Showing 75 of total 75 results (show query)
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 20 days ago.
spatial-autocorrelationspatial-dependencespatial-weights
7.5 match 131 stars 16.62 score 6.0k scripts 107 dependents
r-forge
Matrix:Sparse and Dense Matrix Classes and Methods
A rich hierarchy of sparse and dense matrix classes, including general, symmetric, triangular, and diagonal matrices with numeric, logical, or pattern entries. Efficient methods for operating on such matrices, often wrapping the 'BLAS', 'LAPACK', and 'SuiteSparse' libraries.
Maintained by Martin Maechler. Last updated 9 days ago.
7.0 match 1 stars 17.23 score 33k scripts 12k dependents
pachadotdev
cpp11armadillo:An 'Armadillo' Interface
Provides function declarations and inline function definitions that facilitate communication between R and the 'Armadillo' 'C++' library for linear algebra and scientific computing. This implementation is detailed in Vargas Sepulveda and Schneider Malamud (2024) <doi:10.48550/arXiv.2408.11074>.
Maintained by Mauricio Vargas Sepulveda. Last updated 28 days ago.
armadillocppcpp11hacktoberfestlinear-algebra
12.9 match 9 stars 9.14 score 1 scripts 16 dependents
hsbadr
HiClimR:Hierarchical Climate Regionalization
A tool for Hierarchical Climate Regionalization applicable to any correlation-based clustering. It adds several features and a new clustering method (called, 'regional' linkage) to hierarchical clustering in R ('hclust' function in 'stats' library): data regridding, coarsening spatial resolution, geographic masking, contiguity-constrained clustering, data filtering by mean and/or variance thresholds, data preprocessing (detrending, standardization, and PCA), faster correlation function with preliminary big data support, different clustering methods, hybrid hierarchical clustering, multivariate clustering (MVC), cluster validation, visualization of regionalization results, and exporting region map and mean timeseries into NetCDF-4 file. The technical details are described in Badr et al. (2015) <doi:10.1007/s12145-015-0221-7>.
Maintained by Hamada S. Badr. Last updated 2 months ago.
clusteringcontiguityhomogeneitymultivariateregionalizationspatiotemporalfortran
10.5 match 16 stars 8.06 score 53 scripts 3 dependents
reinhardfurrer
spam:SPArse Matrix
Set of functions for sparse matrix algebra. Differences with other sparse matrix packages are: (1) we only support (essentially) one sparse matrix format, (2) based on transparent and simple structure(s), (3) tailored for MCMC calculations within G(M)RF. (4) and it is fast and scalable (with the extension package spam64). Documentation about 'spam' is provided by vignettes included in this package, see also Furrer and Sain (2010) <doi:10.18637/jss.v036.i10>; see 'citation("spam")' for details.
Maintained by Reinhard Furrer. Last updated 2 months ago.
8.6 match 1 stars 9.26 score 420 scripts 433 dependents
colearendt
xlsx:Read, Write, Format Excel 2007 and Excel 97/2000/XP/2003 Files
Provide R functions to read/write/format Excel 2007 and Excel 97/2000/XP/2003 file formats.
Maintained by Cole Arendt. Last updated 3 years ago.
5.2 match 85 stars 14.40 score 14k scripts 35 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 13 days ago.
biodiversityconservationconservation-planneroptimizationprioritizationsolverspatialcpp
5.4 match 124 stars 11.82 score 584 scripts 2 dependents
geodacenter
rgeoda:R Library for Spatial Data Analysis
Provides spatial data analysis functionalities including Exploratory Spatial Data Analysis, Spatial Cluster Detection and Clustering Analysis, Regionalization, etc. based on the C++ source code of 'GeoDa', which is an open-source software tool that serves as an introduction to spatial data analysis. The 'GeoDa' software and its documentation are available at <https://geodacenter.github.io>.
Maintained by Xun Li. Last updated 11 days ago.
dataanalysisgeodageospatialcpp
7.2 match 73 stars 7.85 score 179 scripts 1 dependents
horankev
sfislands:Streamlines the Process of Fitting Areal Spatial Models
Helpers for addressing the issue of disconnected spatial units. It allows for convenient adding and removal of neighbourhood connectivity between areal units prior to modelling, with the visual aid of maps. Post-modelling, it reduces the human workload for extracting, tidying and mapping predictions from areal models.
Maintained by Kevin Horan. Last updated 16 days ago.
10.7 match 7 stars 4.32 score 5 scripts
thijsjanzen
GenomeAdmixR:Simulate Admixture of Genomes
Individual-based simulations forward in time, simulating how patterns in ancestry along the genome change after admixture. Full description can be found in Janzen (2021) <doi:10.1111/2041-210X.13612>.
Maintained by Thijs Janzen. Last updated 1 years ago.
8.4 match 5 stars 5.24 score 14 scripts
bioc
coMethDMR:Accurate identification of co-methylated and differentially methylated regions in epigenome-wide association studies
coMethDMR identifies genomic regions associated with continuous phenotypes by optimally leverages covariations among CpGs within predefined genomic regions. Instead of testing all CpGs within a genomic region, coMethDMR carries out an additional step that selects co-methylated sub-regions first without using any outcome information. Next, coMethDMR tests association between methylation within the sub-region and continuous phenotype using a random coefficient mixed effects model, which models both variations between CpG sites within the region and differential methylation simultaneously.
Maintained by Fernanda Veitzman. Last updated 5 months ago.
dnamethylationepigeneticsmethylationarraydifferentialmethylationgenomewideassociation
6.8 match 7 stars 6.47 score 42 scripts
cran
timeSeries:Financial Time Series Objects (Rmetrics)
'S4' classes and various tools for financial time series: Basic functions such as scaling and sorting, subsetting, mathematical operations and statistical functions.
Maintained by Georgi N. Boshnakov. Last updated 6 months ago.
3.9 match 2 stars 9.90 score 1.3k scripts 145 dependents
sjewo
cartogram:Create Cartograms with R
Construct continuous and non-contiguous area cartograms.
Maintained by Sebastian Jeworutzki. Last updated 2 months ago.
4.3 match 149 stars 8.72 score 732 scripts 3 dependents
christopherkenny
geomander:Geographic Tools for Studying Gerrymandering
A compilation of tools to complete common tasks for studying gerrymandering. This focuses on the geographic tool side of common problems, such as linking different levels of spatial units or estimating how to break up units. Functions exist for creating redistricting-focused data for the US.
Maintained by Christopher T. Kenny. Last updated 20 days ago.
4.0 match 14 stars 7.81 score 191 scripts 1 dependents
mlverse
torch:Tensors and Neural Networks with 'GPU' Acceleration
Provides functionality to define and train neural networks similar to 'PyTorch' by Paszke et al (2019) <doi:10.48550/arXiv.1912.01703> but written entirely in R using the 'libtorch' library. Also supports low-level tensor operations and 'GPU' acceleration.
Maintained by Daniel Falbel. Last updated 8 days ago.
1.8 match 520 stars 16.52 score 1.4k scripts 38 dependentsr-forge
zoo:S3 Infrastructure for Regular and Irregular Time Series (Z's Ordered Observations)
An S3 class with methods for totally ordered indexed observations. It is particularly aimed at irregular time series of numeric vectors/matrices and factors. zoo's key design goals are independence of a particular index/date/time class and consistency with ts and base R by providing methods to extend standard generics.
Maintained by Achim Zeileis. Last updated 15 days ago.
1.8 match 16.23 score 33k scripts 2.2k dependents
svmiller
peacesciencer:Tools and Data for Quantitative Peace Science Research
These are useful tools and data sets for the study of quantitative peace science. The goal for this package is to include tools and data sets for doing original research that mimics well what a user would have to previously get from a software package that may not be well-sourced or well-supported. Those software bundles were useful the extent to which they encourage replications of long-standing analyses by starting the data-generating process from scratch. However, a lot of the functionality can be done relatively quickly and more transparently in the R programming language.
Maintained by Steve Miller. Last updated 5 days ago.
5.1 match 29 stars 5.49 score 211 scripts
asgr
imager:Image Processing Library Based on 'CImg'
Fast image processing for images in up to 4 dimensions (two spatial dimensions, one time/depth dimension, one colour dimension). Provides most traditional image processing tools (filtering, morphology, transformations, etc.) as well as various functions for easily analysing image data using R. The package wraps 'CImg', <http://cimg.eu>, a simple, modern C++ library for image processing.
Maintained by Aaron Robotham. Last updated 29 days ago.
2.0 match 17 stars 13.62 score 2.4k scripts 45 dependents
sparklyr
sparklyr:R Interface to Apache Spark
R interface to Apache Spark, a fast and general engine for big data processing, see <https://spark.apache.org/>. This package supports connecting to local and remote Apache Spark clusters, provides a 'dplyr' compatible back-end, and provides an interface to Spark's built-in machine learning algorithms.
Maintained by Edgar Ruiz. Last updated 8 hours ago.
apache-sparkdistributeddplyridelivymachine-learningremote-clusterssparksparklyr
1.7 match 959 stars 15.20 score 4.0k scripts 21 dependents
rstudio
keras3:R Interface to 'Keras'
Interface to 'Keras' <https://keras.io>, a high-level neural networks API. 'Keras' was developed with a focus on enabling fast experimentation, supports both convolution based networks and recurrent networks (as well as combinations of the two), and runs seamlessly on both CPU and GPU devices.
Maintained by Tomasz Kalinowski. Last updated 2 days ago.
1.9 match 845 stars 13.60 score 264 scripts 2 dependents
henrikbengtsson
R.utils:Various Programming Utilities
Utility functions useful when programming and developing R packages.
Maintained by Henrik Bengtsson. Last updated 1 years ago.
1.8 match 63 stars 13.74 score 5.7k scripts 814 dependents
nsaph-software
CausalGPS:Matching on Generalized Propensity Scores with Continuous Exposures
Provides a framework for estimating causal effects of a continuous exposure using observational data, and implementing matching and weighting on the generalized propensity score. Wu, X., Mealli, F., Kioumourtzoglou, M.A., Dominici, F. and Braun, D., 2022. Matching on generalized propensity scores with continuous exposures. Journal of the American Statistical Association, pp.1-29.
Maintained by Naeem Khoshnevis. Last updated 9 months ago.
3.2 match 24 stars 7.67 score 39 scripts
stocnet
manynet:Many Ways to Make, Modify, Map, Mark, and Measure Myriad Networks
Many tools for making, modifying, mapping, marking, measuring, and motifs and memberships of many different types of networks. All functions operate with matrices, edge lists, and 'igraph', 'network', and 'tidygraph' objects, and on one-mode, two-mode (bipartite), and sometimes three-mode networks. The package includes functions for importing and exporting, creating and generating networks, modifying networks and node and tie attributes, and describing and visualizing networks with sensible defaults.
Maintained by James Hollway. Last updated 3 months ago.
diffusion-modelsgraphsnetwork-analysis
3.3 match 13 stars 6.41 score 35 scripts 1 dependents
bnosac
udpipe:Tokenization, Parts of Speech Tagging, Lemmatization and Dependency Parsing with the 'UDPipe' 'NLP' Toolkit
This natural language processing toolkit provides language-agnostic 'tokenization', 'parts of speech tagging', 'lemmatization' and 'dependency parsing' of raw text. Next to text parsing, the package also allows you to train annotation models based on data of 'treebanks' in 'CoNLL-U' format as provided at <https://universaldependencies.org/format.html>. The techniques are explained in detail in the paper: 'Tokenizing, POS Tagging, Lemmatizing and Parsing UD 2.0 with UDPipe', available at <doi:10.18653/v1/K17-3009>. The toolkit also contains functionalities for commonly used data manipulations on texts which are enriched with the output of the parser. Namely functionalities and algorithms for collocations, token co-occurrence, document term matrix handling, term frequency inverse document frequency calculations, information retrieval metrics (Okapi BM25), handling of multi-word expressions, keyword detection (Rapid Automatic Keyword Extraction, noun phrase extraction, syntactical patterns) sentiment scoring and semantic similarity analysis.
Maintained by Jan Wijffels. Last updated 2 years ago.
conlldependency-parserlemmatizationnatural-language-processingnlppos-taggingr-pkgrcpptext-miningtokenizerudpipecpp
1.8 match 215 stars 11.83 score 1.2k scripts 9 dependents
rozetasimonovska
SDPDmod:Spatial Dynamic Panel Data Modeling
Spatial model calculation for static and dynamic panel data models, weights matrix creation and Bayesian model comparison. Bayesian model comparison methods were described by 'LeSage' (2014) <doi:10.1016/j.spasta.2014.02.002>. The 'Lee'-'Yu' transformation approach is described in 'Yu', 'De Jong' and 'Lee' (2008) <doi:10.1016/j.jeconom.2008.08.002>, 'Lee' and 'Yu' (2010) <doi:10.1016/j.jeconom.2009.08.001> and 'Lee' and 'Yu' (2010) <doi:10.1017/S0266466609100099>.
Maintained by Rozeta Simonovska. Last updated 11 months ago.
4.1 match 5 stars 4.98 score 19 scripts
t-kalinowski
keras:R Interface to 'Keras'
Interface to 'Keras' <https://keras.io>, a high-level neural networks 'API'. 'Keras' was developed with a focus on enabling fast experimentation, supports both convolution based networks and recurrent networks (as well as combinations of the two), and runs seamlessly on both 'CPU' and 'GPU' devices.
Maintained by Tomasz Kalinowski. Last updated 11 months ago.
1.7 match 10.93 score 10k scripts 55 dependents
spatlyu
tidyrgeoda:A tidy interface for rgeoda
An interface for 'rgeoda' to integrate with 'sf' objects and the 'tidyverse'.
Maintained by Wenbo Lv. Last updated 7 months ago.
geocomputationgeoinformaticsgisciencespatial-analysisspatial-statistics
3.5 match 16 stars 5.11 score 5 scriptsr-forge
latticeExtra:Extra Graphical Utilities Based on Lattice
Building on the infrastructure provided by the lattice package, this package provides several new high-level functions and methods, as well as additional utilities such as panel and axis annotation functions.
Maintained by Deepayan Sarkar. Last updated 3 years ago.
1.8 match 10.18 score 2.6k scripts 233 dependents
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.
bayesianbayesian-inferencebayesian-statisticsepidemiologymodelingpublic-healthrspatialspatialstancpp
2.0 match 80 stars 8.80 score 46 scripts
chavent
ClustGeo:Hierarchical Clustering with Spatial Constraints
Implements a Ward-like hierarchical clustering algorithm including soft spatial/geographical constraints.
Maintained by Marie Chavent. Last updated 3 years ago.
3.0 match 7 stars 5.85 score 67 scripts 1 dependents
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.
geospatialgerrymanderingredistrictingsamplingopenblascppopenmp
1.9 match 68 stars 9.17 score 259 scriptsr-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 5 days ago.
bayesianimpactsmaximum-likelihoodspatial-dependencespatial-econometricsspatial-regressionopenblas
1.2 match 46 stars 12.92 score 916 scripts 24 dependents
adw96
breakaway:Species Richness Estimation and Modeling
Understanding the drivers of microbial diversity is an important frontier of microbial ecology, and investigating the diversity of samples from microbial ecosystems is a common step in any microbiome analysis. 'breakaway' is the premier package for statistical analysis of microbial diversity. 'breakaway' implements the latest and greatest estimates of species richness, described in Willis and Bunge (2015) <doi:10.1111/biom.12332>, Willis et al. (2017) <doi:10.1111/rssc.12206>, and Willis (2016) <arXiv:1604.02598>, as well as the most commonly used estimates, including the objective Bayes approach described in Barger and Bunge (2010) <doi:10.1214/10-BA527>.
Maintained by Amy D Willis. Last updated 1 years ago.
1.8 match 68 stars 8.18 score 211 scripts
cbhurley
gclus:Clustering Graphics
Orders panels in scatterplot matrices and parallel coordinate displays by some merit index. Package contains various indices of merit, ordering functions, and enhanced versions of pairs and parcoord which color panels according to their merit level.
Maintained by Catherine Hurley. Last updated 6 years ago.
1.7 match 8.23 score 406 scripts 82 dependents
thocevar
orca:Computation of Graphlet Orbit Counts in Sparse Graphs
Implements orbit counting using a fast combinatorial approach. Counts orbits of nodes and edges from edge matrix or data frame, or a graph object from the graph package.
Maintained by Tomaz Hocevar. Last updated 6 months ago.
4.0 match 3.34 score 116 scripts 1 dependents
ekstroem
MESS:Miscellaneous Esoteric Statistical Scripts
A mixed collection of useful and semi-useful diverse statistical functions, some of which may even be referenced in The R Primer book. See Ekstrøm, C. T. (2016). The R Primer. 2nd edition. Chapman & Hall.
Maintained by Claus Thorn Ekstrøm. Last updated 1 months ago.
biostatisticspower-analysisstatistical-analysisstatistical-methodsstatistical-modelsopenblascpp
1.7 match 4 stars 7.69 score 328 scripts 13 dependents
davidchall
ipaddress:Data Analysis for IP Addresses and Networks
Classes and functions for working with IP (Internet Protocol) addresses and networks, inspired by the Python 'ipaddress' module. Offers full support for both IPv4 and IPv6 (Internet Protocol versions 4 and 6) address spaces. It is specifically designed to work well with the 'tidyverse'.
Maintained by David Hall. Last updated 1 years ago.
cyberdata-analysisip-addressipv4ipv6vctrscpp
1.9 match 32 stars 7.02 score 27 scripts 2 dependents
nredell
forecastML:Time Series Forecasting with Machine Learning Methods
The purpose of 'forecastML' is to simplify the process of multi-step-ahead forecasting with standard machine learning algorithms. 'forecastML' supports lagged, dynamic, static, and grouping features for modeling single and grouped numeric or factor/sequence time series. In addition, simple wrapper functions are used to support model-building with most R packages. This approach to forecasting is inspired by Bergmeir, Hyndman, and Koo's (2018) paper "A note on the validity of cross-validation for evaluating autoregressive time series prediction" <doi:10.1016/j.csda.2017.11.003>.
Maintained by Nickalus Redell. Last updated 5 years ago.
deep-learningdirect-forecastingforecastforecastingmachine-learningmulti-step-ahead-forecastingneural-networkpythontime-series
1.7 match 131 stars 7.64 score 134 scripts
josiahparry
sfdep:Spatial Dependence for Simple Features
An interface to 'spdep' to integrate with 'sf' objects and the 'tidyverse'.
Maintained by Dexter Locke. Last updated 6 months ago.
1.8 match 130 stars 7.01 score 130 scripts
theomichelot
hmmTMB:Fit Hidden Markov Models using Template Model Builder
Fitting hidden Markov models using automatic differentiation and Laplace approximation, allowing for fast inference and flexible covariate effects (including random effects and smoothing splines) on model parameters. The package is described by Michelot (2022) <arXiv:2211.14139>.
Maintained by Theo Michelot. Last updated 1 months ago.
1.9 match 53 stars 6.57 score 64 scripts
stscl
sdsfun:Spatial Data Science Complementary Features
Wrapping and supplementing commonly used functions in the R ecosystem related to spatial data science, while serving as a basis for other packages maintained by Wenbo Lv.
Maintained by Wenbo Lv. Last updated 17 days ago.
geoinformaticsspatial-data-analysisspatial-data-sciencespatial-statisticsopenblascppopenmp
1.8 match 16 stars 6.58 score 6 scripts 8 dependents
microsoft
wpa:Tools for Analysing and Visualising Viva Insights Data
Opinionated functions that enable easier and faster analysis of Viva Insights data. There are three main types of functions in 'wpa': (i) Standard functions create a 'ggplot' visual or a summary table based on a specific Viva Insights metric; (2) Report Generation functions generate HTML reports on a specific analysis area, e.g. Collaboration; (3) Other miscellaneous functions cover more specific applications (e.g. Subject Line text mining) of Viva Insights data. This package adheres to 'tidyverse' principles and works well with the pipe syntax. 'wpa' is built with the beginner-to-intermediate R users in mind, and is optimised for simplicity.
Maintained by Martin Chan. Last updated 4 months ago.
1.7 match 30 stars 6.69 score 39 scripts 1 dependents
tmieno2
r.spatial.workshop.datasets:Collection of spatial datasets
This packages provides spatial datasets in various format. They are used for demonstrating spatial operations and map creation using R spatial pacakges (e.g., sf, terra, tmap).
Maintained by Taro Mieno. Last updated 6 months ago.
3.6 match 2.96 score 23 scriptsmicrosoft
vivainsights:Analyze and Visualize Data from 'Microsoft Viva Insights'
Provides a versatile range of functions, including exploratory data analysis, time-series analysis, organizational network analysis, and data validation, whilst at the same time implements a set of best practices in analyzing and visualizing data specific to 'Microsoft Viva Insights'.
Maintained by Martin Chan. Last updated 25 days ago.
1.7 match 11 stars 6.12 score 68 scriptsbioc
seqsetvis:Set Based Visualizations for Next-Gen Sequencing Data
seqsetvis enables the visualization and analysis of sets of genomic sites in next gen sequencing data. Although seqsetvis was designed for the comparison of mulitple ChIP-seq samples, this package is domain-agnostic and allows the processing of multiple genomic coordinate files (bed-like files) and signal files (bigwig files pileups from bam file). seqsetvis has multiple functions for fetching data from regions into a tidy format for analysis in data.table or tidyverse and visualization via ggplot2.
Maintained by Joseph R Boyd. Last updated 3 months ago.
softwarechipseqmultiplecomparisonsequencingvisualization
1.7 match 5.82 score 82 scriptscran
HTRX:Haplotype Trend Regression with eXtra Flexibility (HTRX)
Detection of haplotype patterns that include single nucleotide polymorphisms (SNPs) and non-contiguous haplotypes that are associated with a phenotype. Methods for implementing HTRX are described in Yang Y, Lawson DJ (2023) <doi:10.1093/bioadv/vbad038> and Barrie W, Yang Y, Irving-Pease E.K, et al (2024) <doi:10.1038/s41586-023-06618-z>.
Maintained by Yaoling Yang. Last updated 1 years ago.
3.4 match 2.70 score
eitsupi
neopolars:R Bindings for the 'polars' Rust Library
Lightning-fast 'DataFrame' library written in 'Rust'. Convert R data to 'Polars' data and vice versa. Perform fast, lazy, larger-than-memory and optimized data queries. 'Polars' is interoperable with the package 'arrow', as both are based on the 'Apache Arrow' Columnar Format.
Maintained by Tatsuya Shima. Last updated 1 days ago.
1.8 match 40 stars 4.87 score 1 scriptsbioc
dStruct:Identifying differentially reactive regions from RNA structurome profiling data
dStruct identifies differentially reactive regions from RNA structurome profiling data. dStruct is compatible with a broad range of structurome profiling technologies, e.g., SHAPE-MaP, DMS-MaPseq, Structure-Seq, SHAPE-Seq, etc. See Choudhary et al., Genome Biology, 2019 for the underlying method.
Maintained by Krishna Choudhary. Last updated 5 months ago.
statisticalmethodstructuralpredictionsequencingsoftware
1.8 match 2 stars 4.86 score 12 scriptsbioc
UPDhmm:Detecting Uniparental Disomy through NGS trio data
Uniparental disomy (UPD) is a genetic condition where an individual inherits both copies of a chromosome or part of it from one parent, rather than one copy from each parent. This package contains a HMM for detecting UPDs through HTS (High Throughput Sequencing) data from trio assays. By analyzing the genotypes in the trio, the model infers a hidden state (normal, father isodisomy, mother isodisomy, father heterodisomy and mother heterodisomy).
Maintained by Marta Sevilla. Last updated 5 months ago.
softwarehiddenmarkovmodelgenetics
1.8 match 1 stars 4.54 score 3 scriptsbioc
rnaEditr:Statistical analysis of RNA editing sites and hyper-editing regions
RNAeditr analyzes site-specific RNA editing events, as well as hyper-editing regions. The editing frequencies can be tested against binary, continuous or survival outcomes. Multiple covariate variables as well as interaction effects can also be incorporated in the statistical models.
Maintained by Lanyu Zhang. Last updated 5 months ago.
genetargetepigeneticsdimensionreductionfeatureextractionregressionsurvivalrnaseq
1.7 match 3 stars 4.48 score 9 scripts
rorynolan
nandb:Number and Brightness Image Analysis
Calculation of molecular number and brightness from fluorescence microscopy image series. The software was published in a 2016 paper <doi:10.1093/bioinformatics/btx434>. The seminal paper for the technique is Digman et al. 2008 <doi:10.1529/biophysj.107.114645>. A review of the technique was published in 2017 <doi:10.1016/j.ymeth.2017.12.001>.
Maintained by Rory Nolan. Last updated 2 months ago.
1.3 match 2 stars 5.24 score 29 scriptsbioc
metagene2:A package to produce metagene plots
This package produces metagene plots to compare coverages of sequencing experiments at selected groups of genomic regions. It can be used for such analyses as assessing the binding of DNA-interacting proteins at promoter regions or surveying antisense transcription over the length of a gene. The metagene2 package can manage all aspects of the analysis, from normalization of coverages to plot facetting according to experimental metadata. Bootstraping analysis is used to provide confidence intervals of per-sample mean coverages.
Maintained by Eric Fournier. Last updated 5 months ago.
chipseqgeneticsmultiplecomparisoncoveragealignmentsequencing
1.1 match 4 stars 5.45 score 8 scripts
kjetil1001
SenSrivastava:Datasets from Sen & Srivastava
Collection of datasets from Sen & Srivastava: "Regression Analysis, Theory, Methods and Applications", Springer. Sources for individual data files are more fully documented in the book.
Maintained by Kjetil B Halvorsen. Last updated 1 years ago.
3.5 match 1.76 score 57 scripts
adamlilith
statisfactory:Statistical and Geometrical Tools
A collection of statistical and geometrical tools including the aligned rank transform (ART; Higgins et al. 1990 <doi:10.4148/2475-7772.1443>; Peterson 2002 <doi:10.22237/jmasm/1020255240>; Wobbrock et al. 2011 <doi:10.1145/1978942.1978963>), 2-D histograms and histograms with overlapping bins, a function for making all possible formulae within a set of constraints, amongst others.
Maintained by Adam B. Smith. Last updated 5 months ago.
2d-histogramsaligned-rank-transformsampling
1.8 match 3.38 score 16 scripts 1 dependents
impaug
GmooG:Datasets for the Book 'Getting (more out of) Graphics'
Datasets analysed in the book Antony Unwin (2024, ISBN:978-0367674007) "Getting (more out of) Graphics".
Maintained by Antony Unwin. Last updated 7 months ago.
3.5 match 1.70 score
sustainscapes
TroublemakeR:Generates Spatial Problems in R for 'AMPL'
Provides methods for generating .dat files for use with the 'AMPL' software using spatial data, particularly rasters. It includes support for various spatial data formats and different problem types. By automating the process of generating 'AMPL' datasets, this package can help streamline optimization workflows and make it easier to solve complex optimization problems. The methods implemented in this package are described in detail in a publication by Fourer et al. (<doi:10.1287/mnsc.36.5.519>).
Maintained by Derek Corcoran. Last updated 2 months ago.
1.8 match 3.18 score 4 scriptscran
lctools:Local Correlation, Spatial Inequalities, Geographically Weighted Regression and Other Tools
Provides researchers and educators with easy-to-learn user friendly tools for calculating key spatial statistics and to apply simple as well as advanced methods of spatial analysis in real data. These include: Local Pearson and Geographically Weighted Pearson Correlation Coefficients, Spatial Inequality Measures (Gini, Spatial Gini, LQ, Focal LQ), Spatial Autocorrelation (Global and Local Moran's I), several Geographically Weighted Regression techniques and other Spatial Analysis tools (other geographically weighted statistics). This package also contains functions for measuring the significance of each statistic calculated, mainly based on Monte Carlo simulations.
Maintained by Stamatis Kalogirou. Last updated 12 months ago.
1.8 match 1 stars 3.03 score 53 scripts
hz6yc3
CSeqpat:Frequent Contiguous Sequential Pattern Mining of Text
Mines contiguous sequential patterns in text.
Maintained by Anantha Janakiraman. Last updated 7 years ago.
5.2 match 1.00 score 3 scripts
doktorandahl
pintervals:Model Agnostic Prediction Intervals
Provides tools for estimating model-agnostic prediction intervals using conformal prediction, bootstrapping, and parametric prediction intervals. The package is designed for ease of use, offering intuitive functions for both binned and full conformal prediction methods, as well as parametric interval estimation with diagnostic checks. Currently only working for continuous predictions. For details on the conformal and bin-conditional conformal prediction methods, see Randahl, Williams, and Hegre (2024) <DOI:10.48550/arXiv.2410.14507>.
Maintained by David Randahl. Last updated 13 days ago.
5.1 match 1.00 score
zcolburn
Bioi:Biological Image Analysis
Single linkage clustering and connected component analyses are often performed on biological images. 'Bioi' provides a set of functions for performing these tasks. This functionality is implemented in several key functions that can extend to from 1 to many dimensions. The single linkage clustering method implemented here can be used on n-dimensional data sets, while connected component analyses are limited to 3 or fewer dimensions.
Maintained by Zachary Colburn. Last updated 5 years ago.
biological-data-analysisbiologycellcppimage-analysismicroscopycpp
1.1 match 3.81 score 13 scriptscran
OasisR:Outright Tool for the Analysis of Spatial Inequalities and Segregation
A comprehensive set of indexes and tests for social segregation analysis, as described in Tivadar (2019) - 'OasisR': An R Package to Bring Some Order to the World of Segregation Measurement <doi:10.18637/jss.v089.i07>. The package is the most complete existing tool and it clarifies many ambiguities and errors regarding the definition of segregation indices. Additionally, 'OasisR' introduces several resampling methods that enable testing their statistical significance (randomization tests, bootstrapping, and jackknife methods).
Maintained by Mihai Tivadar. Last updated 4 months ago.
1.9 match 2 stars 1.78 score 1 dependentsbioc
CatsCradle:This package provides methods for analysing spatial transcriptomics data and for discovering gene clusters
This package addresses two broad areas. It allows for in-depth analysis of spatial transcriptomic data by identifying tissue neighbourhoods. These are contiguous regions of tissue surrounding individual cells. 'CatsCradle' allows for the categorisation of neighbourhoods by the cell types contained in them and the genes expressed in them. In particular, it produces Seurat objects whose individual elements are neighbourhoods rather than cells. In addition, it enables the categorisation and annotation of genes by producing Seurat objects whose elements are genes.
Maintained by Michael Shapiro. Last updated 1 days ago.
biologicalquestionstatisticalmethodgeneexpressionsinglecelltranscriptomicsspatial
0.5 match 3 stars 6.52 score
dimitri-justeau
restoptr:Ecological Restoration Planning
Flexible framework for ecological restoration planning. It aims to identify priority areas for restoration efforts using optimization algorithms (based on Justeau-Allaire et al. 2021 <doi:10.1111/1365-2664.13803>). Priority areas can be identified by maximizing landscape indices, such as the effective mesh size (Jaeger 2000 <doi:10.1023/A:1008129329289>), or the integral index of connectivity (Pascual-Hortal & Saura 2006 <doi:10.1007/s10980-006-0013-z>). Additionally, constraints can be used to ensure that priority areas exhibit particular characteristics (e.g., ensure that particular places are not selected for restoration, ensure that priority areas form a single contiguous network). Furthermore, multiple near-optimal solutions can be generated to explore multiple options in restoration planning. The package leverages the 'Choco-solver' software to perform optimization using constraint programming (CP) techniques (<https://choco-solver.org/>).
Maintained by Dimitri Justeau-Allaire. Last updated 8 months ago.
0.5 match 11 stars 5.04 score 6 scripts
chainsawriot
ngramrr:A Simple General Purpose N-Gram Tokenizer
A simple n-gram (contiguous sequences of n items from a given sequence of text) tokenizer to be used with the 'tm' package with no 'rJava'/'RWeka' dependency.
Maintained by Chung-hong Chan. Last updated 9 years ago.
0.5 match 10 stars 4.48 score 5 scripts 2 dependents
hafen
housingData:U.S. Housing Data from 2008 to 2016
Monthly median home listing, sale price per square foot, and number of units sold for 2984 counties in the contiguous United States From 2008 to January 2016. Additional data sets containing geographical information and links to Wikipedia are also included.
Maintained by Ryan Hafen. Last updated 9 years ago.
0.5 match 9 stars 4.55 score 79 scripts
fmarotta
fplyr:Apply Functions to Blocks of Files
Read and process a large delimited file block by block. A block consists of all the contiguous rows that have the same value in the first field. The result can be returned as a list or a data.table, or even directly printed to an output file.
Maintained by Federico Marotta. Last updated 2 years ago.
0.5 match 3 stars 4.18 score 6 scriptsbioc
genomicInstability:Genomic Instability estimation for scRNA-Seq
This package contain functions to run genomic instability analysis (GIA) from scRNA-Seq data. GIA estimates the association between gene expression and genomic location of the coding genes. It uses the aREA algorithm to quantify the enrichment of sets of contiguous genes (loci-blocks) on the gene expression profiles and estimates the Genomic Instability Score (GIS) for each analyzed cell.
Maintained by Mariano Alvarez. Last updated 5 months ago.
systemsbiologygeneexpressionsinglecell
0.5 match 5 stars 4.00 score 3 scripts
nikdata
avocado:Weekly Hass Avocado Sales Summary
Provides a weekly summary of Hass Avocado sales for the contiguous US from January 2017 through December 20204. See the package website for more information, documentation, and examples. Data source: Haas Avocado Board <https://hassavocadoboard.com/category-data/>.
Maintained by Nikhil Agarwal. Last updated 3 hours ago.
0.5 match 3.74 score 11 scripts
giraultg
SpiceFP:Sparse Method to Identify Joint Effects of Functional Predictors
A set of functions allowing to implement the 'SpiceFP' approach which is iterative. It involves transformation of functional predictors into several candidate explanatory matrices (based on contingency tables), to which relative edge matrices with contiguity constraints are associated. Generalized Fused Lasso regression are performed in order to identify the best candidate matrix, the best class intervals and related coefficients at each iteration. The approach is stopped when the maximal number of iterations is reached or when retained coefficients are zeros. Supplementary functions allow to get coefficients of any candidate matrix or mean of coefficients of many candidates.
Maintained by Girault Gnanguenon Guesse. Last updated 2 years ago.
0.5 match 3.70 score 1 scriptspachadotdev
cepiigeodist:CEPII's GeoDist datasets in R
Provides data on countries and their main city or agglomeration and the different distance measures and dummy variables indicating whether two countries are contiguous, share a common language or a colonial relationship. The reference article for these datasets is Mayer and Zignago (2011).
Maintained by Mauricio Vargas. Last updated 2 years ago.
borderscolonizationgeodistancegravitylanguagestrade
0.5 match 3 stars 3.54 score 23 scripts
stla
intmap:Ordered Containers with Integer Keys
Provides a key-value store data structure. The keys are integers and the values can be any R object. This is like a list but indexed by a set of integers, not necessarily contiguous and possibly negative. The implementation uses a 'R6' class. These containers are not faster than lists but their usage can be more convenient for certain situations.
Maintained by Stéphane Laurent. Last updated 2 years ago.
0.5 match 1 stars 3.18 score 1 dependents
mingsnu
stfit:Spatio-Temporal Functional Imputation Tool
A general spatiotemporal satellite image imputation method based on sparse functional data analytic techniques. The imputation method applies and extends the Functional Principal Analysis by Conditional Estimation (PACE). The underlying idea for the proposed procedure is to impute a missing pixel by borrowing information from temporally and spatially contiguous pixels based on the best linear unbiased prediction.
Maintained by Weicheng Zhu. Last updated 2 years ago.
0.5 match 2.61 score 41 scripts
geomarker-io
appc:Air Pollution Predictor Commons
Functions for geomarker assessment for s2 locations and dates. These are used to train and predict daily ambient air pollution concentrations across the contiguous US 2016 - 2022.
Maintained by Cole Brokamp. Last updated 3 months ago.
0.5 match 2.54 score 6 scriptscran
LabourMarketAreas:Identification, Tuning, Visualisation and Analysis of Labour Market Areas
Produces Labour Market Areas from commuting flows available at elementary territorial units. It provides tools for automatic tuning based on spatial contiguity. It also allows for statistical analyses and visualisation of the new functional geography.
Maintained by Luisa Franconi. Last updated 1 years ago.
0.5 match 2.00 score
