment patterns, tessellations and hyperframes. Capabilities include creation and manipulation of data (using command line or graphical interaction), plotting, geometrical operations (rotation, shift, rescale, affine transformation), convex hull, discretisation and pixellation, Dirichlet tessellation, Delaunay triangulation, pairwise distances, nearest-neighbour distances, distance transform, morphological operations (erosion, dilation, closing, opening), quadrat counting, geometrical measurement, geometrical covariance, colour maps, calculus on spatial domains, Gaussian blur, level sets of images, transects of images, intersections between objects, minimum distance matching. (Excludes spatial data on a network, which are supported by the package 'spatstat.linnet'.)

Maintained by Adrian Baddeley. Last updated 2 days ago.

classes-and-objects distance-calculation geometry geometry-processing images mensuration plotting point-patterns spatial-data spatial-data-analysis

58.5 match 7 stars 12.11 score 241 scripts 227 dependents

riatelab

cartography:Thematic Cartography

Create and integrate maps in your R workflow. This package helps to design cartographic representations such as proportional symbols, choropleth, typology, flows or discontinuities maps. It also offers several features that improve the graphic presentation of maps, for instance, map palettes, layout elements (scale, north arrow, title...), labels or legends. See Giraud and Lambert (2017) <doi:10.1007/978-3-319-57336-6_13>.

Maintained by Timothée Giraud. Last updated 2 years ago.

cartography map thematic-maps cpp

60.5 match 399 stars 10.47 score 460 scripts 2 dependents

dankelley

oce:Analysis of Oceanographic Data

Supports the analysis of Oceanographic data, including 'ADCP' measurements, measurements made with 'argo' floats, 'CTD' measurements, sectional data, sea-level time series, coastline and topographic data, etc. Provides specialized functions for calculating seawater properties such as potential temperature in either the 'UNESCO' or 'TEOS-10' equation of state. Produces graphical displays that conform to the conventions of the Oceanographic literature. This package is discussed extensively by Kelley (2018) "Oceanographic Analysis with R" <doi:10.1007/978-1-4939-8844-0>.

Maintained by Dan Kelley. Last updated 1 days ago.

oceanography fortran cpp

41.0 match 146 stars 15.42 score 4.2k scripts 18 dependents

celehs

MAP:Multimodal Automated Phenotyping

Electronic health records (EHR) linked with biorepositories are a powerful platform for translational studies. A major bottleneck exists in the ability to phenotype patients accurately and efficiently. Towards that end, we developed an automated high-throughput phenotyping method integrating International Classification of Diseases (ICD) codes and narrative data extracted using natural language processing (NLP). Specifically, our proposed method, called MAP (Map Automated Phenotyping algorithm), fits an ensemble of latent mixture models on aggregated ICD and NLP counts along with healthcare utilization. The MAP algorithm yields a predicted probability of phenotype for each patient and a threshold for classifying subjects with phenotype yes/no (See Katherine P. Liao, et al. (2019) <doi:10.1093/jamia/ocz066>.).

Maintained by Thomas Charlon. Last updated 2 months ago.

70.4 match 6 stars 8.58 score 177 scripts 1 dependents

csids

csmaps:Preformatted Maps of Norway that Don't Need Geolibraries

Provides datasets containing preformatted maps of Norway at the county, municipality, and ward (Oslo only) level for redistricting in 2024, 2020, 2018, and 2017. Multiple layouts are provided (normal, split, and with an insert for Oslo), allowing the user to rapidly create choropleth maps of Norway without any geolibraries.

Maintained by Richard Aubrey White. Last updated 6 months ago.

csverse

116.7 match 3 stars 5.08 score 20 scripts

mmollina

mappoly:Genetic Linkage Maps in Autopolyploids

Construction of genetic maps in autopolyploid full-sib populations. Uses pairwise recombination fraction estimation as the first source of information to sequentially position allelic variants in specific homologous chromosomes. For situations where pairwise analysis has limited power, the algorithm relies on the multilocus likelihood obtained through a hidden Markov model (HMM). For more detail, please see Mollinari and Garcia (2019) <doi:10.1534/g3.119.400378> and Mollinari et al. (2020) <doi:10.1534/g3.119.400620>.

Maintained by Marcelo Mollinari. Last updated 11 days ago.

polyploid polyploid-genetic-mapping polyploidy cpp

71.6 match 27 stars 7.56 score 111 scripts 1 dependents

lindbrook

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

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

Maintained by lindbrook. Last updated 1 days ago.

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

57.8 match 136 stars 9.33 score 95 scripts

symbolixau

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

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

Maintained by David Cooley. Last updated 6 months ago.

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

54.9 match 236 stars 9.67 score 536 scripts 2 dependents

tidyverse

ggplot2:Create Elegant Data Visualisations Using the Grammar of Graphics

A system for 'declaratively' creating graphics, based on "The Grammar of Graphics". You provide the data, tell 'ggplot2' how to map variables to aesthetics, what graphical primitives to use, and it takes care of the details.

Maintained by Thomas Lin Pedersen. Last updated 9 days ago.

data-visualisation visualisation

17.2 match 6.6k stars 25.10 score 645k scripts 7.5k 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 23 hours ago.

geospatial raster spatial vector onetbb proj gdal geos cpp

24.4 match 559 stars 17.64 score 17k scripts 851 dependents

bioc

ensembldb:Utilities to create and use Ensembl-based annotation databases

The package provides functions to create and use transcript centric annotation databases/packages. The annotation for the databases are directly fetched from Ensembl using their Perl API. The functionality and data is similar to that of the TxDb packages from the GenomicFeatures package, but, in addition to retrieve all gene/transcript models and annotations from the database, ensembldb provides a filter framework allowing to retrieve annotations for specific entries like genes encoded on a chromosome region or transcript models of lincRNA genes. EnsDb databases built with ensembldb contain also protein annotations and mappings between proteins and their encoding transcripts. Finally, ensembldb provides functions to map between genomic, transcript and protein coordinates.

Maintained by Johannes Rainer. Last updated 5 months ago.

genetics annotationdata sequencing coverage annotation bioconductor bioconductor-packages ensembl

30.2 match 35 stars 14.08 score 892 scripts 108 dependents

pdil

usmap:US Maps Including Alaska and Hawaii

Obtain United States map data frames of varying region types (e.g. county, state). The map data frames include Alaska and Hawaii conveniently placed to the bottom left, as they appear in most maps of the US. Convenience functions for plotting choropleths, visualizing spatial data, and working with FIPS codes are also provided.

Maintained by Paolo Di Lorenzo. Last updated 3 months ago.

counties data fips geodata mapping states usa

36.3 match 75 stars 11.22 score 1.7k scripts 2 dependents

bioc

pathview:a tool set for pathway based data integration and visualization

Pathview is a tool set for pathway based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs. All users need is to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, Pathview also seamlessly integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.

Maintained by Weijun Luo. Last updated 5 months ago.

pathways graphandnetwork visualization genesetenrichment differentialexpression geneexpression microarray rnaseq genetics metabolomics proteomics systemsbiology sequencing

34.6 match 40 stars 11.24 score 1.6k scripts 10 dependents

mappinguniverse

mapping:Automatic Download, Linking, Manipulating Coordinates for Maps

Maps are an important tool to visualise variables distribution across different spatial objects. The mapping process requires to link the data with coordinates and then generate the correspondent map. This package provide coordinates, linking and mapping functions for an automatic, flexible and easy approach of external functions. The package provides an easy, flexible and automatic unit. Geographical coordinates are provided in the package and automatically linked with the input data to generate maps with internal provided functions or external functions. Provide an easy, flexible and automatic approach to potentially download updated coordinates, to link statistical units with coordinates and to aggregate variables based on the spatial hierarchy of units. The object returned from the package can be used for thematic maps with the build-in functions provided in mapping or with other packages already available.

Maintained by Alessio Serafini. Last updated 1 years ago.

81.1 match 4 stars 4.79 score 31 scripts

predictiveecology

map:Defines a meta class of geographical objects, the 'map' class, and associated tools

The 'map' class is a collection of geospatial objects (e.g., from the 'sp', 'raster', 'sf', and 'terra' packages), with a number of metadata additions to enable powerful methods, e.g., for leaflet, reproducible GIS etc.

Maintained by Alex M Chubaty. Last updated 1 months ago.

89.4 match 2 stars 4.33 score 178 scripts 1 dependents

ifellows

OpenStreetMap:Access to Open Street Map Raster Images

Accesses high resolution raster maps using the OpenStreetMap protocol. Dozens of road, satellite, and topographic map servers are directly supported, including Apple, Mapnik, Bing, and stamen. Additionally raster maps may be constructed using custom tile servers. Maps can be plotted using either base graphics, or ggplot2. This package is not affiliated with the OpenStreetMap.org mapping project.

Maintained by Ian Fellows. Last updated 1 years ago.

openjdk

47.8 match 11 stars 8.09 score 498 scripts 4 dependents

dkahle

ggmap:Spatial Visualization with ggplot2

A collection of functions to visualize spatial data and models on top of static maps from various online sources (e.g Google Maps and Stamen Maps). It includes tools common to those tasks, including functions for geolocation and routing.

Maintained by David Kahle. Last updated 1 years ago.

26.3 match 770 stars 14.17 score 12k scripts 31 dependents

riatelab

mapsf:Thematic Cartography

Create and integrate thematic maps in your workflow. This package helps to design various cartographic representations such as proportional symbols, choropleth or typology maps. It also offers several functions to display layout elements that improve the graphic presentation of maps (e.g. scale bar, north arrow, title, labels). 'mapsf' maps 'sf' objects on 'base' graphics.

Maintained by Timothée Giraud. Last updated 4 days ago.

cartography map spatial spatial-analysis

32.5 match 228 stars 11.28 score 414 scripts 11 dependents

r-spatial

mapview:Interactive Viewing of Spatial Data in R

Quickly and conveniently create interactive visualisations of spatial data with or without background maps. Attributes of displayed features are fully queryable via pop-up windows. Additional functionality includes methods to visualise true- and false-color raster images and bounding boxes.

Maintained by Tim Appelhans. Last updated 3 months ago.

gis leaflet maps spatial visualization web-mapping

25.1 match 525 stars 14.28 score 7.3k scripts 25 dependents

r-spatial

leafem:'leaflet' Extensions for 'mapview'

Provides extensions for packages 'leaflet' & 'mapdeck', many of which are used by package 'mapview'. Focus is on functionality readily available in Geographic Information Systems such as 'Quantum GIS'. Includes functions to display coordinates of mouse pointer position, query image values via mouse pointer and zoom-to-layer buttons. Additionally, provides a feature type agnostic function to add points, lines, polygons to a map.

Maintained by Tim Appelhans. Last updated 17 days ago.

28.2 match 108 stars 12.36 score 704 scripts 53 dependents

richardli

SUMMER:Small-Area-Estimation Unit/Area Models and Methods for Estimation in R

Provides methods for spatial and spatio-temporal smoothing of demographic and health indicators using survey data, with particular focus on estimating and projecting under-five mortality rates, described in Mercer et al. (2015) <doi:10.1214/15-AOAS872>, Li et al. (2019) <doi:10.1371/journal.pone.0210645>, Wu et al. (DHS Spatial Analysis Reports No. 21, 2021), and Li et al. (2023) <doi:10.48550/arXiv.2007.05117>.

Maintained by Zehang R Li. Last updated 2 months ago.

bayesian-inference small-area-estimation space-time

33.1 match 23 stars 10.28 score 134 scripts 2 dependents

urbananalyst

dodgr:Distances on Directed Graphs

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

Maintained by Mark Padgham. Last updated 5 days ago.

distance openstreetmap router shortest-paths street-networks cpp

29.3 match 129 stars 11.53 score 229 scripts 4 dependents

terminological

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

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

Maintained by Robert Challen. Last updated 11 months ago.

101.9 match 4 stars 3.30 score 4 scripts

jbkunst

highcharter:A Wrapper for the 'Highcharts' Library

A wrapper for the 'Highcharts' library including shortcut functions to plot R objects. 'Highcharts' <https://www.highcharts.com/> is a charting library offering numerous chart types with a simple configuration syntax.

Maintained by Joshua Kunst. Last updated 1 years ago.

highcharts htmlwidgets shiny shiny-r visualization wrapper

22.8 match 725 stars 13.93 score 4.9k scripts 18 dependents

bioc

rhdf5:R Interface to HDF5

This package provides an interface between HDF5 and R. HDF5's main features are the ability to store and access very large and/or complex datasets and a wide variety of metadata on mass storage (disk) through a completely portable file format. The rhdf5 package is thus suited for the exchange of large and/or complex datasets between R and other software package, and for letting R applications work on datasets that are larger than the available RAM.

Maintained by Mike Smith. Last updated 2 months ago.

infrastructure dataimport hdf5 rhdf5 openssl curl zlib cpp

18.9 match 62 stars 15.93 score 4.2k scripts 232 dependents

michaeldorman

mapsapi:'sf'-Compatible Interface to 'Google Maps' APIs

Interface to the 'Google Maps' APIs: (1) routing directions based on the 'Directions' API, returned as 'sf' objects, either as single feature per alternative route, or a single feature per segment per alternative route; (2) travel distance or time matrices based on the 'Distance Matrix' API; (3) geocoded locations based on the 'Geocode' API, returned as 'sf' objects, either points or bounds; (4) map images using the 'Maps Static' API, returned as 'stars' objects.

Maintained by Michael Dorman. Last updated 2 years ago.

41.1 match 51 stars 7.10 score 99 scripts

ropensci

terrainr:Landscape Visualizations in R and 'Unity'

Functions for the retrieval, manipulation, and visualization of 'geospatial' data, with an aim towards producing '3D' landscape visualizations in the 'Unity' '3D' rendering engine. Functions are also provided for retrieving elevation data and base map tiles from the 'USGS' National Map <https://apps.nationalmap.gov/services/>.

Maintained by Michael Mahoney. Last updated 8 months ago.

datasets dems map map-tiles mapping national-map nhd orthoimagery peer-reviewed progressr retrieve-data terrainr unity unity-rendering-engine usgs

38.4 match 72 stars 7.40 score 87 scripts

ropensci

rotl:Interface to the 'Open Tree of Life' API

An interface to the 'Open Tree of Life' API to retrieve phylogenetic trees, information about studies used to assemble the synthetic tree, and utilities to match taxonomic names to 'Open Tree identifiers'. The 'Open Tree of Life' aims at assembling a comprehensive phylogenetic tree for all named species.

Maintained by Francois Michonneau. Last updated 2 years ago.

metadata ropensci phylogenetics independant-contrasts biodiversity peer-reviewed phylogeny taxonomy

22.9 match 40 stars 12.05 score 356 scripts 29 dependents

rsoc

soc.ca:Specific Correspondence Analysis for the Social Sciences

Specific and class specific multiple correspondence analysis on survey-like data. Soc.ca is optimized to the needs of the social scientist and presents easily interpretable results in near publication ready quality.

Maintained by Anton Grau Larsen. Last updated 1 years ago.

66.0 match 14 stars 4.15 score 50 scripts

ropensci

lingtypology:Linguistic Typology and Mapping

Provides R with the Glottolog database <https://glottolog.org/> and some more abilities for purposes of linguistic mapping. The Glottolog database contains the catalogue of languages of the world. This package helps researchers to make a linguistic maps, using philosophy of the Cross-Linguistic Linked Data project <https://clld.org/>, which allows for while at the same time facilitating uniform access to the data across publications. A tutorial for this package is available on GitHub pages <https://docs.ropensci.org/lingtypology/> and package vignette. Maps created by this package can be used both for the investigation and linguistic teaching. In addition, package provides an ability to download data from typological databases such as WALS, AUTOTYP and some others and to create your own database website.

Maintained by George Moroz. Last updated 5 months ago.

abvd afbo atlas autotype bivaltyp clld glottolog-database linguistic-maps linguistics phoible sails typology wals

27.5 match 51 stars 9.58 score 694 scripts

easystats

bayestestR:Understand and Describe Bayesian Models and Posterior Distributions

Provides utilities to describe posterior distributions and Bayesian models. It includes point-estimates such as Maximum A Posteriori (MAP), measures of dispersion (Highest Density Interval - HDI; Kruschke, 2015 <doi:10.1016/C2012-0-00477-2>) and indices used for null-hypothesis testing (such as ROPE percentage, pd and Bayes factors). References: Makowski et al. (2021) <doi:10.21105/joss.01541>.

Maintained by Dominique Makowski. Last updated 9 hours ago.

bayes-factors bayesfactor bayesian bayesian-framework credible-interval easystats hacktoberfest hdi map posterior-distributions rope

15.0 match 579 stars 16.84 score 2.2k scripts 82 dependents

pharmaverse

admiral:ADaM in R Asset Library

A toolbox for programming Clinical Data Interchange Standards Consortium (CDISC) compliant Analysis Data Model (ADaM) datasets in R. ADaM datasets are a mandatory part of any New Drug or Biologics License Application submitted to the United States Food and Drug Administration (FDA). Analysis derivations are implemented in accordance with the "Analysis Data Model Implementation Guide" (CDISC Analysis Data Model Team, 2021, <https://www.cdisc.org/standards/foundational/adam>).

Maintained by Ben Straub. Last updated 4 days ago.

cdisc clinical-trials open-source

18.0 match 236 stars 13.89 score 486 scripts 4 dependents

markusloecher

RgoogleMaps:Overlays on Static Maps

Serves two purposes: (i) Provide a comfortable R interface to query the Google server for static maps, and (ii) Use the map as a background image to overlay plots within R. This requires proper coordinate scaling.

Maintained by Markus Loecher. Last updated 1 years ago.

42.9 match 1 stars 5.80 score 516 scripts 9 dependents

md-anderson-bioinformatics

NGCHM:Next Generation Clustered Heat Maps

Next-Generation Clustered Heat Maps (NG-CHMs) allow for dynamic exploration of heat map data in a web browser. 'NGCHM' allows users to create both stand-alone HTML files containing a Next-Generation Clustered Heat Map, and .ngchm files to view in the NG-CHM viewer. See Ryan MC, Stucky M, et al (2020) <doi:10.12688/f1000research.20590.2> for more details.

Maintained by Mary A Rohrdanz. Last updated 9 days ago.

heatmap nci-itcr ng-chm

45.2 match 9 stars 5.48 score 28 scripts

malaria-atlas-project

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

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

Maintained by Mauricio van den Berg. Last updated 8 months ago.

database malaria opendata raster

27.0 match 44 stars 9.10 score 118 scripts 3 dependents

trafficonese

leaflet.extras:Extra Functionality for 'leaflet' Package

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

Maintained by Sebastian Gatscha. Last updated 2 months ago.

data-visualization geospatial leaflet

18.2 match 218 stars 13.27 score 2.5k scripts 25 dependents

safetygraphics

safetyCharts:Charts for Monitoring Clinical Trial Safety

Contains chart code for monitoring clinical trial safety. Charts can be used as standalone output, but are also designed for use with the 'safetyGraphics' package, which makes it easy to load data and customize the charts using an interactive web-based interface created with Shiny.

Maintained by Jeremy Wildfire. Last updated 6 months ago.

44.8 match 9 stars 5.36 score 21 scripts 1 dependents

bioc

destiny:Creates diffusion maps

Create and plot diffusion maps.

Maintained by Philipp Angerer. Last updated 4 months ago.

cellbiology cellbasedassays clustering software visualization diffusion-maps dimensionality-reduction cpp

21.7 match 81 stars 10.94 score 792 scripts

adeckmyn

mapdata:Extra Map Databases

Supplement to maps package, providing some larger and/or higher-resolution databases. NOTE: this is a legacy package. The world map is out-dated.

Maintained by Alex Deckmyn. Last updated 2 years ago.

33.3 match 7.10 score 3.9k scripts 11 dependents

a-b-street

abstr:R Interface to the A/B Street Transport System Simulation Software

Provides functions to convert origin-destination data, represented as straight 'desire lines' in the 'sf' Simple Features class system, into JSON files that can be directly imported into A/B Street <https://www.abstreet.org>, a free and open source tool for simulating urban transport systems and scenarios of change <doi:10.1007/s10109-020-00342-2>.

Maintained by Nathanael Sheehan. Last updated 3 years ago.

34.3 match 34 stars 6.87 score 27 scripts

massimoaria

bibliometrix:Comprehensive Science Mapping Analysis

Tool for quantitative research in scientometrics and bibliometrics. It implements the comprehensive workflow for science mapping analysis proposed in Aria M. and Cuccurullo C. (2017) <doi:10.1016/j.joi.2017.08.007>. 'bibliometrix' provides various routines for importing bibliographic data from 'SCOPUS', 'Clarivate Analytics Web of Science' (<https://www.webofknowledge.com/>), 'Digital Science Dimensions' (<https://www.dimensions.ai/>), 'OpenAlex' (<https://openalex.org/>), 'Cochrane Library' (<https://www.cochranelibrary.com/>), 'Lens' (<https://lens.org>), and 'PubMed' (<https://pubmed.ncbi.nlm.nih.gov/>) databases, performing bibliometric analysis and building networks for co-citation, coupling, scientific collaboration and co-word analysis.

Maintained by Massimo Aria. Last updated 7 days ago.

bibliometric-analysis bibliometrics citation citation-network citations co-authors co-occurence co-word-analysis correspondence-analysis coupling isi-web journal manuscript quantitative-analysis scholars science science-mapping scientific scientometrics scopus

18.6 match 545 stars 12.54 score 518 scripts 2 dependents

cristianetaniguti

onemap:Construction of Genetic Maps in Experimental Crosses

Analysis of molecular marker data from model (backcrosses, F2 and recombinant inbred lines) and non-model systems (i. e. outcrossing species). For the later, it allows statistical analysis by simultaneously estimating linkage and linkage phases (genetic map construction) according to Wu et al. (2002) <doi:10.1006/tpbi.2002.1577>. All analysis are based on multipoint approaches using hidden Markov models.

Maintained by Cristiane Taniguti. Last updated 2 months ago.

cpp

35.3 match 3 stars 6.58 score 183 scripts

elipousson

mapbaltimore:Make maps for Baltimore City with open data

This package provides data from the Baltimore City, the state of Maryland, and other sources, functions to access additional data, and function to create and modify simple maps of Baltimore neighborhoods using sf and ggplot2.

Maintained by Eli Pousson. Last updated 4 months ago.

baltimore rspatial

60.1 match 17 stars 3.85 score 14 scripts

tidyverse

purrr:Functional Programming Tools

A complete and consistent functional programming toolkit for R.

Maintained by Hadley Wickham. Last updated 1 months ago.

functional-programming

10.4 match 1.3k stars 22.12 score 59k scripts 6.9k dependents

ncss-tech

soilDB:Soil Database Interface

A collection of functions for reading soil data from U.S. Department of Agriculture Natural Resources Conservation Service (USDA-NRCS) and National Cooperative Soil Survey (NCSS) databases.

Maintained by Andrew Brown. Last updated 7 days ago.

kssl nasis nrcs soil soil-data-access soil-survey soilweb sql usda

20.2 match 87 stars 11.34 score 1.0k scripts 1 dependents

benjaminrich

mappings:Functions for Transforming Categorical Variables

Easily create functions to map between different sets of values, such as for re-labeling categorical variables.

Maintained by Benjamin Rich. Last updated 9 months ago.

71.5 match 3 stars 3.18 score 1 scripts

datastorm-open

visNetwork:Network Visualization using 'vis.js' Library

Provides an R interface to the 'vis.js' JavaScript charting library. It allows an interactive visualization of networks.

Maintained by Benoit Thieurmel. Last updated 2 years ago.

15.0 match 549 stars 15.14 score 4.1k scripts 195 dependents

openml

OpenML:Open Machine Learning and Open Data Platform

We provide an R interface to 'OpenML.org' which is an online machine learning platform where researchers can access open data, download and upload data sets, share their machine learning tasks and experiments and organize them online to work and collaborate with other researchers. The R interface allows to query for data sets with specific properties, and allows the downloading and uploading of data sets, tasks, flows and runs. See <https://www.openml.org/guide/api> for more information.

Maintained by Giuseppe Casalicchio. Last updated 10 months ago.

arff benchmarking benchmarking-suite classification data-science database dataset datasets machine-learning machine-learning-algorithms open-data open-science opendata openml openscience regression reproducible-research statistics

20.5 match 97 stars 11.04 score 7.1k scripts

friendly

HistData:Data Sets from the History of Statistics and Data Visualization

The 'HistData' package provides a collection of small data sets that are interesting and important in the history of statistics and data visualization. The goal of the package is to make these available, both for instructional use and for historical research. Some of these present interesting challenges for graphics or analysis in R.

Maintained by Michael Friendly. Last updated 10 months ago.

graphics historical-data

23.7 match 63 stars 9.19 score 732 scripts 2 dependents

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

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

pbourkey

polymapR:Linkage Analysis in Outcrossing Polyploids

Creation of linkage maps in polyploid species from marker dosage scores of an F1 cross from two heterozygous parents. Currently works for outcrossing diploid, autotriploid, autotetraploid and autohexaploid species, as well as segmental allotetraploids. Methods are described in a manuscript of Bourke et al. (2018) <doi:10.1093/bioinformatics/bty371>. Since version 1.1.0, both discrete and probabilistic genotypes are acceptable input; for more details on the latter see Liao et al. (2021) <doi:10.1007/s00122-021-03834-x>.

Maintained by Peter Bourke. Last updated 10 months ago.

53.1 match 1 stars 4.03 score 54 scripts

adeverse

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

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

Maintained by Aurélie Siberchicot. Last updated 12 days ago.

openblas cpp

14.3 match 39 stars 14.96 score 2.2k scripts 256 dependents

thinkr-open

golem:A Framework for Robust Shiny Applications

An opinionated framework for building a production-ready 'Shiny' application. This package contains a series of tools for building a robust 'Shiny' application from start to finish.

Maintained by Colin Fay. Last updated 7 months ago.

golemverse hacktoberfest shiny shiny-apps shiny-r shinyapps

15.0 match 921 stars 14.23 score 167 scripts 62 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

23.7 match 48 stars 9.00 score 93 scripts 5 dependents

jonathanlees

GEOmap:Topographic and Geologic Mapping

Set of routines for making map projections (forward and inverse), topographic maps, perspective plots, geological maps, geological map symbols, geological databases, interactive plotting and selection of focus regions.

Maintained by Jonathan M. Lees. Last updated 8 months ago.

61.8 match 3.38 score 162 scripts 3 dependents

safetygraphics

safetyGraphics:Interactive Graphics for Monitoring Clinical Trial Safety

A framework for evaluation of clinical trial safety. Users can interactively explore their data using the included 'Shiny' application.

Maintained by Jeremy Wildfire. Last updated 2 years ago.

25.5 match 98 stars 8.18 score 111 scripts

insee-psar-at

oceanis:Cartography for Statistical Analysis

Creating maps for statistical analysis such as proportional circles, choropleth, typology and flows. Some functions use 'shiny' or 'leaflet' technologies for dynamism and interactivity. The great features are : - Create maps in a web environment where the parameters are modifiable on the fly ('shiny' and 'leaflet' technologies). - Create interactive maps through zoom and pop-up ('leaflet' technology). - Create frozen maps with the possibility to add labels.

Maintained by Sébastien Novella. Last updated 1 months ago.

35.8 match 12 stars 5.79 score 17 scripts

drj001

ASMap:Linkage Map Construction using the MSTmap Algorithm

Functions for Accurate and Speedy linkage map construction, manipulation and diagnosis of Doubled Haploid, Backcross and Recombinant Inbred 'R/qtl' objects. This includes extremely fast linkage map clustering and optimal marker ordering using 'MSTmap' (see Wu et al.,2008).

Maintained by Julian Taylor. Last updated 4 months ago.

cpp

30.6 match 2 stars 6.73 score 79 scripts

bupaverse

processmapR:Construct Process Maps Using Event Data

Visualize event logs using directed graphs, i.e. process maps. Part of the 'bupaR' framework.

Maintained by Gert Janssenswillen. Last updated 7 months ago.

cpp

26.4 match 9 stars 7.70 score 169 scripts 3 dependents

tiledb-inc

tiledb:Modern Database Engine for Complex Data Based on Multi-Dimensional Arrays

The modern database 'TileDB' introduces a powerful on-disk format for storing and accessing any complex data based on multi-dimensional arrays. It supports dense and sparse arrays, dataframes and key-values stores, cloud storage ('S3', 'GCS', 'Azure'), chunked arrays, multiple compression, encryption and checksum filters, uses a fully multi-threaded implementation, supports parallel I/O, data versioning ('time travel'), metadata and groups. It is implemented as an embeddable cross-platform C++ library with APIs from several languages, and integrations. This package provides the R support.

Maintained by Isaiah Norton. Last updated 4 days ago.

array hdfs s3 storage-manager tiledb cpp

16.8 match 107 stars 11.96 score 306 scripts 4 dependents

crazycapivara

mapboxer:An R Interface to 'Mapbox GL JS'

Makes 'Mapbox GL JS' <https://docs.mapbox.com/mapbox-gl-js/api/>, an open source JavaScript library that uses WebGL to render interactive maps, available within R via the 'htmlwidgets' package. Visualizations can be used from the R console, in R Markdown documents and in Shiny apps.

Maintained by Stefan Kuethe. Last updated 3 years ago.

htmlwidgets mapbox-gl-js spatial webgl

29.6 match 55 stars 6.61 score 49 scripts 1 dependents

rqtl

qtl2:Quantitative Trait Locus Mapping in Experimental Crosses

Provides a set of tools to perform quantitative trait locus (QTL) analysis in experimental crosses. It is a reimplementation of the 'R/qtl' package to better handle high-dimensional data and complex cross designs. Broman et al. (2019) <doi:10.1534/genetics.118.301595>.

Maintained by Karl W Broman. Last updated 8 days ago.

cpp

20.5 match 34 stars 9.48 score 1.1k scripts 5 dependents

igraph

igraph:Network Analysis and Visualization

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

Maintained by Kirill Müller. Last updated 11 hours ago.

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

9.2 match 582 stars 21.11 score 31k scripts 1.9k dependents

riatelab

maptiles:Download and Display Map Tiles

To create maps from tiles, 'maptiles' downloads, composes and displays tiles from a large number of providers (e.g. 'OpenStreetMap', 'Stadia', 'Esri', 'CARTO', or 'Thunderforest').

Maintained by Timothée Giraud. Last updated 2 months ago.

map rspatial tiles

20.3 match 106 stars 9.40 score 199 scripts 14 dependents

ramiromagno

gwasrapidd:'REST' 'API' Client for the 'NHGRI'-'EBI' 'GWAS' Catalog

'GWAS' R 'API' Data Download. This package provides easy access to the 'NHGRI'-'EBI' 'GWAS' Catalog data by accessing the 'REST' 'API' <https://www.ebi.ac.uk/gwas/rest/docs/api/>.

Maintained by Ramiro Magno. Last updated 1 years ago.

thirdpartyclient biomedicalinformatics genomewideassociation snp association-studies gwas-catalog human rest-client trait trait-ontology

22.5 match 95 stars 8.10 score 49 scripts 1 dependents

openair-project

openairmaps:Create Maps of Air Pollution Data

Combine the air quality data analysis methods of 'openair' with the JavaScript 'Leaflet' (<https://leafletjs.com/>) library. Functionality includes plotting site maps, "directional analysis" figures such as polar plots, and air mass trajectories.

Maintained by Jack Davison. Last updated 1 days ago.

openair

30.2 match 21 stars 6.04 score 47 scripts

bioc

ORFik:Open Reading Frames in Genomics

R package for analysis of transcript and translation features through manipulation of sequence data and NGS data like Ribo-Seq, RNA-Seq, TCP-Seq and CAGE. It is generalized in the sense that any transcript region can be analysed, as the name hints to it was made with investigation of ribosomal patterns over Open Reading Frames (ORFs) as it's primary use case. ORFik is extremely fast through use of C++, data.table and GenomicRanges. Package allows to reassign starts of the transcripts with the use of CAGE-Seq data, automatic shifting of RiboSeq reads, finding of Open Reading Frames for whole genomes and much more.

Maintained by Haakon Tjeldnes. Last updated 28 days ago.

immunooncology software sequencing riboseq rnaseq functionalgenomics coverage alignment dataimport cpp

17.1 match 33 stars 10.63 score 115 scripts 2 dependents

bioc

Rsamtools:Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.

Maintained by Bioconductor Package Maintainer. Last updated 4 months ago.

dataimport sequencing coverage alignment qualitycontrol bioconductor-package core-package curl bzip2 xz-utils zlib cpp

11.8 match 28 stars 15.42 score 3.2k scripts 566 dependents

edzer

sp:Classes and Methods for Spatial Data

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

Maintained by Edzer Pebesma. Last updated 2 months ago.

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

milesmcbain

slippymath:Slippy Map Tile Tools

Provides functions for performing common tasks when working with slippy map tile service APIs e.g. Google maps, Open Street Map, Mapbox, Stamen, among others. Functionality includes converting from latitude and longitude to tile numbers, determining tile bounding boxes, and compositing tiles to a georeferenced raster image.

Maintained by Miles McBain. Last updated 6 years ago.

google-maps mapbox osm slippy-map

20.1 match 66 stars 8.91 score 32 scripts 19 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

9.9 match 91 stars 17.49 score 7.3k scripts 300 dependents

ropensci

osmapiR:'OpenStreetMap' API

Interface to 'OpenStreetMap API' for fetching and saving data from/to the 'OpenStreetMap' database (<https://wiki.openstreetmap.org/wiki/API_v0.6>).

Maintained by Joan Maspons. Last updated 4 months ago.

open street map openstreetmap osm openstreetmap-api osmapi api

23.3 match 22 stars 7.42 score 6 scripts

apache

arrow:Integration to 'Apache' 'Arrow'

'Apache' 'Arrow' <https://arrow.apache.org/> is a cross-language development platform for in-memory data. It specifies a standardized language-independent columnar memory format for flat and hierarchical data, organized for efficient analytic operations on modern hardware. This package provides an interface to the 'Arrow C++' library.

Maintained by Jonathan Keane. Last updated 1 months ago.

arrow curl openssl cpp

9.0 match 15k stars 19.22 score 10k scripts 81 dependents

ropensci

osmextract:Download and Import Open Street Map Data Extracts

Match, download, convert and import Open Street Map data extracts obtained from several providers.

Maintained by Andrea Gilardi. Last updated 2 months ago.

geo geofabrik-zone open-data osm osm-pbf

17.7 match 173 stars 9.73 score 342 scripts

ropensci

mapscanner:Print Maps, Draw on Them, Scan Them Back in

Enables preparation of maps to be printed and drawn on. Modified maps can then be scanned back in, and hand-drawn marks converted to spatial objects.

Maintained by Mark Padgham. Last updated 1 months ago.

maps scan spatial cpp

24.0 match 90 stars 7.13 score 2 scripts

hughjonesd

huxtable:Easily Create and Style Tables for LaTeX, HTML and Other Formats

Creates styled tables for data presentation. Export to HTML, LaTeX, RTF, 'Word', 'Excel', and 'PowerPoint'. Simple, modern interface to manipulate borders, size, position, captions, colours, text styles and number formatting. Table cells can span multiple rows and/or columns. Includes a 'huxreg' function for creation of regression tables, and 'quick_*' one-liners to print data to a new document.

Maintained by David Hugh-Jones. Last updated 12 days ago.

html huxtable latex microsoft-word powerpoint reproducible-research tables

12.3 match 323 stars 13.93 score 1.9k scripts 16 dependents

rspatial

raster:Geographic Data Analysis and Modeling

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

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

cpp

9.9 match 164 stars 17.05 score 58k scripts 555 dependents

bioc

mixOmics:Omics Data Integration Project

Multivariate methods are well suited to large omics data sets where the number of variables (e.g. genes, proteins, metabolites) is much larger than the number of samples (patients, cells, mice). They have the appealing properties of reducing the dimension of the data by using instrumental variables (components), which are defined as combinations of all variables. Those components are then used to produce useful graphical outputs that enable better understanding of the relationships and correlation structures between the different data sets that are integrated. mixOmics offers a wide range of multivariate methods for the exploration and integration of biological datasets with a particular focus on variable selection. The package proposes several sparse multivariate models we have developed to identify the key variables that are highly correlated, and/or explain the biological outcome of interest. The data that can be analysed with mixOmics may come from high throughput sequencing technologies, such as omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but also beyond the realm of omics (e.g. spectral imaging). The methods implemented in mixOmics can also handle missing values without having to delete entire rows with missing data. A non exhaustive list of methods include variants of generalised Canonical Correlation Analysis, sparse Partial Least Squares and sparse Discriminant Analysis. Recently we implemented integrative methods to combine multiple data sets: N-integration with variants of Generalised Canonical Correlation Analysis and P-integration with variants of multi-group Partial Least Squares.

Maintained by Eva Hamrud. Last updated 4 days ago.

immunooncology microarray sequencing metabolomics metagenomics proteomics geneprediction multiplecomparison classification regression bioconductor genomics genomics-data genomics-visualization multivariate-analysis multivariate-statistics omics r-pkg r-project

12.2 match 182 stars 13.71 score 1.3k scripts 22 dependents

okamumu

mapfit:PH/MAP Parameter Estimation

Estimation methods for phase-type distribution (PH) and Markovian arrival process (MAP) from empirical data (point and grouped data) and density function. The tool is based on the following researches: Okamura et al. (2009) <doi:10.1109/TNET.2008.2008750>, Okamura and Dohi (2009) <doi:10.1109/QEST.2009.28>, Okamura et al. (2011) <doi:10.1016/j.peva.2011.04.001>, Okamura et al. (2013) <doi:10.1002/asmb.1919>, Horvath and Okamura (2013) <doi:10.1007/978-3-642-40725-3_10>, Okamura and Dohi (2016) <doi:10.15807/jorsj.59.72>.

Maintained by Hiroyuki Okamura. Last updated 2 years ago.

openblas cpp

50.2 match 2 stars 3.34 score 22 scripts

rstudio

keras3:R Interface to 'Keras'

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

Maintained by Tomasz Kalinowski. Last updated 4 days ago.

12.1 match 845 stars 13.57 score 264 scripts 2 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

17.0 match 173 stars 9.65 score 203 scripts 2 dependents

sjmgarnier

viridis:Colorblind-Friendly Color Maps for R

Color maps designed to improve graph readability for readers with common forms of color blindness and/or color vision deficiency. The color maps are also perceptually-uniform, both in regular form and also when converted to black-and-white for printing. This package also contains 'ggplot2' bindings for discrete and continuous color and fill scales. A lean version of the package called 'viridisLite' that does not include the 'ggplot2' bindings can be found at <https://cran.r-project.org/package=viridisLite>.

Maintained by Simon Garnier. Last updated 1 years ago.

color-blindness color-scheme

9.2 match 299 stars 17.92 score 49k scripts 1.2k dependents

anushapb

wingen:Continuous Mapping of Genetic Diversity

Generate continuous maps of genetic diversity using moving windows with options for rarefaction, interpolation, and masking as described in Bishop et al. (2023) <doi:10.1111/2041-210X.14090>.

Maintained by Anusha Bishop. Last updated 2 months ago.

26.0 match 12 stars 6.24 score 24 scripts

cran

queueing:Analysis of Queueing Networks and Models

It provides versatile tools for analysis of birth and death based Markovian Queueing Models and Single and Multiclass Product-Form Queueing Networks. It implements M/M/1, M/M/c, M/M/Infinite, M/M/1/K, M/M/c/K, M/M/c/c, M/M/1/K/K, M/M/c/K/K, M/M/c/K/m, M/M/Infinite/K/K, Multiple Channel Open Jackson Networks, Multiple Channel Closed Jackson Networks, Single Channel Multiple Class Open Networks, Single Channel Multiple Class Closed Networks and Single Channel Multiple Class Mixed Networks. Also it provides a B-Erlang, C-Erlang and Engset calculators. This work is dedicated to the memory of D. Sixto Rios Insua.

Maintained by Pedro Canadilla. Last updated 5 years ago.

62.9 match 2.58 score 376 scripts

roelandkindt

BiodiversityR:Package for Community Ecology and Suitability Analysis

Graphical User Interface (via the R-Commander) and utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and cluster, constrained and unconstrained ordination analysis. A book on biodiversity and community ecology analysis is available for free download from the website. In 2012, methods for (ensemble) suitability modelling and mapping were expanded in the package.

Maintained by Roeland Kindt. Last updated 2 months ago.

21.8 match 16 stars 7.42 score 390 scripts 2 dependents

r-tmap

tmaptools:Thematic Map Tools

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

Maintained by Martijn Tennekes. Last updated 2 months ago.

13.8 match 42 stars 11.67 score 1.8k scripts 26 dependents

statistikat

VIM:Visualization and Imputation of Missing Values

New tools for the visualization of missing and/or imputed values are introduced, which can be used for exploring the data and the structure of the missing and/or imputed values. Depending on this structure of the missing values, the corresponding methods may help to identify the mechanism generating the missing values and allows to explore the data including missing values. In addition, the quality of imputation can be visually explored using various univariate, bivariate, multiple and multivariate plot methods. A graphical user interface available in the separate package VIMGUI allows an easy handling of the implemented plot methods.

Maintained by Matthias Templ. Last updated 7 months ago.

hotdeck imputation-methods model-predictions visualization cpp

11.1 match 85 stars 14.44 score 2.6k scripts 19 dependents

pbs-software

PBSmapping:Mapping Fisheries Data and Spatial Analysis Tools

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

Maintained by Rowan Haigh. Last updated 6 months ago.

cpp

15.4 match 11 stars 10.29 score 652 scripts 9 dependents

clementcalenge

adehabitatMA:Tools to Deal with Raster Maps

A collection of tools to deal with raster maps.

Maintained by Clement Calenge. Last updated 6 months ago.

25.0 match 1 stars 6.34 score 43 scripts 15 dependents

datastorm-open

shinymanager:Authentication Management for 'Shiny' Applications

Simple and secure authentification mechanism for single 'Shiny' applications. Credentials can be stored in an encrypted 'SQLite' database or on your own SQL Database (Postgres, MySQL, ...). Source code of main application is protected until authentication is successful.

Maintained by Benoit Thieurmel. Last updated 10 months ago.

shiny shiny-server shinyapps

15.0 match 391 stars 10.51 score 316 scripts 2 dependents

kwstat

pals:Color Palettes, Colormaps, and Tools to Evaluate Them

A comprehensive collection of color palettes, colormaps, and tools to evaluate them. See Kovesi (2015) <doi:10.48550/arXiv.1509.03700>.

Maintained by Kevin Wright. Last updated 9 days ago.

13.8 match 83 stars 11.39 score 2.1k scripts 8 dependents

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

20.8 match 66 stars 7.54 score 106 scripts

thinkr-open

attachment:Deal with Dependencies

Manage dependencies during package development. This can retrieve all dependencies that are used in ".R" files in the "R/" directory, in ".Rmd" files in "vignettes/" directory and in 'roxygen2' documentation of functions. There is a function to update the "DESCRIPTION" file of your package with 'CRAN' packages or any other remote package. All functions to retrieve dependencies of ".R" scripts and ".Rmd" or ".qmd" files can be used independently of a package development.

Maintained by Vincent Guyader. Last updated 2 days ago.

hacktoberfest

15.0 match 110 stars 10.44 score 48 scripts 5 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.

17.5 match 64 stars 8.87 score 173 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

19.8 match 42 stars 7.85 score 31 scripts 2 dependents

sinhrks

ggfortify:Data Visualization Tools for Statistical Analysis Results

Unified plotting tools for statistics commonly used, such as GLM, time series, PCA families, clustering and survival analysis. The package offers a single plotting interface for these analysis results and plots in a unified style using 'ggplot2'.

Maintained by Yuan Tang. Last updated 9 months ago.

10.6 match 529 stars 14.49 score 9.1k scripts 22 dependents

projectmosaic

mosaic:Project MOSAIC Statistics and Mathematics Teaching Utilities

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

Maintained by Randall Pruim. Last updated 1 years ago.

11.6 match 93 stars 13.32 score 7.2k scripts 7 dependents

sparklyr

sparklyr:R Interface to Apache Spark

R interface to Apache Spark, a fast and general engine for big data processing, see <https://spark.apache.org/>. This package supports connecting to local and remote Apache Spark clusters, provides a 'dplyr' compatible back-end, and provides an interface to Spark's built-in machine learning algorithms.

Maintained by Edgar Ruiz. Last updated 10 days ago.

apache-spark distributed dplyr ide livy machine-learning remote-clusters spark sparklyr

10.0 match 959 stars 15.16 score 4.0k scripts 21 dependents

stephenslab

susieR:Sum of Single Effects Linear Regression

Implements methods for variable selection in linear regression based on the "Sum of Single Effects" (SuSiE) model, as described in Wang et al (2020) <DOI:10.1101/501114> and Zou et al (2021) <DOI:10.1101/2021.11.03.467167>. These methods provide simple summaries, called "Credible Sets", for accurately quantifying uncertainty in which variables should be selected. The methods are motivated by genetic fine-mapping applications, and are particularly well-suited to settings where variables are highly correlated and detectable effects are sparse. The fitting algorithm, a Bayesian analogue of stepwise selection methods called "Iterative Bayesian Stepwise Selection" (IBSS), is simple and fast, allowing the SuSiE model be fit to large data sets (thousands of samples and hundreds of thousands of variables).

Maintained by Peter Carbonetto. Last updated 17 days ago.

14.2 match 197 stars 10.38 score 728 scripts 6 dependents

polkas

cat2cat:Handling an Inconsistently Coded Categorical Variable in a Longitudinal Dataset

Unifying an inconsistently coded categorical variable between two different time points in accordance with a mapping table. The main rule is to replicate the observation if it could be assigned to a few categories. Then using frequencies or statistical methods to approximate the probabilities of being assigned to each of them. This procedure was invented and implemented in the paper by Nasinski, Majchrowska, and Broniatowska (2020) <doi:10.24425/cejeme.2020.134747>.

Maintained by Maciej Nasinski. Last updated 1 years ago.

categories encoding encodings factor longitudinal mapping mappings panel transitions

34.3 match 4 stars 4.30 score 2 scripts

paleolimbot

rosm:Plot Raster Map Tiles from Open Street Map and Other Sources

Download and plot Open Street Map <https://www.openstreetmap.org/>, Bing Maps <https://www.bing.com/maps> and other tiled map sources. Use to create basemaps quickly and add hillshade to vector-based maps.

Maintained by Dewey Dunnington. Last updated 2 years ago.

17.9 match 27 stars 8.23 score 130 scripts 26 dependents

winvector

wrapr:Wrap R Tools for Debugging and Parametric Programming

Tools for writing and debugging R code. Provides: '%.>%' dot-pipe (an 'S3' configurable pipe), unpack/to (R style multiple assignment/return), 'build_frame()'/'draw_frame()' ('data.frame' example tools), 'qc()' (quoting concatenate), ':=' (named map builder), 'let()' (converts non-standard evaluation interfaces to parametric standard evaluation interfaces, inspired by 'gtools::strmacro()' and 'base::bquote()'), and more.

Maintained by John Mount. Last updated 2 years ago.

13.0 match 137 stars 11.11 score 390 scripts 12 dependents

renkun-ken

rlist:A Toolbox for Non-Tabular Data Manipulation

Provides a set of functions for data manipulation with list objects, including mapping, filtering, grouping, sorting, updating, searching, and other useful functions. Most functions are designed to be pipeline friendly so that data processing with lists can be chained.

Maintained by Kun Ren. Last updated 2 years ago.

10.5 match 206 stars 13.73 score 2.2k scripts 123 dependents

ropenspain

mapSpain:Administrative Boundaries of Spain

Administrative Boundaries of Spain at several levels (Autonomous Communities, Provinces, Municipalities) based on the 'GISCO' 'Eurostat' database <https://ec.europa.eu/eurostat/web/gisco> and 'CartoBase SIANE' from 'Instituto Geografico Nacional' <https://www.ign.es/>. It also provides a 'leaflet' plugin and the ability of downloading and processing static tiles.

Maintained by Diego Hernangómez. Last updated 1 months ago.

ropenspain tiles maps spatial municipalities spain gisco provinces ign administrative-boundaries ccaa static-tiles ggplot2 gis

16.2 match 42 stars 8.83 score 244 scripts 2 dependents

pecanproject

PEcAn.visualization:PEcAn visualization functions

The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PECAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation. This module is used to create more complex visualizations from the data generated by PEcAn code, specifically the models.

Maintained by David LeBauer. Last updated 2 days ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants

13.0 match 216 stars 10.95 score 74 scripts 11 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

10.9 match 4 stars 13.03 score 652 scripts 12 dependents

thinkr-open

fusen:Build a Package from Rmarkdown Files

Use Rmarkdown First method to build your package. Start your package with documentation, functions, examples and tests in the same unique file. Everything can be set from the Rmarkdown template file provided in your project, then inflated as a package. Inflating the template copies the relevant chunks and sections in the appropriate files required for package development.

Maintained by Vincent Guyader. Last updated 2 months ago.

hacktoberfest rmd-first

15.0 match 163 stars 9.45 score 35 scripts

constantino-garcia

nonlinearTseries:Nonlinear Time Series Analysis

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

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

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

15.8 match 35 stars 8.98 score 123 scripts 7 dependents

bioc

annotate:Annotation for microarrays

Using R enviroments for annotation.

Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.

annotation pathways go

12.4 match 11.41 score 812 scripts 243 dependents

thinkr-open

gitlabr:Access to the 'GitLab' API

Provides R functions to access the API of the project and repository management web application 'GitLab'. For many common tasks (repository file access, issue assignment and status, commenting) convenience wrappers are provided, and in addition the full API can be used by specifying request locations. 'GitLab' is open-source software and can be self-hosted or used on <https://about.gitlab.com>.

Maintained by Sébastien Rochette. Last updated 10 months ago.

gitlab

16.8 match 40 stars 8.40 score 69 scripts 1 dependents

datastorm-open

suncalc:Compute Sun Position, Sunlight Phases, Moon Position and Lunar Phase

Get sun position, sunlight phases (times for sunrise, sunset, dusk, etc.), moon position and lunar phase for the given location and time. Most calculations are based on the formulas given in Astronomy Answers articles about position of the sun and the planets : <https://www.aa.quae.nl/en/reken/zonpositie.html>.

Maintained by Benoit Thieurmel. Last updated 1 years ago.

15.0 match 44 stars 9.43 score 372 scripts 16 dependents

r-dbi

DBI:R Database Interface

A database interface definition for communication between R and relational database management systems. All classes in this package are virtual and need to be extended by the various R/DBMS implementations.

Maintained by Kirill Müller. Last updated 3 months ago.

database interface

6.8 match 302 stars 20.88 score 19k scripts 2.9k 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

13.6 match 363 stars 10.30 score 368 scripts 1 dependents

exaexa

EmbedSOM:Fast Embedding Guided by Self-Organizing Map

Provides a smooth mapping of multidimensional points into low-dimensional space defined by a self-organizing map. Designed to work with 'FlowSOM' and flow-cytometry use-cases. See Kratochvil et al. (2019) <doi:10.12688/f1000research.21642.1>.

Maintained by Mirek Kratochvil. Last updated 1 months ago.

cytometry som visualization cpp

23.1 match 26 stars 6.02 score 8 scripts

ropensci

rsi:Efficiently Retrieve and Process Satellite Imagery

Downloads spatial data from spatiotemporal asset catalogs ('STAC'), computes standard spectral indices from the Awesome Spectral Indices project (Montero et al. (2023) <doi:10.1038/s41597-023-02096-0>) against raster data, and glues the outputs together into predictor bricks. Methods focus on interoperability with the broader spatial ecosystem; function arguments and outputs use classes from 'sf' and 'terra', and data downloading functions support complex 'CQL2' queries using 'rstac'.

Maintained by Michael Mahoney. Last updated 2 months ago.

19.3 match 49 stars 7.20 score 38 scripts

nflverse

nflreadr:Download 'nflverse' Data

A minimal package for downloading data from 'GitHub' repositories of the 'nflverse' project.

Maintained by Tan Ho. Last updated 4 months ago.

nfl nflfastr nflverse sports-data

11.1 match 66 stars 12.46 score 476 scripts 10 dependents

emcramer

CHOIRBM:Plots the CHOIR Body Map

Collection of utility functions for visualizing body map data collected with the Collaborative Health Outcomes Information Registry.

Maintained by Eric Cramer. Last updated 1 years ago.

body-map cbm choir data-visualization visualization

25.1 match 5 stars 5.51 score 26 scripts

bruneiverse

bruneimap:Maps and Spatial Data of Brunei

Provides spatial data for mapping Brunei, including boundaries for districts, mukims, and kampongs, as well as locations of key infrastructure such as masjids, hospitals, clinics, and schools. The package supports researchers, analysts, and developers working with Brunei’s geographic and demographic data, offering a quick and accessible foundation for creating maps and conducting spatial studies.

Maintained by Haziq Jamil. Last updated 29 days ago.

brunei census maps

22.7 match 1 stars 6.10 score 25 scripts

mpjashby

sfhotspot:Hot-Spot Analysis with Simple Features

Identify and understand clusters of points (typically representing the locations of places or events) stored in simple-features (SF) objects. This is useful for analysing, for example, hot-spots of crime events. The package emphasises producing results from point SF data in a single step using reasonable default values for all other arguments, to aid rapid data analysis by users who are starting out. Functions available include kernel density estimation (for details, see Yip (2020) <doi:10.22224/gistbok/2020.1.12>), analysis of spatial association (Getis and Ord (1992) <doi:10.1111/j.1538-4632.1992.tb00261.x>) and hot-spot classification (Chainey (2020) ISBN:158948584X).

Maintained by Matt Ashby. Last updated 24 days ago.

hotspot hotspots hotspots-analysis mapping mapping-tools

24.9 match 12 stars 5.56 score 30 scripts

bioc

nucleoSim:Generate synthetic nucleosome maps

This package can generate a synthetic map with reads covering the nucleosome regions as well as a synthetic map with forward and reverse reads emulating next-generation sequencing. The synthetic hybridization data of “Tiling Arrays” can also be generated. The user has choice between three different distributions for the read positioning: Normal, Student and Uniform. In addition, a visualization tool is provided to explore the synthetic nucleosome maps.

Maintained by Astrid Deschênes. Last updated 5 months ago.

genetics sequencing software statisticalmethod alignment bioconductor nucleosome-maps nucleosomes simulation simulator synthetic-nucleosomes

27.5 match 2 stars 5.00 score 8 scripts

bioc

GenomicFeatures:Query the gene models of a given organism/assembly

Extract the genomic locations of genes, transcripts, exons, introns, and CDS, for the gene models stored in a TxDb object. A TxDb object is a small database that contains the gene models of a given organism/assembly. Bioconductor provides a small collection of TxDb objects in the form of ready-to-install TxDb packages for the most commonly studied organisms. Additionally, the user can easily make a TxDb object (or package) for the organism/assembly of their choice by using the tools from the txdbmaker package.

Maintained by H. Pagès. Last updated 4 months ago.

genetics infrastructure annotation sequencing genomeannotation bioconductor-package core-package

8.9 match 26 stars 15.34 score 5.3k scripts 339 dependents

arilamstein

choroplethrMaps:Contains Maps Used by the 'choroplethr' Package

Contains 3 maps. 1) US States 2) US Counties 3) Countries of the world.

Maintained by Ari Lamstein. Last updated 7 years ago.

28.5 match 4.80 score 418 scripts 1 dependents

geanders

hurricaneexposure:Explore and Map County-Level Hurricane Exposure in the United States

Allows users to create time series of tropical storm exposure histories for chosen counties for a number of hazard metrics (wind, rain, distance from the storm, etc.). This package interacts with data available through the 'hurricaneexposuredata' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/geanders/hurricaneexposure>. The size of the 'hurricaneexposuredata' package is approximately 20 MB. This work was supported in part by grants from the National Institute of Environmental Health Sciences (R00ES022631), the National Science Foundation (1331399), and a NASA Applied Sciences Program/Public Health Program Grant (NNX09AV81G).

Maintained by Brooke Anderson. Last updated 5 years ago.

20.3 match 35 stars 6.71 score 49 scripts 1 dependents

ggobi

GGally:Extension to 'ggplot2'

The R package 'ggplot2' is a plotting system based on the grammar of graphics. 'GGally' extends 'ggplot2' by adding several functions to reduce the complexity of combining geometric objects with transformed data. Some of these functions include a pairwise plot matrix, a two group pairwise plot matrix, a parallel coordinates plot, a survival plot, and several functions to plot networks.

Maintained by Barret Schloerke. Last updated 10 months ago.

8.4 match 597 stars 16.15 score 17k scripts 154 dependents

gaynorr

AlphaSimR:Breeding Program Simulations

The successor to the 'AlphaSim' software for breeding program simulation [Faux et al. (2016) <doi:10.3835/plantgenome2016.02.0013>]. Used for stochastic simulations of breeding programs to the level of DNA sequence for every individual. Contained is a wide range of functions for modeling common tasks in a breeding program, such as selection and crossing. These functions allow for constructing simulations of highly complex plant and animal breeding programs via scripting in the R software environment. Such simulations can be used to evaluate overall breeding program performance and conduct research into breeding program design, such as implementation of genomic selection. Included is the 'Markovian Coalescent Simulator' ('MaCS') for fast simulation of biallelic sequences according to a population demographic history [Chen et al. (2009) <doi:10.1101/gr.083634.108>].

Maintained by Chris Gaynor. Last updated 5 months ago.

breeding genomics simulation openblas cpp openmp

13.3 match 47 stars 10.22 score 534 scripts 2 dependents

spatialnous

alcyon:Spatial Network Analysis

Interface package for 'sala', the spatial network analysis library from the 'depthmapX' software application. The R parts of the code are based on the 'rdepthmap' package. Allows for the analysis of urban and building-scale networks and provides metrics and methods usually found within the Space Syntax domain. Methods in this package are described by K. Al-Sayed, A. Turner, B. Hillier, S. Iida and A. Penn (2014) "Space Syntax methodology", and also by A. Turner (2004) <https://discovery.ucl.ac.uk/id/eprint/2651> "Depthmap 4: a researcher's handbook".

Maintained by Petros Koutsolampros. Last updated 2 months ago.

cpp openmp

21.4 match 2 stars 6.34 score 13 scripts

tbep-tech

tbeptools:Data and Indicators for the Tampa Bay Estuary Program

Several functions are provided for working with Tampa Bay Estuary Program data and indicators, including the water quality report card, tidal creek assessments, Tampa Bay Nekton Index, Tampa Bay Benthic Index, seagrass transect data, habitat report card, and fecal indicator bacteria. Additional functions are provided for miscellaneous tasks, such as reference library curation.

Maintained by Marcus Beck. Last updated 9 days ago.

data-analysis tampa-bay tbep water-quality

17.2 match 10 stars 7.86 score 133 scripts

ropensci

osfr:Interface to the 'Open Science Framework' ('OSF')

An interface for interacting with 'OSF' (<https://osf.io>). 'osfr' enables you to access open research materials and data, or create and manage your own private or public projects.

Maintained by Aaron Wolen. Last updated 8 months ago.

open-science osf reproducible-research

13.3 match 145 stars 10.18 score 588 scripts 3 dependents

gabrielgesteira

qtlpoly:Random-Effect Multiple QTL Mapping in Autopolyploids

Performs random-effect multiple interval mapping (REMIM) in full-sib families of autopolyploid species based on restricted maximum likelihood (REML) estimation and score statistics, as described in Pereira et al. (2020) <doi:10.1534/genetics.120.303080>.

Maintained by Gabriel de Siqueira Gesteira. Last updated 4 months ago.

polyploid qtl-mapping openblas cpp openmp

25.9 match 6 stars 5.17 score 61 scripts

bioc

BridgeDbR:Code for using BridgeDb identifier mapping framework from within R

Use BridgeDb functions and load identifier mapping databases in R. It uses GitHub, Zenodo, and Figshare if you use this package to download identifier mappings files.

Maintained by Egon Willighagen. Last updated 4 months ago.

software annotation metabolomics cheminformatics bioconductor-package bridgedb genes identifiers life-sciences metabolites proteins openjdk

19.2 match 4 stars 6.97 score 43 scripts

r-spatial

rgee:R Bindings for Calling the 'Earth Engine' API

Earth Engine <https://earthengine.google.com/> client library for R. All of the 'Earth Engine' API classes, modules, and functions are made available. Additional functions implemented include importing (exporting) of Earth Engine spatial objects, extraction of time series, interactive map display, assets management interface, and metadata display. See <https://r-spatial.github.io/rgee/> for further details.

Maintained by Cesar Aybar. Last updated 4 days ago.

earth-engine earthengine google-earth-engine googleearthengine spatial-analysis spatial-data

9.7 match 715 stars 13.77 score 1.9k scripts 3 dependents

coatless-rpkg

cetcolor:CET Perceptually Uniform Colour Maps

Collection of perceptually uniform colour maps made by Peter Kovesi (2015) "Good Colour Maps: How to Design Them" <arXiv:1509.03700> at the Centre for Exploration Targeting (CET).

Maintained by James Balamuta. Last updated 1 years ago.

cet color-palettes color-scheme

21.9 match 31 stars 6.08 score 78 scripts

cran

MDSMap:High Density Genetic Linkage Mapping using Multidimensional Scaling

Estimate genetic linkage maps for markers on a single chromosome (or in a single linkage group) from pairwise recombination fractions or intermarker distances using weighted metric multidimensional scaling. The methods are suitable for autotetraploid as well as diploid populations. Options for assessing the fit to a known map are also provided. Methods are discussed in detail in Preedy and Hackett (2016) <doi:10.1007/s00122-016-2761-8>.

Maintained by Bram Boskamp. Last updated 7 years ago.

42.7 match 3.08 score 1 dependents

ropengov

giscoR:Download Map Data from GISCO API - Eurostat

Tools to download data from the GISCO (Geographic Information System of the Commission) Eurostat database <https://ec.europa.eu/eurostat/web/gisco>. Global and European map data available. This package is in no way officially related to or endorsed by Eurostat.

Maintained by Diego Hernangómez. Last updated 30 days ago.

ropengov spatial api-wrapper eurostat gisco thematic-maps eurostat-data ggplot2 gis

12.3 match 75 stars 10.70 score 424 scripts 5 dependents

chris-prener

biscale:Tools and Palettes for Bivariate Thematic Mapping

Provides a 'ggplot2' centric approach to bivariate mapping. This is a technique that maps two quantities simultaneously rather than the single value that most thematic maps display. The package provides a suite of tools for calculating breaks using multiple different approaches, a selection of palettes appropriate for bivariate mapping and scale functions for 'ggplot2' calls that adds those palettes to maps. Tools for creating bivariate legends are also included.

Maintained by Christopher Prener. Last updated 3 years ago.

15.3 match 122 stars 8.53 score 466 scripts

ropensci

tiler:Create Geographic and Non-Geographic Map Tiles

Creates geographic map tiles from geospatial map files or non-geographic map tiles from simple image files. This package provides a tile generator function for creating map tile sets for use with packages such as 'leaflet'. In addition to generating map tiles based on a common raster layer source, it also handles the non-geographic edge case, producing map tiles from arbitrary images. These map tiles, which have a non-geographic, simple coordinate reference system (CRS), can also be used with 'leaflet' when applying the simple CRS option. Map tiles can be created from an input file with any of the following extensions: tif, grd and nc for spatial maps and png, jpg and bmp for basic images. This package requires 'Python' and the 'gdal' library for 'Python'. 'Windows' users are recommended to install 'OSGeo4W' (<https://trac.osgeo.org/osgeo4w/>) as an easy way to obtain the required 'gdal' support for 'Python'.

Maintained by Matthew Leonawicz. Last updated 6 months ago.

16.8 match 64 stars 7.78 score 39 scripts 2 dependents

open-eo

openeo:Client Interface for 'openEO' Servers

Access data and processing functionalities of 'openEO' compliant back-ends in R.

Maintained by Florian Lahn. Last updated 2 months ago.

openeo openeo-user

15.0 match 64 stars 8.65 score 128 scripts

adeverse

adespatial:Multivariate Multiscale Spatial Analysis

Tools for the multiscale spatial analysis of multivariate data. Several methods are based on the use of a spatial weighting matrix and its eigenvector decomposition (Moran's Eigenvectors Maps, MEM). Several approaches are described in the review Dray et al (2012) <doi:10.1890/11-1183.1>.

Maintained by Aurélie Siberchicot. Last updated 12 days ago.

openblas

11.7 match 36 stars 11.06 score 398 scripts 2 dependents

cogdisreslab

KRSA:KRSA: Kinome Random Sampling Analyzer

The goal of this package is to analyze the PamChip data and identify the changes in the active kinome. The package can preprocess the PamChip data output from BioNavigator and use Random Sampling and Permutation Analysis to identify upstream kinases. Additionally, this package provides a set of useful visualizations for the PamChip data.

Maintained by Ali Sajid Imami. Last updated 11 days ago.

kinase phosphatases pamchip kinome random sampling permutation analysis

29.1 match 4 stars 4.42 score 49 scripts

riatelab

maplegend:Legends for Maps

Create legends for maps and other graphics. Thematic maps need to be accompanied by legible legends to be fully comprehensible. This package offers a wide range of legends useful for cartography, some of which may also be useful for other types of graphics.

Maintained by Timothée Giraud. Last updated 5 months ago.

legend maps

20.3 match 13 stars 6.33 score 5 scripts 14 dependents

jrnold

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

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

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

data-visualisation ggplot2 ggplot2-themes plot plotting theme visualization

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

pbs-software

PBSmodelling:GUI Tools Made Easy: Interact with Models and Explore Data

Provides software to facilitate the design, testing, and operation of computer models. It focuses particularly on tools that make it easy to construct and edit a customized graphical user interface ('GUI'). Although our simplified 'GUI' language depends heavily on the R interface to the 'Tcl/Tk' package, a user does not need to know 'Tcl/Tk'. Examples illustrate models built with other R packages, including 'PBSmapping', 'PBSddesolve', and 'BRugs'. A complete user's guide 'PBSmodelling-UG.pdf' shows how to use this package effectively.

Maintained by Rowan Haigh. Last updated 4 months ago.

18.7 match 2 stars 6.76 score 120 scripts 4 dependents

pdil

usmapdata:Mapping Data for 'usmap' Package

Provides a container for data used by the 'usmap' package. The data used by 'usmap' has been extracted into this package so that the file size of the 'usmap' package can be reduced greatly. The data in this package will be updated roughly once per year as new map data files are provided by the US Census Bureau.

Maintained by Paolo Di Lorenzo. Last updated 10 days ago.

counties data fips mapping states usa

19.1 match 5 stars 6.59 score 35 scripts 3 dependents

thinkr-open

togglr:'Toggl.com' Api for 'Rstudio'

Use the <https://toggl.com> time tracker api through R.

Maintained by Vincent Guyader. Last updated 1 years ago.

hacktoberfest toggl-api toggler

18.5 match 49 stars 6.81 score 33 scripts

sjmgarnier

viridisLite:Colorblind-Friendly Color Maps (Lite Version)

Color maps designed to improve graph readability for readers with common forms of color blindness and/or color vision deficiency. The color maps are also perceptually-uniform, both in regular form and also when converted to black-and-white for printing. This is the 'lite' version of the 'viridis' package that also contains 'ggplot2' bindings for discrete and continuous color and fill scales and can be found at <https://cran.r-project.org/package=viridis>.

Maintained by Simon Garnier. Last updated 2 years ago.

color-blindness color-scheme

7.9 match 67 stars 15.75 score 2.3k scripts 8.0k dependents

ericpante

marmap:Import, Plot and Analyze Bathymetric and Topographic Data

Import xyz data from the NOAA (National Oceanic and Atmospheric Administration, <https://www.noaa.gov>), GEBCO (General Bathymetric Chart of the Oceans, <https://www.gebco.net>) and other sources, plot xyz data to prepare publication-ready figures, analyze xyz data to extract transects, get depth / altitude based on geographical coordinates, or calculate z-constrained least-cost paths.

Maintained by Benoit Simon-Bouhet. Last updated 8 months ago.

14.0 match 32 stars 8.86 score 524 scripts 1 dependents

open-and-sustainable

prismaid:Open Science AI Tools for Systematic, Protocol-Based Literature Reviews

prismAId uses generative AI models to extract data from scientific literature. It offers simple-to-use, efficient, and replicable methods for analyzing literature when conducting systematic reviews.

Maintained by Riccardo Boero. Last updated 1 months ago.

generative-ai open-science open-source systematic-literature-reviews

32.8 match 5 stars 3.76 score 1 scripts

moosa-r

rbioapi:User-Friendly R Interface to Biologic Web Services' API

Currently fully supports Enrichr, JASPAR, miEAA, PANTHER, Reactome, STRING, and UniProt! The goal of rbioapi is to provide a user-friendly and consistent interface to biological databases and services. In a way that insulates the user from the technicalities of using web services API and creates a unified and easy-to-use interface to biological and medical web services. This is an ongoing project; New databases and services will be added periodically. Feel free to suggest any databases or services you often use.

Maintained by Moosa Rezwani. Last updated 1 months ago.

api-client bioinformatics biology enrichment enrichment-analysis enrichr jaspar mieaa over-representation-analysis panther reactome string uniprot

16.1 match 20 stars 7.60 score 55 scripts

open-aims

bayesnec:A Bayesian No-Effect- Concentration (NEC) Algorithm

Implementation of No-Effect-Concentration estimation that uses 'brms' (see Burkner (2017)<doi:10.18637/jss.v080.i01>; Burkner (2018)<doi:10.32614/RJ-2018-017>; Carpenter 'et al.' (2017)<doi:10.18637/jss.v076.i01> to fit concentration(dose)-response data using Bayesian methods for the purpose of estimating 'ECx' values, but more particularly 'NEC' (see Fox (2010)<doi:10.1016/j.ecoenv.2009.09.012>), 'NSEC' (see Fisher and Fox (2023)<doi:10.1002/etc.5610>), and 'N(S)EC (see Fisher et al. 2023<doi:10.1002/ieam.4809>). A full description of this package can be found in Fisher 'et al.' (2024)<doi:10.18637/jss.v110.i05>. This package expands and supersedes an original version implemented in 'R2jags' (see Su and Yajima (2020)<https://CRAN.R-project.org/package=R2jags>; Fisher et al. (2020)<doi:10.5281/ZENODO.3966864>).

Maintained by Rebecca Fisher. Last updated 7 months ago.

bayesian-inference concentration-response ecotoxicology no-effect-concentration non-linear-decay threshold-derivation toxicology

15.0 match 12 stars 8.11 score 360 scripts

thinkr-open

fakir:Generate Fake Datasets for Prototyping and Teaching

Create fake datasets that can be used for prototyping and teaching. This package provides a set of functions to generate fake data for a variety of data types, such as dates, addresses, and names. It can be used for prototyping (notably in 'shiny') or as a tool to teach data manipulation and data visualization.

Maintained by Colin Fay. Last updated 7 months ago.

charlatan fake-datasets golemverse hacktoberfest

19.5 match 133 stars 6.24 score 26 scripts

alarm-redist

redist:Simulation Methods for Legislative Redistricting

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

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

geospatial gerrymandering redistricting sampling openblas cpp openmp

13.3 match 68 stars 9.17 score 259 scripts

thinkr-open

remedy:'RStudio' Addins to Simplify 'Markdown' Writing

An 'RStudio' addin providing shortcuts for writing in 'Markdown'. This package provides a series of functions that allow the user to be more efficient when using 'Markdown'. For example, you can select a word, and put it in bold or in italics, or change the alignment of elements inside you Rmd. The idea is to map all the functionalities from 'remedy' on keyboard shortcuts, so that it provides an interface close to what you can find in any other text editor.

Maintained by Colin Fay. Last updated 5 years ago.

hacktoberfest

15.5 match 452 stars 7.83 score 50 scripts

rcapell

HYPEtools:Tools for Processing and Analyzing Files from the Hydrological Catchment Model HYPE

Work with model files (setup, input, output) from the hydrological catchment model HYPE: Streamlined file import and export, standard evaluation plot routines, diverse post-processing and aggregation routines for hydrological model analysis. The HYPEtools package is also archived at <doi:10.5281/zenodo.7627955> and can be cited in publications with Brendel et al. (2024) <doi:10.1016/j.envsoft.2024.106094>.

Maintained by Rene Capell. Last updated 26 days ago.

16.0 match 17 stars 7.54 score 26 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.

9.8 match 368 stars 12.33 score 1.7k scripts 3 dependents

cogdisreslab

creedenzymatic:creedenzymatic

Combine kinome results from KRSA and UKA and other tools A package for integrating upstream kinases analyses

Maintained by Ali Sajid Imami. Last updated 12 months ago.

bioconductor bioconductor-package kinome

33.4 match 1 stars 3.60 score 20 scripts

ms609

TreeDist:Calculate and Map Distances Between Phylogenetic Trees

Implements measures of tree similarity, including information-based generalized Robinson-Foulds distances (Phylogenetic Information Distance, Clustering Information Distance, Matching Split Information Distance; Smith 2020) <doi:10.1093/bioinformatics/btaa614>; Jaccard-Robinson-Foulds distances (Bocker et al. 2013) <doi:10.1007/978-3-642-40453-5_13>, including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>; the Matching Split Distance (Bogdanowicz & Giaro 2012) <doi:10.1109/TCBB.2011.48>; Maximum Agreement Subtree distances; the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the Nearest Neighbour Interchange (NNI) distance, approximated per Li et al. (1996) <doi:10.1007/3-540-61332-3_168>. Includes tools for visualizing mappings of tree space (Smith 2022) <doi:10.1093/sysbio/syab100>, for identifying islands of trees (Silva and Wilkinson 2021) <doi:10.1093/sysbio/syab015>, for calculating the median of sets of trees, and for computing the information content of trees and splits.

Maintained by Martin R. Smith. Last updated 1 months ago.

phylogenetics tree-distance phylogenetic-trees tree-distances trees cpp

11.5 match 32 stars 10.32 score 97 scripts 5 dependents

r-spatial

sf:Simple Features for R

Support for simple feature access, a standardized way to encode and analyze spatial vector data. Binds to 'GDAL' <doi: 10.5281/zenodo.5884351> for reading and writing data, to 'GEOS' <doi: 10.5281/zenodo.11396894> for geometrical operations, and to 'PROJ' <doi: 10.5281/zenodo.5884394> for projection conversions and datum transformations. Uses by default the 's2' package for geometry operations on geodetic (long/lat degree) coordinates.

Maintained by Edzer Pebesma. Last updated 16 days ago.

gdal geos proj spatial cpp

5.3 match 1.4k stars 22.42 score 117k scripts 1.2k dependents

fragla

eq5d:Methods for Analysing 'EQ-5D' Data and Calculating 'EQ-5D' Index Scores

EQ-5D is a popular health related quality of life instrument used in the clinical and economic evaluation of health care. Developed by the EuroQol group <https://euroqol.org/>, the instrument consists of two components: health state description and evaluation. For the description component a subject self-rates their health in terms of five dimensions; mobility, self-care, usual activities, pain/discomfort, and anxiety/depression using either a three-level (EQ-5D-3L, <https://euroqol.org/information-and-support/euroqol-instruments/eq-5d-3l/>) or a five-level (EQ-5D-5L, <https://euroqol.org/information-and-support/euroqol-instruments/eq-5d-5l/>) scale. Frequently the scores on these five dimensions are converted to a single utility index using country specific value sets, which can be used in the clinical and economic evaluation of health care as well as in population health surveys. The eq5d package provides methods to calculate index scores from a subject's dimension scores. 32 TTO and 11 VAS EQ-5D-3L value sets including those for countries in Szende et al (2007) <doi:10.1007/1-4020-5511-0> and Szende et al (2014) <doi:10.1007/978-94-007-7596-1>, 47 EQ-5D-5L EQ-VT value sets, the EQ-5D-5L crosswalk value sets developed by van Hout et al. (2012) <doi:10.1016/j.jval.2012.02.008>, the crosswalk value sets for Bermuda, Jordan and Russia and the reverse crosswalk value sets. 10 EQ-5D-Y value sets are also included as are the NICE 'DSU' age-sex based EQ-5D-3L to EQ-5D-5L and EQ-5D-5L to EQ-5D-3L mappings. Methods are also included for the analysis of EQ-5D profiles, including those from the book "Methods for Analyzing and Reporting EQ-5D data" by Devlin et al. (2020) <doi:10.1007/978-3-030-47622-9>. Additionally a shiny web tool is included to enable the calculation, visualisation and automated statistical analysis of EQ-5D data via a web browser using EQ-5D dimension scores stored in CSV or Excel files.

Maintained by Fraser Morton. Last updated 15 days ago.

14.3 match 22 stars 8.19 score 37 scripts

noaa-ocm

SWMPrExtension:Functions for Analyzing and Plotting Estuary Monitoring Data

Tools for performing routine analysis and plotting tasks with environmental data from the System Wide Monitoring Program of the National Estuarine Research Reserve System <https://cdmo.baruch.sc.edu/>. This package builds on the functionality of the 'SWMPr' package <https://cran.r-project.org/package=SWMPr>, which is used to retrieve and organize the data. The combined set of tools address common challenges associated with continuous time series data for environmental decision making, and are intended for use in annual reporting activities. References: Beck, Marcus W. (2016) <ISSN 2073-4859><https://journal.r-project.org/archive/2016-1/beck.pdf> Rudis, Bob (2014) <https://rud.is/b/2014/11/16/moving-the-earth-well-alaska-hawaii-with-r/>. United States Environmental Protection Agency (2015) <https://cfpub.epa.gov/si/si_public_record_Report.cfm?Lab=OWOW&dirEntryId=327030>. United States Environmental Protection Agency (2012) <https://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.646.1973&rep=rep1&type=pdf>.

Maintained by Matt Dornback. Last updated 2 years ago.

22.7 match 12 stars 5.10 score 42 scripts

ropensci

geojsonio:Convert Data from and to 'GeoJSON' or 'TopoJSON'

Convert data to 'GeoJSON' or 'TopoJSON' from various R classes, including vectors, lists, data frames, shape files, and spatial classes. 'geojsonio' does not aim to replace packages like 'sp', 'rgdal', 'rgeos', but rather aims to be a high level client to simplify conversions of data from and to 'GeoJSON' and 'TopoJSON'.

Maintained by Michael Mahoney. Last updated 1 years ago.

geojson topojson geospatial conversion data input-output io

10.7 match 151 stars 10.80 score 2.9k scripts 13 dependents

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

16.0 match 39 stars 7.16 score 59 scripts

dreamrs

billboarder:Create Interactive Chart with the JavaScript 'Billboard' Library

Provides an 'htmlwidgets' interface to 'billboard.js', a re-usable easy interface JavaScript chart library, based on D3 v4+. Chart types include line charts, scatterplots, bar/lollipop charts, histogram/density plots, pie/donut charts and gauge charts. All charts are interactive, and a proxy method is implemented to smoothly update a chart without rendering it again in 'shiny' apps.

Maintained by Victor Perrier. Last updated 5 months ago.

data-visualization htmlwidgets

11.7 match 174 stars 9.74 score 96 scripts 4 dependents

rwehrens

kohonen:Supervised and Unsupervised Self-Organising Maps

Functions to train self-organising maps (SOMs). Also interrogation of the maps and prediction using trained maps are supported. The name of the package refers to Teuvo Kohonen, the inventor of the SOM.

Maintained by Ron Wehrens. Last updated 2 years ago.

cpp openmp

16.4 match 9 stars 6.91 score 724 scripts 14 dependents

mthrun

DataVisualizations:Visualizations of High-Dimensional Data

Gives access to data visualisation methods that are relevant from the data scientist's point of view. The flagship idea of 'DataVisualizations' is the mirrored density plot (MD-plot) for either classified or non-classified multivariate data published in Thrun, M.C. et al.: "Analyzing the Fine Structure of Distributions" (2020), PLoS ONE, <DOI:10.1371/journal.pone.0238835>. The MD-plot outperforms the box-and-whisker diagram (box plot), violin plot and bean plot and geom_violin plot of ggplot2. Furthermore, a collection of various visualization methods for univariate data is provided. In the case of exploratory data analysis, 'DataVisualizations' makes it possible to inspect the distribution of each feature of a dataset visually through a combination of four methods. One of these methods is the Pareto density estimation (PDE) of the probability density function (pdf). Additionally, visualizations of the distribution of distances using PDE, the scatter-density plot using PDE for two variables as well as the Shepard density plot and the Bland-Altman plot are presented here. Pertaining to classified high-dimensional data, a number of visualizations are described, such as f.ex. the heat map and silhouette plot. A political map of the world or Germany can be visualized with the additional information defined by a classification of countries or regions. By extending the political map further, an uncomplicated function for a Choropleth map can be used which is useful for measurements across a geographic area. For categorical features, the Pie charts, slope charts and fan plots, improved by the ABC analysis, become usable. More detailed explanations are found in the book by Thrun, M.C.: "Projection-Based Clustering through Self-Organization and Swarm Intelligence" (2018) <DOI:10.1007/978-3-658-20540-9>.

Maintained by Michael Thrun. Last updated 2 months ago.

cpp

14.5 match 7 stars 7.72 score 118 scripts 7 dependents

lbbe-software

MareyMap:Estimation of Meiotic Recombination Rates Using Marey Maps

Local recombination rates are graphically estimated across a genome using Marey maps.

Maintained by Aurélie Siberchicot. Last updated 13 days ago.

21.0 match 1 stars 5.30 score 20 scripts

datastorm-open

rAmCharts:JavaScript Charts Tool

Provides an R interface for using 'AmCharts' Library. Based on 'htmlwidgets', it provides a global architecture to generate 'JavaScript' source code for charts. Most of classes in the library have their equivalent in R with S4 classes; for those classes, not all properties have been referenced but can easily be added in the constructors. Complex properties (e.g. 'JavaScript' object) can be passed as named list. See examples at <https://datastorm-open.github.io/introduction_ramcharts/> and <https://www.amcharts.com/> for more information about the library. The package includes the free version of 'AmCharts' Library. Its only limitation is a small link to the web site displayed on your charts. If you enjoy this library, do not hesitate to refer to this page <https://www.amcharts.com/online-store/> to purchase a licence, and thus support its creators and get a period of Priority Support. See also <https://www.amcharts.com/about/> for more information about 'AmCharts' company.

Maintained by Benoit Thieurmel. Last updated 2 months ago.

15.5 match 49 stars 7.17 score 153 scripts 4 dependents

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

11.4 match 87 stars 9.70 score 432 scripts 1 dependents

christopherkenny

feltr:Access the Felt API

Upload, download, and edit internet maps with the Felt API (<https://feltmaps.notion.site/Felt-Public-API-reference-c01e0e6b0d954a678c608131b894e8e1>). Allows users to create new maps, edit existing maps, and extract data. Provides tools for working with layers, which represent geographic data, and elements, which are interactive annotations. Spatial data accessed from the API is transformed to work with 'sf'.

Maintained by Christopher T. Kenny. Last updated 9 months ago.

22.5 match 4 stars 4.86 score 9 scripts 6 dependents

mages

googleVis:R Interface to Google Charts

R interface to Google's chart tools, allowing users to create interactive charts based on data frames. Charts are displayed locally via the R HTTP help server. A modern browser with an Internet connection is required. The data remains local and is not uploaded to Google.

Maintained by Markus Gesmann. Last updated 10 months ago.

8.4 match 361 stars 12.98 score 2.4k scripts 11 dependents

e-sensing

sits:Satellite Image Time Series Analysis for Earth Observation Data Cubes

An end-to-end toolkit for land use and land cover classification using big Earth observation data, based on machine learning methods applied to satellite image data cubes, as described in Simoes et al (2021) <doi:10.3390/rs13132428>. Builds regular data cubes from collections in AWS, Microsoft Planetary Computer, Brazil Data Cube, Copernicus Data Space Environment (CDSE), Digital Earth Africa, Digital Earth Australia, NASA HLS using the Spatio-temporal Asset Catalog (STAC) protocol (<https://stacspec.org/>) and the 'gdalcubes' R package developed by Appel and Pebesma (2019) <doi:10.3390/data4030092>. Supports visualization methods for images and time series and smoothing filters for dealing with noisy time series. Includes functions for quality assessment of training samples using self-organized maps as presented by Santos et al (2021) <doi:10.1016/j.isprsjprs.2021.04.014>. Includes methods to reduce training samples imbalance proposed by Chawla et al (2002) <doi:10.1613/jair.953>. Provides machine learning methods including support vector machines, random forests, extreme gradient boosting, multi-layer perceptrons, temporal convolutional neural networks proposed by Pelletier et al (2019) <doi:10.3390/rs11050523>, and temporal attention encoders by Garnot and Landrieu (2020) <doi:10.48550/arXiv.2007.00586>. Supports GPU processing of deep learning models using torch <https://torch.mlverse.org/>. Performs efficient classification of big Earth observation data cubes and includes functions for post-classification smoothing based on Bayesian inference as described by Camara et al (2024) <doi:10.3390/rs16234572>, and methods for active learning and uncertainty assessment. Supports region-based time series analysis using package supercells <https://jakubnowosad.com/supercells/>. Enables best practices for estimating area and assessing accuracy of land change as recommended by Olofsson et al (2014) <doi:10.1016/j.rse.2014.02.015>. Minimum recommended requirements: 16 GB RAM and 4 CPU dual-core.

Maintained by Gilberto Camara. Last updated 1 months ago.

big-earth-data cbers earth-observation eo-datacubes geospatial image-time-series land-cover-classification landsat planetary-computer r-spatial remote-sensing rspatial satellite-image-time-series satellite-imagery sentinel-2 stac-api stac-catalog cpp

11.5 match 494 stars 9.50 score 384 scripts

bioc

slingshot:Tools for ordering single-cell sequencing

Provides functions for inferring continuous, branching lineage structures in low-dimensional data. Slingshot was designed to model developmental trajectories in single-cell RNA sequencing data and serve as a component in an analysis pipeline after dimensionality reduction and clustering. It is flexible enough to handle arbitrarily many branching events and allows for the incorporation of prior knowledge through supervised graph construction.

Maintained by Kelly Street. Last updated 5 months ago.

clustering differentialexpression geneexpression rnaseq sequencing software singlecell transcriptomics visualization

9.1 match 283 stars 12.01 score 1.0k scripts 4 dependents

bioc

OmnipathR:OmniPath web service client and more

A client for the OmniPath web service (https://www.omnipathdb.org) and many other resources. It also includes functions to transform and pretty print some of the downloaded data, functions to access a number of other resources such as BioPlex, ConsensusPathDB, EVEX, Gene Ontology, Guide to Pharmacology (IUPHAR/BPS), Harmonizome, HTRIdb, Human Phenotype Ontology, InWeb InBioMap, KEGG Pathway, Pathway Commons, Ramilowski et al. 2015, RegNetwork, ReMap, TF census, TRRUST and Vinayagam et al. 2011. Furthermore, OmnipathR features a close integration with the NicheNet method for ligand activity prediction from transcriptomics data, and its R implementation `nichenetr` (available only on github).

Maintained by Denes Turei. Last updated 19 days ago.

graphandnetwork network pathways software thirdpartyclient dataimport datarepresentation genesignaling generegulation systemsbiology transcriptomics singlecell annotation kegg complexes enzyme-ptm networks networks-biology omnipath proteins quarto

10.9 match 126 stars 9.90 score 226 scripts 2 dependents

gisma

uavRmp:UAV Mission Planner

The Unmanned Aerial Vehicle Mission Planner provides an easy to use work flow for planning autonomous obstacle avoiding surveys of ready to fly unmanned aerial vehicles to retrieve aerial or spot related data. It creates either intermediate flight control files for the DJI-Litchi supported series or ready to upload control files for the pixhawk-based flight controller as used in the 3DR-Solo or Yuneec series. Additionally it contains some useful tools for digitizing and data manipulation.

Maintained by Chris Reudenbach. Last updated 9 months ago.

cultural-heritage dji drone flight-planning forest-mapping litchi low-budget-uav mission-planning photogrammetry pixhawk pixhawk-controller qgroundcontrol2litchi solo survey terrain-following terrain-mapping uavs yuneec

16.7 match 25 stars 6.48 score 6 scripts

ropensci

ruODK:An R Client for the ODK Central API

Access and tidy up data from the 'ODK Central' API. 'ODK Central' is a clearinghouse for digitally captured data using ODK <https://docs.getodk.org/central-intro/>. It manages user accounts and permissions, stores form definitions, and allows data collection clients like 'ODK Collect' to connect to it for form download and submission upload. The 'ODK Central' API is documented at <https://docs.getodk.org/central-api/>.

Maintained by Florian W. Mayer. Last updated 4 months ago.

database open-data odk api data dataset odata odata-client odk-central opendatakit

13.9 match 42 stars 7.73 score 57 scripts 1 dependents

ropensci

rangr:Mechanistic Simulation of Species Range Dynamics

Integrates population dynamics and dispersal into a mechanistic virtual species simulator. The package can be used to study the effects of environmental change on population growth and range shifts. It allows for simple and straightforward definition of population dynamics (including positive density dependence), extensive possibilities for defining dispersal kernels, and the ability to generate virtual ecologist data. Learn more about the 'rangr' at <https://docs.ropensci.org/rangr/>.

Maintained by Katarzyna Markowska. Last updated 12 days ago.

20.7 match 2 stars 5.18 score 5 scripts

okgreece

DescriptiveStats.OBeu:Descriptive Statistics 'OpenBudgets.eu'

Estimate and return the needed parameters for visualizations designed for 'OpenBudgets.eu' <http://openbudgets.eu/> datasets. Calculate descriptive statistical measures in budget data of municipalities across Europe, according to the 'OpenBudgets.eu' data model. There are functions for measuring central tendency and dispersion of amount variables along with their distributions and correlations and the frequencies of categorical variables for a given dataset. Also, can be used generally to other datasets, to extract visualization parameters, convert them to 'JSON' format and use them as input in a different graphical interface.

Maintained by Kleanthis Koupidis. Last updated 4 years ago.

boxplot correlation descriptive-statistics estimate frequencies obeu open-budgets openbudgets

19.7 match 1 stars 5.40 score 28 scripts 1 dependents

urbananalyst

m4ra:Many-to-Many Multi-Modal Routing Aggregator

Many-to-many multi-modal routing aggregator, combining 'dodgr' and 'gtfsrouter' for complete routing through urban networks.

Maintained by Mark Padgham. Last updated 1 months ago.

gtfs open-street-map routing-engine cpp

25.0 match 15 stars 4.26 score 1 scripts 2 dependents

jeroen

jsonlite:A Simple and Robust JSON Parser and Generator for R

A reasonably fast JSON parser and generator, optimized for statistical data and the web. Offers simple, flexible tools for working with JSON in R, and is particularly powerful for building pipelines and interacting with a web API. The implementation is based on the mapping described in the vignette (Ooms, 2014). In addition to converting JSON data from/to R objects, 'jsonlite' contains functions to stream, validate, and prettify JSON data. The unit tests included with the package verify that all edge cases are encoded and decoded consistently for use with dynamic data in systems and applications.

Maintained by Jeroen Ooms. Last updated 22 days ago.

json parser

5.0 match 384 stars 21.15 score 27k scripts 8.6k dependents

thinkr-open

fcuk:The Ultimate Helper for Clumsy Fingers

Automatically suggests a correction when a typo occurs.

Maintained by Vincent Guyader. Last updated 1 years ago.

error fcuk

15.0 match 92 stars 7.05 score 49 scripts

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

24.2 match 3 stars 4.35 score 15 scripts

bleutner

RStoolbox:Remote Sensing Data Analysis

Toolbox for remote sensing image processing and analysis such as calculating spectral indexes, principal component transformation, unsupervised and supervised classification or fractional cover analyses.

Maintained by Konstantin Mueller. Last updated 1 months ago.

ggplot2 land-cover-mapping remote-sensing spectral-unmixing supervised-classification unsupervised-classification openblas cpp

10.4 match 275 stars 10.10 score 1.1k scripts

ropensci

rvertnet:Search 'Vertnet', a 'Database' of Vertebrate Specimen Records

Retrieve, map and summarize data from the 'VertNet.org' archives (<https://vertnet.org/>). Functions allow searching by many parameters, including 'taxonomic' names, places, and dates. In addition, there is an interface for conducting spatially delimited searches, and another for requesting large 'datasets' via email.

Maintained by Dave Slager. Last updated 5 months ago.

species occurrences biodiversity maps vertnet mammals mammalia specimens api-wrapper specimen spocc

12.3 match 7 stars 8.51 score 35 scripts 6 dependents

thinkr-open

thinkr:Tools for Cleaning Up Messy Files

Some tools for cleaning up messy 'Excel' files to be suitable for R. People who have been working with 'Excel' for years built more or less complicated sheets with names, characters, formats that are not homogeneous. To be able to use them in R nowadays, we built a set of functions that will avoid the majority of importation problems and keep all the data at best.

Maintained by Vincent Guyader. Last updated 3 years ago.

hacktoberfest thinkr-not-maintained

15.0 match 29 stars 6.96 score 45 scripts

kisungyou

Rdimtools:Dimension Reduction and Estimation Methods

We provide linear and nonlinear dimension reduction techniques. Intrinsic dimension estimation methods for exploratory analysis are also provided. For more details on the package, see the paper by You and Shung (2022) <doi:10.1016/j.simpa.2022.100414>.

Maintained by Kisung You. Last updated 2 years ago.

dimension-estimation dimension-reduction manifold-learning subspace-learning openblas cpp openmp

12.3 match 52 stars 8.37 score 186 scripts 8 dependents

ropensci

rnaturalearth:World Map Data from Natural Earth

Facilitates mapping by making natural earth map data from <https://www.naturalearthdata.com/> more easily available to R users.

Maintained by Philippe Massicotte. Last updated 1 days ago.

peer-reviewed

6.6 match 234 stars 15.52 score 7.2k scripts 47 dependents

bioc

lumi:BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. It also includes the functions of processing Illumina methylation microarrays, especially Illumina Infinium methylation microarrays.

Maintained by Lei Huang. Last updated 5 months ago.

microarray onechannel preprocessing dnamethylation qualitycontrol twochannel

16.3 match 6.27 score 294 scripts 5 dependents

ropensci

landscapetools:Landscape Utility Toolbox

Provides utility functions for some of the less-glamorous tasks involved in landscape analysis. It includes functions to coerce raster data to the common tibble format and vice versa, it helps with flexible reclassification tasks of raster data and it provides a function to merge multiple raster. Furthermore, 'landscapetools' helps landscape scientists to visualize their data by providing optional themes and utility functions to plot single landscapes, rasterstacks, -bricks and lists of raster.

Maintained by Marco Sciaini. Last updated 2 years ago.

landscape landscape-ecology raster visualization workflow

15.4 match 46 stars 6.60 score 191 scripts

thinkr-open

checkhelper:Deal with Check Outputs

Deal with packages 'check' outputs and reduce the risk of rejection by 'CRAN' by following policies.

Maintained by Sebastien Rochette. Last updated 1 years ago.

15.0 match 34 stars 6.74 score 18 scripts

pythonhealthdatascience

treat.sim:Nelson's Treatment Centre Simulation in Simmer

A discrete-event simulation of a simple urgent care treatment centre simulation from Nelson (2013). Implemented in R Simmer. The model is packaged to allow for easy experimentation, summary of results, and implementation in other software such as a Shiny interface.

Maintained by Thomas Monks. Last updated 8 months ago.

computer-simulation discrete-event-simulation health open-modelling open-science open-source r-language reproducible-research simmer

22.5 match 2 stars 4.48 score 5 scripts

eguidotti

bidask:Efficient Estimation of Bid-Ask Spreads from Open, High, Low, and Close Prices

Implements the efficient estimator of bid-ask spreads from open, high, low, and close prices described in Ardia, Guidotti, & Kroencke (JFE, 2024) <doi:10.1016/j.jfineco.2024.103916>. It also provides an implementation of the estimators described in Roll (JF, 1984) <doi:10.1111/j.1540-6261.1984.tb03897.x>, Corwin & Schultz (JF, 2012) <doi:10.1111/j.1540-6261.2012.01729.x>, and Abdi & Ranaldo (RFS, 2017) <doi:10.1093/rfs/hhx084>.

Maintained by Emanuele Guidotti. Last updated 19 days ago.

finance

14.4 match 107 stars 6.98 score 6 scripts

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

8.8 match 603 stars 11.45 score 1.3k scripts 11 dependents

maps:Draw Geographical Maps

tmap:Thematic Maps

RCy3:Functions to Access and Control Cytoscape

qtl:Tools for Analyzing QTL Experiments

Racmacs:Antigenic Cartography Macros

mapgl:Interactive Maps with 'Mapbox GL JS' and 'MapLibre GL JS'

leaflet:Create Interactive Web Maps with the JavaScript 'Leaflet' Library

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

rworldmap:Mapping Global Data

spatstat.geom:Geometrical Functionality of the 'spatstat' Family

cartography:Thematic Cartography

oce:Analysis of Oceanographic Data

MAP:Multimodal Automated Phenotyping

csmaps:Preformatted Maps of Norway that Don't Need Geolibraries

mappoly:Genetic Linkage Maps in Autopolyploids

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

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

ggplot2:Create Elegant Data Visualisations Using the Grammar of Graphics

terra:Spatial Data Analysis

ensembldb:Utilities to create and use Ensembl-based annotation databases

usmap:US Maps Including Alaska and Hawaii

pathview:a tool set for pathway based data integration and visualization

mapping:Automatic Download, Linking, Manipulating Coordinates for Maps

map:Defines a meta class of geographical objects, the 'map' class, and associated tools

OpenStreetMap:Access to Open Street Map Raster Images

ggmap:Spatial Visualization with ggplot2

mapsf:Thematic Cartography

mapview:Interactive Viewing of Spatial Data in R

leafem:'leaflet' Extensions for 'mapview'

SUMMER:Small-Area-Estimation Unit/Area Models and Methods for Estimation in R

dodgr:Distances on Directed Graphs

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

highcharter:A Wrapper for the 'Highcharts' Library

rhdf5:R Interface to HDF5

mapsapi:'sf'-Compatible Interface to 'Google Maps' APIs

terrainr:Landscape Visualizations in R and 'Unity'

rotl:Interface to the 'Open Tree of Life' API

soc.ca:Specific Correspondence Analysis for the Social Sciences

lingtypology:Linguistic Typology and Mapping

bayestestR:Understand and Describe Bayesian Models and Posterior Distributions

admiral:ADaM in R Asset Library

RgoogleMaps:Overlays on Static Maps

NGCHM:Next Generation Clustered Heat Maps

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

leaflet.extras:Extra Functionality for 'leaflet' Package

safetyCharts:Charts for Monitoring Clinical Trial Safety

destiny:Creates diffusion maps

mapdata:Extra Map Databases

abstr:R Interface to the A/B Street Transport System Simulation Software

bibliometrix:Comprehensive Science Mapping Analysis

onemap:Construction of Genetic Maps in Experimental Crosses

mapbaltimore:Make maps for Baltimore City with open data

purrr:Functional Programming Tools

soilDB:Soil Database Interface

mappings:Functions for Transforming Categorical Variables

visNetwork:Network Visualization using 'vis.js' Library

OpenML:Open Machine Learning and Open Data Platform

HistData:Data Sets from the History of Statistics and Data Visualization

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

polymapR:Linkage Analysis in Outcrossing Polyploids

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

golem:A Framework for Robust Shiny Applications

loon:Interactive Statistical Data Visualization

GEOmap:Topographic and Geologic Mapping

safetyGraphics:Interactive Graphics for Monitoring Clinical Trial Safety

oceanis:Cartography for Statistical Analysis

ASMap:Linkage Map Construction using the MSTmap Algorithm

processmapR:Construct Process Maps Using Event Data

tiledb:Modern Database Engine for Complex Data Based on Multi-Dimensional Arrays

mapboxer:An R Interface to 'Mapbox GL JS'

qtl2:Quantitative Trait Locus Mapping in Experimental Crosses

igraph:Network Analysis and Visualization

maptiles:Download and Display Map Tiles

gwasrapidd:'REST' 'API' Client for the 'NHGRI'-'EBI' 'GWAS' Catalog

openairmaps:Create Maps of Air Pollution Data

ORFik:Open Reading Frames in Genomics

Rsamtools:Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

sp:Classes and Methods for Spatial Data

slippymath:Slippy Map Tile Tools

rgl:3D Visualization Using OpenGL