R-universe search: exports:project

rstudio

renv:Project Environments

A dependency management toolkit for R. Using 'renv', you can create and manage project-local R libraries, save the state of these libraries to a 'lockfile', and later restore your library as required. Together, these tools can help make your projects more isolated, portable, and reproducible.

Maintained by Kevin Ushey. Last updated 2 days ago.

1.0k stars 18.59 score 1.5k scripts 114 dependents

rspatial

terra:Spatial Data Analysis

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

Maintained by Robert J. Hijmans. Last updated 5 hours ago.

geospatial raster spatial vector onetbb proj gdal geos cpp

560 stars 17.65 score 17k scripts 856 dependents

projectmosaic

mosaic:Project MOSAIC Statistics and Mathematics Teaching Utilities

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

Maintained by Randall Pruim. Last updated 1 years ago.

93 stars 13.32 score 7.2k scripts 7 dependents

cvxgrp

CVXR:Disciplined Convex Optimization

An object-oriented modeling language for disciplined convex programming (DCP) as described in Fu, Narasimhan, and Boyd (2020, <doi:10.18637/jss.v094.i14>). It allows the user to formulate convex optimization problems in a natural way following mathematical convention and DCP rules. The system analyzes the problem, verifies its convexity, converts it into a canonical form, and hands it off to an appropriate solver to obtain the solution. Interfaces to solvers on CRAN and elsewhere are provided, both commercial and open source.

Maintained by Anqi Fu. Last updated 5 months ago.

cpp

207 stars 12.89 score 768 scripts 51 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 4 hours ago.

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

205 stars 11.04 score 848 scripts 1 dependents

zdebruine

RcppML:Rcpp Machine Learning Library

Fast machine learning algorithms including matrix factorization and divisive clustering for large sparse and dense matrices.

Maintained by Zach DeBruine. Last updated 2 years ago.

clustering matrix-factorization nmf rcpp rcppeigen sparse-matrix cpp openmp

107 stars 10.66 score 125 scripts 50 dependents

stan-dev

projpred:Projection Predictive Feature Selection

Performs projection predictive feature selection for generalized linear models (Piironen, Paasiniemi, and Vehtari, 2020, <doi:10.1214/20-EJS1711>) with or without multilevel or additive terms (Catalina, Bürkner, and Vehtari, 2022, <https://proceedings.mlr.press/v151/catalina22a.html>), for some ordinal and nominal regression models (Weber, Glass, and Vehtari, 2023, <arXiv:2301.01660>), and for many other regression models (using the latent projection by Catalina, Bürkner, and Vehtari, 2021, <arXiv:2109.04702>, which can also be applied to most of the former models). The package is compatible with the 'rstanarm' and 'brms' packages, but other reference models can also be used. See the vignettes and the documentation for more information and examples.

Maintained by Frank Weber. Last updated 7 hours ago.

bayes bayesian bayesian-inference rstanarm stan statistics variable-selection openblas cpp

112 stars 10.12 score 241 scripts

winvector

rquery:Relational Query Generator for Data Manipulation at Scale

A piped query generator based on Edgar F. Codd's relational algebra, and on production experience using 'SQL' and 'dplyr' at big data scale. The design represents an attempt to make 'SQL' more teachable by denoting composition by a sequential pipeline notation instead of nested queries or functions. The implementation delivers reliable high performance data processing on large data systems such as 'Spark', databases, and 'data.table'. Package features include: data processing trees or pipelines as observable objects (able to report both columns produced and columns used), optimized 'SQL' generation as an explicit user visible table modeling step, plus explicit query reasoning and checking.

Maintained by John Mount. Last updated 2 years ago.

110 stars 9.53 score 126 scripts 3 dependents

sizespectrum

mizer:Dynamic Multi-Species Size Spectrum Modelling

A set of classes and methods to set up and run multi-species, trait based and community size spectrum ecological models, focused on the marine environment.

Maintained by Gustav Delius. Last updated 2 months ago.

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

39 stars 9.41 score 207 scripts

iandryden

shapes:Statistical Shape Analysis

Routines for the statistical analysis of landmark shapes, including Procrustes analysis, graphical displays, principal components analysis, permutation and bootstrap tests, thin-plate spline transformation grids and comparing covariance matrices. See Dryden, I.L. and Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd Edition), John Wiley and Sons.

Maintained by Ian Dryden. Last updated 2 days ago.

7 stars 8.61 score 225 scripts 24 dependents

s-u

proj4:A simple interface to the PROJ.4 cartographic projections library

A simple interface to lat/long projection and datum transformation of the PROJ.4 cartographic projections library. It allows transformation of geographic coordinates from one projection and/or datum to another.

Maintained by Simon Urbanek. Last updated 8 days ago.

proj

3 stars 7.96 score 408 scripts 39 dependents

adamlilith

fasterRaster:Faster Raster and Spatial Vector Processing Using 'GRASS GIS'

Processing of large-in-memory/large-on disk rasters and spatial vectors using 'GRASS GIS' <https://grass.osgeo.org/>. Most functions in the 'terra' package are recreated. Processing of medium-sized and smaller spatial objects will nearly always be faster using 'terra' or 'sf', but for large-in-memory/large-on-disk objects, 'fasterRaster' may be faster. To use most of the functions, you must have the stand-alone version (not the 'OSGeoW4' installer version) of 'GRASS GIS' 8.0 or higher.

Maintained by Adam B. Smith. Last updated 2 days ago.

aspect distance fragmentation fragmentation-indices gis grass grass-gis raster raster-projection rasterize slope topography vectorization

57 stars 7.68 score 8 scripts

pachadotdev

analogsea:Interface to 'DigitalOcean'

Provides a set of functions for interacting with the 'DigitalOcean' API <https://www.digitalocean.com/>, including creating images, destroying them, rebooting, getting details on regions, and available images.

Maintained by Mauricio Vargas. Last updated 2 years ago.

cloud-computing droplet ssh

159 stars 7.54 score 100 scripts 1 dependents

syncrosim

rsyncrosim:The R Interface to 'SyncroSim'

'SyncroSim' is a generalized framework for managing scenario-based datasets (<https://syncrosim.com/>). 'rsyncrosim' provides an interface to 'SyncroSim'. Simulation models can be added to 'SyncroSim' in order to transform these datasets, taking advantage of general features such as defining scenarios of model inputs, running Monte Carlo simulations, and summarizing model outputs. 'rsyncrosim' requires 'SyncroSim' 2.3.5 or higher (API documentation: <https://docs.syncrosim.com/>).

Maintained by Katie Birchard. Last updated 21 days ago.

9 stars 7.09 score 189 scripts

sylvainschmitt

SSDM:Stacked Species Distribution Modelling

Allows to map species richness and endemism based on stacked species distribution models (SSDM). Individuals SDMs can be created using a single or multiple algorithms (ensemble SDMs). For each species, an SDM can yield a habitat suitability map, a binary map, a between-algorithm variance map, and can assess variable importance, algorithm accuracy, and between- algorithm correlation. Methods to stack individual SDMs include summing individual probabilities and thresholding then summing. Thresholding can be based on a specific evaluation metric or by drawing repeatedly from a Bernoulli distribution. The SSDM package also provides a user-friendly interface.

Maintained by Sylvain Schmitt. Last updated 11 months ago.

44 stars 6.99 score 44 scripts

reconhub

projections:Project Future Case Incidence

Provides functions and graphics for projecting daily incidence based on past incidence, and estimates of the serial interval and reproduction number. Projections are based on a branching process using a Poisson-distributed number of new cases per day, similar to the model used for estimating R in 'EpiEstim' or in 'earlyR', and described by Nouvellet et al. (2017) <doi:10.1016/j.epidem.2017.02.012>. The package provides the S3 class 'projections' which extends 'matrix', with accessors and additional helpers for handling, subsetting, merging, or adding these objects, as well as dedicated printing and plotting methods.

Maintained by Thibaut Jombart. Last updated 4 months ago.

14 stars 6.47 score 175 scripts

cran

gss:General Smoothing Splines

A comprehensive package for structural multivariate function estimation using smoothing splines.

Maintained by Chong Gu. Last updated 6 months ago.

fortran openblas

3 stars 6.40 score 137 dependents

blue-matter

SAMtool:Stock Assessment Methods Toolkit

Simulation tools for closed-loop simulation are provided for the 'MSEtool' operating model to inform data-rich fisheries. 'SAMtool' provides a conditioning model, assessment models of varying complexity with standardized reporting, model-based management procedures, and diagnostic tools for evaluating assessments inside closed-loop simulation.

Maintained by Quang Huynh. Last updated 1 months ago.

cpp

3 stars 6.39 score 36 scripts 1 dependents

greta-dev

greta.gp:Gaussian Process Modelling in 'greta'

Provides a syntax to create and combine Gaussian process kernels in 'greta'. You can then them to define either full rank or sparse Gaussian processes. This is an extension to the 'greta' software, Golding (2019) <doi:10.21105/joss.01601>.

Maintained by Nicholas Tierney. Last updated 2 months ago.

19 stars 6.33 score 28 scripts

hughparsonage

grattan:Australian Tax Policy Analysis

Utilities to cost and evaluate Australian tax policy, including fast projections of personal income tax collections, high-performance tax and transfer calculators, and an interface to common indices from the Australian Bureau of Statistics. Written to support Grattan Institute's Australian Perspectives program, and related projects. Access to the Australian Taxation Office's sample files of personal income tax returns is assumed.

Maintained by Hugh Parsonage. Last updated 1 years ago.

australian-analysts tax openmp

25 stars 6.04 score 124 scripts

csids

org:Organising Projects

A framework for organizing R projects with a standardized structure. Most analyses consist of three main components: code, results, and data, each with different requirements such as version control, sharing, and encryption. This package provides tools to set up and manage project directories, handle file paths consistently across operating systems, organize results using date-based structures, source code from specified directories, create and manage Quarto documents, and perform file operations safely. It ensures consistency across projects while accommodating different requirements for various types of content.

Maintained by Richard Aubrey White. Last updated 10 days ago.

csverse

1 stars 5.95 score 60 scripts

matthieu-bruneaux

isotracer:Isotopic Tracer Analysis Using MCMC

Implements Bayesian models to analyze data from tracer addition experiments. The implemented method was originally described in the article "A New Method to Reconstruct Quantitative Food Webs and Nutrient Flows from Isotope Tracer Addition Experiments" by López-Sepulcre et al. (2020) <doi:10.1086/708546>.

Maintained by Matthieu Bruneaux. Last updated 5 months ago.

cpp

5.92 score 60 scripts

swarm-lab

trackdf:Data Frame Class for Tracking Data

Data frame class for storing collective movement data (e.g. fish schools, ungulate herds, baboon troops) collected from GPS trackers or computer vision tracking software.

Maintained by Simon Garnier. Last updated 2 years ago.

animal-behavior animal-behaviour gps gps-data

4 stars 5.42 score 11 scripts 1 dependents

data-cleaning

lintools:Manipulation of Linear Systems of (in)Equalities

Variable elimination (Gaussian elimination, Fourier-Motzkin elimination), Moore-Penrose pseudoinverse, reduction to reduced row echelon form, value substitution, projecting a vector on the convex polytope described by a system of (in)equations, simplify systems by removing spurious columns and rows and collapse implied equalities, test if a matrix is totally unimodular, compute variable ranges implied by linear (in)equalities.

Maintained by Mark van der Loo. Last updated 10 months ago.

4 stars 5.19 score 13 scripts 2 dependents

iainmstott

popdemo:Demographic Modelling Using Projection Matrices

Tools for modelling populations and demography using matrix projection models, with deterministic and stochastic model implementations. Includes population projection, indices of short- and long-term population size and growth, perturbation analysis, convergence to stability or stationarity, and diagnostic and manipulation tools.

Maintained by Iain Stott. Last updated 3 years ago.

5.16 score 172 scripts 7 dependents

bioc

snifter:R wrapper for the python openTSNE library

Provides an R wrapper for the implementation of FI-tSNE from the python package openTNSE. See Poličar et al. (2019) <doi:10.1101/731877> and the algorithm described by Linderman et al. (2018) <doi:10.1038/s41592-018-0308-4>.

Maintained by Alan OCallaghan. Last updated 5 months ago.

dimensionreduction visualization software singlecell sequencing

3 stars 4.95 score 3 scripts

hendersontrent

theftdlc:Analyse and Interpret Time Series Features

Provides a suite of functions for analysing, interpreting, and visualising time-series features calculated from different feature sets from the 'theft' package. Implements statistical learning methodologies described in Henderson, T., Bryant, A., and Fulcher, B. (2023) <arXiv:2303.17809>.

Maintained by Trent Henderson. Last updated 2 months ago.

data-science data-visualization machine-learning statistics time-series

4 stars 4.94 score 11 scripts

diegommcc

SpatialDDLS:Deconvolution of Spatial Transcriptomics Data Based on Neural Networks

Deconvolution of spatial transcriptomics data based on neural networks and single-cell RNA-seq data. SpatialDDLS implements a workflow to create neural network models able to make accurate estimates of cell composition of spots from spatial transcriptomics data using deep learning and the meaningful information provided by single-cell RNA-seq data. See Torroja and Sanchez-Cabo (2019) <doi:10.3389/fgene.2019.00978> and Mañanes et al. (2024) <doi:10.1093/bioinformatics/btae072> to get an overview of the method and see some examples of its performance.

Maintained by Diego Mañanes. Last updated 5 months ago.

deconvolution deep-learning neural-network spatial-transcriptomics

5 stars 4.88 score 1 scripts

iiasa

ibis.iSDM:Modelling framework for integrated biodiversity distribution scenarios

Integrated framework of modelling the distribution of species and ecosystems in a suitability framing. This package allows the estimation of integrated species distribution models (iSDM) based on several sources of evidence and provided presence-only and presence-absence datasets. It makes heavy use of point-process models for estimating habitat suitability and allows to include spatial latent effects and priors in the estimation. To do so 'ibis.iSDM' supports a number of engines for Bayesian and more non-parametric machine learning estimation. Further, the 'ibis.iSDM' is specifically customized to support spatial-temporal projections of habitat suitability into the future.

Maintained by Martin Jung. Last updated 5 months ago.

bayesian biodiversity integrated-framework poisson-process scenarios sdm spatial-grain spatial-predictions species-distribution-modelling

21 stars 4.36 score 12 scripts 1 dependents

blecigne

VoxR:Trees Geometry and Morphology from Unstructured TLS Data

Tools for 3D point cloud voxelisation, projection, geometrical and morphological description of trees (DBH, height, volume, crown diameter), analyses of temporal changes between different measurement times, distance based clustering and visualisation of 3D voxel clouds and 2D projection. Most analyses and algorithms provided in the package are based on the concept of space exploration and are described in Lecigne et al. (2018, https://doi.org/10.1093/aob/mcx095).

Maintained by Bastien Lecigne. Last updated 4 years ago.

6 stars 4.21 score 18 scripts 1 dependents

datawookie

clockify:A Wrapper for the 'Clockify' API

A wrapper for the Clockify API <https://docs.clockify.me/>, making it possible to query, insert and update time keeping data.

Maintained by Andrew B. Collier. Last updated 10 months ago.

hacktoberfest

2 stars 3.95 score 6 scripts

simon-lenau

prolific.api:A User-Friendly Interface for Accessing the Prolific API

A user-friendly interface for creating and managing empirical crowd-sourcing studies via API access to <https://www.prolific.co>.

Maintained by Simon Lenau. Last updated 2 years ago.

crowd-sourcing crowdsourcing-experiments crowdsourcing-platforms empirical-research participants sampling

3.70 score 8 scripts

bbuchsbaum

multivarious:Extensible Data Structures for Multivariate Analysis

Provides a set of basic and extensible data structures and functions for multivariate analysis, including dimensionality reduction techniques, projection methods, and preprocessing functions. The aim of this package is to offer a flexible and user-friendly framework for multivariate analysis that can be easily extended for custom requirements and specific data analysis tasks.

Maintained by Bradley Buchsbaum. Last updated 3 months ago.

3.53 score 17 scripts

adamkocsis

via:Virtual Arrays

The base class 'VirtualArray' is defined, which acts as a wrapper around lists allowing users to fold arbitrary sequential data into n-dimensional, R-style virtual arrays. The derived 'XArray' class is defined to be used for homogeneous lists that contain a single class of objects. The 'RasterArray' and 'SfArray' classes enable the use of stacked spatial data instead of lists.

Maintained by Adam T. Kocsis. Last updated 2 years ago.

3 stars 3.18 score 8 scripts

gchapron

pop.wolf:Models for Simulating Wolf Populations

Simulate the dynamic of wolf populations using a specific Individual-Based Model (IBM) compiled in C, see Chapron et al. (2016) <doi:10.1016/j.ecolmodel.2016.08.012>.

Maintained by Guillaume Chapron. Last updated 3 years ago.

2.70 score 2 scripts

mikelydeamore

condensr:Academic Group Website Generator

Helps automate 'Quarto' website creation for small academic groups. Builds a database-like structure of people, projects and publications, linking them together with a string-based ID system. Then, provides functions to automate production of clean markdown for these structures, and in-built CSS formatting using CSS flexbox.

Maintained by Michael Lydeamore. Last updated 2 years ago.

1 stars 2.70 score 6 scripts

gchapron

pop.lion:Models for Simulating Lion Populations

Simulate the dynamic of lion populations using a specific Individual-Based Model (IBM) compiled in C.

Maintained by Guillaume Chapron. Last updated 3 years ago.

2.70 score 1 scripts

gchapron

population:Models for Simulating Populations

Run population simulations using an Individual-Based Model (IBM) compiled in C.

Maintained by Guillaume Chapron. Last updated 3 years ago.

2.00 score 5 scripts

cran

mongopipe:Query MongoDB Documents with R

Translate R code into MongoDB aggregation pipelines.

Maintained by Oliver Haag. Last updated 4 years ago.

1.70 score

cran

manifold:Operations for Riemannian Manifolds

Implements operations for Riemannian manifolds, e.g., geodesic distance, Riemannian metric, exponential and logarithm maps, etc. Also incorporates random object generator on the manifolds. See Dai, Lin, and Müller (2021) <doi:10.1111/biom.13385>.

Maintained by Xiongtao Dai. Last updated 2 years ago.

openblas cpp

1 stars 1.48 score 1 dependents

f-rousset

Infusion:Inference Using Simulation

Implements functions for simulation-based inference. In particular, implements functions to perform likelihood inference from data summaries whose distributions are simulated. The package implements more advanced methods than the ones first described in: Rousset, Gouy, Almoyna and Courtiol (2017) <doi:10.1111/1755-0998.12627>.

Maintained by François Rousset. Last updated 6 months ago.

1.18 score 15 scripts

cran

SISIR:Select Intervals Suited for Functional Regression

Interval fusion and selection procedures for regression with functional inputs. Methods include a semiparametric approach based on Sliced Inverse Regression (SIR), as described in <doi:10.1007/s11222-018-9806-6> (standard ridge and sparse SIR are also included in the package) and a random forest based approach, as described in <doi:10.1002/sam.11705>.

Maintained by Nathalie Vialaneix. Last updated 7 months ago.

1.00 score