R-universe search: abs

mattcowgill

readabs:Download and Tidy Time Series Data from the Australian Bureau of Statistics

Downloads, imports, and tidies time series data from the Australian Bureau of Statistics <https://www.abs.gov.au/>.

Maintained by Matt Cowgill. Last updated 15 days ago.

abs australia australian-bureau-of-statistics australian-data statistics tidy-data time-series

52.4 match 104 stars 8.85 score 180 scripts

idem-lab

conmat:Builds Contact Matrices using GAMs and Population Data

Builds contact matrices using GAMs and population data. This package incorporates data that is copyright Commonwealth of Australia (Australian Electoral Commission and Australian Bureau of Statistics) 2020.

Maintained by Nicholas Tierney. Last updated 7 days ago.

contact-matrices infectious-diseases population-data public-health

56.7 match 19 stars 7.21 score 47 scripts

tyee001

VGAM:Vector Generalized Linear and Additive Models

An implementation of about 6 major classes of statistical regression models. The central algorithm is Fisher scoring and iterative reweighted least squares. At the heart of this package are the vector generalized linear and additive model (VGLM/VGAM) classes. VGLMs can be loosely thought of as multivariate GLMs. VGAMs are data-driven VGLMs that use smoothing. The book "Vector Generalized Linear and Additive Models: With an Implementation in R" (Yee, 2015) <DOI:10.1007/978-1-4939-2818-7> gives details of the statistical framework and the package. Currently only fixed-effects models are implemented. Many (100+) models and distributions are estimated by maximum likelihood estimation (MLE) or penalized MLE. The other classes are RR-VGLMs (reduced-rank VGLMs), quadratic RR-VGLMs, doubly constrained RR-VGLMs, quadratic RR-VGLMs, reduced-rank VGAMs, RCIMs (row-column interaction models)---these classes perform constrained and unconstrained quadratic ordination (CQO/UQO) models in ecology, as well as constrained additive ordination (CAO). Hauck-Donner effect detection is implemented. Note that these functions are subject to change; see the NEWS and ChangeLog files for latest changes.

Maintained by Thomas Yee. Last updated 1 months ago.

fortran

25.8 match 10 stars 10.67 score 3.6k scripts 169 dependents

iembry

ie2miscdata:Irucka Embry's Miscellaneous USGS Data Collection

A collection of Irucka Embry's miscellaneous USGS data sets (USGS Parameter codes with fixed values, USGS global time zone codes, and US Air Force Global Engineering Weather Data). Irucka created these data sets while a Cherokee Nation Technology Solutions (CNTS) United States Geological Survey (USGS) Contractor and/or USGS employee.

Maintained by Irucka Embry. Last updated 2 years ago.

29.8 match 4.00 score

frankportman

bayesAB:Fast Bayesian Methods for AB Testing

A suite of functions that allow the user to analyze A/B test data in a Bayesian framework. Intended to be a drop-in replacement for common frequentist hypothesis test such as the t-test and chi-sq test.

Maintained by Frank Portman. Last updated 4 years ago.

ab-testing bayesian-methods bayesian-tests cpp

10.5 match 308 stars 7.43 score 88 scripts

msberends

AMR:Antimicrobial Resistance Data Analysis

Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by using evidence-based methods, as described in <doi:10.18637/jss.v104.i03>.

Maintained by Matthijs S. Berends. Last updated 2 hours ago.

amr antimicrobial-data epidemiology microbiology software

6.0 match 92 stars 11.87 score 182 scripts 6 dependents

asgr

imager:Image Processing Library Based on 'CImg'

Fast image processing for images in up to 4 dimensions (two spatial dimensions, one time/depth dimension, one colour dimension). Provides most traditional image processing tools (filtering, morphology, transformations, etc.) as well as various functions for easily analysing image data using R. The package wraps 'CImg', <http://cimg.eu>, a simple, modern C++ library for image processing.

Maintained by Aaron Robotham. Last updated 27 days ago.

libx11 fftw3 tiff cpp openmp

4.5 match 17 stars 13.62 score 2.4k scripts 45 dependents

eagerai

fastai:Interface to 'fastai'

The 'fastai' <https://docs.fast.ai/index.html> library simplifies training fast and accurate neural networks using modern best practices. It is based on research in to deep learning best practices undertaken at 'fast.ai', including 'out of the box' support for vision, text, tabular, audio, time series, and collaborative filtering models.

Maintained by Turgut Abdullayev. Last updated 11 months ago.

audio collaborative-filtering darknet darknet-image-classification fastai medical object-detection tabular text vision

6.0 match 118 stars 9.40 score 76 scripts

mlverse

torch:Tensors and Neural Networks with 'GPU' Acceleration

Provides functionality to define and train neural networks similar to 'PyTorch' by Paszke et al (2019) <doi:10.48550/arXiv.1912.01703> but written entirely in R using the 'libtorch' library. Also supports low-level tensor operations and 'GPU' acceleration.

Maintained by Daniel Falbel. Last updated 6 days ago.

autograd deep-learning torch cpp

3.0 match 520 stars 16.52 score 1.4k scripts 38 dependents

ab-sa

daySupply:Calculating Days' Supply and Daily Dose of Prescriptions

Allows clinicians and researchers to compute daily dose (and subsequently days' supply) for prescription refills using the following methods: Fixed window, fixed tablet, defined daily dose (DDD), and Random Effects Warfarin Days' Supply (REWarDS). Daily dose is the computed dose that the patient takes every day. For medications with fixed dosing (e.g. direct oral anticoagulants) this is known and does not need to be estimated. For medications with varying dose such as warfarin, however, the daily dose should be assumed or estimated to allow measurement of drug exposure. Days’ supply is the number of days that patients’ supply of medication will last after each prescription fill. Estimating days’ supply is necessary to calculate drug exposure. The package computes days’ supply and daily dose at both the prescription and patient levels. Results at the prescription level are denoted with “-Rx-” and those at patient level are denoted with “-Pt-”.

Maintained by Abdollah Safari. Last updated 4 years ago.

15.0 match 1 stars 2.70 score

business-science

tidyquant:Tidy Quantitative Financial Analysis

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

Maintained by Matt Dancho. Last updated 1 months ago.

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

3.0 match 872 stars 13.34 score 5.2k scripts

jinghuazhao

gap:Genetic Analysis Package

As first reported [Zhao, J. H. 2007. "gap: Genetic Analysis Package". J Stat Soft 23(8):1-18. <doi:10.18637/jss.v023.i08>], it is designed as an integrated package for genetic data analysis of both population and family data. Currently, it contains functions for sample size calculations of both population-based and family-based designs, probability of familial disease aggregation, kinship calculation, statistics in linkage analysis, and association analysis involving genetic markers including haplotype analysis with or without environmental covariates. Over years, the package has been developed in-between many projects hence also in line with the name (gap).

Maintained by Jing Hua Zhao. Last updated 16 days ago.

genetics imputation lmm fortran

3.3 match 12 stars 11.88 score 448 scripts 16 dependents

harrelfe

Hmisc:Harrell Miscellaneous

Contains many functions useful for data analysis, high-level graphics, utility operations, functions for computing sample size and power, simulation, importing and annotating datasets, imputing missing values, advanced table making, variable clustering, character string manipulation, conversion of R objects to LaTeX and html code, recoding variables, caching, simplified parallel computing, encrypting and decrypting data using a safe workflow, general moving window statistical estimation, and assistance in interpreting principal component analysis.

Maintained by Frank E Harrell Jr. Last updated 6 hours ago.

fortran

2.0 match 210 stars 17.61 score 17k scripts 750 dependents

r-lib

bit64:A S3 Class for Vectors of 64bit Integers

Package 'bit64' provides serializable S3 atomic 64bit (signed) integers. These are useful for handling database keys and exact counting in +-2^63. WARNING: do not use them as replacement for 32bit integers, integer64 are not supported for subscripting by R-core and they have different semantics when combined with double, e.g. integer64 + double => integer64. Class integer64 can be used in vectors, matrices, arrays and data.frames. Methods are available for coercion from and to logicals, integers, doubles, characters and factors as well as many elementwise and summary functions. Many fast algorithmic operations such as 'match' and 'order' support inter- active data exploration and manipulation and optionally leverage caching.

Maintained by Michael Chirico. Last updated 4 days ago.

2.3 match 35 stars 14.91 score 1.5k scripts 3.2k dependents

hoxo-m

deltatest:Statistical Hypothesis Testing Using the Delta Method

Statistical hypothesis testing using the Delta method as proposed by Deng et al. (2018) <doi:10.1145/3219819.3219919>. This method replaces the standard variance estimation formula in the Z-test with an approximate formula derived via the Delta method, which can account for within-user correlation.

Maintained by Koji Makiyama. Last updated 1 days ago.

ab-testing data-science statistics

7.5 match 4 stars 4.26 score

tomasfryda

h2o:R Interface for the 'H2O' Scalable Machine Learning Platform

R interface for 'H2O', the scalable open source machine learning platform that offers parallelized implementations of many supervised and unsupervised machine learning algorithms such as Generalized Linear Models (GLM), Gradient Boosting Machines (including XGBoost), Random Forests, Deep Neural Networks (Deep Learning), Stacked Ensembles, Naive Bayes, Generalized Additive Models (GAM), ANOVA GLM, Cox Proportional Hazards, K-Means, PCA, ModelSelection, Word2Vec, as well as a fully automatic machine learning algorithm (H2O AutoML).

Maintained by Tomas Fryda. Last updated 1 years ago.

3.8 match 3 stars 8.20 score 7.8k scripts 11 dependents

rstudio

tfprobability:Interface to 'TensorFlow Probability'

Interface to 'TensorFlow Probability', a 'Python' library built on 'TensorFlow' that makes it easy to combine probabilistic models and deep learning on modern hardware ('TPU', 'GPU'). 'TensorFlow Probability' includes a wide selection of probability distributions and bijectors, probabilistic layers, variational inference, Markov chain Monte Carlo, and optimizers such as Nelder-Mead, BFGS, and SGLD.

Maintained by Tomasz Kalinowski. Last updated 3 years ago.

3.4 match 54 stars 8.63 score 221 scripts 3 dependents

cvxgrp

CVXR:Disciplined Convex Optimization

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

Maintained by Anqi Fu. Last updated 4 months ago.

cpp

2.3 match 207 stars 12.89 score 768 scripts 51 dependents

bertcarnell

lhs:Latin Hypercube Samples

Provides a number of methods for creating and augmenting Latin Hypercube Samples and Orthogonal Array Latin Hypercube Samples.

Maintained by Rob Carnell. Last updated 9 months ago.

latin-hypercube latin-hypercube-sample latin-hypercube-sampling lhs orthogonal-arrays cpp

2.1 match 44 stars 13.95 score 1.5k scripts 108 dependents

hdvinod

generalCorr:Generalized Correlations, Causal Paths and Portfolio Selection

Function gmcmtx0() computes a more reliable (general) correlation matrix. Since causal paths from data are important for all sciences, the package provides many sophisticated functions. causeSummBlk() and causeSum2Blk() give easy-to-interpret causal paths. Let Z denote control variables and compare two flipped kernel regressions: X=f(Y, Z)+e1 and Y=g(X, Z)+e2. Our criterion Cr1 says that if |e1*Y|>|e2*X| then variation in X is more "exogenous or independent" than in Y, and the causal path is X to Y. Criterion Cr2 requires |e2|<|e1|. These inequalities between many absolute values are quantified by four orders of stochastic dominance. Our third criterion Cr3, for the causal path X to Y, requires new generalized partial correlations to satisfy |r*(x|y,z)|< |r*(y|x,z)|. The function parcorVec() reports generalized partials between the first variable and all others. The package provides several R functions including get0outliers() for outlier detection, bigfp() for numerical integration by the trapezoidal rule, stochdom2() for stochastic dominance, pillar3D() for 3D charts, canonRho() for generalized canonical correlations, depMeas() measures nonlinear dependence, and causeSummary(mtx) reports summary of causal paths among matrix columns. Portfolio selection: decileVote(), momentVote(), dif4mtx(), exactSdMtx() can rank several stocks. Functions whose names begin with 'boot' provide bootstrap statistical inference, including a new bootGcRsq() test for "Granger-causality" allowing nonlinear relations. A new tool for evaluation of out-of-sample portfolio performance is outOFsamp(). Panel data implementation is now included. See eight vignettes of the package for theory, examples, and usage tips. See Vinod (2019) \doi{10.1080/03610918.2015.1122048}.

Maintained by H. D. Vinod. Last updated 1 years ago.

6.5 match 2 stars 4.48 score 63 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

danheck

multinomineq:Bayesian Inference for Multinomial Models with Inequality Constraints

Implements Gibbs sampling and Bayes factors for multinomial models with linear inequality constraints on the vector of probability parameters. As special cases, the model class includes models that predict a linear order of binomial probabilities (e.g., p[1] < p[2] < p[3] < .50) and mixture models assuming that the parameter vector p must be inside the convex hull of a finite number of predicted patterns (i.e., vertices). A formal definition of inequality-constrained multinomial models and the implemented computational methods is provided in: Heck, D.W., & Davis-Stober, C.P. (2019). Multinomial models with linear inequality constraints: Overview and improvements of computational methods for Bayesian inference. Journal of Mathematical Psychology, 91, 70-87. <doi:10.1016/j.jmp.2019.03.004>. Inequality-constrained multinomial models have applications in the area of judgment and decision making to fit and test random utility models (Regenwetter, M., Dana, J., & Davis-Stober, C.P. (2011). Transitivity of preferences. Psychological Review, 118, 42–56, <doi:10.1037/a0021150>) or to perform outcome-based strategy classification to select the decision strategy that provides the best account for a vector of observed choice frequencies (Heck, D.W., Hilbig, B.E., & Moshagen, M. (2017). From information processing to decisions: Formalizing and comparing probabilistic choice models. Cognitive Psychology, 96, 26–40. <doi:10.1016/j.cogpsych.2017.05.003>).

Maintained by Daniel W. Heck. Last updated 1 years ago.

openblas cpp openmp

6.6 match 4 stars 4.30 score 4 scripts

rstudio

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

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

Maintained by Joe Cheng. Last updated 13 days ago.

gis leaflet-map spatial

1.5 match 821 stars 17.20 score 39k scripts 178 dependents

rstudio

httpuv:HTTP and WebSocket Server Library

Provides low-level socket and protocol support for handling HTTP and WebSocket requests directly from within R. It is primarily intended as a building block for other packages, rather than making it particularly easy to create complete web applications using httpuv alone. httpuv is built on top of the libuv and http-parser C libraries, both of which were developed by Joyent, Inc. (See LICENSE file for libuv and http-parser license information.)

Maintained by Winston Chang. Last updated 12 months ago.

libuv1 cpp

1.5 match 235 stars 15.09 score 708 scripts 2.1k dependents

bioc

AnVILAz:R / Bioconductor Support for the AnVIL Azure Platform

The AnVIL is a cloud computing resource developed in part by the National Human Genome Research Institute. The AnVILAz package supports end-users and developers using the AnVIL platform in the Azure cloud. The package provides a programmatic interface to AnVIL resources, including workspaces, notebooks, tables, and workflows. The package also provides utilities for managing resources, including copying files to and from Azure Blob Storage, and creating shared access signatures (SAS) for secure access to Azure resources.

Maintained by Marcel Ramos. Last updated 5 months ago.

software infrastructure thirdpartyclient

4.0 match 5.45 score 5 scripts

tvganesh

cricketr:Analyze Cricketers and Cricket Teams Based on ESPN Cricinfo Statsguru

Tools for analyzing performances of cricketers based on stats in ESPN Cricinfo Statsguru. The toolset can be used for analysis of Tests,ODIs and Twenty20 matches of both batsmen and bowlers. The package can also be used to analyze team performances.

Maintained by Tinniam V Ganesh. Last updated 4 years ago.

3.8 match 62 stars 5.55 score 115 scripts

ropensci

stplanr:Sustainable Transport Planning

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

Maintained by Robin Lovelace. Last updated 7 months ago.

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

1.7 match 427 stars 12.31 score 684 scripts 3 dependents

bioc

daMA:Efficient design and analysis of factorial two-colour microarray data

This package contains functions for the efficient design of factorial two-colour microarray experiments and for the statistical analysis of factorial microarray data. Statistical details are described in Bretz et al. (2003, submitted)

Maintained by Jobst Landgrebe. Last updated 5 months ago.

microarray twochannel differentialexpression

8.1 match 2.30 score

wuqian77

TrialSize:R Functions for Chapter 3,4,6,7,9,10,11,12,14,15 of Sample Size Calculation in Clinical Research

Functions and Examples in Sample Size Calculation in Clinical Research.

Maintained by Vicky Qian Wu. Last updated 4 months ago.

cpp

4.5 match 3 stars 3.78 score 95 scripts 1 dependents

skranz

RoundingMatters:Tools for adjusting for rounding problems in metastudies about p-hacking and publication bias

Tools for adjusting for rounding problems in metastudies about p-hacking and publication bias

Maintained by Sebastian Kranz. Last updated 4 years ago.

9.8 match 1.70 score 8 scripts

linlf

pcnetmeta:Patient-Centered Network Meta-Analysis

Performs Bayesian arm-based network meta-analysis for datasets with binary, continuous, and count outcomes (Zhang et al., 2014 <doi:10.1177/1740774513498322>; Lin et al., 2017 <doi:10.18637/jss.v080.i05>).

Maintained by Lifeng Lin. Last updated 3 years ago.

jags cpp

8.0 match 1 stars 2.08 score 12 scripts

mtennekes

treemap:Treemap Visualization

A treemap is a space-filling visualization of hierarchical structures. This package offers great flexibility to draw treemaps.

Maintained by Martijn Tennekes. Last updated 2 years ago.

1.8 match 8.88 score 2.2k scripts 7 dependents

thinkr-open

lozen:Management tools for missions

Management tools for missions (internal and external). Includes weekly, GL projects, etc.

Maintained by Sébastien Rochette. Last updated 12 months ago.

experimental

3.0 match 7 stars 5.42 score 14 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

cran

CircNNTSR:Statistical Analysis of Circular Data using Nonnegative Trigonometric Sums (NNTS) Models

Includes functions for the analysis of circular data using distributions based on Nonnegative Trigonometric Sums (NNTS). The package includes functions for calculation of densities and distributions, for the estimation of parameters, for plotting and more.

Maintained by Maria Mercedes Gregorio-Dominguez. Last updated 2 years ago.

8.3 match 1.78 score 2 dependents

sqyu

genscore:Generalized Score Matching Estimators

Implementation of the Generalized Score Matching estimator in Yu et al. (2019) <http://jmlr.org/papers/v20/18-278.html> for non-negative graphical models (truncated Gaussian, exponential square-root, gamma, a-b models) and univariate truncated Gaussian distributions. Also includes the original estimator for untruncated Gaussian graphical models from Lin et al. (2016) <doi:10.1214/16-EJS1126>, with the addition of a diagonal multiplier.

Maintained by Shiqing Yu. Last updated 5 years ago.

density-estimation graphical-models interaction-models score-matching undirected-graphs

3.4 match 1 stars 4.18 score 3 scripts 1 dependents

uupharmacometrics

xpose4:Diagnostics for Nonlinear Mixed-Effect Models

A model building aid for nonlinear mixed-effects (population) model analysis using NONMEM, facilitating data set checkout, exploration and visualization, model diagnostics, candidate covariate identification and model comparison. The methods are described in Keizer et al. (2013) <doi:10.1038/psp.2013.24>, and Jonsson et al. (1999) <doi:10.1016/s0169-2607(98)00067-4>.

Maintained by Andrew C. Hooker. Last updated 1 years ago.

diagnostics nonmem pharmacometrics population-model xpose

1.9 match 35 stars 7.30 score 315 scripts

jamesliley

SPARRAfairness:Analysis of Differential Behaviour of SPARRA Score Across Demographic Groups

The SPARRA risk score (Scottish Patients At Risk of admission and Re-Admission) estimates yearly risk of emergency hospital admission using electronic health records on a monthly basis for most of the Scottish population. This package implements a suite of functions used to analyse the behaviour and performance of the score, focusing particularly on differential performance over demographically-defined groups. It includes useful utility functions to plot receiver-operator-characteristic, precision-recall and calibration curves, draw stock human figures, estimate counterfactual quantities without the need to re-compute risk scores, to simulate a semi-realistic dataset.

Maintained by James Liley. Last updated 4 months ago.

5.0 match 2.70 score 4 scripts

chawm

pwrAB:Power Analysis for AB Testing

Power analysis for AB testing. The calculations are based on the Welch's unequal variances t-test, which is generally preferred over the Student's t-test when sample sizes and variances of the two groups are unequal, which is frequently the case in AB testing. In such situations, the Student's t-test will give biased results due to using the pooled standard deviation, unlike the Welch's t-test.

Maintained by William Cha. Last updated 8 years ago.

3.9 match 5 stars 3.40 score 6 scripts

statnmap

tweetrbot:Functions for a Twitter bot

Functions to allow retrieve, store and retweet regularly.

Maintained by Sebastien Rochette. Last updated 2 years ago.

3.8 match 3 stars 3.48 score 4 scripts

bioc

QSutils:Quasispecies Diversity

Set of utility functions for viral quasispecies analysis with NGS data. Most functions are equally useful for metagenomic studies. There are three main types: (1) data manipulation and exploration—functions useful for converting reads to haplotypes and frequencies, repairing reads, intersecting strand haplotypes, and visualizing haplotype alignments. (2) diversity indices—functions to compute diversity and entropy, in which incidence, abundance, and functional indices are considered. (3) data simulation—functions useful for generating random viral quasispecies data.

Maintained by Mercedes Guerrero-Murillo. Last updated 5 months ago.

software genetics dnaseq geneticvariability sequencing alignment sequencematching dataimport

2.3 match 5.56 score 8 scripts 1 dependents

ddalthorp

dwp:Density-Weighted Proportion

Fit a Poisson regression to carcass distance data and integrate over the searched area at a wind farm to estimate the fraction of carcasses falling in the searched area and format the output for use as the dwp parameter in the 'GenEst' or 'eoa' package for estimating bird and bat mortality, following Dalthorp, et al. (2022) <arXiv:2201.10064>.

Maintained by Daniel Dalthorp. Last updated 2 years ago.

4.5 match 1 stars 2.70 score

hughparsonage

grattanInflators:Inflators for Australian Policy Analysis

Using Australian Bureau of Statistics indices, provides functions that convert historical, nominal statistics to real, contemporary values without worrying about date input quality, performance, or the ABS catalogue.

Maintained by Hugh Parsonage. Last updated 3 months ago.

openmp

2.8 match 2 stars 4.32 score 6 scripts 1 dependents

robinhankin

freegroup:The Free Group

The free group in R; juxtaposition is represented by a plus. Includes inversion, multiplication by a scalar, group-theoretic power operation, and Tietze forms. To cite the package in publications please use Hankin (2022) <doi:10.48550/ARXIV.2212.05883>.

Maintained by Robin K. S. Hankin. Last updated 2 months ago.

2.3 match 5.06 score 33 scripts

cmsaf

cmsafops:Tools for CM SAF NetCDF Data

The Satellite Application Facility on Climate Monitoring (CM SAF) is a ground segment of the European Organization for the Exploitation of Meteorological Satellites (EUMETSAT) and one of EUMETSATs Satellite Application Facilities. The CM SAF contributes to the sustainable monitoring of the climate system by providing essential climate variables related to the energy and water cycle of the atmosphere (<https://www.cmsaf.eu>). It is a joint cooperation of eight National Meteorological and Hydrological Services. The 'cmsafops' R-package provides a collection of R-operators for the analysis and manipulation of CM SAF NetCDF formatted data. Other CF conform NetCDF data with time, longitude and latitude dimension should be applicable, but there is no guarantee for an error-free application. CM SAF climate data records are provided for free via (<https://wui.cmsaf.eu/safira>). Detailed information and test data are provided on the CM SAF webpage (<http://www.cmsaf.eu/R_toolbox>).

Maintained by Steffen Kothe. Last updated 6 months ago.

2.3 match 2 stars 5.03 score 4 scripts 2 dependents

bioc

PROMISE:PRojection Onto the Most Interesting Statistical Evidence

A general tool to identify genomic features with a specific biologically interesting pattern of associations with multiple endpoint variables as described in Pounds et. al. (2009) Bioinformatics 25: 2013-2019

Maintained by Stan Pounds. Last updated 5 months ago.

microarray onechannel multiplecomparison geneexpression

2.0 match 5.44 score 46 scripts 1 dependents

rmheiberger

HH:Statistical Analysis and Data Display: Heiberger and Holland

Support software for Statistical Analysis and Data Display (Second Edition, Springer, ISBN 978-1-4939-2121-8, 2015) and (First Edition, Springer, ISBN 0-387-40270-5, 2004) by Richard M. Heiberger and Burt Holland. This contemporary presentation of statistical methods features extensive use of graphical displays for exploring data and for displaying the analysis. The second edition includes redesigned graphics and additional chapters. The authors emphasize how to construct and interpret graphs, discuss principles of graphical design, and show how accompanying traditional tabular results are used to confirm the visual impressions derived directly from the graphs. Many of the graphical formats are novel and appear here for the first time in print. All chapters have exercises. All functions introduced in the book are in the package. R code for all examples, both graphs and tables, in the book is included in the scripts directory of the package.

Maintained by Richard M. Heiberger. Last updated 1 months ago.

1.7 match 3 stars 6.42 score 752 scripts 5 dependents

jzl-ck

pattern.checks:Identifies Patterned Responses in Scales

Identifies the entries with patterned responses for psychometric scales. The patterns included in the package are identical (a, a, a), ascending (a, b, c), descending (c, b, a), alternative (a, b, a, b / a, b, c, a, b, c).

Maintained by JZL. Last updated 2 months ago.

3.7 match 2.70 score

phamdn

peramo:Permutation Tests for Randomization Model

Perform permutation-based hypothesis testing for randomized experiments as suggested in Ludbrook & Dudley (1998) <doi:10.2307/2685470> and Ernst (2004) <doi:10.1214/088342304000000396>, introduced in Pham et al. (2022) <doi:10.1016/j.chemosphere.2022.136736>.

Maintained by Duy Nghia Pham. Last updated 7 months ago.

3.3 match 3.00 score

bioc

OLIN:Optimized local intensity-dependent normalisation of two-color microarrays

Functions for normalisation of two-color microarrays by optimised local regression and for detection of artefacts in microarray data

Maintained by Matthias Futschik. Last updated 5 months ago.

microarray twochannel qualitycontrol preprocessing visualization

2.0 match 4.78 score 2 scripts 1 dependents

ropengov

sweidnumbr:Handling of Swedish Identity Numbers

Structural handling of identity numbers used in the Swedish administration such as personal identity numbers ('personnummer') and organizational identity numbers ('organisationsnummer').

Maintained by Mans Magnusson. Last updated 1 years ago.

ropengov

1.8 match 8 stars 5.38 score

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.

2.0 match 8 stars 4.70 score 42 scripts

bioc

MsDataHub:Mass Spectrometry Data on ExperimentHub

The MsDataHub package uses the ExperimentHub infrastructure to distribute raw mass spectrometry data files, peptide spectrum matches or quantitative data from proteomics and metabolomics experiments.

Maintained by Laurent Gatto. Last updated 23 days ago.

experimenthubsoftware massspectrometry proteomics metabolomics bioconductor data mass-spectrometry

1.8 match 1 stars 4.95 score 2 scripts

jmzobitz

neonSoilFlux:Compute Soil Carbon Fluxes for the National Ecological Observatory Network Sites

Acquires and synthesizes soil carbon fluxes at sites located in the National Ecological Observatory Network (NEON). Provides flux estimates and associated uncertainty as well as key environmental measurements (soil water, temperature, CO2 concentration) that are used to compute soil fluxes.

Maintained by John Zobitz. Last updated 10 months ago.

1.5 match 6 stars 5.43 score 2 scripts

cran

Platypus:Single-Cell Immune Repertoire and Gene Expression Analysis

We present 'Platypus', an open-source software platform providing a user-friendly interface to investigate B-cell receptor and T-cell receptor repertoires from scSeq experiments. 'Platypus' provides a framework to automate and ease the analysis of single-cell immune repertoires while also incorporating transcriptional information involving unsupervised clustering, gene expression and gene ontology. This R version of 'Platypus' is part of the 'ePlatypus' ecosystem for computational analysis of immunogenomics data: Yermanos et al. (2021) <doi:10.1093/nargab/lqab023>, Cotet et al. (2023) <doi:10.1093/bioinformatics/btad553>.

Maintained by Alexander Yermanos. Last updated 5 months ago.

1.8 match 4.58 score 38 scripts

emilhvitfeldt

extrasteps:More Miscellaneous Steps for the 'recipes' Package

Contains additional miscellaneous steps for the 'recipes' package. These steps are useful, but doesn't have a good home in other 'recipes' packages or its extensions.

Maintained by Emil Hvitfeldt. Last updated 5 months ago.

1.9 match 10 stars 4.15 score 14 scripts

robinhankin

freealg:The Free Algebra

The free algebra in R with non-commuting indeterminates. Uses 'disordR' discipline (Hankin, 2022, <doi:10.48550/ARXIV.2210.03856>). To cite the package in publications please use Hankin (2022) <doi:10.48550/ARXIV.2211.04002>.

Maintained by Robin K. S. Hankin. Last updated 5 days ago.

cpp

1.1 match 3 stars 7.07 score 10 dependents

cran

asnipe:Animal Social Network Inference and Permutations for Ecologists

Implements several tools that are used in animal social network analysis, as described in Whitehead (2007) Analyzing Animal Societies <University of Chicago Press> and Farine & Whitehead (2015) <doi: 10.1111/1365-2656.12418>. In particular, this package provides the tools to infer groups and generate networks from observation data, perform permutation tests on the data, calculate lagged association rates, and performed multiple regression analysis on social network data.

Maintained by Damien R. Farine. Last updated 2 years ago.

1.7 match 2 stars 4.36 score 173 scripts 2 dependents

jensharbers

agricolaeplotr:Visualization of Design of Experiments from the 'agricolae' Package

Visualization of Design of Experiments from the 'agricolae' package with 'ggplot2' framework The user provides an experiment design from the 'agricolae' package, calls the corresponding function and will receive a visualization with 'ggplot2' based functions that are specific for each design. As there are many different designs, each design is tested on its type. The output can be modified with standard 'ggplot2' commands or with other packages with 'ggplot2' function extensions.

Maintained by Jens Harbers. Last updated 1 months ago.

1.2 match 8 stars 6.27 score 78 scripts

uncertaintyquantification

AIUQ:Ab Initio Uncertainty Quantification

Uncertainty quantification and inverse estimation by probabilistic generative models from the beginning of the data analysis. An example is a Fourier basis method for inverse estimation in scattering analysis of microscopy videos. It does not require specifying a certain range of Fourier bases and it substantially reduces computational cost via the generalized Schur algorithm. See the reference: Mengyang Gu, Yue He, Xubo Liu and Yimin Luo (2023), <doi:10.48550/arXiv.2309.02468>.

Maintained by Mengyang Gu. Last updated 9 months ago.

3.1 match 2.30 score 1 scripts

cran

iAdapt:Two-Stage Adaptive Dose-Finding Clinical Trial Design

Simulate and implement early phase two-stage adaptive dose-finding design for binary and quasi-continuous toxicity endpoints. See Chiuzan et al. (2018) for further reading <DOI:10.1080/19466315.2018.1462727>.

Maintained by Alyssa Vanderbeek. Last updated 4 years ago.

2.3 match 3.18 score 7 scripts

cran

qrnn:Quantile Regression Neural Network

Fit quantile regression neural network models with optional left censoring, partial monotonicity constraints, generalized additive model constraints, and the ability to fit multiple non-crossing quantile functions following Cannon (2011) <doi:10.1016/j.cageo.2010.07.005> and Cannon (2018) <doi:10.1007/s00477-018-1573-6>.

Maintained by Alex J. Cannon. Last updated 1 years ago.

2.3 match 8 stars 3.08 score 1 dependents

junyuchen-econ

ablasso:Arellano-Bond LASSO Estimator for Dynamic Linear Panel Models

Implements the Arellano-Bond estimation method combined with LASSO for dynamic linear panel models. See Chernozhukov et al. (2024) "Arellano-Bond LASSO Estimator for Dynamic Linear Panel Models". arXiv preprint <doi:10.48550/arXiv.2402.00584>.

Maintained by Junyu Chen. Last updated 1 months ago.

5.2 match 1 stars 1.30 score 1 scripts

cran

NST:Normalized Stochasticity Ratio

To estimate ecological stochasticity in community assembly. Understanding the community assembly mechanisms controlling biodiversity patterns is a central issue in ecology. Although it is generally accepted that both deterministic and stochastic processes play important roles in community assembly, quantifying their relative importance is challenging. The new index, normalized stochasticity ratio (NST), is to estimate ecological stochasticity, i.e. relative importance of stochastic processes, in community assembly. With functions in this package, NST can be calculated based on different similarity metrics and/or different null model algorithms, as well as some previous indexes, e.g. previous Stochasticity Ratio (ST), Standard Effect Size (SES), modified Raup-Crick metrics (RC). Functions for permutational test and bootstrapping analysis are also included. Previous ST is published by Zhou et al (2014) <doi:10.1073/pnas.1324044111>. NST is modified from ST by considering two alternative situations and normalizing the index to range from 0 to 1 (Ning et al 2019) <doi:10.1073/pnas.1904623116>. A modified version, MST, is a special case of NST, used in some recent or upcoming publications, e.g. Liang et al (2020) <doi:10.1016/j.soilbio.2020.108023>. SES is calculated as described in Kraft et al (2011) <doi:10.1126/science.1208584>. RC is calculated as reported by Chase et al (2011) <doi:10.1890/ES10-00117.1> and Stegen et al (2013) <doi:10.1038/ismej.2013.93>. Version 3 added NST based on phylogenetic beta diversity, used by Ning et al (2020) <doi:10.1038/s41467-020-18560-z>.

Maintained by Daliang Ning. Last updated 3 years ago.

2.3 match 2 stars 2.85 score 35 scripts

theropod1

paleoDiv:Extracting and Visualizing Paleobiodiversity

Contains various tools for conveniently downloading and editing taxon-specific datasets from the Paleobiology Database <https://paleobiodb.org>, extracting information on abundance, temporal distribution of subtaxa and taxonomic diversity through deep time, and visualizing these data in relation to phylogeny and stratigraphy.

Maintained by Darius Nau. Last updated 5 months ago.

2.3 match 2 stars 2.78 score

biocool-lab

PSSMCOOL:Features Extracted from Position Specific Scoring Matrix (PSSM)

Returns almost all features that has been extracted from Position Specific Scoring Matrix (PSSM) so far, which is a matrix of L rows (L is protein length) and 20 columns produced by 'PSI-BLAST' which is a program to produce PSSM Matrix from multiple sequence alignment of proteins see <https://www.ncbi.nlm.nih.gov/books/NBK2590/> for mor details. some of these features are described in Zahiri, J., et al.(2013) <DOI:10.1016/j.ygeno.2013.05.006>, Saini, H., et al.(2016) <DOI:10.17706/jsw.11.8.756-767>, Ding, S., et al.(2014) <DOI:10.1016/j.biochi.2013.09.013>, Cheng, C.W., et al.(2008) <DOI:10.1186/1471-2105-9-S12-S6>, Juan, E.Y., et al.(2009) <DOI:10.1109/CISIS.2009.194>.

Maintained by Alireza mohammadi. Last updated 3 years ago.

1.8 match 4 stars 3.53 score 17 scripts

cran

caroline:A Collection of Database, Data Structure, Visualization, and Utility Functions for R

The caroline R library contains dozens of functions useful for: database migration (dbWriteTable2), database style joins & aggregation (nerge, groupBy, & bestBy), data structure conversion (nv, tab2df), legend table making (sstable & leghead), automatic legend positioning for scatter and box plots (), plot annotation (labsegs & mvlabs), data visualization (pies, sparge, confound.grid & raPlot), character string manipulation (m & pad), file I/O (write.delim), batch scripting, data exploration, and more. The package's greatest contributions lie in the database style merge, aggregation and interface functions as well as in it's extensive use and propagation of row, column and vector names in most functions.

Maintained by David Schruth. Last updated 5 months ago.

1.9 match 3.29 score 108 scripts 3 dependents

bioc

deltaCaptureC:This Package Discovers Meso-scale Chromatin Remodeling from 3C Data

This package discovers meso-scale chromatin remodelling from 3C data. 3C data is local in nature. It givens interaction counts between restriction enzyme digestion fragments and a preferred 'viewpoint' region. By binning this data and using permutation testing, this package can test whether there are statistically significant changes in the interaction counts between the data from two cell types or two treatments.

Maintained by Michael Shapiro. Last updated 5 months ago.

biologicalquestion statisticalmethod

1.7 match 3.48 score 1 scripts

sarahkatharine

pbANOVA:Parametric Bootstrap for ANOVA Models

Parametric bootstrap (PB) has been used for three-way ANOVA model with unequal group variances.

Maintained by Sarah Alver. Last updated 3 years ago.

5.5 match 1.00 score 3 scripts

cran

hbim:Hill/Bliss Independence Model for Combination Vaccines

Calculate expected relative risk and proportion protected assuming normally distributed log10 transformed antibody dose for a several component vaccine. Uses Hill models for each component which are combined under Bliss independence. See Saul and Fay, 2007 <DOI:10.1371/journal.pone.0000850>.

Maintained by Michael P. Fay. Last updated 2 years ago.

2.3 match 2.30 score

rapidsurveys

odkr:'Open Data Kit' ('ODK') R API

Utility functions for working with datasets gathered using 'Open Data Kit' ('ODK') <https://opendatakit.org/>. These include an API to interface with 'ODK Briefcase', a 'Java' application for fetching and pushing 'ODK' forms and their contents, that allows pulling of data from either a remote 'ODK Aggregate Server' or a local 'ODK' folder, a rename function to give more human readable variable names for 'ODK' datasets, a merge function to create a single dataframe from a nested 'ODK' dataset and an expand function to disaggregate multiple choice answers that have been collapsed into single code by 'ODK'.

Maintained by Ernest Guevarra. Last updated 5 months ago.

odk odk-briefcase open-data-kit openjdk

1.6 match 11 stars 3.32 score 19 scripts

repboxr

repboxRfun:Repbox functions called by code injections into R scripts

Try to use as little special dependencies as reasonably possible

Maintained by Sebastian Kranz. Last updated 1 years ago.

2.3 match 2.18 score 1 dependents

tdaverse

ripserr:Calculate Persistent Homology with Ripser-Based Engines

Ports the Ripser <https://arxiv.org/abs/1908.02518> and Cubical Ripser <https://arxiv.org/abs/2005.12692> persistent homology calculation engines from C++. Can be used as a rapid calculation tool in topological data analysis pipelines.

Maintained by Raoul Wadhwa. Last updated 2 days ago.

algebraic-topology cohomology cpp cubical-complex persistent-homology pixel point-cloud r-language r-programming rcpp rips-complex ripser simplicial-complex simplicial-homology topological-data-analysis topology vietoris-complex voxel cpp

0.8 match 7 stars 5.80 score 6 scripts

jamesuanhoro

ssrhom:Hierarchical ordinal models for analyzing single subject designs

Hierarchical ordinal models for analyzing single subject designs using Bayesian models fit with Stan.

Maintained by James Uanhoro. Last updated 6 months ago.

bayesian-statistics hierarchical-models mcmc single-case-design stan cpp

2.0 match 2.30 score 3 scripts

ddalthorp

eoa3:Wildlife Mortality Estimator for Low Fatality Rates and Imperfect Detection

Evidence of Absence software (EoA) is a user-friendly application for estimating bird and bat fatalities at wind farms and designing search protocols. The software is particularly useful in addressing whether the number of fatalities has exceeded a given threshold and what search parameters are needed to give assurance that thresholds were not exceeded. The models are applicable even when zero carcasses have been found in searches, following Huso et al. (2015) <doi:10.1890/14-0764.1>, Dalthorp et al. (2017) <doi:10.3133/ds1055>, and Dalthorp and Huso (2015) <doi:10.3133/ofr20151227>.

Maintained by Daniel Dalthorp. Last updated 4 months ago.

jags cpp

4.5 match 1.00 score

hkestler

GiANT:Gene Set Uncertainty in Enrichment Analysis

Toolbox for various enrichment analysis methods and quantification of uncertainty of gene sets, Schmid et al. (2016) <doi:10.1093/bioinformatics/btw030>.

Maintained by Hans A. Kestler. Last updated 6 months ago.

2.3 match 2.00 score 4 scripts

dranthropoid

mmodely:Modeling Multivariate Origins Determinants - Evolutionary Lineages in Ecology

Perform multivariate modeling of evolved traits, with special attention to understanding the interplay of the multi-factorial determinants of their origins in complex ecological settings (Stephens, 2007 <doi:10.1016/j.tree.2006.12.003>). This software primarily concentrates on phylogenetic regression analysis, enabling implementation of tree transformation averaging and visualization functionality. Functions additionally support information theoretic approaches (Grueber, 2011 <doi:10.1111/j.1420-9101.2010.02210.x>; Garamszegi, 2011 <doi:10.1007/s00265-010-1028-7>) such as model averaging and selection of phylogenetic models. Accessory functions are also implemented for coef standardization (Cade 2015), selection uncertainty, and variable importance (Burnham & Anderson 2000). There are other numerous functions for visualizing confounded variables, plotting phylogenetic trees, as well as reporting and exporting modeling results. Lastly, as challenges to ecology are inherently multifarious, and therefore often multi-dataset, this package features several functions to support the identification, interpolation, merging, and updating of missing data and outdated nomenclature.

Maintained by David M Schruth. Last updated 2 years ago.

1.9 match 2.30 score 4 scripts

dmohit

MuViCP:MultiClass Visualizable Classification using Combination of Projections

An ensemble classifier for multiclass classification. This is a novel classifier that natively works as an ensemble. It projects data on a large number of matrices, and uses very simple classifiers on each of these projections. The results are then combined, ideally via Dempster-Shafer Calculus.

Maintained by Mohit Dayal. Last updated 9 years ago.

4.3 match 1.00 score 8 scripts

billvenables

MASSExtra:Some 'MASS' Enhancements

Some enhancements, extensions and additions to the facilities of the recommended 'MASS' package that are useful mainly for teaching purposes, with more convenient default settings and user interfaces. Key functions from 'MASS' are imported and re-exported to avoid masking conflicts. In addition we provide some additional functions mainly used to illustrate coding paradigms and techniques, such as Gramm-Schmidt orthogonalisation and generalised eigenvalue problems.

Maintained by Bill Venables. Last updated 2 years ago.

1.5 match 2.74 score 11 scripts

cran

SCVA:Single-Case Visual Analysis

Make graphical representations of single case data and transform graphical displays back to raw data, as discussed in Bulte and Onghena (2013) <doi:10.22237/jmasm/1383280020>. The package also includes tools for visually analyzing single-case data, by displaying central location, variability and trend.

Maintained by Tamal Kumar De. Last updated 5 years ago.

4.0 match 1.00 score

cran

SCMA:Single-Case Meta-Analysis

Perform meta-analysis of single-case experiments, including calculating various effect size measures (SMD, PND, PEM and NAP) and probability combining (additive and multiplicative method), as discussed in Bulte and Onghena (2013) <doi:10.22237/jmasm/1383280020>.

Maintained by Tamal Kumar De. Last updated 5 years ago.

4.0 match 1.00 score

cristiancastiglione

sgdGMF:Estimation of Generalized Matrix Factorization Models via Stochastic Gradient Descent

Efficient framework to estimate high-dimensional generalized matrix factorization models using penalized maximum likelihood under a dispersion exponential family specification. Either deterministic and stochastic methods are implemented for the numerical maximization. In particular, the package implements the stochastic gradient descent algorithm with a block-wise mini-batch strategy to speed up the computations and an efficient adaptive learning rate schedule to stabilize the convergence. All the theoretical details can be found in Castiglione, Segers, Clement, Risso (2024, <https://arxiv.org/abs/2412.20509>). Other methods considered for the optimization are the alternated iterative re-weighted least squares and the quasi-Newton method with diagonal approximation of the Fisher information matrix discussed in Kidzinski, Hui, Warton, Hastie (2022, <http://jmlr.org/papers/v23/20-1104.html>).

Maintained by Cristian Castiglione. Last updated 11 days ago.

openblas cpp openmp

0.5 match 10 stars 7.75 score 108 scripts

quentingronau

abtest:Bayesian A/B Testing

Provides functions for Bayesian A/B testing including prior elicitation options based on Kass and Vaidyanathan (1992) <doi:10.1111/j.2517-6161.1992.tb01868.x>. Gronau, Raj K. N., & Wagenmakers (2021) <doi:10.18637/jss.v100.i17>.

Maintained by Quentin F. Gronau. Last updated 3 years ago.

cpp

3.9 match 1.00 score 9 scripts

jacquesallard

TaxicabCA:Taxicab Correspondence Analysis

Computation and visualization of Taxicab Correspondence Analysis, Choulakian (2006) <doi:10.1007/s11336-004-1231-4>. Classical correspondence analysis (CA) is a statistical method to analyse 2-dimensional tables of positive numbers and is typically applied to contingency tables (Benzecri, J.-P. (1973). L'Analyse des Donnees. Volume II. L'Analyse des Correspondances. Paris, France: Dunod). Classical CA is based on the Euclidean distance. Taxicab CA is like classical CA but is based on the Taxicab or Manhattan distance. For some tables, Taxicab CA gives more informative results than classical CA.

Maintained by Jacques Allard. Last updated 5 years ago.

2.8 match 1.36 score 23 scripts

riccarl

JFM:Rock Mass Structural Analysis from 3D Mesh of Point Cloud

Provides functions to extract joint planes from 3D triangular mesh derived from point cloud and makes data available for structural analysis.

Maintained by Riccardo Campana. Last updated 3 years ago.

openblas cpp

3.6 match 1.00 score 1 scripts

cran

refineR:Reference Interval Estimation using Real-World Data

Indirect method for the estimation of reference intervals using Real-World Data ('RWD'). It takes routine measurements of diagnostic tests, containing pathological and non-pathological samples as input and uses sophisticated statistical methods to derive a model describing the distribution of the non-pathological samples. This distribution can then be used to derive reference intervals. Furthermore, the package offers functions for printing and plotting the results of the algorithm. See ?refineR for a more comprehensive description of the features. Version 1.0 of the algorithm is described in detail in 'Ammer et al. (2021)' <doi:10.1038/s41598-021-95301-2>. Additional guidance on the usage of the algorithm is given in 'Ammer et al. (2023)' <doi:10.1093/jalm/jfac101>.

Maintained by Tatjana Ammer. Last updated 7 months ago.

1.6 match 1 stars 2.18 score 15 scripts

cran

pubmed.mineR:Text Mining of PubMed Abstracts

Text mining of PubMed Abstracts (text and XML) from <https://pubmed.ncbi.nlm.nih.gov/>.

Maintained by S. Ramachandran. Last updated 6 months ago.

1.6 match 6 stars 2.08 score

cran

salad:Simple Automatic Differentiation

Handles both vector and matrices, using a flexible S4 class for automatic differentiation. The method used is forward automatic differentiation. Many functions and methods have been defined, so that in most cases, functions written without automatic differentiation in mind can be used without change.

Maintained by Hervé Perdry. Last updated 3 months ago.

1.3 match 2.48 score 9 scripts

mfacevedol

renpow:Renewable Power Systems and the Environment

Supports calculations and visualization for renewable power systems and the environment. Analysis and graphical tools for DC and AC circuits and their use in electric power systems. Analysis and graphical tools for thermodynamic cycles and heat engines, supporting efficiency calculations in coal-fired power plants, gas-fired power plants. Calculations of carbon emissions and atmospheric CO2 dynamics. Analysis of power flow and demand for the grid, as well as power models for microgrids and off-grid systems. Provides resource and power generation for hydro power, wind power, and solar power.

Maintained by Miguel F. Acevedo. Last updated 7 years ago.

2.0 match 1.48 score 30 scripts

vitara-p

icmm:Empirical Bayes Variable Selection via ICM/M Algorithm

Empirical Bayes variable selection via ICM/M algorithm for normal, binary logistic, and Cox's regression. The basic problem is to fit high-dimensional regression which sparse coefficients. This package allows incorporating the Ising prior to capture structure of predictors in the modeling process. More information can be found in the papers listed in the URL below.

Maintained by Vitara Pungpapong. Last updated 4 years ago.

2.3 match 1.28 score 19 scripts

bioc

lionessR:Modeling networks for individual samples using LIONESS

LIONESS, or Linear Interpolation to Obtain Network Estimates for Single Samples, can be used to reconstruct single-sample networks (https://arxiv.org/abs/1505.06440). This code implements the LIONESS equation in the lioness function in R to reconstruct single-sample networks. The default network reconstruction method we use is based on Pearson correlation. However, lionessR can run on any network reconstruction algorithms that returns a complete, weighted adjacency matrix. lionessR works for both unipartite and bipartite networks.

Maintained by Ping-Han Hsieh. Last updated 5 months ago.

network networkinference geneexpression

0.5 match 22 stars 5.57 score 17 scripts

mattsheng

iBART:Iterative Bayesian Additive Regression Trees Descriptor Selection Method

A statistical method based on Bayesian Additive Regression Trees with Global Standard Error Permutation Test (BART-G.SE) for descriptor selection and symbolic regression. It finds the symbolic formula of the regression function y=f(x) as described in Ye, Senftle, and Li (2023) <https://www.tandfonline.com/doi/abs/10.1080/01621459.2023.2294527>.

Maintained by Shengbin Ye. Last updated 1 months ago.

openjdk

0.5 match 7 stars 5.53 score 16 scripts

lleisong

itsdm:Isolation Forest-Based Presence-Only Species Distribution Modeling

Collection of R functions to do purely presence-only species distribution modeling with isolation forest (iForest) and its variations such as Extended isolation forest and SCiForest. See the details of these methods in references: Liu, F.T., Ting, K.M. and Zhou, Z.H. (2008) <doi:10.1109/ICDM.2008.17>, Hariri, S., Kind, M.C. and Brunner, R.J. (2019) <doi:10.1109/TKDE.2019.2947676>, Liu, F.T., Ting, K.M. and Zhou, Z.H. (2010) <doi:10.1007/978-3-642-15883-4_18>, Guha, S., Mishra, N., Roy, G. and Schrijvers, O. (2016) <https://proceedings.mlr.press/v48/guha16.html>, Cortes, D. (2021) <arXiv:2110.13402>. Additionally, Shapley values are used to explain model inputs and outputs. See details in references: Shapley, L.S. (1953) <doi:10.1515/9781400881970-018>, Lundberg, S.M. and Lee, S.I. (2017) <https://dl.acm.org/doi/abs/10.5555/3295222.3295230>, Molnar, C. (2020) <ISBN:978-0-244-76852-2>, Štrumbelj, E. and Kononenko, I. (2014) <doi:10.1007/s10115-013-0679-x>. itsdm also provides functions to diagnose variable response, analyze variable importance, draw spatial dependence of variables and examine variable contribution. As utilities, the package includes a few functions to download bioclimatic variables including 'WorldClim' version 2.0 (see Fick, S.E. and Hijmans, R.J. (2017) <doi:10.1002/joc.5086>) and 'CMCC-BioClimInd' (see Noce, S., Caporaso, L. and Santini, M. (2020) <doi:10.1038/s41597-020-00726-5>.

Maintained by Lei Song. Last updated 2 years ago.

isolation-forest outlier-detection presence-onlymodel shapley-value species-distribution-modelling

0.5 match 4 stars 5.59 score 65 scripts

eriqande

CKMRpop:Forward-in-Time Simulation and Tallying of Pairwise Relationships

Provides an R wrapper around the program 'spip' (<https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1471-8286.2005.00884.x>), a C program for the simulation of pedigrees within age-structured populations with user-specified life histories. Also includes a variety of functions to parse 'spip' output to compile information about related pairs amongst simulated, sampled individuals, to assess the feasibility and potential accuracy of close-kin mark-recapture (CKMR). Full documentation and vignettes are mirrored at <https://eriqande.github.io/CKMRpop/index.html> and can be read online there.

Maintained by Eric C. Anderson. Last updated 1 years ago.

noaa-omics-software cpp

0.5 match 4 stars 5.38 score 24 scripts

canyi-chen

abima:Adaptive Bootstrap Inference for Mediation Analysis with Enhanced Statistical Power

Assess whether and how a specific continuous or categorical exposure affects the outcome of interest through one- or multi-dimensional mediators using an adaptive bootstrap (AB) approach. The AB method allows to make inference for composite null hypotheses of no mediation effect, providing valid type I error control and thus optimizes statistical power. For more technical details, refer to He, Song and Xu (2024) <doi:10.1093/jrsssb/qkad129>.

Maintained by Canyi Chen. Last updated 5 months ago.

enhanced-power mediation-analysis type-i-error-control

0.8 match 1 stars 3.30 score 7 scripts

cran

MChtest:Monte Carlo Hypothesis Tests with Sequential Stopping

Performs Monte Carlo hypothesis tests, allowing a couple of different sequential stopping boundaries. For example, a truncated sequential probability ratio test boundary (Fay, Kim and Hachey, 2007 <DOI:10.1198/106186007X257025>) and a boundary proposed by Besag and Clifford, 1991 <DOI:10.1093/biomet/78.2.301>. Gives valid p-values and confidence intervals on p-values.

Maintained by Michael P. Fay. Last updated 6 years ago.

2.3 match 1.00 score

rohelab

fastadi:Self-Tuning Data Adaptive Matrix Imputation

Implements the AdaptiveImpute matrix completion algorithm of 'Intelligent Initialization and Adaptive Thresholding for Iterative Matrix Completion', <https://amstat.tandfonline.com/doi/abs/10.1080/10618600.2018.1518238>. AdaptiveImpute is useful for embedding sparsely observed matrices, often out performs competing matrix completion algorithms, and self-tunes its hyperparameter, making usage easy.

Maintained by Alex Hayes. Last updated 9 months ago.

openblas cpp openmp

0.5 match 9 stars 4.26 score 6 scripts

hugogogo

varband:Variable Banding of Large Precision Matrices

Implementation of the variable banding procedure for modeling local dependence and estimating precision matrices that is introduced in Yu & Bien (2016) and is available at <https://arxiv.org/abs/1604.07451>.

Maintained by Guo Yu. Last updated 7 years ago.

openblas cpp

0.5 match 2 stars 4.00 score 10 scripts

heplersa

multiocc:Fits Multivariate Spatio-Temporal Occupancy Model

Spatio-temporal multivariate occupancy models can handle multiple species in occupancy models. This method for fitting such models is described in Hepler and Erhardt (2021) "A spatiotemporal model for multivariate occupancy data" <https://onlinelibrary.wiley.com/doi/abs/10.1002/env.2657>.

Maintained by Staci Hepler. Last updated 2 years ago.

0.5 match 3.70 score 4 scripts

illustratien

toolStability:Tool for Stability Indices Calculation

Tools to calculate stability indices with parametric, non-parametric and probabilistic approaches. The basic data format requirement for 'toolStability' is a data frame with 3 columns including numeric trait values, genotype,and environmental labels. Output format of each function is the dataframe with chosen stability index for each genotype. Function "table_stability" offers the summary table of all stability indices in this package. This R package toolStability is part of the main publication: Wang, Casadebaig and Chen (2023) <doi:10.1007/s00122-023-04264-7>. Analysis pipeline for main publication can be found on github: <https://github.com/Illustratien/Wang_2023_TAAG/tree/V1.0.0>. Sample dataset in this package is derived from another publication: Casadebaig P, Zheng B, Chapman S et al. (2016) <doi:10.1371/journal.pone.0146385>. For detailed documentation of dataset, please see on Zenodo <doi:10.5281/zenodo.4729636>. Indices used in this package are from: Döring TF, Reckling M (2018) <doi:10.1016/j.eja.2018.06.007>. Eberhart SA, Russell WA (1966) <doi:10.2135/cropsci1966.0011183X000600010011x>. Eskridge KM (1990) <doi:10.2135/cropsci1990.0011183X003000020025x>. Finlay KW, Wilkinson GN (1963) <doi:10.1071/AR9630742>. Hanson WD (1970) Genotypic stability. <doi:10.1007/BF00285245>. Lin CS, Binns MR (1988) <https://cdnsciencepub.com/doi/abs/10.4141/cjps88-018>. Nassar R, Hühn M (1987). Pinthus MJ (1973) <doi:10.1007/BF00021563>. Römer T (1917). Shukla GK (1972). Wricke G (1962).

Maintained by Tien-Cheng Wang. Last updated 1 years ago.

analysis-package reproducible-research stability

0.5 match 1 stars 3.74 score 11 scripts

lechmadeyski

reproducer:Reproduce Statistical Analyses and Meta-Analyses

Includes data analysis and meta-analysis functions (e.g., to calculate effect sizes and 95% Confidence Intervals (CI) on Standardised Effect Sizes (d) for AB/BA cross-over repeated-measures experimental designs), data presentation functions (e.g., density curve overlaid on histogram),and the data sets analyzed in different research papers in software engineering (e.g., related to software defect prediction or multi- site experiment concerning the extent to which structured abstracts were clearer and more complete than conventional abstracts) to streamline reproducible research in software engineering.

Maintained by Lech Madeyski. Last updated 1 years ago.

0.5 match 3.50 score 63 scripts

carlosyanez

aussiemaps:Maps of Australia

Granular maps of Australia using ABS boundaries from 2006-2021.

Maintained by Carlos Yáñez Santibáñez. Last updated 2 years ago.

australia maps r-spatial sf-objects

0.6 match 1 stars 3.06 score 23 scripts

nano-optics

RcppFaddeeva:'Rcpp' Bindings for the 'Faddeeva' Package

Access to a family of Gauss error functions for arbitrary complex arguments is provided via the 'Faddeeva' package by Steven G. Johnson (see <http://ab-initio.mit.edu/wiki/index.php/Faddeeva_Package> for more information).

Maintained by Baptiste Auguié. Last updated 7 months ago.

cpp

0.5 match 3.20 score 16 scripts

gwpcor

gwpcormapper:Geographically Weighted Partial Correlation Mapper

An interactive mapping tool for geographically weighted correlation and partial correlation. Geographically weighted partial correlation coefficients are calculated following (Percival and Tsutsumida, 2017)<doi:10.1553/giscience2017_01_s36> and are described in greater detail in (Tsutsumida et al., 2019)<doi:10.5194/ica-abs-1-372-2019> and (Percival et al., 2021)<arXiv:2101.03491>.

Maintained by Joseph Emile Honour Percival. Last updated 3 years ago.

cpp

0.5 match 3 stars 3.18 score 1 scripts

gardiners

ozgs:Use the Australian Statistical Geography Standard in R

Access maps, layers and data provided by the Australian Statistical Geography Standard (ASGS) via the ABS web service. Available spatial objects include Indigenous Structures, Statistical Areas (SA1, SA2, SA3 and SA4), states and territories, postcode approximations (POAs), suburbs and localities, local government areas (LGAs), state and federal electorates, remoteness areas and the mesh blocks from which each of these are constructed. Requests are cached to avoid repeatedly fetching large quantities of data from the ABS web servers.

Maintained by Sam Gardiner. Last updated 12 months ago.

0.8 match 2.00 score

david-cortes

nonneg.cg:Non-Negative Conjugate-Gradient Minimizer

Minimize a differentiable function subject to all the variables being non-negative (i.e. >= 0), using a Conjugate-Gradient algorithm based on a modified Polak-Ribiere-Polyak formula as described in (Li, (2013) <https://www.hindawi.com/journals/jam/2013/986317/abs/>).

Maintained by David Cortes. Last updated 5 years ago.

conjugate-gradient minimize optimization openblas cpp openmp

0.5 match 2 stars 3.00 score 1 scripts

cran

CircNNTSRSymmetric:Circular Data using Symmetric NNTS Models

The statistical analysis of circular data using distributions based on symmetric Nonnegative Trigonometric Sums (NNTS). It includes functions to perform empirical analysis and estimate the parameters of density functions. Fernandez-Duran, J.J. and Gregorio-Dominguez, M.M. (2025), "Multimodal Symmetric Circular Distributions Based on Nonnegative Trigonometric Sums and a Likelihood Ratio Test for Reflective Symmetry", <doi:10.48550/arXiv.2412.19501>.

Maintained by Maria Mercedes Gregorio-Dominguez. Last updated 1 months ago.

1.5 match 1.00 score

uwemenzel

EMT:Exact Multinomial Test: Goodness-of-Fit Test for Discrete Multivariate Data

Goodness-of-fit tests for discrete multivariate data. It is tested if a given observation is likely to have occurred under the assumption of an ab-initio model. Monte Carlo methods are provided to make the package capable of solving high-dimensional problems.

Maintained by Uwe Menzel. Last updated 12 months ago.

0.5 match 2.67 score 47 scripts

jdgonzalezwork

RMBC:Robust Model Based Clustering

A robust clustering algorithm (Model-Based) similar to Expectation Maximization for finite mixture normal distributions is implemented, its main advantage is that the estimator is resistant to outliers, that means that results of parameter estimation are still correct when there are atypical values in the sample (see Gonzalez, Maronna, Yohai and Zamar (2021) <https://arxiv.org/abs/2102.06851>).

Maintained by Juan Domingo Gonzalez. Last updated 4 years ago.

0.5 match 2.70 score

jzhou54

TestsSymmetry:Tests for Symmetry when the Center of Symmetry is Unknown

Provides functionality of a statistical testing implementation whether a dataset comes from a symmetric distribution when the center of symmetry is unknown, including Wilcoxon test and sign test procedure. In addition, sample size determination for both tests is provided. The Wilcoxon test procedure is described in Vexler et al. (2023) <https://www.sciencedirect.com/science/article/abs/pii/S0167947323000579>, and the sign test is outlined in Gastwirth (1971) <https://www.jstor.org/stable/2284233>.

Maintained by Jiaojiao Zhou. Last updated 1 years ago.

cpp

0.5 match 2.70 score 1 scripts

weiyangyu

HiGarrote:Nonnegative Garrote Method Incorporating Hierarchical Relationships

An implementation of the nonnegative garrote method that incorporates hierarchical relationships among variables. The core function, HiGarrote, offers an automated approach for analyzing experiments while respecting hierarchical structures among effects. For methodological details, refer to Yu and Joseph (2024) <https://arxiv.org/abs/2411.01383>. This work is supported by U.S. National Foundation grant DMS-2310637.

Maintained by Wei-Yang Yu. Last updated 4 months ago.

cpp

0.5 match 2.00 score

davidzarruk

IGCities:Simulate Impact of Different Urban Policies Through a General Equilibrium Model

Develops a General Equilibrium (GE) Model, which estimates key variables such as wages, the number of residents and workers, the prices of the floor space, and its distribution between commercial and residential use, as in Ahlfeldt et al., (2015) <https://onlinelibrary.wiley.com/doi/abs/10.3982/ECTA10876>. By doing so, the model allows understanding the economic influence of different urban policies.

Maintained by David Zarruk. Last updated 2 years ago.

0.5 match 1 stars 1.70 score

djpedregal

UComp:Automatic Univariate Time Series Modelling of many Kinds

Comprehensive analysis and forecasting of univariate time series using automatic time series models of many kinds. Harvey AC (1989) <doi:10.1017/CBO9781107049994>. Pedregal DJ and Young PC (2002) <doi:10.1002/9780470996430>. Durbin J and Koopman SJ (2012) <doi:10.1093/acprof:oso/9780199641178.001.0001>. Hyndman RJ, Koehler AB, Ord JK, and Snyder RD (2008) <doi:10.1007/978-3-540-71918-2>. Gómez V, Maravall A (2000) <doi:10.1002/9781118032978>. Pedregal DJ, Trapero JR and Holgado E (2024) <doi:10.1016/j.ijforecast.2023.09.004>.

Maintained by Diego J. Pedregal. Last updated 16 days ago.

openblas cpp openmp

0.5 match 1 stars 1.70 score 1 scripts

sophie-lebre

DCODE:List Linear n-Peptide Constraints for Overlapping Protein Regions

Traversal graph algorithm for listing linear n-peptide constraints for overlapping protein regions. (Lebre and Gascuel, The combinatorics of overlapping genes, freely available from arXiv at : http://arxiv.org/abs/1602.04971).

Maintained by Sophie Lebre. Last updated 9 years ago.

0.5 match 1.60 score 3 scripts

argju

gpmap:Analysing and Plotting Genotype-Phenotype Maps

Tools for studying genotype-phenotype maps for bi-allelic loci underlying quantitative phenotypes. The 0.1 version is released in connection with the publication of Gjuvsland et al (2013) and implements basic line plots and the monotonicity measures for GP maps presented in the paper. Reference: Gjuvsland AB, Wang Y, Plahte E and Omholt SW (2013) Monotonicity is a key feature of genotype-phenotype maps. Frontier in Genetics 4:216 <doi:10.3389/fgene.2013.00216>.

Maintained by Arne B. Gjuvsland. Last updated 4 years ago.

0.5 match 1.34 score 11 scripts

rluo

cord:Community Estimation in G-Models via CORD

Partition data points (variables) into communities/clusters, similar to clustering algorithms, such as k-means and hierarchical clustering. This package implements a clustering algorithm based on a new metric CORD, defined for high dimensional parametric or semi-parametric distributions. Read http://arxiv.org/abs/1508.01939 for more details.

Maintained by Xi (Rossi) LUO. Last updated 9 years ago.

cpp

0.5 match 1.00 score 1 scripts

janhoutveen

pdt:Permutation Distancing Test

Permutation (randomisation) test for single-case phase design data with two phases (e.g., pre- and post-treatment). Correction for dependency of observations is done through stepwise resampling the time series while varying the distance between observations. The required distance 0,1,2,3.. is determined based on repeated dependency testing while stepwise increasing the distance. In preparation: Vroegindeweij et al. "A Permutation distancing test for single-case observational AB phase design data: A Monte Carlo simulation study".

Maintained by Jan Houtveen. Last updated 2 years ago.

0.5 match 1.00 score 5 scripts

daiscode

ROCpsych:Compute and Compare Diagnostic Test Statistics Across Groups

Functions for (1) computing diagnostic test statistics (sensitivity, specificity, etc.) from confusion matrices with adjustment for various base rates or known prevalence based on McCaffrey et al (2003) <doi:10.1007/978-1-4615-0079-7_1>, (2) computing optimal cut-off scores with different criteria including maximizing sensitivity, maximizing specificity, and maximizing the Youden Index from Youden (1950) <https://acsjournals.onlinelibrary.wiley.com/doi/abs/10.1002/1097-0142%281950%293%3A1%3C32%3A%3AAID-CNCR2820030106%3E3.0.CO%3B2-3>, and (3) displaying and comparing classification statistics and area under the receiver operating characteristic (ROC) curves or area under the curves (AUC) across consecutive categories for ordinal variables.

Maintained by Shenghai Dai. Last updated 5 years ago.

0.5 match 1.00 score