R-universe search: sp

edzer

sp:Classes and Methods for Spatial Data

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

Maintained by Edzer Pebesma. Last updated 2 months ago.

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

bhaskarvk

tilegramsR:R Spatial Data for Tilegrams

R spatial objects for Tilegrams. Tilegrams are tiled maps where the region size is proportional to the certain characteristics of the dataset.

Maintained by Bhaskar Karambelkar. Last updated 3 years ago.

geospatial tilegrams

54.0 match 52 stars 6.03 score 41 scripts

tomaspinall

FKF.SP:Fast Kalman Filtering Through Sequential Processing

Fast and flexible Kalman filtering and smoothing implementation utilizing sequential processing, designed for efficient parameter estimation through maximum likelihood estimation. Sequential processing is a univariate treatment of a multivariate series of observations and can benefit from computational efficiency over traditional Kalman filtering when independence is assumed in the variance of the disturbances of the measurement equation. Sequential processing is described in the textbook of Durbin and Koopman (2001, ISBN:978-0-19-964117-8). 'FKF.SP' was built upon the existing 'FKF' package and is, in general, a faster Kalman filter/smoother.

Maintained by Thomas Aspinall. Last updated 5 months ago.

kalman-filter kalman-filtering maximum-likelihood-estimation sequential-processing time-series-analysis openblas

42.5 match 2 stars 4.78 score 3 scripts 1 dependents

nowosad

spData:Datasets for Spatial Analysis

Diverse spatial datasets for demonstrating, benchmarking and teaching spatial data analysis. It includes R data of class sf (defined by the package 'sf'), Spatial ('sp'), and nb ('spdep'). Unlike other spatial data packages such as 'rnaturalearth' and 'maps', it also contains data stored in a range of file formats including GeoJSON and GeoPackage, but from version 2.3.4, no longer ESRI Shapefile - use GeoPackage instead. Some of the datasets are designed to illustrate specific analysis techniques. cycle_hire() and cycle_hire_osm(), for example, is designed to illustrate point pattern analysis techniques.

Maintained by Jakub Nowosad. Last updated 2 months ago.

datasets raster sf sp spatial spdep

11.5 match 82 stars 13.23 score 3.4k scripts 116 dependents

bioc

RBGL:An interface to the BOOST graph library

A fairly extensive and comprehensive interface to the graph algorithms contained in the BOOST library.

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

graphandnetwork network cpp

17.3 match 8.59 score 320 scripts 132 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 18 days ago.

spatial-autocorrelation spatial-dependence spatial-weights

5.5 match 131 stars 16.62 score 6.0k scripts 107 dependents

cmlmagneville

mFD:Compute and Illustrate the Multiple Facets of Functional Diversity

Computing functional traits-based distances between pairs of species for species gathered in assemblages allowing to build several functional spaces. The package allows to compute functional diversity indices assessing the distribution of species (and of their dominance) in a given functional space for each assemblage and the overlap between assemblages in a given functional space, see: Chao et al. (2018) <doi:10.1002/ecm.1343>, Maire et al. (2015) <doi:10.1111/geb.12299>, Mouillot et al. (2013) <doi:10.1016/j.tree.2012.10.004>, Mouillot et al. (2014) <doi:10.1073/pnas.1317625111>, Ricotta and Szeidl (2009) <doi:10.1016/j.tpb.2009.10.001>. Graphical outputs are included. Visit the 'mFD' website for more information, documentation and examples.

Maintained by Camille Magneville. Last updated 3 months ago.

12.4 match 26 stars 7.35 score 61 scripts

r-spatial

sf:Simple Features for R

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

Maintained by Edzer Pebesma. Last updated 16 days ago.

gdal geos proj spatial cpp

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

cran

mgcv:Mixed GAM Computation Vehicle with Automatic Smoothness Estimation

Generalized additive (mixed) models, some of their extensions and other generalized ridge regression with multiple smoothing parameter estimation by (Restricted) Marginal Likelihood, Generalized Cross Validation and similar, or using iterated nested Laplace approximation for fully Bayesian inference. See Wood (2017) <doi:10.1201/9781315370279> for an overview. Includes a gam() function, a wide variety of smoothers, 'JAGS' support and distributions beyond the exponential family.

Maintained by Simon Wood. Last updated 1 years ago.

openblas openmp

6.8 match 32 stars 12.71 score 17k scripts 7.8k dependents

eblondel

cleangeo:Cleaning Geometries from Spatial Objects

Provides a set of utility tools to inspect spatial objects, facilitate handling and reporting of topology errors and geometry validity issue with sp objects. Finally, it provides a geometry cleaner that will fix all geometry problems, and eliminate (at least reduce) the likelihood of having issues when doing spatial data processing.

Maintained by Emmanuel Blondel. Last updated 2 years ago.

cleaning cleaning-geometries gis sp spatial

11.5 match 45 stars 6.82 score 99 scripts 1 dependents

pboutros

VennDiagram:Generate High-Resolution Venn and Euler Plots

A set of functions to generate high-resolution Venn and Euler plots. Includes handling for several special cases, including two-case scaling, and extensive customization of plot shape and structure.

Maintained by Paul Boutros. Last updated 3 years ago.

8.0 match 3 stars 8.53 score 5.7k scripts 41 dependents

r-forge

car:Companion to Applied Regression

Functions to Accompany J. Fox and S. Weisberg, An R Companion to Applied Regression, Third Edition, Sage, 2019.

Maintained by John Fox. Last updated 5 months ago.

3.3 match 15.29 score 43k scripts 901 dependents

bayesiandemography

bage:Bayesian Estimation and Forecasting of Age-Specific Rates

Fast Bayesian estimation and forecasting of age-specific rates, probabilities, and means, based on 'Template Model Builder'.

Maintained by John Bryant. Last updated 2 months ago.

cpp

6.6 match 3 stars 7.30 score 39 scripts

helixcn

spaa:SPecies Association Analysis

Miscellaneous functions for analysing species association and niche overlap.

Maintained by Jinlong Zhang. Last updated 4 years ago.

6.5 match 12 stars 7.40 score 155 scripts 1 dependents

bioc

syntenet:Inference And Analysis Of Synteny Networks

syntenet can be used to infer synteny networks from whole-genome protein sequences and analyze them. Anchor pairs are detected with the MCScanX algorithm, which was ported to this package with the Rcpp framework for R and C++ integration. Anchor pairs from synteny analyses are treated as an undirected unweighted graph (i.e., a synteny network), and users can perform: i. network clustering; ii. phylogenomic profiling (by identifying which species contain which clusters) and; iii. microsynteny-based phylogeny reconstruction with maximum likelihood.

Maintained by Fabrício Almeida-Silva. Last updated 3 months ago.

software networkinference functionalgenomics comparativegenomics phylogenetics systemsbiology graphandnetwork wholegenome network comparative-genomics evolutionary-genomics network-science phylogenomics synteny synteny-network cpp

7.1 match 26 stars 6.67 score 12 scripts 1 dependents

christopherkenny

dots:Dot Density Maps

Generate point data for representing people within spatial data. This collects a suite of tools for creating simple dot density maps. Several functions from different spatial packages are standardized to take the same arguments so that they can be easily substituted for each other.

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

11.3 match 3 stars 4.18 score 8 scripts

tilburgnetworkgroup

remstats:Computes Statistics for Relational Event History Data

Computes a variety of statistics for relational event models. Relational event models enable researchers to investigate both exogenous and endogenous factors influencing the evolution of a time-ordered sequence of events. These models are categorized into tie-oriented models (Butts, C., 2008, <doi:10.1111/j.1467-9531.2008.00203.x>), where the probability of a dyad interacting next is modeled in a single step, and actor-oriented models (Stadtfeld, C., & Block, P., 2017, <doi:10.15195/v4.a14>), which first model the probability of a sender initiating an interaction and subsequently the probability of the sender's choice of receiver. The package is designed to compute a variety of statistics that summarize exogenous and endogenous influences on the event stream for both types of models.

Maintained by Giuseppe Arena. Last updated 2 months ago.

cpp

6.6 match 8 stars 6.72 score 44 scripts 1 dependents

bpfaff

evir:Extreme Values in R

Functions for extreme value theory, which may be divided into the following groups; exploratory data analysis, block maxima, peaks over thresholds (univariate and bivariate), point processes, gev/gpd distributions.

Maintained by Bernhard Pfaff. Last updated 8 years ago.

7.3 match 2 stars 5.89 score 211 scripts 6 dependents

skranz

gtree:gtree basic functionality to model and solve games

gtree basic functionality to model and solve games

Maintained by Sebastian Kranz. Last updated 4 years ago.

economic-experiments economics gambit game-theory nash-equilibrium

11.3 match 18 stars 3.79 score 23 scripts 1 dependents

spatstat

spatstat.model:Parametric Statistical Modelling and Inference for the 'spatstat' Family

Functionality for parametric statistical modelling and inference for spatial data, mainly spatial point patterns, in the 'spatstat' family of packages. (Excludes analysis of spatial data on a linear network, which is covered by the separate package 'spatstat.linnet'.) Supports parametric modelling, formal statistical inference, and model validation. Parametric models include Poisson point processes, Cox point processes, Neyman-Scott cluster processes, Gibbs point processes and determinantal point processes. Models can be fitted to data using maximum likelihood, maximum pseudolikelihood, maximum composite likelihood and the method of minimum contrast. Fitted models can be simulated and predicted. Formal inference includes hypothesis tests (quadrat counting tests, Cressie-Read tests, Clark-Evans test, Berman test, Diggle-Cressie-Loosmore-Ford test, scan test, studentised permutation test, segregation test, ANOVA tests of fitted models, adjusted composite likelihood ratio test, envelope tests, Dao-Genton test, balanced independent two-stage test), confidence intervals for parameters, and prediction intervals for point counts. Model validation techniques include leverage, influence, partial residuals, added variable plots, diagnostic plots, pseudoscore residual plots, model compensators and Q-Q plots.

Maintained by Adrian Baddeley. Last updated 7 days ago.

analysis-of-variance cluster-process confidence-intervals cox-process determinantal-point-processes gibbs-process influence leverage model-diagnostics neyman-scott parameter-estimation poisson-process spatial-analysis spatial-modelling spatial-point-processes statistical-inference

4.5 match 5 stars 9.09 score 6 scripts 46 dependents

gacarrillor

vec2dtransf:2D Cartesian Coordinate Transformation

Applies affine and similarity transformations on vector spatial data (sp objects). Transformations can be defined from control points or directly from parameters. If redundant control points are provided Least Squares is applied allowing to obtain residuals and RMSE.

Maintained by German Carrillo. Last updated 3 months ago.

2d affine affine-transformation coordinates least-squares rmse similarity-transformations sp-objects transformations

9.9 match 5 stars 3.97 score 37 scripts

gabrielblain

PowerSDI:Calculate Standardised Drought Indices Using NASA POWER Data

A set of functions designed to calculate the standardised precipitation and standardised precipitation evapotranspiration indices using NASA POWER data as described in Blain et al. (2023) <doi:10.2139/ssrn.4442843>. These indices are calculated using a reference data source. The functions verify if the indices' estimates meet the assumption of normality and how well NASA POWER estimates represent real-world data. Indices are calculated in a routine mode. Potential evapotranspiration amounts and the difference between rainfall and potential evapotranspiration are also calculated. The functions adopt a basic time scale that splits each month into four periods. Days 1 to 7, days 8 to 14, days 15 to 21, and days 22 to 28, 29, 30, or 31, where 'TS=4' corresponds to a 1-month length moving window (calculated 4 times per month) and 'TS=48' corresponds to a 12-month length moving window (calculated 4 times per month).

Maintained by Gabriel Constantino Blain. Last updated 8 months ago.

7.7 match 4 stars 5.08 score 1 scripts 1 dependents

bpfaff

urca:Unit Root and Cointegration Tests for Time Series Data

Unit root and cointegration tests encountered in applied econometric analysis are implemented.

Maintained by Bernhard Pfaff. Last updated 10 months ago.

fortran

4.1 match 6 stars 8.91 score 1.4k scripts 269 dependents

rfastofficial

Rfast2:A Collection of Efficient and Extremely Fast R Functions II

A collection of fast statistical and utility functions for data analysis. Functions for regression, maximum likelihood, column-wise statistics and many more have been included. C++ has been utilized to speed up the functions. References: Tsagris M., Papadakis M. (2018). Taking R to its limits: 70+ tips. PeerJ Preprints 6:e26605v1 <doi:10.7287/peerj.preprints.26605v1>.

Maintained by Manos Papadakis. Last updated 1 years ago.

openblas cpp openmp

4.5 match 38 stars 8.09 score 75 scripts 26 dependents

xrobin

pROC:Display and Analyze ROC Curves

Tools for visualizing, smoothing and comparing receiver operating characteristic (ROC curves). (Partial) area under the curve (AUC) can be compared with statistical tests based on U-statistics or bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.

Maintained by Xavier Robin. Last updated 4 months ago.

bootstrapping covariance hypothesis-testing machine-learning plot plotting roc roc-curve variance cpp

2.3 match 125 stars 15.18 score 16k scripts 445 dependents

bioc

Rgraphviz:Provides plotting capabilities for R graph objects

Interfaces R with the AT and T graphviz library for plotting R graph objects from the graph package.

Maintained by Kasper Daniel Hansen. Last updated 3 days ago.

graphandnetwork visualization zlib

3.3 match 10.14 score 1.2k scripts 109 dependents

cschwarz-stat-sfu-ca

SPAS:Stratified-Petersen Analysis System

The Stratified-Petersen Analysis System (SPAS) is designed to estimate abundance in two-sample capture-recapture experiments where the capture and recaptures are stratified. This is a generalization of the simple Lincoln-Petersen estimator. Strata may be defined in time or in space or both, and the s strata in which marking takes place may differ from the t strata in which recoveries take place. When s=t, SPAS reduces to the method described by Darroch (1961) <doi:10.2307/2332748>. When s<t, SPAS implements the methods described in Plante, Rivest, and Tremblay (1988) <doi:10.2307/2533994>. Schwarz and Taylor (1998) <doi:10.1139/f97-238> describe the use of SPAS in estimating return of salmon stratified by time and geography. A related package, BTSPAS, deals with temporal stratification where a spline is used to model the distribution of the population over time as it passes the second capture location. This is the R-version of the (now obsolete) standalone Windows program of the same name.

Maintained by Carl James Schwarz. Last updated 1 months ago.

cpp

4.9 match 2 stars 6.55 score 28 scripts 1 dependents

ropensci

osmdata:Import 'OpenStreetMap' Data as Simple Features or Spatial Objects

Download and import of 'OpenStreetMap' ('OSM') data as 'sf' or 'sp' objects. 'OSM' data are extracted from the 'Overpass' web server (<https://overpass-api.de/>) and processed with very fast 'C++' routines for return to 'R'.

Maintained by Mark Padgham. Last updated 1 months ago.

open0street0map openstreetmap overpass0api osm cpp osm-data overpass-api peer-reviewed cpp

2.2 match 322 stars 14.53 score 2.8k scripts 14 dependents

kjhealy

gssrdoc:Document General Social Survey Variable

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

Maintained by Kieran Healy. Last updated 11 months ago.

14.1 match 2.28 score 38 scripts

jhelvy

logitr:Logit Models w/Preference & WTP Space Utility Parameterizations

Fast estimation of multinomial (MNL) and mixed logit (MXL) models in R. Models can be estimated using "Preference" space or "Willingness-to-pay" (WTP) space utility parameterizations. Weighted models can also be estimated. An option is available to run a parallelized multistart optimization loop with random starting points in each iteration, which is useful for non-convex problems like MXL models or models with WTP space utility parameterizations. The main optimization loop uses the 'nloptr' package to minimize the negative log-likelihood function. Additional functions are available for computing and comparing WTP from both preference space and WTP space models and for predicting expected choices and choice probabilities for sets of alternatives based on an estimated model. Mixed logit models can include uncorrelated or correlated heterogeneity covariances and are estimated using maximum simulated likelihood based on the algorithms in Train (2009) <doi:10.1017/CBO9780511805271>. More details can be found in Helveston (2023) <doi:10.18637/jss.v105.i10>.

Maintained by John Helveston. Last updated 5 months ago.

log-likelihood logit logit-model mixed-logit mlogit multinomial-regression mxl mxl-models preference-space preferences willingness-to-pay wtp

3.4 match 54 stars 9.10 score 119 scripts 1 dependents

forestgeo

fgeo.plot:Plot ForestGEO Data

To help you access, transform, analyze, and visualize ForestGEO data, we developed a collection of R packages (<https://forestgeo.github.io/fgeo/>). This package, in particular, helps you to plot ForestGEO data. To learn more about ForestGEO visit <https://forestgeo.si.edu/>.

Maintained by Mauro Lepore. Last updated 3 years ago.

7.0 match 4 stars 4.26 score 5 scripts 1 dependents

flr

FLCore:Core Package of FLR, Fisheries Modelling in R

Core classes and methods for FLR, a framework for fisheries modelling and management strategy simulation in R. Developed by a team of fisheries scientists in various countries. More information can be found at <http://flr-project.org/>.

Maintained by Iago Mosqueira. Last updated 9 days ago.

fisheries flr fisheries-modelling

3.3 match 16 stars 8.78 score 956 scripts 23 dependents

rsquaredacademy

olsrr:Tools for Building OLS Regression Models

Tools designed to make it easier for users, particularly beginner/intermediate R users to build ordinary least squares regression models. Includes comprehensive regression output, heteroskedasticity tests, collinearity diagnostics, residual diagnostics, measures of influence, model fit assessment and variable selection procedures.

Maintained by Aravind Hebbali. Last updated 4 months ago.

collinearity-diagnostics linear-models regression stepwise-regression

2.3 match 103 stars 12.19 score 1.4k scripts 4 dependents

rubenfcasal

npsp:Nonparametric Spatial Statistics

Multidimensional nonparametric spatial (spatio-temporal) geostatistics. S3 classes and methods for multidimensional: linear binning, local polynomial kernel regression (spatial trend estimation), density and variogram estimation. Nonparametric methods for simultaneous inference on both spatial trend and variogram functions (for spatial processes). Nonparametric residual kriging (spatial prediction). For details on these methods see, for example, Fernandez-Casal and Francisco-Fernandez (2014) <doi:10.1007/s00477-013-0817-8> or Castillo-Paez et al. (2019) <doi:10.1016/j.csda.2019.01.017>.

Maintained by Ruben Fernandez-Casal. Last updated 4 months ago.

geostatistics spatial-data-analysis statistics fortran openblas

4.8 match 4 stars 5.71 score 64 scripts

jfrench

SpatialTools:Tools for Spatial Data Analysis

Tools for spatial data analysis. Emphasis on kriging. Provides functions for prediction and simulation. Intended to be relatively straightforward, fast, and flexible.

Maintained by Joshua French. Last updated 2 years ago.

openblas cpp

6.3 match 2 stars 4.38 score 100 scripts 4 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 9 days ago.

dataanalysis geoda geospatial cpp

3.4 match 73 stars 7.85 score 179 scripts 1 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

2.4 match 16 stars 11.18 score 261 scripts 26 dependents

phytoclass

phytoclass:Estimate Chla Concentrations of Phytoplankton Groups

Determine the chlorophyll a (Chl a) concentrations of different phytoplankton groups based on their pigment biomarkers. The method uses non-negative matrix factorisation and simulated annealing to minimise error between the observed and estimated values of pigment concentrations (Hayward et al. (2023) <doi:10.1002/lom3.10541>). The approach is similar to the widely used 'CHEMTAX' program (Mackey et al. 1996) <doi:10.3354/meps144265>, but is more straightforward, accurate, and not reliant on initial guesses for the pigment to Chl a ratios for phytoplankton groups.

Maintained by Alexander Hayward. Last updated 10 days ago.

4.5 match 2 stars 5.88 score 9 scripts

sinhrks

ggfortify:Data Visualization Tools for Statistical Analysis Results

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

Maintained by Yuan Tang. Last updated 9 months ago.

1.8 match 529 stars 14.49 score 9.1k scripts 22 dependents

iohprofiler

IOHanalyzer:Data Analysis Part of 'IOHprofiler'

The data analysis module for the Iterative Optimization Heuristics Profiler ('IOHprofiler'). This module provides statistical analysis methods for the benchmark data generated by optimization heuristics, which can be visualized through a web-based interface. The benchmark data is usually generated by the experimentation module, called 'IOHexperimenter'. 'IOHanalyzer' also supports the widely used 'COCO' (Comparing Continuous Optimisers) data format for benchmarking.

Maintained by Diederick Vermetten. Last updated 10 months ago.

cpp

5.1 match 24 stars 5.10 score 13 scripts

kenaho1

asbio:A Collection of Statistical Tools for Biologists

Contains functions from: Aho, K. (2014) Foundational and Applied Statistics for Biologists using R. CRC/Taylor and Francis, Boca Raton, FL, ISBN: 978-1-4398-7338-0.

Maintained by Ken Aho. Last updated 2 months ago.

3.5 match 5 stars 7.32 score 310 scripts 3 dependents

pablosanmar

amazonspR:Get Amazon Sp Data via the 'Windsor.ai' API

Collect your data on digital marketing campaigns from Amazon Sp using the 'Windsor.ai' API <https://windsor.ai/api-fields/>.

Maintained by Pablo Sanchez. Last updated 2 years ago.

9.5 match 2.70 score 3 scripts

wadpac

GGIR:Raw Accelerometer Data Analysis

A tool to process and analyse data collected with wearable raw acceleration sensors as described in Migueles and colleagues (JMPB 2019), and van Hees and colleagues (JApplPhysiol 2014; PLoSONE 2015). The package has been developed and tested for binary data from 'GENEActiv' <https://activinsights.com/>, binary (.gt3x) and .csv-export data from 'Actigraph' <https://theactigraph.com> devices, and binary (.cwa) and .csv-export data from 'Axivity' <https://axivity.com>. These devices are currently widely used in research on human daily physical activity. Further, the package can handle accelerometer data file from any other sensor brand providing that the data is stored in csv format. Also the package allows for external function embedding.

Maintained by Vincent T van Hees. Last updated 2 days ago.

accelerometer activity-recognition circadian-rhythm movement-sensor sleep

1.9 match 109 stars 13.20 score 342 scripts 3 dependents

dgerbing

lessR:Less Code, More Results

Each function replaces multiple standard R functions. For example, two function calls, Read() and CountAll(), generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for summary statistics via pivot tables, a comprehensive regression analysis, ANOVA and t-test, visualizations including the Violin/Box/Scatter plot for a numerical variable, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function call, variable labels, time series with aggregation and forecasting, color themes, and Trellis (facet) graphics. Also includes a confirmatory factor analysis of multiple indicator measurement models, pedagogical routines for data simulation such as for the Central Limit Theorem, generation and rendering of regression instructions for interpretative output, and interactive visualizations.

Maintained by David W. Gerbing. Last updated 1 months ago.

3.3 match 6 stars 7.47 score 394 scripts 3 dependents

tarnduong

ks:Kernel Smoothing

Kernel smoothers for univariate and multivariate data, with comprehensive visualisation and bandwidth selection capabilities, including for densities, density derivatives, cumulative distributions, clustering, classification, density ridges, significant modal regions, and two-sample hypothesis tests. Chacon & Duong (2018) <doi:10.1201/9780429485572>.

Maintained by Tarn Duong. Last updated 6 months ago.

2.3 match 6 stars 10.14 score 920 scripts 262 dependents

adeverse

adephylo:Exploratory Analyses for the Phylogenetic Comparative Method

Multivariate tools to analyze comparative data, i.e. a phylogeny and some traits measured for each taxa. The package contains functions to represent comparative data, compute phylogenetic proximities, perform multivariate analysis with phylogenetic constraints and test for the presence of phylogenetic autocorrelation. The package is described in Jombart et al (2010) <doi:10.1093/bioinformatics/btq292>.

Maintained by Aurélie Siberchicot. Last updated 2 days ago.

2.3 match 9 stars 10.05 score 312 scripts 4 dependents

gabrielshimizu

AgroR:Experimental Statistics and Graphics for Agricultural Sciences

Performs the analysis of completely randomized experimental designs (CRD), randomized blocks (RBD) and Latin square (LSD), experiments in double and triple factorial scheme (in CRD and RBD), experiments in subdivided plot scheme (in CRD and RBD), subdivided and joint analysis of experiments in CRD and RBD, linear regression analysis, test for two samples. The package performs analysis of variance, ANOVA assumptions and multiple comparison test of means or regression, according to Pimentel-Gomes (2009, ISBN: 978-85-7133-055-9), nonparametric test (Conover, 1999, ISBN: 0471160687), test for two samples, joint analysis of experiments according to Ferreira (2018, ISBN: 978-85-7269-566-4) and generalized linear model (glm) for binomial and Poisson family in CRD and RBD (Carvalho, FJ (2019), <doi:10.14393/ufu.te.2019.1244>). It can also be used to obtain descriptive measures and graphics, in addition to correlations and creative graphics used in agricultural sciences (Agronomy, Zootechnics, Food Science and related areas).

Maintained by Gabriel Danilo Shimizu. Last updated 11 months ago.

7.2 match 1 stars 3.11 score 173 scripts

flr

FLBRP:Reference Points for Fisheries Management

Calculates a range of biological reference points based upon yield per recruit and stock recruit based equilibrium calculations. These include F based reference points like F0.1, FMSY and biomass based reference points like BMSY.

Maintained by Iago Mosqueira. Last updated 3 months ago.

reference points fisheries flr cpp

3.3 match 2 stars 6.58 score 350 scripts 4 dependents

clementcalenge

adehabitatMA:Tools to Deal with Raster Maps

A collection of tools to deal with raster maps.

Maintained by Clement Calenge. Last updated 6 months ago.

3.4 match 1 stars 6.34 score 43 scripts 15 dependents

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 13 days ago.

biodiversity conservation ecology r-spatial raster spatial vector

2.3 match 110 stars 9.55 score 736 scripts 2 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 19 days ago.

cpp

3.3 match 3 stars 6.49 score 36 scripts 1 dependents

trevorhastie

gam:Generalized Additive Models

Functions for fitting and working with generalized additive models, as described in chapter 7 of "Statistical Models in S" (Chambers and Hastie (eds), 1991), and "Generalized Additive Models" (Hastie and Tibshirani, 1990).

Maintained by Trevor Hastie. Last updated 6 months ago.

fortran openblas

2.3 match 4 stars 9.50 score 2.2k scripts 61 dependents

r-forge

skellam:Densities and Sampling for the Skellam Distribution

Functions for the Skellam distribution, including: density (pmf), cdf, quantiles and regression.

Maintained by Patrick E. Brown. Last updated 1 years ago.

4.5 match 4.75 score 62 scripts 3 dependents

flr

mse:Tools for Running Management Strategy Evaluations using FLR

A set of functions and methods to enable the development and running of Management Strategy Evaluation (MSE) analyses, using the FLR packages and classes and the a4a methods and algorithms.

Maintained by Iago Mosqueira. Last updated 21 days ago.

simulation mse fisheries flr a4a

3.0 match 4 stars 7.04 score 137 scripts 3 dependents

rtsay1

MTS:All-Purpose Toolkit for Analyzing Multivariate Time Series (MTS) and Estimating Multivariate Volatility Models

Multivariate Time Series (MTS) is a general package for analyzing multivariate linear time series and estimating multivariate volatility models. It also handles factor models, constrained factor models, asymptotic principal component analysis commonly used in finance and econometrics, and principal volatility component analysis. (a) For the multivariate linear time series analysis, the package performs model specification, estimation, model checking, and prediction for many widely used models, including vector AR models, vector MA models, vector ARMA models, seasonal vector ARMA models, VAR models with exogenous variables, multivariate regression models with time series errors, augmented VAR models, and Error-correction VAR models for co-integrated time series. For model specification, the package performs structural specification to overcome the difficulties of identifiability of VARMA models. The methods used for structural specification include Kronecker indices and Scalar Component Models. (b) For multivariate volatility modeling, the MTS package handles several commonly used models, including multivariate exponentially weighted moving-average volatility, Cholesky decomposition volatility models, dynamic conditional correlation (DCC) models, copula-based volatility models, and low-dimensional BEKK models. The package also considers multiple tests for conditional heteroscedasticity, including rank-based statistics. (c) Finally, the MTS package also performs forecasting using diffusion index , transfer function analysis, Bayesian estimation of VAR models, and multivariate time series analysis with missing values.Users can also use the package to simulate VARMA models, to compute impulse response functions of a fitted VARMA model, and to calculate theoretical cross-covariance matrices of a given VARMA model.

Maintained by Ruey S. Tsay. Last updated 3 years ago.

cpp

3.2 match 6 stars 6.52 score 272 scripts 6 dependents

appsilon

shiny.semantic:Semantic UI Support for Shiny

Creating a great user interface for your Shiny apps can be a hassle, especially if you want to work purely in R and don't want to use, for instance HTML templates. This package adds support for a powerful UI library Fomantic UI - <https://fomantic-ui.com/> (before Semantic). It also supports universal UI input binding that works with various DOM elements.

Maintained by Jakub Nowicki. Last updated 11 months ago.

appsilon fomantic-ui rhinoverse semantic semantic-components semantic-ui shiny

1.5 match 506 stars 13.00 score 586 scripts 3 dependents

jrowen

rhandsontable:Interface to the 'Handsontable.js' Library

An R interface to the 'Handsontable' JavaScript library, which is a minimalist Excel-like data grid editor. See <https://handsontable.com/> for details.

Maintained by Jonathan Owen. Last updated 3 years ago.

handsontable htmlwidgets javascript shiny sparkline

1.5 match 389 stars 12.31 score 1.0k scripts 46 dependents

gabrielblain

CropWaterBalance:Climate Water Balance for Irrigation Purposes

Calculates daily climate water balance for irrigation purposes and also calculates the reference evapotranspiration (ET) using three methods, Penman and Monteith (Allen et al. 1998, ISBN:92-5-104219-5); Priestley and Taylor (1972) <doi:10/cr3qwn>; or Hargreaves and Samani (1985) <doi:10.13031/2013.26773>. Users may specify a management allowed depletion (MAD), which is used to suggest when to irrigate. The functionality allows for the use of crop and water stress coefficients as well.

Maintained by Gabriel Constantino Blain. Last updated 8 months ago.

3.4 match 7 stars 5.54 score 3 scripts

rostats

RSurveillance:Design and Analysis of Disease Surveillance Activities

A range of functions for the design and analysis of disease surveillance activities. These functions were originally developed for animal health surveillance activities but can be equally applied to aquatic animal, wildlife, plant and human health surveillance activities. Utilities are included for sample size calculation and analysis of representative surveys for disease freedom, risk-based studies for disease freedom and for prevalence estimation. This package is based on Cameron A., Conraths F., Frohlich A., Schauer B., Schulz K., Sergeant E., Sonnenburg J., Staubach C. (2015). R package of functions for risk-based surveillance. Deliverable 6.24, WP 6 - Decision making tools for implementing risk-based surveillance, Grant Number no. 310806, RISKSUR (<https://www.fp7-risksur.eu/sites/default/files/documents/Deliverables/RISKSUR_%28310806%29_D6.24.pdf>). Many of the 'RSurveillance' functions are incorporated into the 'epitools' website: Sergeant, ESG, 2019. Epitools epidemiological calculators. Ausvet Pty Ltd. Available at: <http://epitools.ausvet.com.au>.

Maintained by Rohan Sadler. Last updated 5 years ago.

4.5 match 3.98 score 64 scripts

milesott

strategicplayers:Strategic Players

Identifies individuals in a social network who should be the intervention subjects for a network intervention in which you have a group of targets, a group of avoiders, and a group that is neither.

Maintained by Miles Ott. Last updated 1 years ago.

6.6 match 2.70 score 1 scripts

malaria-atlas-project

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

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

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

database malaria opendata raster

1.9 match 44 stars 9.10 score 118 scripts 3 dependents

danielquiroz97

RGCxGC:Preprocessing and Multivariate Analysis of Bidimensional Gas Chromatography Data

Toolbox for chemometrics analysis of bidimensional gas chromatography data. This package import data for common scientific data format (NetCDF) and fold it to 2D chromatogram. Then, it can perform preprocessing and multivariate analysis. In the preprocessing algorithms, baseline correction, smoothing, and peak alignment are available. While in multivariate analysis, multiway principal component analysis is incorporated.

Maintained by Cristian Quiroz-Moreno. Last updated 2 years ago.

chemphys chemometrics gcxgc multiway-algorithms preprocessing

3.5 match 7 stars 4.77 score 17 scripts

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.

1.5 match 82 stars 10.93 score 306 scripts 3 dependents

predictiveecology

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

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

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

3.8 match 2 stars 4.33 score 178 scripts 1 dependents

appsilon

shiny.react:Tools for Using React in Shiny

A toolbox for defining React component wrappers which can be used seamlessly in Shiny apps.

Maintained by Jakub Sobolewski. Last updated 10 months ago.

react rhinoverse shiny

1.6 match 97 stars 10.20 score 83 scripts 4 dependents

nsj3

rioja:Analysis of Quaternary Science Data

Constrained clustering, transfer functions, and other methods for analysing Quaternary science data.

Maintained by Steve Juggins. Last updated 6 months ago.

cpp

2.3 match 10 stars 7.21 score 191 scripts 3 dependents

jwindle

BayesLogit:PolyaGamma Sampling

Tools for sampling from the PolyaGamma distribution based on Polson, Scott, and Windle (2013) <doi:10.1080/01621459.2013.829001>. Useful for logistic regression.

Maintained by Jesse Windle. Last updated 5 years ago.

cpp

2.3 match 16 stars 7.13 score 100 scripts 7 dependents

animint

animint2:Animated Interactive Grammar of Graphics

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

Maintained by Toby Hocking. Last updated 27 days ago.

1.8 match 64 stars 8.87 score 173 scripts

appsilon

shiny.fluent:Microsoft Fluent UI for Shiny Apps

A rich set of UI components for building Shiny applications, including inputs, containers, overlays, menus, and various utilities. All components from Fluent UI (the underlying JavaScript library) are available and have usage examples in R.

Maintained by Jakub Sobolewski. Last updated 10 months ago.

microsoft-fluent-ui react rhinoverse shiny

1.6 match 280 stars 9.91 score 656 scripts

cran

agricolae:Statistical Procedures for Agricultural Research

Original idea was presented in the thesis "A statistical analysis tool for agricultural research" to obtain the degree of Master on science, National Engineering University (UNI), Lima-Peru. Some experimental data for the examples come from the CIP and others research. Agricolae offers extensive functionality on experimental design especially for agricultural and plant breeding experiments, which can also be useful for other purposes. It supports planning of lattice, Alpha, Cyclic, Complete Block, Latin Square, Graeco-Latin Squares, augmented block, factorial, split and strip plot designs. There are also various analysis facilities for experimental data, e.g. treatment comparison procedures and several non-parametric tests comparison, biodiversity indexes and consensus cluster.

Maintained by Felipe de Mendiburu. Last updated 1 years ago.

2.3 match 7 stars 7.01 score 15 dependents

appsilon

shiny.i18n:Shiny Applications Internationalization

It provides easy internationalization of Shiny applications. It can be used as standalone translation package to translate reports, interactive visualizations or graphical elements as well.

Maintained by Jakub Nowicki. Last updated 11 months ago.

internationalization language rhinoverse shiny translation

1.6 match 168 stars 9.97 score 312 scripts 6 dependents

rdinnager

slimr:Create, Run and Post-Process 'SLiM' Population Genetics Forward Simulations

Lets you write 'SLiM' scripts (population genomics simulation) using your favourite R IDE, using a syntax as close as possible to the original 'SLiM' language. It offer many tools to manipulate those scripts, as well as run them in the 'SLiM' software from R, as well as capture and post-process their output, after or even during a simulation.

Maintained by Russell Dinnage. Last updated 4 months ago.

3.3 match 8 stars 4.70 score 42 scripts

clementcalenge

adehabitatLT:Analysis of Animal Movements

A collection of tools for the analysis of animal movements.

Maintained by Clement Calenge. Last updated 6 months ago.

1.8 match 6 stars 8.60 score 370 scripts 12 dependents

appsilon

shiny.telemetry:'Shiny' App Usage Telemetry

Enables instrumentation of 'Shiny' apps for tracking user session events such as input changes, browser type, and session duration. These events can be sent to any of the available storage backends and analyzed using the included 'Shiny' app to gain insights about app usage and adoption.

Maintained by André Veríssimo. Last updated 3 months ago.

analytics rhinoverse shiny

1.6 match 67 stars 9.69 score 29 scripts

cran

queueing:Analysis of Queueing Networks and Models

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

Maintained by Pedro Canadilla. Last updated 5 years ago.

5.6 match 2.58 score 376 scripts

mrc-ide

malariasimulation:An individual based model for malaria

Specifies the latest and greatest malaria model.

Maintained by Giovanni Charles. Last updated 27 days ago.

cpp

1.7 match 16 stars 8.17 score 146 scripts

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

1.3 match 399 stars 10.47 score 460 scripts 2 dependents

appsilon

rhino:A Framework for Enterprise Shiny Applications

A framework that supports creating and extending enterprise Shiny applications using best practices.

Maintained by Kamil Żyła. Last updated 3 days ago.

rhinoverse shiny

1.5 match 304 stars 8.99 score 145 scripts

ateucher

lutz:Look Up Time Zones of Point Coordinates

Input latitude and longitude values or an 'sf/sfc' POINT object and get back the time zone in which they exist. Two methods are implemented. One is very fast and uses 'Rcpp' in conjunction with data from the 'Javascript' library (<https://github.com/darkskyapp/tz-lookup-oss/>). This method also works outside of countries' borders and in international waters, however speed comes at the cost of accuracy - near time zone borders away from populated centres there is a chance that it will return the incorrect time zone. The other method is slower but more accurate - it uses the 'sf' package to intersect points with a detailed map of time zones from here: <https://github.com/evansiroky/timezone-boundary-builder/>. The package also contains several utility functions for helping to understand and visualize time zones, such as listing of world time zones, including information about daylight savings times and their offsets from UTC. You can also plot a time zone to visualize the UTC offset over a year and when daylight savings times are in effect.

Maintained by Andy Teucher. Last updated 1 years ago.

cpp

1.8 match 60 stars 7.76 score 163 scripts 10 dependents

fschaffner

websearchr:Access Domains and Search Popular Websites

Functions for accessing domains and a number of search engines.

Maintained by Florian S. Schaffner. Last updated 5 years ago.

internet search search-engine web

3.3 match 11 stars 4.04 score 20 scripts

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.

1.5 match 93 stars 8.88 score 106 scripts 4 dependents

azvoleff

gfcanalysis:Tools for Working with Hansen et al. Global Forest Change Dataset

Supports analyses using the Global Forest Change dataset released by Hansen et al. gfcanalysis was originally written for the Tropical Ecology Assessment and Monitoring (TEAM) Network. For additional details on the Global Forest Change dataset, see: Hansen, M. et al. 2013. "High-Resolution Global Maps of 21st-Century Forest Cover Change." Science 342 (15 November): 850-53. The forest change data and more information on the product is available at <http://earthenginepartners.appspot.com>.

Maintained by Matthew Cooper. Last updated 1 years ago.

2.7 match 17 stars 4.93 score 33 scripts

appsilon

shiny.router:Basic Routing for Shiny Web Applications

It is a simple router for your Shiny apps. The router allows you to create dynamic web applications with real-time User Interface and easily share url to pages within your Shiny apps.

Maintained by Ryszard Szymański. Last updated 11 months ago.

rhinoverse routing shiny

1.6 match 257 stars 8.50 score 165 scripts

bioc

SPsimSeq:Semi-parametric simulation tool for bulk and single-cell RNA sequencing data

SPsimSeq uses a specially designed exponential family for density estimation to constructs the distribution of gene expression levels from a given real RNA sequencing data (single-cell or bulk), and subsequently simulates a new dataset from the estimated marginal distributions using Gaussian-copulas to retain the dependence between genes. It allows simulation of multiple groups and batches with any required sample size and library size.

Maintained by Joris Meys. Last updated 5 months ago.

geneexpression rnaseq singlecell sequencing dnaseq

1.8 match 10 stars 7.14 score 29 scripts 1 dependents

michaelchirico

geohashTools:Tools for Working with Geohashes

Tools for working with Gustavo Niemeyer's geohash coordinate system, including API for interacting with other common R GIS libraries.

Maintained by Michael Chirico. Last updated 1 years ago.

1.8 match 52 stars 7.18 score 30 scripts 6 dependents

onofriandreapg

lmDiallel:Linear Fixed/Mixed Effects Models for Diallel Crosses

Several service functions to be used to analyse datasets obtained from diallel experiments within the frame of linear models in R, as described in Onofri et al (2020) <DOI:10.1007/s00122-020-03716-8>.

Maintained by Andrea Onofri. Last updated 2 years ago.

3.3 match 5 stars 3.74 score 22 scripts

kbhoehn

dowser:B Cell Receptor Phylogenetics Toolkit

Provides a set of functions for inferring, visualizing, and analyzing B cell phylogenetic trees. Provides methods to 1) reconstruct unmutated ancestral sequences, 2) build B cell phylogenetic trees using multiple methods, 3) visualize trees with metadata at the tips, 4) reconstruct intermediate sequences, 5) detect biased ancestor-descendant relationships among metadata types Workflow examples available at documentation site (see URL). Citations: Hoehn et al (2022) <doi:10.1371/journal.pcbi.1009885>, Hoehn et al (2021) <doi:10.1101/2021.01.06.425648>.

Maintained by Kenneth Hoehn. Last updated 2 months ago.

1.7 match 6.81 score 84 scripts

f8l5h9

spqdep:Testing for Spatial Independence of Cross-Sectional Qualitative Data

Testing for Spatial Dependence of Qualitative Data in Cross Section. The list of functions includes join-count tests, Q test, spatial scan test, similarity test and spatial runs test. The methodology of these models can be found in <doi:10.1007/s10109-009-0100-1> and <doi:10.1080/13658816.2011.586327>.

Maintained by Fernando Lopez. Last updated 3 months ago.

categorical-data qualitative-analysis spatial-data-analysis spatial-econometrics statistical-tests

3.9 match 3.00 score 3 scripts

cran

espadon:Easy Study of Patient DICOM Data in Oncology

Exploitation, processing and 2D-3D visualization of DICOM-RT files (structures, dosimetry, imagery) for medical physics and clinical research, in a patient-oriented perspective.

Maintained by Cathy Fontbonne. Last updated 1 months ago.

cpp

4.0 match 2.85 score

appsilon

box.linters:Linters for 'box' Modules

Static code analysis of 'box' modules. The package enhances code quality by providing linters that check for common issues, enforce best practices, and ensure consistent coding standards.

Maintained by Ricardo Rodrigo Basa. Last updated 6 months ago.

box linter rhinoverse shiny

1.6 match 10 stars 6.96 score 1 scripts 1 dependents

ropensci

lingtypology:Linguistic Typology and Mapping

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

Maintained by George Moroz. Last updated 5 months ago.

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

1.1 match 51 stars 9.58 score 694 scripts

appsilon

shiny.info:'shiny' Info

Displays simple diagnostic information of the 'shiny' project in the user interface of the app.

Maintained by Jakub Nowicki. Last updated 11 months ago.

rhinoverse shiny

1.6 match 61 stars 6.73 score 25 scripts

appsilon

data.validator:Automatic Data Validation and Reporting

Validate dataset by columns and rows using convenient predicates inspired by 'assertr' package. Generate good looking HTML report or print console output to display in logs of your data processing pipeline.

Maintained by Marcin Dubel. Last updated 11 months ago.

data reporting rhinoverse rstudio validation

1.6 match 147 stars 6.67 score 40 scripts

appsilon

box.lsp:Provides 'box' Compatibility for 'languageserver'

A 'box' compatible custom language parser for the 'languageserver' package to provide completion and signature hints in code editors.

Maintained by Ricardo Rodrigo Basa. Last updated 6 months ago.

1.6 match 5 stars 6.48 score 2 scripts 1 dependents

bappa10085

soilchemistry:Computation of Properties Related to Soil Chemical Environment and Nutrient Availability

Facilitates basic and equation-based analyses of some important soil properties related to soil chemical environment and nutrient availability to plants. Freundlich H (1907). <doi:10.1515/zpch-1907-5723>. Datta SP, Bhadoria PBS (1999). <doi:10.1002%2F%28SICI%291522-2624%28199903%29162%3A2%3C183%3A%3AAID-JPLN183%3E3.0.CO%3B2-A>."Boron adsorption and desorption in some acid soils of West Bengal, India". Langmuir I (1918). <doi:10.1021/ja02242a004> "The adsorption of gases on plane surfaces of glass, mica, and platinum". Khasawneh FE (1971). <doi:10.2136/sssaj1971.03615995003500030029x> "Solution ion activity and plant growth".

Maintained by Bappa Das. Last updated 3 months ago.

3.8 match 2.70 score

paulowhite

timeROC:Time-Dependent ROC Curve and AUC for Censored Survival Data

Estimation of time-dependent ROC curve and area under time dependent ROC curve (AUC) in the presence of censored data, with or without competing risks. Confidence intervals of AUCs and tests for comparing AUCs of two rival markers measured on the same subjects can be computed, using the iid-representation of the AUC estimator. Plot functions for time-dependent ROC curves and AUC curves are provided. Time-dependent Positive Predictive Values (PPV) and Negative Predictive Values (NPV) can also be computed. See Blanche et al. (2013) <doi:10.1002/sim.5958> and references therein for the details of the methods implemented in the package.

Maintained by Paul Blanche. Last updated 5 years ago.

1.6 match 9 stars 6.24 score 342 scripts 8 dependents

markusloecher

RgoogleMaps:Overlays on Static Maps

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

Maintained by Markus Loecher. Last updated 1 years ago.

1.7 match 1 stars 5.80 score 516 scripts 9 dependents

appsilon

shiny.benchmark:Benchmark the Performance of 'shiny' Applications

Compare performance between different versions of a 'shiny' application based on 'git' references.

Maintained by Douglas Azevedo. Last updated 11 months ago.

performance-testing rhinoverse shiny

1.7 match 31 stars 5.79 score 6 scripts

appsilon

reactable.extras:Extra Features for 'reactable' Package

Enhanced functionality for 'reactable' in 'shiny' applications, offering interactive and dynamic data table capabilities with ease. With 'reactable.extras', easily integrate a range of functions and components to enrich your 'shiny' apps and facilitate user-friendly data exploration.

Maintained by Recle Vibal. Last updated 5 months ago.

reactable shiny

1.6 match 43 stars 5.96 score 20 scripts

andrefujita

statGraph:Statistical Methods for Graphs

Contains statistical methods to analyze graphs, such as graph parameter estimation, model selection based on the Graph Information Criterion, statistical tests to discriminate two or more populations of graphs, correlation between graphs, and clustering of graphs. References: Takahashi et al. (2012) <doi:10.1371/journal.pone.0049949>, Fujita et al. (2017) <doi:10.3389/fnins.2017.00066>, Fujita et al. (2017) <doi:10.1016/j.csda.2016.11.016>, Fujita et al. (2019) <doi:10.1093/comnet/cnz028>.

Maintained by Andre Fujita. Last updated 7 months ago.

4.0 match 2 stars 2.29 score 14 scripts

bioc

CexoR:An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates

Strand specific peak-pair calling in ChIP-exo replicates. The cumulative Skellam distribution function is used to detect significant normalised count differences of opposed sign at each DNA strand (peak-pairs). Then, irreproducible discovery rate for overlapping peak-pairs across biological replicates is computed.

Maintained by Pedro Madrigal. Last updated 5 months ago.

functionalgenomics sequencing coverage chipseq peakdetection

2.3 match 4.00 score 1 scripts

mdbahadur

rhcoclust:Robust Hierarchical Co-Clustering to Identify Significant Co-Cluster

Here we performs robust hierarchical co-clustering between row and column entities of a data matrix in absence and presence of outlying observations. It can be used to explore important co-clusters consisting of important samples and their regulatory significant features. Please see Hasan, Badsha and Mollah (2020) <doi:10.1101/2020.05.13.094946>.

Maintained by Md. Bahadur Badsha. Last updated 2 years ago.

3.3 match 2.70 score 9 scripts

cran

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.

5.1 match 2 stars 1.78 score 1 dependents

mikejohnson51

AOI:Areas of Interest

A consistent tool kit for forward and reverse geocoding and defining boundaries for spatial analysis.

Maintained by Mike Johnson. Last updated 1 years ago.

aoi area-of-interest bounding-boxes gis spatial subset

1.7 match 37 stars 4.98 score 174 scripts 1 dependents

apwheele

ptools:Tools for Poisson Data

Functions used for analyzing count data, mostly crime counts. Includes checking difference in two Poisson counts (e-test), checking the fit for a Poisson distribution, small sample tests for counts in bins, Weighted Displacement Difference test (Wheeler and Ratcliffe, 2018) <doi:10.1186/s40163-018-0085-5>, to evaluate crime changes over time in treated/control areas. Additionally includes functions for aggregating spatial data and spatial feature engineering.

Maintained by Andrew Wheeler. Last updated 1 years ago.

crime-analysis criminal-justice criminology

1.8 match 5 stars 4.44 score 11 scripts

daijiang

lirrr:Functions collected/wrote by Daijiang Li

To keep all my functions in one place, and to use them more easily.

Maintained by Daijiang Li. Last updated 1 years ago.

4.6 match 1 stars 1.70 score 3 scripts

protviz

prozor:Minimal Protein Set Explaining Peptide Spectrum Matches

Determine minimal protein set explaining peptide spectrum matches. Utility functions for creating fasta amino acid databases with decoys and contaminants. Peptide false discovery rate estimation for target decoy search results on psm, precursor, peptide and protein level. Computing dynamic swath window sizes based on MS1 or MS2 signal distributions.

Maintained by Witold Wolski. Last updated 4 months ago.

software massspectrometry proteomics experimenthubsoftware

1.7 match 6 stars 4.45 score 93 scripts

cantonfe

sitree:Single Tree Simulator

Framework to build an individual tree simulator.

Maintained by Clara Anton Fernandez. Last updated 1 years ago.

2.3 match 3.37 score 39 scripts 1 dependents

vmoprojs

GeoModels:Procedures for Gaussian and Non Gaussian Geostatistical (Large) Data Analysis

Functions for Gaussian and Non Gaussian (bivariate) spatial and spatio-temporal data analysis are provided for a) (fast) simulation of random fields, b) inference for random fields using standard likelihood and a likelihood approximation method called weighted composite likelihood based on pairs and b) prediction using (local) best linear unbiased prediction. Weighted composite likelihood can be very efficient for estimating massive datasets. Both regression and spatial (temporal) dependence analysis can be jointly performed. Flexible covariance models for spatial and spatial-temporal data on Euclidean domains and spheres are provided. There are also many useful functions for plotting and performing diagnostic analysis. Different non Gaussian random fields can be considered in the analysis. Among them, random fields with marginal distributions such as Skew-Gaussian, Student-t, Tukey-h, Sin-Arcsin, Two-piece, Weibull, Gamma, Log-Gaussian, Binomial, Negative Binomial and Poisson. See the URL for the papers associated with this package, as for instance, Bevilacqua and Gaetan (2015) <doi:10.1007/s11222-014-9460-6>, Bevilacqua et al. (2016) <doi:10.1007/s13253-016-0256-3>, Vallejos et al. (2020) <doi:10.1007/978-3-030-56681-4>, Bevilacqua et. al (2020) <doi:10.1002/env.2632>, Bevilacqua et. al (2021) <doi:10.1111/sjos.12447>, Bevilacqua et al. (2022) <doi:10.1016/j.jmva.2022.104949>, Morales-Navarrete et al. (2023) <doi:10.1080/01621459.2022.2140053>, and a large class of examples and tutorials.

Maintained by Moreno Bevilacqua. Last updated 2 months ago.

fortran openblas glibc

1.8 match 3 stars 4.17 score 83 scripts

mxrodriguezuvigo

ROCnReg:ROC Curve Inference with and without Covariates

Estimates the pooled (unadjusted) Receiver Operating Characteristic (ROC) curve, the covariate-adjusted ROC (AROC) curve, and the covariate-specific/conditional ROC (cROC) curve by different methods, both Bayesian and frequentist. Also, it provides functions to obtain ROC-based optimal cutpoints utilizing several criteria. Based on Erkanli, A. et al. (2006) <doi:10.1002/sim.2496>; Faraggi, D. (2003) <doi:10.1111/1467-9884.00350>; Gu, J. et al. (2008) <doi:10.1002/sim.3366>; Inacio de Carvalho, V. et al. (2013) <doi:10.1214/13-BA825>; Inacio de Carvalho, V., and Rodriguez-Alvarez, M.X. (2022) <doi:10.1214/21-STS839>; Janes, H., and Pepe, M.S. (2009) <doi:10.1093/biomet/asp002>; Pepe, M.S. (1998) <http://www.jstor.org/stable/2534001?seq=1>; Rodriguez-Alvarez, M.X. et al. (2011a) <doi:10.1016/j.csda.2010.07.018>; Rodriguez-Alvarez, M.X. et al. (2011a) <doi:10.1007/s11222-010-9184-1>. Please see Rodriguez-Alvarez, M.X. and Inacio, V. (2021) <doi:10.32614/RJ-2021-066> for more details.

Maintained by Maria Xose Rodriguez-Alvarez. Last updated 10 months ago.

4.5 match 1 stars 1.66 score 46 scripts

hypertidy

graticule:Meridional and Parallel Lines for Maps

Create graticule lines and labels for maps. Control the creation of lines or tiles by setting their placement (at particular meridians and parallels) and extent (along parallels and meridians). Labels are created independently of lines.

Maintained by Michael D. Sumner. Last updated 1 years ago.

1.3 match 18 stars 5.94 score 97 scripts

professorbeautiful

NNTbiomarker:Calculate Design Parameters for Biomarker Validation Studies

Helps a clinical trial team discuss the clinical goals of a well-defined biomarker with a diagnostic, staging, prognostic, or predictive purpose. From this discussion will come a statistical plan for a (non-randomized) validation trial. Both prospective and retrospective trials are supported. In a specific focused discussion, investigators should determine the range of "discomfort" for the NNT, number needed to treat. The meaning of the discomfort range, [NNTlower, NNTupper], is that within this range most physicians would feel discomfort either in treating or withholding treatment. A pair of NNT values bracketing that range, NNTpos and NNTneg, become the targets of the study's design. If the trial can demonstrate that a positive biomarker test yields an NNT less than NNTlower, and that a negative biomarker test yields an NNT less than NNTlower, then the biomarker may be useful for patients. A highlight of the package is visualization of a "contra-Bayes" theorem, which produces criteria for retrospective case-controls studies.

Maintained by Roger Day. Last updated 6 years ago.

2.0 match 3.65 score 15 scripts

luismurao

tenm:Temporal Ecological Niche Models

Implements methods and functions to calibrate time-specific niche models (multi-temporal calibration), letting users execute a strict calibration and selection process of niche models based on ellipsoids, as well as functions to project the potential distribution in the present and in global change scenarios.The 'tenm' package has functions to recover information that may be lost or overlooked while applying a data curation protocol. This curation involves preserving occurrences that may appear spatially redundant (occurring in the same pixel) but originate from different time periods. A novel aspect of this package is that it might reconstruct the fundamental niche more accurately than mono-calibrated approaches. The theoretical background of the package can be found in Peterson et al. (2011)<doi:10.5860/CHOICE.49-6266>.

Maintained by Luis Osorio-Olvera. Last updated 8 months ago.

1.3 match 5 stars 5.77 score 34 scripts

freezenik

BayesX:R Utilities Accompanying the Software Package BayesX

Functions for exploring and visualising estimation results obtained with BayesX, a free software for estimating structured additive regression models (<https://www.uni-goettingen.de/de/bayesx/550513.html>). In addition, functions that allow to read, write and manipulate map objects that are required in spatial analyses performed with BayesX.

Maintained by Nikolaus Umlauf. Last updated 1 years ago.

1.9 match 3.71 score 48 scripts 3 dependents

yongkai17

spFSR:Feature Selection and Ranking by Simultaneous Perturbation Stochastic Approximation

An implementation of feature selection and ranking via simultaneous perturbation stochastic approximation (SPSA-FSR) based on works by V. Aksakalli and M. Malekipirbazari (2015) <arXiv:1508.07630> and Zeren D. Yenice and et al. (2018) <arXiv:1804.05589>. The SPSA-FSR algorithm searches for a locally optimal set of features that yield the best predictive performance using a specified error measure such as mean squared error (for regression problems) and accuracy rate (for classification problems). This package requires an object of class 'task' and an object of class 'Learner' from the 'mlr' package.

Maintained by Vural Aksakalli. Last updated 6 years ago.

1.7 match 2 stars 4.00 score 8 scripts

rubens2005

criticalpath:An Implementation of the Critical Path Method

An R implementation of the Critical Path Method (CPM). CPM is a method used to estimate the minimum project duration and determine the amount of scheduling flexibility on the logical network paths within the schedule model. The flexibility is in terms of early start, early finish, late start, late finish, total float and free float. Beside, it permits to quantify the complexity of network diagram through the analysis of topological indicators. Finally, it permits to change the activities duration to perform what-if scenario analysis. The package was built based on following references: To make topological sorting and other graph operation, we use Csardi, G. & Nepusz, T. (2005) <https://www.researchgate.net/publication/221995787_The_Igraph_Software_Package_for_Complex_Network_Research>; For schedule concept, the reference was Project Management Institute (2017) <https://www.pmi.org/pmbok-guide-standards/foundational/pmbok>; For standards terms, we use Project Management Institute (2017) <https://www.pmi.org/pmbok-guide-standards/lexicon>; For algorithms on Critical Path Method development, we use Vanhoucke, M. (2013) <doi:10.1007/978-3-642-40438-2> and Vanhoucke, M. (2014) <doi:10.1007/978-3-319-04331-9>; And, finally, for topological definitions, we use Vanhoucke, M. (2009) <doi:10.1007/978-1-4419-1014-1>.

Maintained by Rubens Jose Rosa. Last updated 3 years ago.

1.8 match 1 stars 3.70 score 5 scripts

freezenik

R2BayesX:Estimate Structured Additive Regression Models with 'BayesX'

An R interface to estimate structured additive regression (STAR) models with 'BayesX'.

Maintained by Nikolaus Umlauf. Last updated 1 years ago.

1.9 match 1 stars 3.55 score 118 scripts 1 dependents

cran

MSclassifR:Automated Classification of Mass Spectra

Functions to classify mass spectra in known categories, and to determine discriminant mass-over-charge values. It includes easy-to-use functions for pre-processing mass spectra, functions to determine discriminant mass-over-charge values (m/z) from a library of mass spectra corresponding to different categories, and functions to predict the category (species, phenotypes, etc.) associated to a mass spectrum from a list of selected mass-over-charge values. Three vignettes illustrating how to use the functions of this package from real data sets are also available online to help users: <https://agodmer.github.io/MSclassifR_examples/Vignettes/Vignettemsclassifr_Ecrobiav3.html>, <https://agodmer.github.io/MSclassifR_examples/Vignettes/Vignettemsclassifr_Klebsiellav3.html> and <https://agodmer.github.io/MSclassifR_examples/Vignettes/Vignettemsclassifr_DAv3.html>.

Maintained by Alexandre Godmer. Last updated 2 years ago.

6.3 match 1 stars 1.00 score

ksbakar

spTDyn:Spatially Varying and Spatio-Temporal Dynamic Linear Models

Fits, spatially predicts, and temporally forecasts space-time data using Gaussian Process (GP): (1) spatially varying coefficient process models and (2) spatio-temporal dynamic linear models. Bakar et al., (2016). Bakar et al., (2015).

Maintained by K. Shuvo Bakar. Last updated 6 months ago.

3.3 match 1 stars 1.82 score 22 scripts 1 dependents

ropensci

antanym:Antarctic Geographic Place Names

Antarctic geographic names from the Composite Gazetteer of Antarctica, and functions for working with those place names.

Maintained by Ben Raymond. Last updated 3 years ago.

antarctic southern ocean place names gazetteer peer-reviewed

1.5 match 7 stars 3.89 score 22 scripts

cran

shiny.blueprint:Palantir's 'Blueprint' for 'Shiny' Apps

Easily use 'Blueprint', the popular 'React' library from Palantir, in your 'Shiny' app. 'Blueprint' provides a rich set of UI components for creating visually appealing applications and is optimized for building complex, data-dense web interfaces. This package provides most components from the underlying library, as well as special wrappers for some components to make it easy to use them in 'R' without writing 'JavaScript' code.

Maintained by Jakub Sobolewski. Last updated 10 months ago.

1.6 match 3.70 score

xiaoruizhu

SPSP:Selection by Partitioning the Solution Paths

An implementation of the feature Selection procedure by Partitioning the entire Solution Paths (namely SPSP) to identify the relevant features rather than using a single tuning parameter. By utilizing the entire solution paths, this procedure can obtain better selection accuracy than the commonly used approach of selecting only one tuning parameter based on existing criteria, cross-validation (CV), generalized CV, AIC, BIC, and extended BIC (Liu, Y., & Wang, P. (2018) <doi:10.1214/18-EJS1434>). It is more stable and accurate (low false positive and false negative rates) than other variable selection approaches. In addition, it can be flexibly coupled with the solution paths of Lasso, adaptive Lasso, ridge regression, and other penalized estimators.

Maintained by Xiaorui (Jeremy) Zhu. Last updated 1 years ago.

feature-selection statistics variable-selection cpp

1.6 match 1 stars 3.60 score 2 scripts

ropensci

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

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

Maintained by Michael Mahoney. Last updated 1 years ago.

geojson topojson geospatial conversion data input-output io

0.5 match 151 stars 10.80 score 2.9k scripts 13 dependents

tianxili

randnet:Random Network Model Estimation, Selection and Parameter Tuning

Model selection and parameter tuning procedures for a class of random network models. The model selection can be done by a general cross-validation framework called ECV from Li et. al. (2016) <arXiv:1612.04717> . Several other model-based and task-specific methods are also included, such as NCV from Chen and Lei (2016) <arXiv:1411.1715>, likelihood ratio method from Wang and Bickel (2015) <arXiv:1502.02069>, spectral methods from Le and Levina (2015) <arXiv:1507.00827>. Many network analysis methods are also implemented, such as the regularized spectral clustering (Amini et. al. 2013 <doi:10.1214/13-AOS1138>) and its degree corrected version and graphon neighborhood smoothing (Zhang et. al. 2015 <arXiv:1509.08588>). It also includes the consensus clustering of Gao et. al. (2014) <arXiv:1410.5837>, the method of moments estimation of nomination SBM of Li et. al. (2020) <arxiv:2008.03652>, and the network mixing method of Li and Le (2021) <arxiv:2106.02803>. It also includes the informative core-periphery data processing method of Miao and Li (2021) <arXiv:2101.06388>. The work to build and improve this package is partially supported by the NSF grants DMS-2015298 and DMS-2015134.

Maintained by Tianxi Li. Last updated 2 years ago.

2.3 match 2.45 score 47 scripts 2 dependents

z0on

MCMC.OTU:Bayesian Analysis of Multivariate Counts Data in DNA Metabarcoding and Ecology

Poisson-lognormal generalized linear mixed model analysis of multivariate counts data using MCMC, aiming to infer the changes in relative proportions of individual variables. The package was originally designed for sequence-based analysis of microbial communities ("metabarcoding", variables = operational taxonomic units, OTUs), but can be used for other types of multivariate counts, such as in ecological applications (variables = species). The results are summarized and plotted using 'ggplot2' functions. Includes functions to remove sample and variable outliers and reformat counts into normalized log-transformed values for correlation and principal component/coordinate analysis. Walkthrough and examples: http://www.bio.utexas.edu/research/matz_lab/matzlab/Methods_files/walkthroughExample_mcmcOTU_R.txt.

Maintained by Mikhail V. Matz. Last updated 9 years ago.

3.4 match 1.53 score 34 scripts

cran

separationplot:Separation Plots

Visual representations of model fit or predictive success in the form of "separation plots." See Greenhill, Brian, Michael D. Ward, and Audrey Sacks. "The separation plot: A new visual method for evaluating the fit of binary models." American Journal of Political Science 55.4 (2011): 991-1002.

Maintained by Brian Greenhill. Last updated 2 years ago.

2.3 match 2.26 score 3 dependents

sunsmiling

PPtreeregViz:Projection Pursuit Regression Tree Visualization

It was developed as a tool for exploring 'PPTreereg' (Projection Pursuit TREE of REGression). It uses various projection pursuit indexes and 'XAI' (eXplainable Artificial Intelligence) methods to help understand the model by finding connections between the input variables and prediction values of the model. The 'KernelSHAP' (Aas, Jullum and Løland (2019) <arXiv:1903.10464>) algorithm was modified to fit ‘PPTreereg’, and some codes were modified from the 'shapr' package (Sellereite, Nikolai, and Martin Jullum (2020) <doi:10.21105/joss.02027>). The implemented methods help to explore the model at the single instance level as well as at the whole dataset level. Users can compare with other machine learning models by applying it to the 'DALEX' package of 'R'.

Maintained by HyunSun Cho. Last updated 1 years ago.

openblas cpp

1.7 match 2 stars 3.00 score 3 scripts

fvidoli

Compind:Composite Indicators Functions

A collection of functions to calculate Composite Indicators methods, focusing, in particular, on the normalisation and weighting-aggregation steps, as described in OECD Handbook on constructing composite indicators: methodology and user guide, 2008, 'Vidoli' and 'Fusco' and 'Mazziotta' <doi:10.1007/s11205-014-0710-y>, 'Mazziotta' and 'Pareto' (2016) <doi:10.1007/s11205-015-0998-2>, 'Van Puyenbroeck and 'Rogge' <doi:10.1016/j.ejor.2016.07.038> and other authors.

Maintained by Francesco Vidoli. Last updated 2 months ago.

1.7 match 1 stars 2.90 score 40 scripts

cran

support.BWS:Tools for Case 1 Best-Worst Scaling

Provides basic functions that support an implementation of object case (Case 1) best-worst scaling: a function for converting a two-level orthogonal main-effect design/balanced incomplete block design into questions; two functions for creating a data set suitable for analysis; a function for calculating count-based scores; a function for calculating shares of preference; and a function for generating artificial responses to questions. See Louviere et al. (2015) <doi:10.1017/CBO9781107337855> for details on best-worst scaling, and Aizaki and Fogarty (2023) <doi:10.1016/j.jocm.2022.100394> for the package.

Maintained by Hideo Aizaki. Last updated 2 years ago.

2.3 match 1 stars 1.95 score 1 dependents

bioc

SPIAT:Spatial Image Analysis of Tissues

SPIAT (**Sp**atial **I**mage **A**nalysis of **T**issues) is an R package with a suite of data processing, quality control, visualization and data analysis tools. SPIAT is compatible with data generated from single-cell spatial proteomics platforms (e.g. OPAL, CODEX, MIBI, cellprofiler). SPIAT reads spatial data in the form of X and Y coordinates of cells, marker intensities and cell phenotypes. SPIAT includes six analysis modules that allow visualization, calculation of cell colocalization, categorization of the immune microenvironment relative to tumor areas, analysis of cellular neighborhoods, and the quantification of spatial heterogeneity, providing a comprehensive toolkit for spatial data analysis.

Maintained by Yuzhou Feng. Last updated 2 days ago.

biomedicalinformatics cellbiology spatial clustering dataimport immunooncology qualitycontrol singlecell software visualization

0.5 match 22 stars 8.59 score 69 scripts

predictiveecology

quickPlot:A System of Plotting Optimized for Speed and Modularity

A high-level plotting system, compatible with `ggplot2` objects, maps from `sf`, `terra`, `raster`, `sp`. It is built primarily on the 'grid' package. The objective of the package is to provide a plotting system that is built for speed and modularity. This is useful for quick visualizations when testing code and for plotting multiple figures to the same device from independent sources that may be independent of one another (i.e., different function or modules the create the visualizations). The suggested package 'fastshp' can be installed from the repository (<https://PredictiveEcology.r-universe.dev>).

Maintained by Eliot J B McIntire. Last updated 4 months ago.

plotting visualization

0.5 match 6 stars 7.92 score 121 scripts 12 dependents

trackage

trip:Tracking Data

Access and manipulate spatial tracking data, with straightforward coercion from and to other formats. Filter for speed and create time spent maps from tracking data. There are coercion methods to convert between 'trip' and 'ltraj' from 'adehabitatLT', and between 'trip' and 'psp' and 'ppp' from 'spatstat'. Trip objects can be created from raw or grouped data frames, and from types in the 'sp', sf', 'amt', 'trackeR', 'mousetrap', and other packages, Sumner, MD (2011) <https://figshare.utas.edu.au/articles/thesis/The_tag_location_problem/23209538>.

Maintained by Michael D. Sumner. Last updated 8 months ago.

0.5 match 13 stars 7.72 score 137 scripts 1 dependents

bayesstats

bamdit:Bayesian Meta-Analysis of Diagnostic Test Data

Provides a new class of Bayesian meta-analysis models that incorporates a model for internal and external validity bias. In this way, it is possible to combine studies of diverse quality and different types. For example, we can combine the results of randomized control trials (RCTs) with the results of observational studies (OS).

Maintained by Pablo Emilio Verde. Last updated 1 months ago.

jags cpp

1.8 match 2.05 score 14 scripts

cran

geoTS:Methods for Handling and Analyzing Time Series of Satellite Images

Provides functions and methods for: splitting large raster objects into smaller chunks, transferring images from a binary format into raster layers, transferring raster layers into an 'RData' file, calculating the maximum gap (amount of consecutive missing values) of a numeric vector, and fitting harmonic regression models to periodic time series. The homoscedastic harmonic regression model is based on G. Roerink, M. Menenti and W. Verhoef (2000) <doi:10.1080/014311600209814>.

Maintained by Inder Tecuapetla-Gómez. Last updated 2 years ago.

1.9 match 1.78 score 9 scripts 2 dependents

stevenpawley

Rsagacmd:Linking R with the Open-Source 'SAGA-GIS' Software

Provides an R scripting interface to the open-source 'SAGA-GIS' (System for Automated Geoscientific Analyses Geographical Information System) software. 'Rsagacmd' dynamically generates R functions for every 'SAGA-GIS' geoprocessing tool based on the user's currently installed 'SAGA-GIS' version. These functions are contained within an S3 object and are accessed as a named list of libraries and tools. This structure facilitates an easier scripting experience by organizing the large number of 'SAGA-GIS' geoprocessing tools (>700) by their respective library. Interactive scripting can fully take advantage of code autocompletion tools (e.g. in 'RStudio'), allowing for each tools syntax to be quickly recognized. Furthermore, the most common types of spatial data (via the 'terra', 'sp', and 'sf' packages) along with non-spatial data are automatically passed from R to the 'SAGA-GIS' command line tool for geoprocessing operations, and the results are loaded as the appropriate R object. Outputs from individual 'SAGA-GIS' tools can also be chained using pipes from the 'magrittr' and 'dplyr' packages to combine complex geoprocessing operations together in a single statement. 'SAGA-GIS' is available under a GPLv2 / LGPLv2 licence from <https://sourceforge.net/projects/saga-gis/> including Windows x86/x64 and macOS binaries. SAGA-GIS is also included in Debian/Ubuntu default software repositories. Rsagacmd has currently been tested on 'SAGA-GIS' versions from 2.3.1 to 9.5.1 on Windows, Linux and macOS.

Maintained by Steven Pawley. Last updated 6 months ago.

0.5 match 32 stars 6.27 score 77 scripts

cran

sidier:Substitution and Indel Distances to Infer Evolutionary Relationships

Evolutionary reconstruction based on substitutions and insertion-deletion (indels) analyses in a distance-based framework.

Maintained by A.J. Muñoz-Pajares. Last updated 4 years ago.

2.0 match 1.56 score 36 scripts

fmmattioni

lactater:Tools for Analyzing Lactate Thresholds

Set of tools for analyzing lactate thresholds from a step incremental test to exhaustion. Easily analyze the methods Log-log, Onset of Blood Lactate Accumulation (OBLA), Baseline plus (Bsln+), Dmax, Lactate Turning Point (LTP), and Lactate / Intensity ratio (LTratio) in cycling, running, or swimming. Beaver WL, Wasserman K, Whipp BJ (1985) <doi:10.1152/jappl.1985.59.6.1936>. Heck H, Mader A, Hess G, Mücke S, Müller R, Hollmann W (1985) <doi:10.1055/s-2008-1025824>. Kindermann W, Simon G, Keul J (1979) <doi:10.1007/BF00421101>. Skinner JS, Mclellan TH (1980) <doi:10.1080/02701367.1980.10609285>. Berg A, Jakob E, Lehmann M, Dickhuth HH, Huber G, Keul J (1990) <PMID:2408033>. Zoladz JA, Rademaker AC, Sargeant AJ (1995) <doi:10.1113/jphysiol.1995.sp020959>. Cheng B, Kuipers H, Snyder A, Keizer H, Jeukendrup A, Hesselink M (1992) <doi:10.1055/s-2007-1021309>. Bishop D, Jenkins DG, Mackinnon LT (1998) <doi:10.1097/00005768-199808000-00014>. Hughson RL, Weisiger KH, Swanson GD (1987) <doi:10.1152/jappl.1987.62.5.1975>. Jamnick NA, Botella J, Pyne DB, Bishop DJ (2018) <doi:10.1371/journal.pone.0199794>. Hofmann P, Tschakert G (2017) <doi:10.3389/fphys.2017.00337>. Hofmann P, Pokan R, von Duvillard SP, Seibert FJ, Zweiker R, Schmid P (1997) <doi:10.1097/00005768-199706000-00005>. Pokan R, Hofmann P, Von Duvillard SP, et al. (1997) <doi:10.1097/00005768-199708000-00009>. Dickhuth H-H, Yin L, Niess A, et al. (1999) <doi:10.1055/s-2007-971105>.

Maintained by Felipe Mattioni Maturana. Last updated 1 years ago.

0.8 match 23 stars 4.06 score 4 scripts

ropensci

qualR:An R package to download São Paulo and Rio de Janeiro air pollution data

A package to download information from CETESB QUALAR <https://cetesb.sp.gov.br/ar/qualar/> and MonitorAr <http://jeap.rio.rj.gov.br/je-metinfosmac/institucional/index.html> systems. It contains function to download different parameters, a set of criteria pollutants and the most frequent meteorological parameters used in air quality data analysis and air quality model evaluation.

Maintained by Mario Gavidia-Calderón. Last updated 26 days ago.

air-pollutants air-quality-data air-quality-measurements brazil cetesb rio-de-janeiro sao-paulo weather-data

0.5 match 25 stars 5.20 score 21 scripts

cran

FAwR:Functions and Datasets for "Forest Analytics with R"

Provides functions and datasets from the book "Forest Analytics with R".

Maintained by Andrew Robinson. Last updated 4 years ago.

2.0 match 2 stars 1.30 score

gplates

rgplates:R Interface for the GPlates Web Service and Desktop Application

Query functions to the GPlates <https://www.gplates.org/> Desktop Application and the GPlates Web Service <https://gws.gplates.org/> allow users to reconstruct past positions of geographic entities based on user-selected rotation models without leaving the R running environment. The online method (GPlates Web Service) makes the rotation of static plates, coastlines, and a low number of geographic coordinates available using nothing but an internet connection. The offline method requires an external installation of the GPlates Desktop Application, but allows the efficient batch rotation of thousands of coordinates, Simple Features (sf) and Spatial (sp) objects with custom reconstruction trees and partitioning polygons. Examples of such plate tectonic models are accessible via the chronosphere <https://cran.r-project.org/package=chronosphere>. This R extension is developed under the umbrella of the DFG (Deutsche Forschungsgemeinschaft) Research Unit TERSANE2 (For 2332, TEmperature Related Stressors in ANcient Extinctions).

Maintained by Adam T. Kocsis. Last updated 6 months ago.

0.5 match 4 stars 4.82 score 55 scripts

jcaledo

EnvNJ:Whole Genome Phylogenies Using Sequence Environments

Contains utilities for the analysis of protein sequences in a phylogenetic context. Allows the generation of phylogenetic trees base on protein sequences in an alignment-independent way. Two different methods have been implemented. One approach is based on the frequency analysis of n-grams, previously described in Stuart et al. (2002) <doi:10.1093/bioinformatics/18.1.100>. The other approach is based on the species-specific neighborhood preference around amino acids. Features include the conversion of a protein set into a vector reflecting these neighborhood preferences, pairwise distances (dissimilarity) between these vectors, and the generation of trees based on these distance matrices.

Maintained by Juan Carlos Aledo. Last updated 3 years ago.

2.3 match 1.04 score 11 scripts

cran

NetworkReg:Generalized Linear Regression Models on Network-Linked Data with Statistical Inference

Linear regression model and generalized linear models with nonparametric network effects on network-linked observations. The model is originally proposed by Le and Li (2022) <doi:10.48550/arXiv.2007.00803> and is assumed on observations that are connected by a network or similar relational data structure. A more recent work by Wang, Le and Li (2024) <doi:10.48550/arXiv.2410.01163> further extends the framework to generalized linear models. All these models are implemented in the current package. The model does not assume that the relational data or network structure to be precisely observed; thus, the method is provably robust to a certain level of perturbation of the network structure. The package contains the estimation and inference function for the model.

Maintained by Jianxiang Wang. Last updated 5 months ago.

2.3 match 1.00 score

lafaye

ConvergenceConcepts:Seeing Convergence Concepts in Action

This is a pedagogical package, designed to help students understanding convergence of random variables. It provides a way to investigate interactively various modes of convergence (in probability, almost surely, in law and in mean) of a sequence of i.i.d. random variables. Visualisation of simulated sample paths is possible through interactive plots. The approach is illustrated by examples and exercises through the function 'investigate', as described in Lafaye de Micheaux and Liquet (2009) <doi:10.1198/tas.2009.0032>. The user can study his/her own sequences of random variables.

Maintained by Pierre Lafaye De Micheaux. Last updated 3 years ago.

2.3 match 1.00 score 10 scripts

ianmcook

wkb:Convert Between Spatial Objects and Well-Known Binary Geometry

Utility functions to convert between the 'Spatial' classes specified by the package 'sp', and the well-known binary '(WKB)' representation for geometry specified by the 'Open Geospatial Consortium'. Supports 'Spatial' objects of class 'SpatialPoints', 'SpatialPointsDataFrame', 'SpatialLines', 'SpatialLinesDataFrame', 'SpatialPolygons', and 'SpatialPolygonsDataFrame'. Supports 'WKB' geometry types 'Point', 'LineString', 'Polygon', 'MultiPoint', 'MultiLineString', and 'MultiPolygon'. Includes extensions to enable creation of maps with 'TIBCO Spotfire'.

Maintained by Ian Cook. Last updated 5 years ago.

0.5 match 6 stars 3.98 score 32 scripts

rte-antares-rpackage

spMaps:Europe SpatialPolygonsDataFrame Builder

Build custom Europe SpatialPolygonsDataFrame, if you don't know what is a SpatialPolygonsDataFrame see SpatialPolygons() in 'sp', by example for mapLayout() in 'antaresViz'. Antares is a powerful software developed by RTE to simulate and study electric power systems (more information about 'Antares' here: <https://antares-simulator.org/>).

Maintained by Tatiana Vargas. Last updated 2 months ago.

maps rte spatialpolygons spatialpolygonsdataframe

0.5 match 1 stars 3.88 score 6 scripts 1 dependents

cran

SALTSampler:Efficient Sampling on the Simplex

The SALTSampler package facilitates Monte Carlo Markov Chain (MCMC) sampling of random variables on a simplex. A Self-Adjusting Logit Transform (SALT) proposal is used so that sampling is still efficient even in difficult cases, such as those in high dimensions or with parameters that differ by orders of magnitude. Special care is also taken to maintain accuracy even when some coordinates approach 0 or 1 numerically. Diagnostic and graphic functions are included in the package, enabling easy assessment of the convergence and mixing of the chain within the constrained space.

Maintained by Scott Vander Wiel. Last updated 8 years ago.

2.0 match 1.00 score

beanb2

intkrige:A Numerical Implementation of Interval-Valued Kriging

An interval-valued extension of ordinary and simple kriging. Optimization of the function is based on a generalized interval distance. This creates a non-differentiable cost function that requires a differentiable approximation to the absolute value function. This differentiable approximation is optimized using a Newton-Raphson algorithm with a penalty function to impose the constraints. Analyses in the package are driven by the 'intsp' and 'intgrd' classes, which are interval-valued extensions of 'SpatialPointsDataFrame' and 'SpatialPixelsDataFrame' respectively. The package includes several wrappers to functions in the 'gstat' and 'sp' packages.

Maintained by Brennan Bean. Last updated 4 years ago.

openblas cpp

0.5 match 3.70 score 6 scripts

garciapintado

SpatialGraph:The SpatialGraph Class and Utilities

Provision of the S4 SpatialGraph class built on top of objects provided by 'igraph' and 'sp' packages, and associated utilities. See the documentation of the SpatialGraph-class within this package for further description. An example of how from a few points one can arrive to a SpatialGraph is provided in the function sl2sg().

Maintained by Javier Garcia-Pintado. Last updated 2 years ago.

0.5 match 5 stars 3.40 score 3 scripts

meer-1

PRNG:A Pseudo-Random Number Generator

Provides functions for generating pseudo-random numbers that follow a uniform distribution [0,1]. Randomness tests were conducted using the National Institute of Standards and Technology test suite<https://csrc.nist.gov/pubs/sp/800/22/r1/upd1/final>, along with additional tests. The sequence generated depends on the initial values and parameters. The package includes a linear congruence map as the decision map and three chaotic maps to generate the pseudo-random sequence, which follow a uniform distribution. Other distributions can be generated from the uniform distribution using the Inversion Principle Method and BOX-Muller transformation. Small perturbations in seed values result in entirely different sequences of numbers due to the sensitive nature of the maps being used. The chaotic nature of the maps helps achieve randomness in the generator. Additionally, the generator is capable of producing random bits.

Maintained by Sajad Ahmad Mir. Last updated 6 months ago.

0.5 match 3.18 score 5 scripts

hanjunwei-lab

DRviaSPCN:Drug Repurposing in Cancer via a Subpathway Crosstalk Network

A systematic biology tool was developed to repurpose drugs via a subpathway crosstalk network. The operation modes include 1) calculating centrality scores of SPs in the context of gene expression data to reflect the influence of SP crosstalk, 2) evaluating drug-disease reverse association based on disease- and drug-induced SPs weighted by the SP crosstalk, 3) identifying cancer candidate drugs through perturbation analysis. There are also several functions used to visualize the results.

Maintained by Junwei Han. Last updated 2 months ago.

0.8 match 2.00 score 5 scripts

s-fleck

smartmap:Smartly Create Maps from R Objects

Preview spatial data as 'leaflet' maps with minimal effort. smartmap is optimized for interactive use and distinguishes itself from similar packages because it does not need real spatial ('sp' or 'sf') objects an input; instead, it tries to automatically coerce everything that looks like spatial data to sf objects or leaflet maps. It - for example - supports direct mapping of: a vector containing a single coordinate pair, a two column matrix, a data.frame with longitude and latitude columns, or the path or URL to a (possibly compressed) 'shapefile'.

Maintained by Stefan Fleck. Last updated 4 years ago.

0.5 match 2.70 score 5 scripts

markusloecher

RapidPolygonLookup:POLYGON LOOKUP USING KD TREES

Facilitates efficient polygon search using kd trees. Coordinate level spatial data can be aggregated to higher geographical identities like census blocks, ZIP codes or police district boundaries. This process requires mapping each point in the given data set to a particular identity of the desired geographical hierarchy. Unless efficient data structures are used, this can be a daunting task. The operation point.in.polygon() from the package sp is computationally expensive. Here, we exploit kd-trees as efficient nearest neighbor search algorithm to dramatically reduce the effective number of polygons being searched.

Maintained by Markus Loecher. Last updated 6 years ago.

0.5 match 1 stars 2.11 score 13 scripts

pvermees

geostats:An Introduction to Statistics for Geoscientists

A collection of datasets and simplified functions for an introductory (geo)statistics module at University College London. Provides functionality for compositional, directional and spatial data, including ternary diagrams, Wulff and Schmidt stereonets, and ordinary kriging interpolation. Implements logistic and (additive and centred) logratio transformations. Computes vector averages and concentration parameters for the von-Mises distribution. Includes a collection of natural and synthetic fractals, and a simulator for deterministic chaos using a magnetic pendulum example. The main purpose of these functions is pedagogical. Researchers can find more complete alternatives for these tools in other packages such as 'compositions', 'robCompositions', 'sp', 'gstat' and 'RFOC'. All the functions are written in plain R, with no compiled code and a minimal number of dependencies. Theoretical background and worked examples are available at <https://tinyurl.com/UCLgeostats/>.

Maintained by Pieter Vermeesch. Last updated 2 years ago.

0.5 match 1.58 score 38 scripts