R-universe search: needs:class

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 3 days ago.

gdal geos proj spatial cpp

1.4k stars 22.44 score 117k scripts 1.2k dependents

topepo

caret:Classification and Regression Training

Misc functions for training and plotting classification and regression models.

Maintained by Max Kuhn. Last updated 4 months ago.

1.6k stars 19.24 score 61k scripts 303 dependents

tidymodels

recipes:Preprocessing and Feature Engineering Steps for Modeling

A recipe prepares your data for modeling. We provide an extensible framework for pipeable sequences of feature engineering steps provides preprocessing tools to be applied to data. Statistical parameters for the steps can be estimated from an initial data set and then applied to other data sets. The resulting processed output can then be used as inputs for statistical or machine learning models.

Maintained by Max Kuhn. Last updated 1 days ago.

586 stars 18.80 score 7.2k scripts 383 dependents

r-spatial

stars:Spatiotemporal Arrays, Raster and Vector Data Cubes

Reading, manipulating, writing and plotting spatiotemporal arrays (raster and vector data cubes) in 'R', using 'GDAL' bindings provided by 'sf', and 'NetCDF' bindings by 'ncmeta' and 'RNetCDF'.

Maintained by Edzer Pebesma. Last updated 1 months ago.

raster satellite-images spatial

571 stars 18.27 score 7.2k scripts 137 dependents

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 26 days ago.

gis leaflet-map spatial

821 stars 17.20 score 39k scripts 178 dependents

andrisignorell

DescTools:Tools for Descriptive Statistics

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

Maintained by Andri Signorell. Last updated 2 days ago.

fortran cpp

86 stars 16.73 score 7.7k scripts 101 dependents

r-spatial

spdep:Spatial Dependence: Weighting Schemes, Statistics

A collection of functions to create spatial weights matrix objects from polygon 'contiguities', from point patterns by distance and tessellations, for summarizing these objects, and for permitting their use in spatial data analysis, including regional aggregation by minimum spanning tree; a collection of tests for spatial 'autocorrelation', including global 'Morans I' and 'Gearys C' proposed by 'Cliff' and 'Ord' (1973, ISBN: 0850860369) and (1981, ISBN: 0850860814), 'Hubert/Mantel' general cross product statistic, Empirical Bayes estimates and 'Assunção/Reis' (1999) <doi:10.1002/(SICI)1097-0258(19990830)18:16%3C2147::AID-SIM179%3E3.0.CO;2-I> Index, 'Getis/Ord' G ('Getis' and 'Ord' 1992) <doi:10.1111/j.1538-4632.1992.tb00261.x> and multicoloured join count statistics, 'APLE' ('Li 'et al.' ) <doi:10.1111/j.1538-4632.2007.00708.x>, local 'Moran's I', 'Gearys C' ('Anselin' 1995) <doi:10.1111/j.1538-4632.1995.tb00338.x> and 'Getis/Ord' G ('Ord' and 'Getis' 1995) <doi:10.1111/j.1538-4632.1995.tb00912.x>, 'saddlepoint' approximations ('Tiefelsdorf' 2002) <doi:10.1111/j.1538-4632.2002.tb01084.x> and exact tests for global and local 'Moran's I' ('Bivand et al.' 2009) <doi:10.1016/j.csda.2008.07.021> and 'LOSH' local indicators of spatial heteroscedasticity ('Ord' and 'Getis') <doi:10.1007/s00168-011-0492-y>. The implementation of most of these measures is described in 'Bivand' and 'Wong' (2018) <doi:10.1007/s11749-018-0599-x>, with further extensions in 'Bivand' (2022) <doi:10.1111/gean.12319>. 'Lagrange' multiplier tests for spatial dependence in linear models are provided ('Anselin et al'. 1996) <doi:10.1016/0166-0462(95)02111-6>, as are 'Rao' score tests for hypothesised spatial 'Durbin' models based on linear models ('Koley' and 'Bera' 2023) <doi:10.1080/17421772.2023.2256810>. A local indicators for categorical data (LICD) implementation based on 'Carrer et al.' (2021) <doi:10.1016/j.jas.2020.105306> and 'Bivand et al.' (2017) <doi:10.1016/j.spasta.2017.03.003> was added in 1.3-7. From 'spdep' and 'spatialreg' versions >= 1.2-1, the model fitting functions previously present in this package are defunct in 'spdep' and may be found in 'spatialreg'.

Maintained by Roger Bivand. Last updated 1 months ago.

spatial-autocorrelation spatial-dependence spatial-weights

131 stars 16.59 score 6.0k scripts 106 dependents

tidymodels

tidymodels:Easily Install and Load the 'Tidymodels' Packages

The tidy modeling "verse" is a collection of packages for modeling and statistical analysis that share the underlying design philosophy, grammar, and data structures of the tidyverse.

Maintained by Max Kuhn. Last updated 1 months ago.

783 stars 16.52 score 66k scripts 15 dependents

r-tmap

tmap:Thematic Maps

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

Maintained by Martijn Tennekes. Last updated 1 days ago.

choropleth-maps maps spatial thematic-maps visualisation

879 stars 16.25 score 13k scripts 24 dependents

r-spatial

classInt:Choose Univariate Class Intervals

Selected commonly used methods for choosing univariate class intervals for mapping or other graphics purposes.

Maintained by Roger Bivand. Last updated 3 months ago.

fortran

34 stars 16.17 score 3.2k scripts 1.2k dependents

r-spatial

gstat:Spatial and Spatio-Temporal Geostatistical Modelling, Prediction and Simulation

Variogram modelling; simple, ordinary and universal point or block (co)kriging; spatio-temporal kriging; sequential Gaussian or indicator (co)simulation; variogram and variogram map plotting utility functions; supports sf and stars.

Maintained by Edzer Pebesma. Last updated 5 days ago.

openblas

197 stars 15.71 score 4.8k scripts 58 dependents

thomasp85

gganimate:A Grammar of Animated Graphics

The grammar of graphics as implemented in the 'ggplot2' package has been successful in providing a powerful API for creating static visualisation. In order to extend the API for animated graphics this package provides a completely new set of grammar, fully compatible with 'ggplot2' for specifying transitions and animations in a flexible and extensible way.

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

animation data-visualization ggplot-extension ggplot2 transition

2.0k stars 15.53 score 13k scripts 24 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 13 days ago.

peer-reviewed

234 stars 15.51 score 7.2k scripts 47 dependents

r-lidar

lidR:Airborne LiDAR Data Manipulation and Visualization for Forestry Applications

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

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

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

623 stars 14.47 score 844 scripts 8 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 8 months ago.

hotdeck imputation-methods model-predictions visualization cpp

85 stars 14.44 score 2.6k scripts 19 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

526 stars 14.39 score 7.3k scripts 27 dependents

tidymodels

tune:Tidy Tuning Tools

The ability to tune models is important. 'tune' contains functions and classes to be used in conjunction with other 'tidymodels' packages for finding reasonable values of hyper-parameters in models, pre-processing methods, and post-processing steps.

Maintained by Max Kuhn. Last updated 25 days ago.

293 stars 14.27 score 756 scripts 39 dependents

business-science

timetk:A Tool Kit for Working with Time Series

Easy visualization, wrangling, and feature engineering of time series data for forecasting and machine learning prediction. Consolidates and extends time series functionality from packages including 'dplyr', 'stats', 'xts', 'forecast', 'slider', 'padr', 'recipes', and 'rsample'.

Maintained by Matt Dancho. Last updated 1 years ago.

coercion coercion-functions data-mining dplyr forecast forecasting forecasting-models machine-learning series-decomposition series-signature tibble tidy tidyquant tidyverse time time-series timeseries

626 stars 14.20 score 4.0k scripts 16 dependents

walkerke

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

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

Maintained by Kyle Walker. Last updated 2 months ago.

648 stars 14.02 score 7.5k scripts 10 dependents

tidymodels

workflows:Modeling Workflows

Managing both a 'parsnip' model and a preprocessor, such as a model formula or recipe from 'recipes', can often be challenging. The goal of 'workflows' is to streamline this process by bundling the model alongside the preprocessor, all within the same object.

Maintained by Simon Couch. Last updated 1 months ago.

207 stars 13.97 score 876 scripts 43 dependents

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 3 days ago.

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

717 stars 13.77 score 1.9k scripts 3 dependents

dieghernan

tidyterra:'tidyverse' Methods and 'ggplot2' Helpers for 'terra' Objects

Extension of the 'tidyverse' for 'SpatRaster' and 'SpatVector' objects of the 'terra' package. It includes also new 'geom_' functions that provide a convenient way of visualizing 'terra' objects with 'ggplot2'.

Maintained by Diego Hernangómez. Last updated 5 days ago.

terra ggplot-extension r-spatial rspatial

190 stars 13.59 score 1.9k scripts 25 dependents

kaz-yos

tableone:Create 'Table 1' to Describe Baseline Characteristics with or without Propensity Score Weights

Creates 'Table 1', i.e., description of baseline patient characteristics, which is essential in every medical research. Supports both continuous and categorical variables, as well as p-values and standardized mean differences. Weighted data are supported via the 'survey' package.

Maintained by Kazuki Yoshida. Last updated 3 years ago.

baseline-characteristics descriptive-statistics statistics

221 stars 13.55 score 2.3k scripts 12 dependents

business-science

tidyquant:Tidy Quantitative Financial Analysis

Bringing business and financial analysis to the 'tidyverse'. The 'tidyquant' package provides a convenient wrapper to various 'xts', 'zoo', 'quantmod', 'TTR' and 'PerformanceAnalytics' package functions and returns the objects in the tidy 'tibble' format. The main advantage is being able to use quantitative functions with the 'tidyverse' functions including 'purrr', 'dplyr', 'tidyr', 'ggplot2', 'lubridate', etc. See the 'tidyquant' website for more information, documentation and examples.

Maintained by Matt Dancho. Last updated 2 months ago.

dplyr financial-analysis financial-data financial-statements multiple-stocks performance-analysis performanceanalytics quantmod stock stock-exchanges stock-indexes stock-lists stock-performance stock-prices stock-symbol tidyverse time-series timeseries xts

872 stars 13.34 score 5.2k scripts

dreamrs

esquisse:Explore and Visualize Your Data Interactively

A 'shiny' gadget to create 'ggplot2' figures interactively with drag-and-drop to map your variables to different aesthetics. You can quickly visualize your data accordingly to their type, export in various formats, and retrieve the code to reproduce the plot.

Maintained by Victor Perrier. Last updated 1 months ago.

addin data-visualization ggplot2 rstudio-addin visualization

1.8k stars 13.31 score 1.1k scripts 1 dependents

oscarkjell

text:Analyses of Text using Transformers Models from HuggingFace, Natural Language Processing and Machine Learning

Link R with Transformers from Hugging Face to transform text variables to word embeddings; where the word embeddings are used to statistically test the mean difference between set of texts, compute semantic similarity scores between texts, predict numerical variables, and visual statistically significant words according to various dimensions etc. For more information see <https://www.r-text.org>.

Maintained by Oscar Kjell. Last updated 7 days ago.

deep-learning machine-learning nlp transformers openjdk

145 stars 13.21 score 436 scripts 1 dependents

r-spatial

spatialreg:Spatial Regression Analysis

A collection of all the estimation functions for spatial cross-sectional models (on lattice/areal data using spatial weights matrices) contained up to now in 'spdep'. These model fitting functions include maximum likelihood methods for cross-sectional models proposed by 'Cliff' and 'Ord' (1973, ISBN:0850860369) and (1981, ISBN:0850860814), fitting methods initially described by 'Ord' (1975) <doi:10.1080/01621459.1975.10480272>. The models are further described by 'Anselin' (1988) <doi:10.1007/978-94-015-7799-1>. Spatial two stage least squares and spatial general method of moment models initially proposed by 'Kelejian' and 'Prucha' (1998) <doi:10.1023/A:1007707430416> and (1999) <doi:10.1111/1468-2354.00027> are provided. Impact methods and MCMC fitting methods proposed by 'LeSage' and 'Pace' (2009) <doi:10.1201/9781420064254> are implemented for the family of cross-sectional spatial regression models. Methods for fitting the log determinant term in maximum likelihood and MCMC fitting are compared by 'Bivand et al.' (2013) <doi:10.1111/gean.12008>, and model fitting methods by 'Bivand' and 'Piras' (2015) <doi:10.18637/jss.v063.i18>; both of these articles include extensive lists of references. A recent review is provided by 'Bivand', 'Millo' and 'Piras' (2021) <doi:10.3390/math9111276>. 'spatialreg' >= 1.1-* corresponded to 'spdep' >= 1.1-1, in which the model fitting functions were deprecated and passed through to 'spatialreg', but masked those in 'spatialreg'. From versions 1.2-*, the functions have been made defunct in 'spdep'. From version 1.3-6, add Anselin-Kelejian (1997) test to `stsls` for residual spatial autocorrelation <doi:10.1177/016001769702000109>.

Maintained by Roger Bivand. Last updated 9 days ago.

bayesian impacts maximum-likelihood spatial-dependence spatial-econometrics spatial-regression openblas

46 stars 12.97 score 916 scripts 24 dependents

r-spatial

lwgeom:Bindings to Selected 'liblwgeom' Functions for Simple Features

Access to selected functions found in 'liblwgeom' <https://github.com/postgis/postgis/tree/master/liblwgeom>, the light-weight geometry library used by 'PostGIS' <http://postgis.net/>.

Maintained by Edzer Pebesma. Last updated 2 months ago.

proj geos cpp

61 stars 12.95 score 1.7k scripts 66 dependents

juba

questionr:Functions to Make Surveys Processing Easier

Set of functions to make the processing and analysis of surveys easier : interactive shiny apps and addins for data recoding, contingency tables, dataset metadata handling, and several convenience functions.

Maintained by Julien Barnier. Last updated 9 days ago.

83 stars 12.93 score 1.1k scripts 19 dependents

walkerke

tigris:Load Census TIGER/Line Shapefiles

Download TIGER/Line shapefiles from the United States Census Bureau (<https://www.census.gov/geographies/mapping-files/time-series/geo/tiger-line-file.html>) and load into R as 'sf' objects.

Maintained by Kyle Walker. Last updated 5 months ago.

331 stars 12.87 score 5.3k scripts 16 dependents

paleolimbot

ggspatial:Spatial Data Framework for ggplot2

Spatial data plus the power of the ggplot2 framework means easier mapping when input data are already in the form of spatial objects.

Maintained by Dewey Dunnington. Last updated 2 years ago.

379 stars 12.85 score 4.1k scripts 24 dependents

inlabru-org

inlabru:Bayesian Latent Gaussian Modelling using INLA and Extensions

Facilitates spatial and general latent Gaussian modeling using integrated nested Laplace approximation via the INLA package (<https://www.r-inla.org>). Additionally, extends the GAM-like model class to more general nonlinear predictor expressions, and implements a log Gaussian Cox process likelihood for modeling univariate and spatial point processes based on ecological survey data. Model components are specified with general inputs and mapping methods to the latent variables, and the predictors are specified via general R expressions, with separate expressions for each observation likelihood model in multi-likelihood models. A prediction method based on fast Monte Carlo sampling allows posterior prediction of general expressions of the latent variables. Ecology-focused introduction in Bachl, Lindgren, Borchers, and Illian (2019) <doi:10.1111/2041-210X.13168>.

Maintained by Finn Lindgren. Last updated 1 days ago.

96 stars 12.59 score 832 scripts 6 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 1 months ago.

108 stars 12.41 score 704 scripts 55 dependents

asardaes

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

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

Maintained by Alexis Sarda. Last updated 8 months ago.

clustering dtw time-series openblas cpp

262 stars 12.35 score 406 scripts 14 dependents

trevorld

ggpattern:'ggplot2' Pattern Geoms

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

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

368 stars 12.33 score 1.7k scripts 3 dependents

ropensci

stplanr:Sustainable Transport Planning

Tools for transport planning with an emphasis on spatial transport data and non-motorized modes. The package was originally developed to support the 'Propensity to Cycle Tool', a publicly available strategic cycle network planning tool (Lovelace et al. 2017) <doi:10.5198/jtlu.2016.862>, but has since been extended to support public transport routing and accessibility analysis (Moreno-Monroy et al. 2017) <doi:10.1016/j.jtrangeo.2017.08.012> and routing with locally hosted routing engines such as 'OSRM' (Lowans et al. 2023) <doi:10.1016/j.enconman.2023.117337>. The main functions are for creating and manipulating geographic "desire lines" from origin-destination (OD) data (building on the 'od' package); calculating routes on the transport network locally and via interfaces to routing services such as <https://cyclestreets.net/> (Desjardins et al. 2021) <doi:10.1007/s11116-021-10197-1>; and calculating route segment attributes such as bearing. The package implements the 'travel flow aggregration' method described in Morgan and Lovelace (2020) <doi:10.1177/2399808320942779> and the 'OD jittering' method described in Lovelace et al. (2022) <doi:10.32866/001c.33873>. Further information on the package's aim and scope can be found in the vignettes and in a paper in the R Journal (Lovelace and Ellison 2018) <doi:10.32614/RJ-2018-053>, and in a paper outlining the landscape of open source software for geographic methods in transport planning (Lovelace, 2021) <doi:10.1007/s10109-020-00342-2>.

Maintained by Robin Lovelace. Last updated 7 months ago.

cycle cycling desire-lines origin-destination peer-reviewed pubic-transport route-network routes routing spatial transport transport-planning transportation walking

427 stars 12.31 score 684 scripts 3 dependents

eliocamp

metR:Tools for Easier Analysis of Meteorological Fields

Many useful functions and extensions for dealing with meteorological data in the tidy data framework. Extends 'ggplot2' for better plotting of scalar and vector fields and provides commonly used analysis methods in the atmospheric sciences.

Maintained by Elio Campitelli. Last updated 10 days ago.

atmospheric-science ggplot2 visualization

146 stars 12.30 score 1000 scripts 22 dependents

isciences

exactextractr:Fast Extraction from Raster Datasets using Polygons

Quickly and accurately summarizes raster values over polygonal areas ("zonal statistics").

Maintained by Daniel Baston. Last updated 8 months ago.

gis raster rcpp geos cpp

286 stars 12.13 score 1.4k scripts 14 dependents

bcallaway11

did:Treatment Effects with Multiple Periods and Groups

The standard Difference-in-Differences (DID) setup involves two periods and two groups -- a treated group and untreated group. Many applications of DID methods involve more than two periods and have individuals that are treated at different points in time. This package contains tools for computing average treatment effect parameters in Difference in Differences setups with more than two periods and with variation in treatment timing using the methods developed in Callaway and Sant'Anna (2021) <doi:10.1016/j.jeconom.2020.12.001>. The main parameters are group-time average treatment effects which are the average treatment effect for a particular group at a a particular time. These can be aggregated into a fewer number of treatment effect parameters, and the package deals with the cases where there is selective treatment timing, dynamic treatment effects, calendar time effects, or combinations of these. There are also functions for testing the Difference in Differences assumption, and plotting group-time average treatment effects.

Maintained by Brantly Callaway. Last updated 3 days ago.

329 stars 12.09 score 696 scripts 3 dependents

tidymodels

probably:Tools for Post-Processing Predicted Values

Models can be improved by post-processing class probabilities, by: recalibration, conversion to hard probabilities, assessment of equivocal zones, and other activities. 'probably' contains tools for conducting these operations as well as calibration tools and conformal inference techniques for regression models.

Maintained by Max Kuhn. Last updated 5 months ago.

115 stars 12.09 score 21k scripts 1 dependents

tidymodels

workflowsets:Create a Collection of 'tidymodels' Workflows

A workflow is a combination of a model and preprocessors (e.g, a formula, recipe, etc.) (Kuhn and Silge (2021) <https://www.tmwr.org/>). In order to try different combinations of these, an object can be created that contains many workflows. There are functions to create workflows en masse as well as training them and visualizing the results.

Maintained by Simon Couch. Last updated 5 months ago.

94 stars 12.04 score 294 scripts 19 dependents

dreamrs

datamods:Modules to Import and Manipulate Data in 'Shiny'

'Shiny' modules to import data into an application or 'addin' from various sources, and to manipulate them after that.

Maintained by Victor Perrier. Last updated 25 days ago.

shiny shiny-modules

144 stars 12.03 score 174 scripts 7 dependents

zachmayer

caretEnsemble:Ensembles of Caret Models

Functions for creating ensembles of caret models: caretList() and caretStack(). caretList() is a convenience function for fitting multiple caret::train() models to the same dataset. caretStack() will make linear or non-linear combinations of these models, using a caret::train() model as a meta-model.

Maintained by Zachary A. Deane-Mayer. Last updated 3 months ago.

226 stars 11.98 score 780 scripts 1 dependents

hannameyer

CAST:'caret' Applications for Spatial-Temporal Models

Supporting functionality to run 'caret' with spatial or spatial-temporal data. 'caret' is a frequently used package for model training and prediction using machine learning. CAST includes functions to improve spatial or spatial-temporal modelling tasks using 'caret'. It includes the newly suggested 'Nearest neighbor distance matching' cross-validation to estimate the performance of spatial prediction models and allows for spatial variable selection to selects suitable predictor variables in view to their contribution to the spatial model performance. CAST further includes functionality to estimate the (spatial) area of applicability of prediction models. Methods are described in Meyer et al. (2018) <doi:10.1016/j.envsoft.2017.12.001>; Meyer et al. (2019) <doi:10.1016/j.ecolmodel.2019.108815>; Meyer and Pebesma (2021) <doi:10.1111/2041-210X.13650>; Milà et al. (2022) <doi:10.1111/2041-210X.13851>; Meyer and Pebesma (2022) <doi:10.1038/s41467-022-29838-9>; Linnenbrink et al. (2023) <doi:10.5194/egusphere-2023-1308>; Schumacher et al. (2024) <doi:10.5194/egusphere-2024-2730>. The package is described in detail in Meyer et al. (2024) <doi:10.48550/arXiv.2404.06978>.

Maintained by Hanna Meyer. Last updated 2 months ago.

autocorrelation caret feature-selection machine-learning overfitting predictive-modeling spatial spatio-temporal variable-selection

114 stars 11.85 score 298 scripts 1 dependents

prioritizr

prioritizr:Systematic Conservation Prioritization in R

Systematic conservation prioritization using mixed integer linear programming (MILP). It provides a flexible interface for building and solving conservation planning problems. Once built, conservation planning problems can be solved using a variety of commercial and open-source exact algorithm solvers. By using exact algorithm solvers, solutions can be generated that are guaranteed to be optimal (or within a pre-specified optimality gap). Furthermore, conservation problems can be constructed to optimize the spatial allocation of different management actions or zones, meaning that conservation practitioners can identify solutions that benefit multiple stakeholders. To solve large-scale or complex conservation planning problems, users should install the Gurobi optimization software (available from <https://www.gurobi.com/>) and the 'gurobi' R package (see Gurobi Installation Guide vignette for details). Users can also install the IBM CPLEX software (<https://www.ibm.com/products/ilog-cplex-optimization-studio/cplex-optimizer>) and the 'cplexAPI' R package (available at <https://github.com/cran/cplexAPI>). Additionally, the 'rcbc' R package (available at <https://github.com/dirkschumacher/rcbc>) can be used to generate solutions using the CBC optimization software (<https://github.com/coin-or/Cbc>). For further details, see Hanson et al. (2025) <doi:10.1111/cobi.14376>.

Maintained by Richard Schuster. Last updated 2 days ago.

biodiversity conservation conservation-planner optimization prioritization solver spatial cpp

124 stars 11.71 score 584 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 3 months ago.

42 stars 11.67 score 1.8k scripts 26 dependents

ateucher

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

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

Maintained by Andy Teucher. Last updated 9 months ago.

rlang

204 stars 11.64 score 2.1k scripts 18 dependents

pecanproject

PEcAn.data.atmosphere:PEcAn Functions Used for Managing Climate Driver Data

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 PECAn.data.atmosphere package converts climate driver data into a standard format for models integrated into PEcAn. As a standalone package, it provides an interface to access diverse climate data sets.

Maintained by David LeBauer. Last updated 3 days ago.

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

216 stars 11.61 score 64 scripts 14 dependents

ggseg

ggseg:Plotting Tool for Brain Atlases

Contains 'ggplot2' geom for plotting brain atlases using simple features. The largest component of the package is the data for the two built-in atlases. Mowinckel & Vidal-Piñeiro (2020) <doi:10.1177/2515245920928009>.

Maintained by Athanasia Mo Mowinckel. Last updated 2 years ago.

221 stars 11.57 score 590 scripts 14 dependents

tidymodels

stacks:Tidy Model Stacking

Model stacking is an ensemble technique that involves training a model to combine the outputs of many diverse statistical models, and has been shown to improve predictive performance in a variety of settings. 'stacks' implements a grammar for 'tidymodels'-aligned model stacking.

Maintained by Simon Couch. Last updated 5 months ago.

298 stars 11.46 score 840 scripts

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

82 stars 11.44 score 792 scripts 1 dependents

doi-usgs

nhdplusTools:NHDPlus Tools

Tools for traversing and working with National Hydrography Dataset Plus (NHDPlus) data. All methods implemented in 'nhdplusTools' are available in the NHDPlus documentation available from the US Environmental Protection Agency <https://www.epa.gov/waterdata/basic-information>.

Maintained by David Blodgett. Last updated 1 months ago.

87 stars 11.38 score 348 scripts 5 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 12 days ago.

cartography map spatial spatial-analysis

229 stars 11.32 score 414 scripts 12 dependents

inlabru-org

fmesher:Triangle Meshes and Related Geometry Tools

Generate planar and spherical triangle meshes, compute finite element calculations for 1- and 2-dimensional flat and curved manifolds with associated basis function spaces, methods for lines and polygons, and transparent handling of coordinate reference systems and coordinate transformation, including 'sf' and 'sp' geometries. The core 'fmesher' library code was originally part of the 'INLA' package, and implements parts of "Triangulations and Applications" by Hjelle and Daehlen (2006) <doi:10.1007/3-540-33261-8>.

Maintained by Finn Lindgren. Last updated 2 days ago.

cpp

16 stars 11.27 score 261 scripts 26 dependents

cran

e1071:Misc Functions of the Department of Statistics, Probability Theory Group (Formerly: E1071), TU Wien

Functions for latent class analysis, short time Fourier transform, fuzzy clustering, support vector machines, shortest path computation, bagged clustering, naive Bayes classifier, generalized k-nearest neighbour ...

Maintained by David Meyer. Last updated 6 months ago.

cpp

29 stars 11.26 score 2.0k dependents

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 10 days ago.

fortran openblas

36 stars 11.16 score 398 scripts 2 dependents

jamiemkass

ENMeval:Automated Tuning and Evaluations of Ecological Niche Models

Runs ecological niche models over all combinations of user-defined settings (i.e., tuning), performs cross validation to evaluate models, and returns data tables to aid in selection of optimal model settings that balance goodness-of-fit and model complexity. Also has functions to partition data spatially (or not) for cross validation, to plot multiple visualizations of results, to run null models to estimate significance and effect sizes of performance metrics, and to calculate range overlap between model predictions, among others. The package was originally built for Maxent models (Phillips et al. 2006, Phillips et al. 2017), but the current version allows possible extensions for any modeling algorithm. The extensive vignette, which guides users through most package functionality but unfortunately has a file size too big for CRAN, can be found here on the package's Github Pages website: <https://jamiemkass.github.io/ENMeval/articles/ENMeval-2.0-vignette.html>.

Maintained by Jamie M. Kass. Last updated 1 days ago.

49 stars 11.16 score 332 scripts 2 dependents

usepa

elevatr:Access Elevation Data from Various APIs

Several web services are available that provide access to elevation data. This package provides access to many of those services and returns elevation data either as an 'sf' simple features object from point elevation services or as a 'raster' object from raster elevation services. In future versions, 'elevatr' will drop support for 'raster' and will instead return 'terra' objects. Currently, the package supports access to the Amazon Web Services Terrain Tiles <https://registry.opendata.aws/terrain-tiles/>, the Open Topography Global Datasets API <https://opentopography.org/developers/>, and the USGS Elevation Point Query Service <https://apps.nationalmap.gov/epqs/>.

Maintained by Jeffrey Hollister. Last updated 7 months ago.

digital-elevation-model elevation-data elevatr epa mapzen-elevation-service r-language

206 stars 11.11 score 1.3k scripts 3 dependents

ropengov

eurostat:Tools for Eurostat Open Data

Tools to download data from the Eurostat database <https://ec.europa.eu/eurostat> together with search and manipulation utilities.

Maintained by Leo Lahti. Last updated 1 months ago.

ropengov eurostat eurostat-data

242 stars 11.07 score 892 scripts 4 dependents

pbs-assess

sdmTMB:Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'

Implements spatial and spatiotemporal GLMMs (Generalized Linear Mixed Effect Models) using 'TMB', 'fmesher', and the SPDE (Stochastic Partial Differential Equation) Gaussian Markov random field approximation to Gaussian random fields. One common application is for spatially explicit species distribution models (SDMs). See Anderson et al. (2024) <doi:10.1101/2022.03.24.485545>.

Maintained by Sean C. Anderson. Last updated 1 days ago.

ecology glmm spatial-analysis species-distribution-modelling tmb cpp

205 stars 11.04 score 848 scripts 1 dependents

bioc

Maaslin2:"Multivariable Association Discovery in Population-scale Meta-omics Studies"

MaAsLin2 is comprehensive R package for efficiently determining multivariable association between clinical metadata and microbial meta'omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods. MaAsLin2 is the next generation of MaAsLin.

Maintained by Lauren McIver. Last updated 5 months ago.

metagenomics software microbiome normalization biobakery bioconductor differential-abundance-analysis false-discovery-rate multiple-covariates public repeated-measures tools

133 stars 11.03 score 532 scripts 3 dependents

uupharmacometrics

xpose:Diagnostics for Pharmacometric Models

Diagnostics for non-linear mixed-effects (population) models from 'NONMEM' <https://www.iconplc.com/solutions/technologies/nonmem/>. 'xpose' facilitates data import, creation of numerical run summary and provide 'ggplot2'-based graphics for data exploration and model diagnostics.

Maintained by Benjamin Guiastrennec. Last updated 3 months ago.

diagnostics ggplot2 nonmem pharmacometrics xpose

62 stars 11.02 score 183 scripts 6 dependents

ropensci

CoordinateCleaner:Automated Cleaning of Occurrence Records from Biological Collections

Automated flagging of common spatial and temporal errors in biological and paleontological collection data, for the use in conservation, ecology and paleontology. Includes automated tests to easily flag (and exclude) records assigned to country or province centroid, the open ocean, the headquarters of the Global Biodiversity Information Facility, urban areas or the location of biodiversity institutions (museums, zoos, botanical gardens, universities). Furthermore identifies per species outlier coordinates, zero coordinates, identical latitude/longitude and invalid coordinates. Also implements an algorithm to identify data sets with a significant proportion of rounded coordinates. Especially suited for large data sets. The reference for the methodology is: Zizka et al. (2019) <doi:10.1111/2041-210X.13152>.

Maintained by Alexander Zizka. Last updated 1 years ago.

82 stars 10.93 score 306 scripts 3 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

75 stars 10.89 score 1.7k scripts 2 dependents

tidymodels

textrecipes:Extra 'Recipes' for Text Processing

Converting text to numerical features requires specifically created procedures, which are implemented as steps according to the 'recipes' package. These steps allows for tokenization, filtering, counting (tf and tfidf) and feature hashing.

Maintained by Emil Hvitfeldt. Last updated 10 days ago.

160 stars 10.86 score 964 scripts 1 dependents

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

151 stars 10.83 score 2.9k scripts 13 dependents

bioc

ANCOMBC:Microbiome differential abudance and correlation analyses with bias correction

ANCOMBC is a package containing differential abundance (DA) and correlation analyses for microbiome data. Specifically, the package includes Analysis of Compositions of Microbiomes with Bias Correction 2 (ANCOM-BC2), Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC), and Analysis of Composition of Microbiomes (ANCOM) for DA analysis, and Sparse Estimation of Correlations among Microbiomes (SECOM) for correlation analysis. Microbiome data are typically subject to two sources of biases: unequal sampling fractions (sample-specific biases) and differential sequencing efficiencies (taxon-specific biases). Methodologies included in the ANCOMBC package are designed to correct these biases and construct statistically consistent estimators.

Maintained by Huang Lin. Last updated 13 days ago.

differentialexpression microbiome normalization sequencing software ancom ancombc ancombc2 correlation differential-abundance-analysis secom

120 stars 10.79 score 406 scripts 1 dependents

thothorn

ipred:Improved Predictors

Improved predictive models by indirect classification and bagging for classification, regression and survival problems as well as resampling based estimators of prediction error.

Maintained by Torsten Hothorn. Last updated 8 months ago.

10.76 score 3.3k scripts 411 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 3 days ago.

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

75 stars 10.70 score 424 scripts 5 dependents

r-spatial

leafgl:High-Performance 'WebGl' Rendering for Package 'leaflet'

Provides bindings to the 'Leaflet.glify' JavaScript library which extends the 'leaflet' JavaScript library to render large data in the browser using 'WebGl'.

Maintained by Tim Appelhans. Last updated 5 months ago.

271 stars 10.63 score 157 scripts 27 dependents

business-science

modeltime:The Tidymodels Extension for Time Series Modeling

The time series forecasting framework for use with the 'tidymodels' ecosystem. Models include ARIMA, Exponential Smoothing, and additional time series models from the 'forecast' and 'prophet' packages. Refer to "Forecasting Principles & Practice, Second edition" (<https://otexts.com/fpp2/>). Refer to "Prophet: forecasting at scale" (<https://research.facebook.com/blog/2017/02/prophet-forecasting-at-scale/>.).

Maintained by Matt Dancho. Last updated 5 months ago.

arima data-science deep-learning ets forecasting machine-learning machine-learning-algorithms modeltime prophet tbats tidymodeling tidymodels time time-series time-series-analysis timeseries timeseries-forecasting

551 stars 10.61 score 1.1k scripts 7 dependents

jmsigner

amt:Animal Movement Tools

Manage and analyze animal movement data. The functionality of 'amt' includes methods to calculate home ranges, track statistics (e.g. step lengths, speed, or turning angles), prepare data for fitting habitat selection analyses, and simulation of space-use from fitted step-selection functions.

Maintained by Johannes Signer. Last updated 5 months ago.

41 stars 10.54 score 418 scripts

ctmm-initiative

ctmm:Continuous-Time Movement Modeling

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

Maintained by Christen H. Fleming. Last updated 9 days ago.

51 stars 10.54 score 534 scripts 4 dependents

rvalavi

blockCV:Spatial and Environmental Blocking for K-Fold and LOO Cross-Validation

Creating spatially or environmentally separated folds for cross-validation to provide a robust error estimation in spatially structured environments; Investigating and visualising the effective range of spatial autocorrelation in continuous raster covariates and point samples to find an initial realistic distance band to separate training and testing datasets spatially described in Valavi, R. et al. (2019) <doi:10.1111/2041-210X.13107>.

Maintained by Roozbeh Valavi. Last updated 5 months ago.

cross-validation spatial spatial-cross-validation spatial-modelling species-distribution-modelling cpp

113 stars 10.49 score 302 scripts 3 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

399 stars 10.47 score 460 scripts 2 dependents

r-transit

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

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

Maintained by Flavio Poletti. Last updated 2 months ago.

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

151 stars 10.47 score 272 scripts 1 dependents

petersonr

bestNormalize:Normalizing Transformation Functions

Estimate a suite of normalizing transformations, including a new adaptation of a technique based on ranks which can guarantee normally distributed transformed data if there are no ties: ordered quantile normalization (ORQ). ORQ normalization combines a rank-mapping approach with a shifted logit approximation that allows the transformation to work on data outside the original domain. It is also able to handle new data within the original domain via linear interpolation. The package is built to estimate the best normalizing transformation for a vector consistently and accurately. It implements the Box-Cox transformation, the Yeo-Johnson transformation, three types of Lambert WxF transformations, and the ordered quantile normalization transformation. It estimates the normalization efficacy of other commonly used transformations, and it allows users to specify custom transformations or normalization statistics. Finally, functionality can be integrated into a machine learning workflow via recipes.

Maintained by Ryan Andrew Peterson. Last updated 1 years ago.

39 stars 10.45 score 510 scripts 5 dependents

dicook

nullabor:Tools for Graphical Inference

Tools for visual inference. Generate null data sets and null plots using permutation and simulation. Calculate distance metrics for a lineup, and examine the distributions of metrics.

Maintained by Di Cook. Last updated 2 months ago.

57 stars 10.38 score 370 scripts 2 dependents

egeulgen

pathfindR:Enrichment Analysis Utilizing Active Subnetworks

Enrichment analysis enables researchers to uncover mechanisms underlying a phenotype. However, conventional methods for enrichment analysis do not take into account protein-protein interaction information, resulting in incomplete conclusions. 'pathfindR' is a tool for enrichment analysis utilizing active subnetworks. The main function identifies active subnetworks in a protein-protein interaction network using a user-provided list of genes and associated p values. It then performs enrichment analyses on the identified subnetworks, identifying enriched terms (i.e. pathways or, more broadly, gene sets) that possibly underlie the phenotype of interest. 'pathfindR' also offers functionalities to cluster the enriched terms and identify representative terms in each cluster, to score the enriched terms per sample and to visualize analysis results. The enrichment, clustering and other methods implemented in 'pathfindR' are described in detail in Ulgen E, Ozisik O, Sezerman OU. 2019. 'pathfindR': An R Package for Comprehensive Identification of Enriched Pathways in Omics Data Through Active Subnetworks. Front. Genet. <doi:10.3389/fgene.2019.00858>.

Maintained by Ege Ulgen. Last updated 1 months ago.

active-subnetworks enrichment pathway pathway-enrichment-analysis subnetwork

187 stars 10.38 score 138 scripts

tidymodels

themis:Extra Recipes Steps for Dealing with Unbalanced Data

A dataset with an uneven number of cases in each class is said to be unbalanced. Many models produce a subpar performance on unbalanced datasets. A dataset can be balanced by increasing the number of minority cases using SMOTE 2011 <doi:10.48550/arXiv.1106.1813>, BorderlineSMOTE 2005 <doi:10.1007/11538059_91> and ADASYN 2008 <https://ieeexplore.ieee.org/document/4633969>. Or by decreasing the number of majority cases using NearMiss 2003 <https://www.site.uottawa.ca/~nat/Workshop2003/jzhang.pdf> or Tomek link removal 1976 <https://ieeexplore.ieee.org/document/4309452>.

Maintained by Emil Hvitfeldt. Last updated 2 months ago.

143 stars 10.37 score 1.3k scripts 2 dependents

bcgov

bcdata:Search and Retrieve Data from the BC Data Catalogue

Search, query, and download tabular and 'geospatial' data from the British Columbia Data Catalogue (<https://catalogue.data.gov.bc.ca/>). Search catalogue data records based on keywords, data licence, sector, data format, and B.C. government organization. View metadata directly in R, download many data formats, and query 'geospatial' data available via the B.C. government Web Feature Service ('WFS') using 'dplyr' syntax.

Maintained by Andy Teucher. Last updated 3 days ago.

bcdc citz data-science env

83 stars 10.36 score 186 scripts 4 dependents

ludvigolsen

cvms:Cross-Validation for Model Selection

Cross-validate one or multiple regression and classification models and get relevant evaluation metrics in a tidy format. Validate the best model on a test set and compare it to a baseline evaluation. Alternatively, evaluate predictions from an external model. Currently supports regression and classification (binary and multiclass). Described in chp. 5 of Jeyaraman, B. P., Olsen, L. R., & Wambugu M. (2019, ISBN: 9781838550134).

Maintained by Ludvig Renbo Olsen. Last updated 23 days ago.

39 stars 10.31 score 492 scripts 5 dependents

bioc

pRoloc:A unifying bioinformatics framework for spatial proteomics

The pRoloc package implements machine learning and visualisation methods for the analysis and interogation of quantitiative mass spectrometry data to reliably infer protein sub-cellular localisation.

Maintained by Lisa Breckels. Last updated 2 days ago.

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

15 stars 10.31 score 101 scripts 2 dependents

hzambran

hydroGOF:Goodness-of-Fit Functions for Comparison of Simulated and Observed Hydrological Time Series

S3 functions implementing both statistical and graphical goodness-of-fit measures between observed and simulated values, mainly oriented to be used during the calibration, validation, and application of hydrological models. Missing values in observed and/or simulated values can be removed before computations. Comments / questions / collaboration of any kind are very welcomed.

Maintained by Mauricio Zambrano-Bigiarini. Last updated 11 months ago.

40 stars 10.29 score 796 scripts 8 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 3 months ago.

bayesian-inference small-area-estimation space-time

23 stars 10.28 score 134 scripts 2 dependents

bioc

EpiDISH:Epigenetic Dissection of Intra-Sample-Heterogeneity

EpiDISH is a R package to infer the proportions of a priori known cell-types present in a sample representing a mixture of such cell-types. Right now, the package can be used on DNAm data of blood-tissue of any age, from birth to old-age, generic epithelial tissue and breast tissue. Besides, the package provides a function that allows the identification of differentially methylated cell-types and their directionality of change in Epigenome-Wide Association Studies.

Maintained by Shijie C. Zheng. Last updated 5 months ago.

dnamethylation methylationarray epigenetics differentialmethylation immunooncology

48 stars 10.28 score 166 scripts 4 dependents

ropensci

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

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

Maintained by OJ Watson. Last updated 30 days ago.

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

37 stars 10.16 score 286 scripts 4 dependents

hzambran

hydroTSM:Time Series Management and Analysis for Hydrological Modelling

S3 functions for management, analysis, interpolation and plotting of time series used in hydrology and related environmental sciences. In particular, this package is highly oriented to hydrological modelling tasks. The focus of this package has been put in providing a collection of tools useful for the daily work of hydrologists (although an effort was made to optimise each function as much as possible, functionality has had priority over speed). Bugs / comments / questions / collaboration of any kind are very welcomed, and in particular, datasets that can be included in this package for academic purposes.

Maintained by Mauricio Zambrano-Bigiarini. Last updated 2 months ago.

hydrology hydrology-modeling hydrology-statistical resource water-resources

45 stars 10.14 score 340 scripts 10 dependents

bioc

SC3:Single-Cell Consensus Clustering

A tool for unsupervised clustering and analysis of single cell RNA-Seq data.

Maintained by Vladimir Kiselev. Last updated 5 months ago.

immunooncology singlecell software classification clustering dimensionreduction supportvectormachine rnaseq visualization transcriptomics datarepresentation gui differentialexpression transcription bioconductor-package human-cell-atlas single-cell-rna-seq openblas cpp

125 stars 10.10 score 374 scripts 1 dependents

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 2 months ago.

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

275 stars 10.10 score 1.1k scripts

jinseob2kim

jstable:Create Tables from Different Types of Regression

Create regression tables from generalized linear model(GLM), generalized estimating equation(GEE), generalized linear mixed-effects model(GLMM), Cox proportional hazards model, survey-weighted generalized linear model(svyglm) and survey-weighted Cox model results for publication.

Maintained by Jinseob Kim. Last updated 1 days ago.

label regression table

28 stars 10.08 score 199 scripts 1 dependents

murrayefford

secr:Spatially Explicit Capture-Recapture

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

Maintained by Murray Efford. Last updated 3 days ago.

cpp

3 stars 10.06 score 410 scripts 5 dependents

mhahsler

stream:Infrastructure for Data Stream Mining

A framework for data stream modeling and associated data mining tasks such as clustering and classification. The development of this package was supported in part by NSF IIS-0948893, NSF CMMI 1728612, and NIH R21HG005912. Hahsler et al (2017) <doi:10.18637/jss.v076.i14>.

Maintained by Michael Hahsler. Last updated 17 days ago.

data-stream-clustering datastream stream-mining cpp

39 stars 10.05 score 132 scripts 3 dependents

r-spatial

sftime:Classes and Methods for Simple Feature Objects that Have a Time Column

Classes and methods for spatial objects that have a registered time column, in particular for irregular spatiotemporal data. The time column can be of any type, but needs to be ordinal. Regularly laid out spatiotemporal data (vector or raster data cubes) are handled by package 'stars'.

Maintained by Henning Teickner. Last updated 1 months ago.

49 stars 9.99 score 27 scripts 60 dependents

ropensci

spatsoc:Group Animal Relocation Data by Spatial and Temporal Relationship

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

Maintained by Alec L. Robitaille. Last updated 2 months ago.

animal gps network social spatial

24 stars 9.97 score 145 scripts 3 dependents

pecanproject

PEcAn.assim.batch:PEcAn Functions Used for Ecological Forecasts and Reanalysis

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.

Maintained by Istem Fer. Last updated 3 days ago.

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

216 stars 9.96 score 20 scripts 2 dependents

tlverse

sl3:Pipelines for Machine Learning and Super Learning

A modern implementation of the Super Learner prediction algorithm, coupled with a general purpose framework for composing arbitrary pipelines for machine learning tasks.

Maintained by Jeremy Coyle. Last updated 5 months ago.

data-science ensemble-learning ensemble-model machine-learning model-selection regression stacking statistics

100 stars 9.94 score 748 scripts 7 dependents

umr-amap

BIOMASS:Estimating Aboveground Biomass and Its Uncertainty in Tropical Forests

Contains functions for estimating above-ground biomass/carbon and its uncertainty in tropical forests. These functions allow to (1) retrieve and correct taxonomy, (2) estimate wood density and its uncertainty, (3) build height-diameter models, (4) manage tree and plot coordinates, (5) estimate above-ground biomass/carbon at stand level with associated uncertainty. To cite ‘BIOMASS’, please use citation(‘BIOMASS’). For more information, see Réjou-Méchain et al. (2017) <doi:10.1111/2041-210X.12753>.

Maintained by Dominique Lamonica. Last updated 9 days ago.

27 stars 9.91 score 68 scripts 1 dependents

r-spatial

leafpop:Include Tables, Images and Graphs in Leaflet Pop-Ups

Creates 'HTML' strings to embed tables, images or graphs in pop-ups of interactive maps created with packages like 'leaflet' or 'mapview'. Handles local images located on the file system or via remote URL. Handles graphs created with 'lattice' or 'ggplot2' as well as interactive plots created with 'htmlwidgets'.

Maintained by Tim Appelhans. Last updated 6 months ago.

114 stars 9.87 score 458 scripts 27 dependents

thomasp85

transformr:Polygon and Path Transformations

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

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

animation data-visualization interpolation matching-shapes tweening cpp

116 stars 9.81 score 772 scripts 26 dependents

hafen

geofacet:'ggplot2' Faceting Utilities for Geographical Data

Provides geographical faceting functionality for 'ggplot2'. Geographical faceting arranges a sequence of plots of data for different geographical entities into a grid that preserves some of the geographical orientation.

Maintained by Ryan Hafen. Last updated 7 months ago.

geography ggplot2 visualization

339 stars 9.79 score 1.5k scripts 4 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

173 stars 9.73 score 342 scripts

rmaia

pavo:Perceptual Analysis, Visualization and Organization of Spectral Colour Data

A cohesive framework for the spectral and spatial analysis of colour described in Maia, Eliason, Bitton, Doucet & Shawkey (2013) <doi:10.1111/2041-210X.12069> and Maia, Gruson, Endler & White (2019) <doi:10.1111/2041-210X.13174>.

Maintained by Thomas White. Last updated 2 months ago.

72 stars 9.72 score 151 scripts 1 dependents

pecanproject

PEcAnRTM:PEcAn Functions Used for Radiative Transfer Modeling

Functions for performing forward runs and inversions of radiative transfer models (RTMs). Inversions can be performed using maximum likelihood, or more complex hierarchical Bayesian methods. Underlying numerical analyses are optimized for speed using Fortran code.

Maintained by Alexey Shiklomanov. Last updated 3 days ago.

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

216 stars 9.70 score 132 scripts

michaeldorman

nngeo:k-Nearest Neighbor Join for Spatial Data

K-nearest neighbor search for projected and non-projected 'sf' spatial layers. Nearest neighbor search uses (1) C code from 'GeographicLib' for lon-lat point layers, (2) function knn() from package 'nabor' for projected point layers, or (3) function st_distance() from package 'sf' for line or polygon layers. The package also includes several other utility functions for spatial analysis.

Maintained by Michael Dorman. Last updated 12 months ago.

81 stars 9.70 score 600 scripts 6 dependents

bblonder

hypervolume:High Dimensional Geometry, Set Operations, Projection, and Inference Using Kernel Density Estimation, Support Vector Machines, and Convex Hulls

Estimates the shape and volume of high-dimensional datasets and performs set operations: intersection / overlap, union, unique components, inclusion test, and hole detection. Uses stochastic geometry approach to high-dimensional kernel density estimation, support vector machine delineation, and convex hull generation. Applications include modeling trait and niche hypervolumes and species distribution modeling.

Maintained by Benjamin Blonder. Last updated 2 months ago.

openblas cpp

23 stars 9.69 score 211 scripts 7 dependents

sdctools

sdcMicro:Statistical Disclosure Control Methods for Anonymization of Data and Risk Estimation

Data from statistical agencies and other institutions are mostly confidential. This package, introduced in Templ, Kowarik and Meindl (2017) <doi:10.18637/jss.v067.i04>, can be used for the generation of anonymized (micro)data, i.e. for the creation of public- and scientific-use files. The theoretical basis for the methods implemented can be found in Templ (2017) <doi:10.1007/978-3-319-50272-4>. Various risk estimation and anonymization methods are included. Note that the package includes a graphical user interface published in Meindl and Templ (2019) <doi:10.3390/a12090191> that allows to use various methods of this package.

Maintained by Matthias Templ. Last updated 1 months ago.

cpp

84 stars 9.63 score 258 scripts

luukvdmeer

sfnetworks:Tidy Geospatial Networks

Provides a tidy approach to spatial network analysis, in the form of classes and functions that enable a seamless interaction between the network analysis package 'tidygraph' and the spatial analysis package 'sf'.

Maintained by Lucas van der Meer. Last updated 3 months ago.

geospatial-networks network-analysis rspatial simple-features spatial-analysis spatial-data-science spatial-networks tidygraph tidyverse

372 stars 9.63 score 332 scripts 6 dependents

business-science

anomalize:Tidy Anomaly Detection

The 'anomalize' package enables a "tidy" workflow for detecting anomalies in data. The main functions are time_decompose(), anomalize(), and time_recompose(). When combined, it's quite simple to decompose time series, detect anomalies, and create bands separating the "normal" data from the anomalous data at scale (i.e. for multiple time series). Time series decomposition is used to remove trend and seasonal components via the time_decompose() function and methods include seasonal decomposition of time series by Loess ("stl") and seasonal decomposition by piecewise medians ("twitter"). The anomalize() function implements two methods for anomaly detection of residuals including using an inner quartile range ("iqr") and generalized extreme studentized deviation ("gesd"). These methods are based on those used in the 'forecast' package and the Twitter 'AnomalyDetection' package. Refer to the associated functions for specific references for these methods.

Maintained by Matt Dancho. Last updated 1 years ago.

anomaly anomaly-detection decomposition detect-anomalies iqr time-series

339 stars 9.56 score 332 scripts

jeffreyevans

spatialEco:Spatial Analysis and Modelling Utilities

Utilities to support spatial data manipulation, query, sampling and modelling in ecological applications. Functions include models for species population density, spatial smoothing, multivariate separability, point process model for creating pseudo- absences and sub-sampling, Quadrant-based sampling and analysis, auto-logistic modeling, sampling models, cluster optimization, statistical exploratory tools and raster-based metrics.

Maintained by Jeffrey S. Evans. Last updated 26 days ago.

biodiversity conservation ecology r-spatial raster spatial vector

110 stars 9.55 score 736 scripts 2 dependents

mstrimas

smoothr:Smooth and Tidy Spatial Features

Tools for smoothing and tidying spatial features (i.e. lines and polygons) to make them more aesthetically pleasing. Smooth curves, fill holes, and remove small fragments from lines and polygons.

Maintained by Matthew Strimas-Mackey. Last updated 2 years ago.

gis spatial

100 stars 9.53 score 440 scripts 9 dependents

ndphillips

FFTrees:Generate, Visualise, and Evaluate Fast-and-Frugal Decision Trees

Create, visualize, and test fast-and-frugal decision trees (FFTs) using the algorithms and methods described by Phillips, Neth, Woike & Gaissmaier (2017), <doi:10.1017/S1930297500006239>. FFTs are simple and transparent decision trees for solving binary classification problems. FFTs can be preferable to more complex algorithms because they require very little information, are easy to understand and communicate, and are robust against overfitting.

Maintained by Hansjoerg Neth. Last updated 5 months ago.

136 stars 9.53 score 144 scripts

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 2 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

494 stars 9.50 score 384 scripts

immunomind

immunarch:Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires

A comprehensive framework for bioinformatics exploratory analysis of bulk and single-cell T-cell receptor and antibody repertoires. It provides seamless data loading, analysis and visualisation for AIRR (Adaptive Immune Receptor Repertoire) data, both bulk immunosequencing (RepSeq) and single-cell sequencing (scRNAseq). Immunarch implements most of the widely used AIRR analysis methods, such as: clonality analysis, estimation of repertoire similarities in distribution of clonotypes and gene segments, repertoire diversity analysis, annotation of clonotypes using external immune receptor databases and clonotype tracking in vaccination and cancer studies. A successor to our previously published 'tcR' immunoinformatics package (Nazarov 2015) <doi:10.1186/s12859-015-0613-1>.

Maintained by Vadim I. Nazarov. Last updated 1 years ago.

airr-analysis b-cell-receptor bcr bcr-repertoire bioinformatics ig ig-repertoire immune-repertoire immune-repertoire-analysis immune-repertoire-data immunoglobulin immunoinformatics immunology rep-seq repertoire-analysis single-cell single-cell-analysis t-cell-receptor tcr tcr-repertoire cpp

316 stars 9.49 score 203 scripts

john-d-fox

Rcmdr:R Commander

A platform-independent basic-statistics GUI (graphical user interface) for R, based on the tcltk package.

Maintained by John Fox. Last updated 5 months ago.

4 stars 9.48 score 636 scripts 38 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

106 stars 9.43 score 199 scripts 15 dependents

bioc

SpatialFeatureExperiment:Integrating SpatialExperiment with Simple Features in sf

A new S4 class integrating Simple Features with the R package sf to bring geospatial data analysis methods based on vector data to spatial transcriptomics. Also implements management of spatial neighborhood graphs and geometric operations. This pakage builds upon SpatialExperiment and SingleCellExperiment, hence methods for these parent classes can still be used.

Maintained by Lambda Moses. Last updated 2 months ago.

datarepresentation transcriptomics spatial

49 stars 9.40 score 322 scripts 1 dependents

r-barnes

dggridR:Discrete Global Grids

Spatial analyses involving binning require that every bin have the same area, but this is impossible using a rectangular grid laid over the Earth or over any projection of the Earth. Discrete global grids use hexagons, triangles, and diamonds to overcome this issue, overlaying the Earth with equally-sized bins. This package provides utilities for working with discrete global grids, along with utilities to aid in plotting such data.

Maintained by Sebastian Krantz. Last updated 6 months ago.

discrete-global-grids geospatial spatial-analysis cpp

168 stars 9.37 score 388 scripts 1 dependents

ecospat

ecospat:Spatial Ecology Miscellaneous Methods

Collection of R functions and data sets for the support of spatial ecology analyses with a focus on pre, core and post modelling analyses of species distribution, niche quantification and community assembly. Written by current and former members and collaborators of the ecospat group of Antoine Guisan, Department of Ecology and Evolution (DEE) and Institute of Earth Surface Dynamics (IDYST), University of Lausanne, Switzerland. Read Di Cola et al. (2016) <doi:10.1111/ecog.02671> for details.

Maintained by Olivier Broennimann. Last updated 2 months ago.

32 stars 9.35 score 418 scripts 1 dependents

tidymodels

embed:Extra Recipes for Encoding Predictors

Predictors can be converted to one or more numeric representations using a variety of methods. Effect encodings using simple generalized linear models <doi:10.48550/arXiv.1611.09477> or nonlinear models <doi:10.48550/arXiv.1604.06737> can be used. There are also functions for dimension reduction and other approaches.

Maintained by Emil Hvitfeldt. Last updated 2 months ago.

142 stars 9.35 score 1.1k scripts

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 3 days ago.

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

134 stars 9.34 score 95 scripts

pecanproject

PEcAn.data.land:PEcAn Functions Used for Ecological Forecasts and Reanalysis

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.

Maintained by Mike Dietze. Last updated 3 days ago.

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

216 stars 9.33 score 19 scripts 10 dependents

chrhennig

fpc:Flexible Procedures for Clustering

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

Maintained by Christian Hennig. Last updated 6 months ago.

11 stars 9.32 score 2.6k scripts 69 dependents

ipeagit

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

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

Maintained by Daniel Herszenhut. Last updated 2 months ago.

gtfs public-transport publictransport cpp

40 stars 9.31 score 126 scripts 3 dependents

microsoft

finnts:Microsoft Finance Time Series Forecasting Framework

Automated time series forecasting developed by Microsoft Finance. The Microsoft Finance Time Series Forecasting Framework, aka Finn, can be used to forecast any component of the income statement, balance sheet, or any other area of interest by finance. Any numerical quantity over time, Finn can be used to forecast it. While it can be applied outside of the finance domain, Finn was built to meet the needs of financial analysts to better forecast their businesses within a company, and has a lot of built in features that are specific to the needs of financial forecasters. Happy forecasting!

Maintained by Mike Tokic. Last updated 1 months ago.

business data-science feature-selection finance finnts forecasting machine-learning microsoft time-series

194 stars 9.30 score 39 scripts

mapme-initiative

mapme.biodiversity:Efficient Monitoring of Global Biodiversity Portfolios

Biodiversity areas, especially primary forest, serve a multitude of functions for local economy, regional functionality of the ecosystems as well as the global health of our planet. Recently, adverse changes in human land use practices and climatic responses to increased greenhouse gas emissions, put these biodiversity areas under a variety of different threats. The present package helps to analyse a number of biodiversity indicators based on freely available geographical datasets. It supports computational efficient routines that allow the analysis of potentially global biodiversity portfolios. The primary use case of the package is to support evidence based reporting of an organization's effort to protect biodiversity areas under threat and to identify regions were intervention is most duly needed.

Maintained by Darius A. Görgen. Last updated 2 days ago.

environment eo gis mapme spatial sustainability

35 stars 9.24 score 287 scripts

business-science

sweep:Tidy Tools for Forecasting

Tidies up the forecasting modeling and prediction work flow, extends the 'broom' package with 'sw_tidy', 'sw_glance', 'sw_augment', and 'sw_tidy_decomp' functions for various forecasting models, and enables converting 'forecast' objects to "tidy" data frames with 'sw_sweep'.

Maintained by Matt Dancho. Last updated 1 years ago.

broom forecast forecasting-models prediction tidy tidyverse time time-series timeseries

155 stars 9.23 score 399 scripts 1 dependents

matthias-da

robCompositions:Compositional Data Analysis

Methods for analysis of compositional data including robust methods (<doi:10.1007/978-3-319-96422-5>), imputation of missing values (<doi:10.1016/j.csda.2009.11.023>), methods to replace rounded zeros (<doi:10.1080/02664763.2017.1410524>, <doi:10.1016/j.chemolab.2016.04.011>, <doi:10.1016/j.csda.2012.02.012>), count zeros (<doi:10.1177/1471082X14535524>), methods to deal with essential zeros (<doi:10.1080/02664763.2016.1182135>), (robust) outlier detection for compositional data, (robust) principal component analysis for compositional data, (robust) factor analysis for compositional data, (robust) discriminant analysis for compositional data (Fisher rule), robust regression with compositional predictors, functional data analysis (<doi:10.1016/j.csda.2015.07.007>) and p-splines (<doi:10.1016/j.csda.2015.07.007>), contingency (<doi:10.1080/03610926.2013.824980>) and compositional tables (<doi:10.1111/sjos.12326>, <doi:10.1111/sjos.12223>, <doi:10.1080/02664763.2013.856871>) and (robust) Anderson-Darling normality tests for compositional data as well as popular log-ratio transformations (addLR, cenLR, isomLR, and their inverse transformations). In addition, visualisation and diagnostic tools are implemented as well as high and low-level plot functions for the ternary diagram.

Maintained by Matthias Templ. Last updated 1 months ago.

cpp

11 stars 9.21 score 226 scripts 2 dependents

ropensci

stats19:Work with Open Road Traffic Casualty Data from Great Britain

Tools to help download, process and analyse the UK road collision data collected using the 'STATS19' form. The datasets are provided as 'CSV' files with detailed road safety information about the circumstances of car crashes and other incidents on the roads resulting in casualties in Great Britain from 1979 to present. Tables are available on 'colissions' with the circumstances (e.g. speed limit of road), information about 'vehicles' involved (e.g. type of vehicle), and 'casualties' (e.g. age). The statistics relate only to events on public roads that were reported to the police, and subsequently recorded, using the 'STATS19' collision reporting form. See the Department for Transport website <https://www.data.gov.uk/dataset/cb7ae6f0-4be6-4935-9277-47e5ce24a11f/road-accidents-safety-data> for more information on these datasets. The package is described in a paper in the Journal of Open Source Software (Lovelace et al. 2019) <doi:10.21105/joss.01181>. See Gilardi et al. (2022) <doi:10.1111/rssa.12823>, Vidal-Tortosa et al. (2021) <doi:10.1016/j.jth.2021.101291>, and Tait et al. (2023) <doi:10.1016/j.aap.2022.106895> for examples of how the data can be used for methodological and empirical road safety research.

Maintained by Robin Lovelace. Last updated 3 months ago.

stats19 road-safety transport car-crashes ropensci data

64 stars 9.20 score 193 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

69 stars 9.18 score 259 scripts

atlasoflivingaustralia

galah:Biodiversity Data from the GBIF Node Network

The Global Biodiversity Information Facility ('GBIF', <https://www.gbif.org>) sources data from an international network of data providers, known as 'nodes'. Several of these nodes - the "living atlases" (<https://living-atlases.gbif.org>) - maintain their own web services using software originally developed by the Atlas of Living Australia ('ALA', <https://www.ala.org.au>). 'galah' enables the R community to directly access data and resources hosted by 'GBIF' and its partner nodes.

Maintained by Martin Westgate. Last updated 2 months ago.

43 stars 9.17 score 275 scripts 1 dependents

alanarnholt

BSDA:Basic Statistics and Data Analysis

Data sets for book "Basic Statistics and Data Analysis" by Larry J. Kitchens.

Maintained by Alan T. Arnholt. Last updated 2 years ago.

7 stars 9.11 score 1.3k scripts 6 dependents

stscl

gdverse:Analysis of Spatial Stratified Heterogeneity

Detecting spatial associations based on the concept of spatial stratified heterogeneity while also considering spatial dependencies, spatial interpretability, complex spatial interactions, and robust spatial stratification. In addition, it supports the spatial stratified heterogeneity family described in Lv et al. (2025)<doi:10.1111/tgis.70032>.

Maintained by Wenbo Lv. Last updated 11 hours ago.

geographical-detector geoinformatics geospatial-analysis spatial-statistics spatial-stratified-heterogeneity cpp

33 stars 9.10 score 41 scripts 2 dependents

malaria-atlas-project

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

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

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

database malaria opendata raster

44 stars 9.10 score 118 scripts 3 dependents

huizezhang-sherry

cubble:A Vector Spatio-Temporal Data Structure for Data Analysis

A spatiotemperal data object in a relational data structure to separate the recording of time variant/ invariant variables. See the Journal of Statistical Software reference: <doi:10.18637/jss.v110.i07>.

Maintained by H. Sherry Zhang. Last updated 6 months ago.

57 stars 9.07 score 83 scripts

joelgombin

concaveman:A Very Fast 2D Concave Hull Algorithm

The concaveman function ports the 'concaveman' (<https://github.com/mapbox/concaveman>) library from 'mapbox'. It computes the concave polygon(s) for one or several set of points.

Maintained by Joël Gombin. Last updated 3 years ago.

concave-hull spatial

66 stars 9.06 score 492 scripts 22 dependents

eblondel

ows4R:Interface to OGC Web-Services (OWS)

Provides an Interface to Web-Services defined as standards by the Open Geospatial Consortium (OGC), including Web Feature Service (WFS) for vector data, Web Coverage Service (WCS), Catalogue Service (CSW) for ISO/OGC metadata, Web Processing Service (WPS) for data processes, and associated standards such as the common web-service specification (OWS) and OGC Filter Encoding. Partial support is provided for the Web Map Service (WMS). The purpose is to add support for additional OGC service standards such as Web Coverage Processing Service (WCPS), the Sensor Observation Service (SOS), or even new standard services emerging such OGC API or SensorThings.

Maintained by Emmanuel Blondel. Last updated 2 months ago.

catalogue-service csw dataaccess fes geospatial iso ogc ows sdi spatial spatial-data standard webfeatureservice wfs

38 stars 9.03 score 99 scripts 5 dependents

ronkeizer

vpc:Create Visual Predictive Checks

Visual predictive checks are a commonly used diagnostic plot in pharmacometrics, showing how certain statistics (percentiles) for observed data compare to those same statistics for data simulated from a model. The package can generate VPCs for continuous, categorical, censored, and (repeated) time-to-event data.

Maintained by Ron Keizer. Last updated 10 months ago.

36 stars 9.01 score 318 scripts 11 dependents

pecanproject

PEcAn.all:PEcAn Functions Used for Ecological Forecasts and Reanalysis

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.

Maintained by David LeBauer. Last updated 3 days ago.

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

216 stars 9.00 score 266 scripts

bioc

scone:Single Cell Overview of Normalized Expression data

SCONE is an R package for comparing and ranking the performance of different normalization schemes for single-cell RNA-seq and other high-throughput analyses.

Maintained by Davide Risso. Last updated 1 months ago.

immunooncology normalization preprocessing qualitycontrol geneexpression rnaseq software transcriptomics sequencing singlecell coverage

53 stars 9.00 score 104 scripts

mlverse

tabnet:Fit 'TabNet' Models for Classification and Regression

Implements the 'TabNet' model by Sercan O. Arik et al. (2019) <doi:10.48550/arXiv.1908.07442> with 'Coherent Hierarchical Multi-label Classification Networks' by Giunchiglia et al. <doi:10.48550/arXiv.2010.10151> and provides a consistent interface for fitting and creating predictions. It's also fully compatible with the 'tidymodels' ecosystem.

Maintained by Christophe Regouby. Last updated 6 months ago.

tabnet

109 stars 9.00 score 65 scripts

r-spatial

link2GI:Linking Geographic Information Systems, Remote Sensing and Other Command Line Tools

Functions and tools for using open GIS and remote sensing command-line interfaces in a reproducible environment.

Maintained by Chris Reudenbach. Last updated 4 months ago.

26 stars 8.99 score 78 scripts 1 dependents

pecanproject

PEcAn.MAAT:PEcAn Package for Integration of the MAAT Model

This module provides functions to wrap the MAAT model into the PEcAn workflows.

Maintained by Shawn Serbin. Last updated 3 days ago.

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

216 stars 8.96 score 12 scripts

sym33

RecordLinkage:Record Linkage Functions for Linking and Deduplicating Data Sets

Provides functions for linking and deduplicating data sets. Methods based on a stochastic approach are implemented as well as classification algorithms from the machine learning domain. For details, see our paper "The RecordLinkage Package: Detecting Errors in Data" Sariyar M / Borg A (2010) <doi:10.32614/RJ-2010-017>.

Maintained by Murat Sariyar. Last updated 2 years ago.

6 stars 8.96 score 454 scripts 8 dependents

bioc

schex:Hexbin plots for single cell omics data

Builds hexbin plots for variables and dimension reduction stored in single cell omics data such as SingleCellExperiment. The ideas used in this package are based on the excellent work of Dan Carr, Nicholas Lewin-Koh, Martin Maechler and Thomas Lumley.

Maintained by Saskia Freytag. Last updated 5 months ago.

software sequencing singlecell dimensionreduction visualization immunooncology dataimport

74 stars 8.96 score 102 scripts 2 dependents

sachaepskamp

bootnet:Bootstrap Methods for Various Network Estimation Routines

Bootstrap methods to assess accuracy and stability of estimated network structures and centrality indices <doi:10.3758/s13428-017-0862-1>. Allows for flexible specification of any undirected network estimation procedure in R, and offers default sets for various estimation routines.

Maintained by Sacha Epskamp. Last updated 5 months ago.

32 stars 8.94 score 155 scripts 3 dependents

ropensci

opentripplanner:Setup and connect to 'OpenTripPlanner'

Setup and connect to 'OpenTripPlanner' (OTP) <http://www.opentripplanner.org/>. OTP is an open source platform for multi-modal and multi-agency journey planning written in 'Java'. The package allows you to manage a local version or connect to remote OTP server to find walking, cycling, driving, or transit routes. This package has been peer-reviewed by rOpenSci (v. 0.2.0.0).

Maintained by Malcolm Morgan. Last updated 3 months ago.

data isochrones java opentripplanner otp public-transport routing transport transportation-planning

83 stars 8.94 score 147 scripts

pecanproject

PEcAn.BIOCRO:PEcAn Package for Integration of the BioCro Model

This module provides functions to link BioCro to PEcAn.

Maintained by David LeBauer. Last updated 3 days ago.

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

216 stars 8.94 score 23 scripts

usepa

spsurvey:Spatial Sampling Design and Analysis

A design-based approach to statistical inference, with a focus on spatial data. Spatially balanced samples are selected using the Generalized Random Tessellation Stratified (GRTS) algorithm. The GRTS algorithm can be applied to finite resources (point geometries) and infinite resources (linear / linestring and areal / polygon geometries) and flexibly accommodates a diverse set of sampling design features, including stratification, unequal inclusion probabilities, proportional (to size) inclusion probabilities, legacy (historical) sites, a minimum distance between sites, and two options for replacement sites (reverse hierarchical order and nearest neighbor). Data are analyzed using a wide range of analysis functions that perform categorical variable analysis, continuous variable analysis, attributable risk analysis, risk difference analysis, relative risk analysis, change analysis, and trend analysis. spsurvey can also be used to summarize objects, visualize objects, select samples that are not spatially balanced, select panel samples, measure the amount of spatial balance in a sample, adjust design weights, and more. For additional details, see Dumelle et al. (2023) <doi:10.18637/jss.v105.i03>.

Maintained by Michael Dumelle. Last updated 7 months ago.

ord

15 stars 8.94 score 241 scripts 1 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 11 days ago.

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

42 stars 8.88 score 244 scripts 2 dependents

pedrohcgs

DRDID:Doubly Robust Difference-in-Differences Estimators

Implements the locally efficient doubly robust difference-in-differences (DiD) estimators for the average treatment effect proposed by Sant'Anna and Zhao (2020) <doi:10.1016/j.jeconom.2020.06.003>. The estimator combines inverse probability weighting and outcome regression estimators (also implemented in the package) to form estimators with more attractive statistical properties. Two different estimation methods can be used to estimate the nuisance functions.

Maintained by Pedro H. C. SantAnna. Last updated 6 months ago.

cpp

92 stars 8.88 score 133 scripts 5 dependents

chris-prener

areal:Areal Weighted Interpolation

A pipeable, transparent implementation of areal weighted interpolation with support for interpolating multiple variables in a single function call. These tools provide a full-featured workflow for validation and estimation that fits into both modern data management (e.g. tidyverse) and spatial data (e.g. sf) frameworks.

Maintained by Christopher Prener. Last updated 3 years ago.

93 stars 8.88 score 106 scripts 4 dependents

macroecology

letsR:Data Handling and Analysis in Macroecology

Handling, processing, and analyzing geographic data on species' distributions and environmental variables. Read Vilela & Villalobos (2015) <doi:10.1111/2041-210X.12401> for details.

Maintained by Bruno Vilela. Last updated 3 months ago.

29 stars 8.87 score 104 scripts

ropensci

nlrx:Setup, Run and Analyze 'NetLogo' Model Simulations from 'R' via 'XML'

Setup, run and analyze 'NetLogo' (<https://ccl.northwestern.edu/netlogo/>) model simulations in 'R'. 'nlrx' experiments use a similar structure as 'NetLogos' Behavior Space experiments. However, 'nlrx' offers more flexibility and additional tools for running and analyzing complex simulation designs and sensitivity analyses. The user defines all information that is needed in an intuitive framework, using class objects. Experiments are submitted from 'R' to 'NetLogo' via 'XML' files that are dynamically written, based on specifications defined by the user. By nesting model calls in future environments, large simulation design with many runs can be executed in parallel. This also enables simulating 'NetLogo' experiments on remote high performance computing machines. In order to use this package, 'Java' and 'NetLogo' (>= 5.3.1) need to be available on the executing system.

Maintained by Sebastian Hanss. Last updated 7 months ago.

agent-based-modeling individual-based-modelling netlogo peer-reviewed

78 stars 8.86 score 195 scripts

usdaforestservice

FIESTA:Forest Inventory Estimation and Analysis

A research estimation tool for analysts that work with sample-based inventory data from the U.S. Department of Agriculture, Forest Service, Forest Inventory and Analysis (FIA) Program.

Maintained by Grayson White. Last updated 3 days ago.

30 stars 8.84 score 62 scripts

pecanproject

PEcAn.workflow:PEcAn Functions Used for Ecological Forecasts and Reanalysis

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 package provides workhorse functions that can be used to run the major steps of a PEcAn analysis.

Maintained by David LeBauer. Last updated 3 days ago.

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

216 stars 8.83 score 15 scripts 4 dependents

evolecolgroup

tidysdm:Species Distribution Models with Tidymodels

Fit species distribution models (SDMs) using the 'tidymodels' framework, which provides a standardised interface to define models and process their outputs. 'tidysdm' expands 'tidymodels' by providing methods for spatial objects, models and metrics specific to SDMs, as well as a number of specialised functions to process occurrences for contemporary and palaeo datasets. The full functionalities of the package are described in Leonardi et al. (2023) <doi:10.1101/2023.07.24.550358>.

Maintained by Andrea Manica. Last updated 23 days ago.

species-distribution-modelling tidymodels

31 stars 8.82 score 51 scripts

bioc

scmap:A tool for unsupervised projection of single cell RNA-seq data

Single-cell RNA-seq (scRNA-seq) is widely used to investigate the composition of complex tissues since the technology allows researchers to define cell-types using unsupervised clustering of the transcriptome. However, due to differences in experimental methods and computational analyses, it is often challenging to directly compare the cells identified in two different experiments. scmap is a method for projecting cells from a scRNA-seq experiment on to the cell-types or individual cells identified in a different experiment.

Maintained by Vladimir Kiselev. Last updated 5 months ago.

immunooncology singlecell software classification supportvectormachine rnaseq visualization transcriptomics datarepresentation transcription sequencing preprocessing geneexpression dataimport bioconductor-package human-cell-atlas projection-mapping single-cell-rna-seq openblas cpp

95 stars 8.82 score 172 scripts

connordonegan

geostan:Bayesian Spatial Analysis

For spatial data analysis; provides exploratory spatial analysis tools, spatial regression, spatial econometric, and disease mapping models, model diagnostics, and special methods for inference with small area survey data (e.g., the America Community Survey (ACS)) and censored population health monitoring data. Models are pre-specified using the Stan programming language, a platform for Bayesian inference using Markov chain Monte Carlo (MCMC). References: Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>; Donegan (2021) <doi:10.31219/osf.io/3ey65>; Donegan (2022) <doi:10.21105/joss.04716>; Donegan, Chun and Hughes (2020) <doi:10.1016/j.spasta.2020.100450>; Donegan, Chun and Griffith (2021) <doi:10.3390/ijerph18136856>; Morris et al. (2019) <doi:10.1016/j.sste.2019.100301>.

Maintained by Connor Donegan. Last updated 3 months ago.

bayesian bayesian-inference bayesian-statistics epidemiology modeling public-health rspatial spatial stan cpp

80 stars 8.80 score 46 scripts

ebird

ebirdst:Access and Analyze eBird Status and Trends Data Products

Tools for accessing and analyzing eBird Status and Trends Data Products (<https://science.ebird.org/en/status-and-trends>). eBird (<https://ebird.org/home>) is a global database of bird observations collected by member of the public. eBird Status and Trends uses these data to model global bird distributions, abundances, and population trends at a high spatial and temporal resolution.

Maintained by Matthew Strimas-Mackey. Last updated 1 months ago.

26 stars 8.77 score 228 scripts

pecanproject

PEcAn.data.remote:PEcAn Functions Used for Extracting Remote Sensing Data

PEcAn module for processing remote data. Python module requirements: requests, json, re, ast, panads, sys. If any of these modules are missing, install using pip install <module name>.

Maintained by Bailey Morrison. Last updated 3 days ago.

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

216 stars 8.75 score 6 scripts 5 dependents

pecanproject

PEcAn.ED2:PEcAn Package for Integration of ED2 Model

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 package provides functions to link the Ecosystem Demography Model, version 2, to PEcAn.

Maintained by Mike Dietze. Last updated 3 days ago.

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

216 stars 8.74 score 145 scripts

atmoschem

vein:Vehicular Emissions Inventories

Elaboration of vehicular emissions inventories, consisting in four stages, pre-processing activity data, preparing emissions factors, estimating the emissions and post-processing of emissions in maps and databases. More details in Ibarra-Espinosa et al (2018) <doi:10.5194/gmd-11-2209-2018>. Before using VEIN you need to know the vehicular composition of your study area, in other words, the combination of of type of vehicles, size and fuel of the fleet. Then, it is recommended to start with the project to download a template to create a structure of directories and scripts.

Maintained by Sergio Ibarra-Espinosa. Last updated 21 hours ago.

atmoschem atmospheric-chemistry atmospheric-science atmospheric-sciences emissions emissions-model vehicular-emissions-inventories vein fortran openmp

46 stars 8.73 score 137 scripts

sjewo

cartogram:Create Cartograms with R

Construct continuous and non-contiguous area cartograms.

Maintained by Sebastian Jeworutzki. Last updated 3 months ago.

149 stars 8.72 score 732 scripts 3 dependents

r-spatial

RSAGA:SAGA Geoprocessing and Terrain Analysis

Provides access to geocomputing and terrain analysis functions of the geographical information system (GIS) 'SAGA' (System for Automated Geoscientific Analyses) from within R by running the command line version of SAGA. This package furthermore provides several R functions for handling ASCII grids, including a flexible framework for applying local functions (including predict methods of fitted models) and focal functions to multiple grids. SAGA GIS is available under GPL-2 / LGPL-2 licences from <https://sourceforge.net/projects/saga-gis/>.

Maintained by Alexander Brenning. Last updated 2 months ago.

23 stars 8.72 score 275 scripts

bioc

Voyager:From geospatial to spatial omics

SpatialFeatureExperiment (SFE) is a new S4 class for working with spatial single-cell genomics data. The voyager package implements basic exploratory spatial data analysis (ESDA) methods for SFE. Univariate methods include univariate global spatial ESDA methods such as Moran's I, permutation testing for Moran's I, and correlograms. Bivariate methods include Lee's L and cross variogram. Multivariate methods include MULTISPATI PCA and multivariate local Geary's C recently developed by Anselin. The Voyager package also implements plotting functions to plot SFE data and ESDA results.

Maintained by Lambda Moses. Last updated 3 months ago.

geneexpression spatial transcriptomics visualization bioconductor eda esda exploratory-data-analysis omics spatial-statistics spatial-transcriptomics

88 stars 8.71 score 173 scripts

adokter

bioRad:Biological Analysis and Visualization of Weather Radar Data

Extract, visualize and summarize aerial movements of birds and insects from weather radar data. See Dokter, A. M. et al. (2018) "bioRad: biological analysis and visualization of weather radar data" <doi:10.1111/ecog.04028> for a software paper describing package and methodologies.

Maintained by Adriaan M. Dokter. Last updated 4 days ago.

aeroecology enram eumetnet-opera lifewatch movement-ecology nexrad oscibio radar weather-radar wsr-88d

29 stars 8.70 score 56 scripts

munterfi

hereR:'sf'-Based Interface to the 'HERE' REST APIs

Interface to the 'HERE' REST APIs <https://developer.here.com/develop/rest-apis>: (1) geocode and autosuggest addresses or reverse geocode POIs using the 'Geocoder' API; (2) route directions, travel distance or time matrices and isolines using the 'Routing', 'Matrix Routing' and 'Isoline Routing' APIs; (3) request real-time traffic flow and incident information from the 'Traffic' API; (4) find request public transport connections and nearby stations from the 'Public Transit' API; (5) request intermodal routes using the 'Intermodal Routing' API; (6) get weather forecasts, reports on current weather conditions, astronomical information and alerts at a specific location from the 'Destination Weather' API. Locations, routes and isolines are returned as 'sf' objects.

Maintained by Merlin Unterfinger. Last updated 1 months ago.

api geocoding gis here-technologies isoline routing rspatial traffic weather

91 stars 8.70 score 63 scripts

andrewzm

FRK:Fixed Rank Kriging

A tool for spatial/spatio-temporal modelling and prediction with large datasets. The approach models the field, and hence the covariance function, using a set of basis functions. This fixed-rank basis-function representation facilitates the modelling of big data, and the method naturally allows for non-stationary, anisotropic covariance functions. Discretisation of the spatial domain into so-called basic areal units (BAUs) facilitates the use of observations with varying support (i.e., both point-referenced and areal supports, potentially simultaneously), and prediction over arbitrary user-specified regions. `FRK` also supports inference over various manifolds, including the 2D plane and 3D sphere, and it provides helper functions to model, fit, predict, and plot with relative ease. Version 2.0.0 and above also supports the modelling of non-Gaussian data (e.g., Poisson, binomial, negative-binomial, gamma, and inverse-Gaussian) by employing a generalised linear mixed model (GLMM) framework. Zammit-Mangion and Cressie <doi:10.18637/jss.v098.i04> describe `FRK` in a Gaussian setting, and detail its use of basis functions and BAUs, while Sainsbury-Dale, Zammit-Mangion, and Cressie <doi:10.18637/jss.v108.i10> describe `FRK` in a non-Gaussian setting; two vignettes are available that summarise these papers and provide additional examples.

Maintained by Andrew Zammit-Mangion. Last updated 6 months ago.

cpp

71 stars 8.70 score 188 scripts 1 dependents

jinseob2kim

jsmodule:'RStudio' Addins and 'Shiny' Modules for Medical Research

'RStudio' addins and 'Shiny' modules for descriptive statistics, regression and survival analysis.

Maintained by Jinseob Kim. Last updated 12 days ago.

medical rstudio-addins shiny shiny-modules statistics

21 stars 8.69 score 61 scripts

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

65 stars 8.65 score 128 scripts

mobiodiv

mobr:Measurement of Biodiversity

Functions for calculating metrics for the measurement biodiversity and its changes across scales, treatments, and gradients. The methods implemented in this package are described in: Chase, J.M., et al. (2018) <doi:10.1111/ele.13151>, McGlinn, D.J., et al. (2019) <doi:10.1111/2041-210X.13102>, McGlinn, D.J., et al. (2020) <doi:10.1101/851717>, and McGlinn, D.J., et al. (2023) <doi:10.1101/2023.09.19.558467>.

Maintained by Daniel McGlinn. Last updated 9 days ago.

biodiversity conservation ecology rarefaction species statistics

23 stars 8.65 score 93 scripts

jniedballa

camtrapR:Camera Trap Data Management and Preparation of Occupancy and Spatial Capture-Recapture Analyses

Management of and data extraction from camera trap data in wildlife studies. The package provides a workflow for storing and sorting camera trap photos (and videos), tabulates records of species and individuals, and creates detection/non-detection matrices for occupancy and spatial capture-recapture analyses with great flexibility. In addition, it can visualise species activity data and provides simple mapping functions with GIS export.

Maintained by Juergen Niedballa. Last updated 4 months ago.

occupancy-modeling spatial-capture-recapture wildlife

35 stars 8.65 score 178 scripts

bcgov

bcmaps:Map Layers and Spatial Utilities for British Columbia

Various layers of B.C., including administrative boundaries, natural resource management boundaries, census boundaries etc. All layers are available in BC Albers (<https://spatialreference.org/ref/epsg/3005/>) equal-area projection, which is the B.C. government standard. The layers are sourced from the British Columbia and Canadian government under open licenses, including B.C. Data Catalogue (<https://data.gov.bc.ca>), the Government of Canada Open Data Portal (<https://open.canada.ca/en/using-open-data>), and Statistics Canada (<https://www.statcan.gc.ca/en/reference/licence>).

Maintained by Andy Teucher. Last updated 3 months ago.

data-science env

73 stars 8.65 score 254 scripts

projectmosaic

mosaicCalc:R-Language Based Calculus Operations for Teaching

Software to support the introductory *MOSAIC Calculus* textbook <https://www.mosaic-web.org/MOSAIC-Calculus/>), one of many data- and modeling-oriented educational resources developed by Project MOSAIC (<https://www.mosaic-web.org/>). Provides symbolic and numerical differentiation and integration, as well as support for applied linear algebra (for data science), and differential equations/dynamics. Includes grammar-of-graphics-based functions for drawing vector fields, trajectories, etc. The software is suitable for general use, but intended mainly for teaching calculus.

Maintained by Daniel Kaplan. Last updated 1 months ago.

13 stars 8.63 score 546 scripts

computationalstylistics

stylo:Stylometric Multivariate Analyses

Supervised and unsupervised multivariate methods, supplemented by GUI and some visualizations, to perform various analyses in the field of computational stylistics, authorship attribution, etc. For further reference, see Eder et al. (2016), <https://journal.r-project.org/archive/2016/RJ-2016-007/index.html>. You are also encouraged to visit the Computational Stylistics Group's website <https://computationalstylistics.github.io/>, where a reasonable amount of information about the package and related projects are provided.

Maintained by Maciej Eder. Last updated 3 months ago.

187 stars 8.58 score 462 scripts

uclahs-cds

BoutrosLab.plotting.general:Functions to Create Publication-Quality Plots

Contains several plotting functions such as barplots, scatterplots, heatmaps, as well as functions to combine plots and assist in the creation of these plots. These functions will give users great ease of use and customization options in broad use for biomedical applications, as well as general purpose plotting. Each of the functions also provides valid default settings to make plotting data more efficient and producing high quality plots with standard colour schemes simpler. All functions within this package are capable of producing plots that are of the quality to be presented in scientific publications and journals. P'ng et al.; BPG: Seamless, automated and interactive visualization of scientific data; BMC Bioinformatics 2019 <doi:10.1186/s12859-019-2610-2>.

Maintained by Paul Boutros. Last updated 8 days ago.

12 stars 8.57 score 414 scripts 7 dependents

philipmostert

PointedSDMs:Fit Models Derived from Point Processes to Species Distributions using 'inlabru'

Integrated species distribution modeling is a rising field in quantitative ecology thanks to significant rises in the quantity of data available, increases in computational speed and the proven benefits of using such models. Despite this, the general software to help ecologists construct such models in an easy-to-use framework is lacking. We therefore introduce the R package 'PointedSDMs': which provides the tools to help ecologists set up integrated models and perform inference on them. There are also functions within the package to help run spatial cross-validation for model selection, as well as generic plotting and predicting functions. An introduction to these methods is discussed in Issac, Jarzyna, Keil, Dambly, Boersch-Supan, Browning, Freeman, Golding, Guillera-Arroita, Henrys, Jarvis, Lahoz-Monfort, Pagel, Pescott, Schmucki, Simmonds and O’Hara (2020) <doi:10.1016/j.tree.2019.08.006>.

Maintained by Philip Mostert. Last updated 3 months ago.

25 stars 8.57 score 50 scripts 1 dependents

riatelab

osrm:Interface Between R and the OpenStreetMap-Based Routing Service OSRM

An interface between R and the 'OSRM' API. 'OSRM' is a routing service based on 'OpenStreetMap' data. See <http://project-osrm.org/> for more information. This package enables the computation of routes, trips, isochrones and travel distances matrices (travel time and kilometric distance).

Maintained by Timothée Giraud. Last updated 5 days ago.

openstreetmap osrm shortest-paths travel

240 stars 8.57 score 452 scripts

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.

122 stars 8.53 score 466 scripts

doi-usgs

hydroloom:Utilities to Weave Hydrologic Fabrics

A collection of utilities that support creation of network attributes for hydrologic networks. Methods and algorithms implemented are documented in Moore et al. (2019) <doi:10.3133/ofr20191096>), Cormen and Leiserson (2022) <ISBN:9780262046305> and Verdin and Verdin (1999) <doi:10.1016/S0022-1694(99)00011-6>.

Maintained by David Blodgett. Last updated 2 months ago.

28 stars 8.53 score 19 scripts 6 dependents

palaeoverse

palaeoverse:Prepare and Explore Data for Palaeobiological Analyses

Provides functionality to support data preparation and exploration for palaeobiological analyses, improving code reproducibility and accessibility. The wider aim of 'palaeoverse' is to bring the palaeobiological community together to establish agreed standards. The package currently includes functionality for data cleaning, binning (time and space), exploration, summarisation and visualisation. Reference datasets (i.e. Geological Time Scales <https://stratigraphy.org/chart>) and auxiliary functions are also provided. Details can be found in: Jones et al., (2023) <doi: 10.1111/2041-210X.14099>.

Maintained by Lewis A. Jones. Last updated 5 months ago.

biodiversity fossil palaeobiology paleobiology

21 stars 8.51 score 44 scripts 1 dependents

hmorlon

RPANDA:Phylogenetic ANalyses of DiversificAtion

Implements macroevolutionary analyses on phylogenetic trees. See Morlon et al. (2010) <DOI:10.1371/journal.pbio.1000493>, Morlon et al. (2011) <DOI:10.1073/pnas.1102543108>, Condamine et al. (2013) <DOI:10.1111/ele.12062>, Morlon et al. (2014) <DOI:10.1111/ele.12251>, Manceau et al. (2015) <DOI:10.1111/ele.12415>, Lewitus & Morlon (2016) <DOI:10.1093/sysbio/syv116>, Drury et al. (2016) <DOI:10.1093/sysbio/syw020>, Manceau et al. (2016) <DOI:10.1093/sysbio/syw115>, Morlon et al. (2016) <DOI:10.1111/2041-210X.12526>, Clavel & Morlon (2017) <DOI:10.1073/pnas.1606868114>, Drury et al. (2017) <DOI:10.1093/sysbio/syx079>, Lewitus & Morlon (2017) <DOI:10.1093/sysbio/syx095>, Drury et al. (2018) <DOI:10.1371/journal.pbio.2003563>, Clavel et al. (2019) <DOI:10.1093/sysbio/syy045>, Maliet et al. (2019) <DOI:10.1038/s41559-019-0908-0>, Billaud et al. (2019) <DOI:10.1093/sysbio/syz057>, Lewitus et al. (2019) <DOI:10.1093/sysbio/syz061>, Aristide & Morlon (2019) <DOI:10.1111/ele.13385>, Maliet et al. (2020) <DOI:10.1111/ele.13592>, Drury et al. (2021) <DOI:10.1371/journal.pbio.3001270>, Perez-Lamarque & Morlon (2022) <DOI:10.1111/mec.16478>, Perez-Lamarque et al. (2022) <DOI:10.1101/2021.08.30.458192>, Mazet et al. (2023) <DOI:10.1111/2041-210X.14195>, Drury et al. (2024) <DOI:10.1016/j.cub.2023.12.055>.

Maintained by Hélène Morlon. Last updated 3 months ago.

24 stars 8.50 score 255 scripts

ropensci

weatherOz:An API Client for Australian Weather and Climate Data Resources

Provides automated downloading, parsing and formatting of weather data for Australia through API endpoints provided by the Department of Primary Industries and Regional Development ('DPIRD') of Western Australia and by the Science and Technology Division of the Queensland Government's Department of Environment and Science ('DES'). As well as the Bureau of Meteorology ('BOM') of the Australian government precis and coastal forecasts, and downloading and importing radar and satellite imagery files. 'DPIRD' weather data are accessed through public 'APIs' provided by 'DPIRD', <https://www.agric.wa.gov.au/weather-api-20>, providing access to weather station data from the 'DPIRD' weather station network. Australia-wide weather data are based on data from the Australian Bureau of Meteorology ('BOM') data and accessed through 'SILO' (Scientific Information for Land Owners) Jeffrey et al. (2001) <doi:10.1016/S1364-8152(01)00008-1>. 'DPIRD' data are made available under a Creative Commons Attribution 3.0 Licence (CC BY 3.0 AU) license <https://creativecommons.org/licenses/by/3.0/au/deed.en>. SILO data are released under a Creative Commons Attribution 4.0 International licence (CC BY 4.0) <https://creativecommons.org/licenses/by/4.0/>. 'BOM' data are (c) Australian Government Bureau of Meteorology and released under a Creative Commons (CC) Attribution 3.0 licence or Public Access Licence ('PAL') as appropriate, see <http://www.bom.gov.au/other/copyright.shtml> for further details.

Maintained by Rodrigo Pires. Last updated 1 months ago.

dpird bom meteorological-data weather-forecast australia weather weather-data meteorology western-australia australia-bureau-of-meteorology western-australia-agriculture australia-agriculture australia-climate australia-weather api-client climate data rainfall weather-api

31 stars 8.47 score 40 scripts

bmcclintock

momentuHMM:Maximum Likelihood Analysis of Animal Movement Behavior Using Multivariate Hidden Markov Models

Extended tools for analyzing telemetry data using generalized hidden Markov models. Features of momentuHMM (pronounced ``momentum'') include data pre-processing and visualization, fitting HMMs to location and auxiliary biotelemetry or environmental data, biased and correlated random walk movement models, discrete- or continuous-time HMMs, continuous- or discrete-space movement models, approximate Langevin diffusion models, hierarchical HMMs, multiple imputation for incorporating location measurement error and missing data, user-specified design matrices and constraints for covariate modelling of parameters, random effects, decoding of the state process, visualization of fitted models, model checking and selection, and simulation. See McClintock and Michelot (2018) <doi:10.1111/2041-210X.12995>.

Maintained by Brett McClintock. Last updated 1 months ago.

openblas cpp

43 stars 8.47 score 162 scripts

bioc

survcomp:Performance Assessment and Comparison for Survival Analysis

Assessment and Comparison for Performance of Risk Prediction (Survival) Models.

Maintained by Benjamin Haibe-Kains. Last updated 5 months ago.

geneexpression differentialexpression visualization cpp

8.46 score 448 scripts 12 dependents

tidymodels

tidyposterior:Bayesian Analysis to Compare Models using Resampling Statistics

Bayesian analysis used here to answer the question: "when looking at resampling results, are the differences between models 'real'?" To answer this, a model can be created were the performance statistic is the resampling statistics (e.g. accuracy or RMSE). These values are explained by the model types. In doing this, we can get parameter estimates for each model's affect on performance and make statistical (and practical) comparisons between models. The methods included here are similar to Benavoli et al (2017) <https://jmlr.org/papers/v18/16-305.html>.

Maintained by Max Kuhn. Last updated 5 months ago.

102 stars 8.44 score 273 scripts

markvanderloo

simputation:Simple Imputation

Easy to use interfaces to a number of imputation methods that fit in the not-a-pipe operator of the 'magrittr' package.

Maintained by Mark van der Loo. Last updated 8 months ago.

data-science imputation officialstatistics

91 stars 8.42 score 350 scripts

trevorld

gridpattern:'grid' Pattern Grobs

Provides 'grid' grobs that fill in a user-defined area with various patterns. Includes enhanced versions of the geometric and image-based patterns originally contained in the 'ggpattern' package as well as original 'pch', 'polygon_tiling', 'regular_polygon', 'rose', 'text', 'wave', and 'weave' patterns plus support for custom user-defined patterns.

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

33 stars 8.42 score 4 scripts 4 dependents

obrl-soil

h3jsr:Access Uber's H3 Library

Provides access to Uber's H3 library for geospatial indexing via its JavaScript transpile 'h3-js' <https://github.com/uber/h3-js> and 'V8' <https://github.com/jeroen/v8>.

Maintained by Lauren OBrien. Last updated 1 years ago.

discrete-global-grids h3 spatial-indexing

67 stars 8.39 score 205 scripts 4 dependents

nlmixr2

nlmixr2:Nonlinear Mixed Effects Models in Population PK/PD

Fit and compare nonlinear mixed-effects models in differential equations with flexible dosing information commonly seen in pharmacokinetics and pharmacodynamics (Almquist, Leander, and Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation solving is by compiled C code provided in the 'rxode2' package (Wang, Hallow, and James 2015 <doi:10.1002/psp4.12052>).

Maintained by Matthew Fidler. Last updated 1 months ago.

52 stars 8.38 score 120 scripts 3 dependents

ncss-tech

sharpshootR:A Soil Survey Toolkit

A collection of data processing, visualization, and export functions to support soil survey operations. Many of the functions build on the `SoilProfileCollection` S4 class provided by the aqp package, extending baseline visualization to more elaborate depictions in the context of spatial and taxonomic data. While this package is primarily developed by and for the USDA-NRCS, in support of the National Cooperative Soil Survey, the authors strive for generalization sufficient to support any soil survey operation. Many of the included functions are used by the SoilWeb suite of websites and movile applications. These functions are provided here, with additional documentation, to enable others to replicate high quality versions of these figures for their own purposes.

Maintained by Dylan Beaudette. Last updated 26 days ago.

18 stars 8.37 score 327 scripts

pecanproject

PEcAn.SIPNET:PEcAn Functions Used for Ecological Forecasts and Reanalysis

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.

Maintained by Mike Dietze. Last updated 3 days ago.

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

216 stars 8.36 score 61 scripts

tidymodels

finetune:Additional Functions for Model Tuning

The ability to tune models is important. 'finetune' enhances the 'tune' package by providing more specialized methods for finding reasonable values of model tuning parameters. Two racing methods described by Kuhn (2014) <arXiv:1405.6974> are included. An iterative search method using generalized simulated annealing (Bohachevsky, Johnson and Stein, 1986) <doi:10.1080/00401706.1986.10488128> is also included.

Maintained by Max Kuhn. Last updated 8 months ago.

62 stars 8.36 score 704 scripts 1 dependents

wallaceecomod

wallace:A Modular Platform for Reproducible Modeling of Species Niches and Distributions

The 'shiny' application Wallace is a modular platform for reproducible modeling of species niches and distributions. Wallace guides users through a complete analysis, from the acquisition of species occurrence and environmental data to visualizing model predictions on an interactive map, thus bundling complex workflows into a single, streamlined interface. An extensive vignette, which guides users through most package functionality can be found on the package's GitHub Pages website: <https://wallaceecomod.github.io/wallace/articles/tutorial-v2.html>.

Maintained by Mary E. Blair. Last updated 22 days ago.

openjdk

133 stars 8.36 score 96 scripts

pecanproject

PEcAn.LINKAGES:PEcAn Package for Integration of the LINKAGES Model

This module provides functions to link the (LINKAGES) to PEcAn.

Maintained by Ann Raiho. Last updated 3 days ago.

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

216 stars 8.35 score 59 scripts

mlr-org

mlr3verse:Easily Install and Load the 'mlr3' Package Family

The 'mlr3' package family is a set of packages for machine-learning purposes built in a modular fashion. This wrapper package is aimed to simplify the installation and loading of the core 'mlr3' packages. Get more information about the 'mlr3' project at <https://mlr3book.mlr-org.com/>.

Maintained by Marc Becker. Last updated 2 months ago.

machine-learning meta mlr3

55 stars 8.32 score 720 scripts 1 dependents

cefet-rj-dal

harbinger:A Unified Time Series Event Detection Framework

By analyzing time series, it is possible to observe significant changes in the behavior of observations that frequently characterize events. Events present themselves as anomalies, change points, or motifs. In the literature, there are several methods for detecting events. However, searching for a suitable time series method is a complex task, especially considering that the nature of events is often unknown. This work presents Harbinger, a framework for integrating and analyzing event detection methods. Harbinger contains several state-of-the-art methods described in Salles et al. (2020) <doi:10.5753/sbbd.2020.13626>.

Maintained by Eduardo Ogasawara. Last updated 4 months ago.

18 stars 8.32 score 216 scripts

mlr-org

mlr3cluster:Cluster Extension for 'mlr3'

Extends the 'mlr3' package with cluster analysis.

Maintained by Maximilian Mücke. Last updated 1 months ago.

cluster-analysis clustering mlr3

23 stars 8.31 score 50 scripts 2 dependents

business-science

modeltime.ensemble:Ensemble Algorithms for Time Series Forecasting with Modeltime

A 'modeltime' extension that implements time series ensemble forecasting methods including model averaging, weighted averaging, and stacking. These techniques are popular methods to improve forecast accuracy and stability.

Maintained by Matt Dancho. Last updated 8 months ago.

ensemble ensemble-learning forecast forecasting modeltime stacking stacking-ensemble tidymodels time time-series timeseries

77 stars 8.30 score 143 scripts