constructive - Display Idiomatic Code to Construct Most R Objects
Prints code that can be used to recreate R objects. In a sense it is similar to 'base::dput()' or 'base::deparse()' but 'constructive' strives to use idiomatic constructors.
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archivedpackagesr-universe
5.06 score 5 stars 4 dependents 1.9k downloadssBIC - Computing the Singular BIC for Multiple Models
Computes the sBIC for various singular model collections including: binomial mixtures, factor analysis models, Gaussian mixtures, latent forests, latent class analyses, and reduced rank regressions.
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archivedpackagesr-universecpp
5.06 score 5 stars 76 scripts 253 downloads
polite - Be Nice on the Web
Be responsible when scraping data from websites by following polite principles: introduce yourself, ask for permission, take slowly and never ask twice.
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archivedpackagesr-universe
4.90 score 5 stars 1 dependents 1.1k scripts 713 downloads
SSM - Fit and Analyze Smooth Supersaturated Models
Creates an S4 class "SSM" and defines functions for fitting smooth supersaturated models, a polynomial model with spline-like behaviour. Functions are defined for the computation of Sobol indices for sensitivity analysis and plotting the main effects using FANOVA methods. It also implements the estimation of the SSM metamodel error using a GP model with a variety of defined correlation functions.
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archivedpackagesr-universe
4.44 score 5 stars 11 scripts 208 downloads
dawaR - An API Wrapper for 'DAWA' - 'The Danish Address Web API'
Functions for interacting with all sections of the official 'Danish Address Web API' (also known as 'DAWA') <https://api.dataforsyningen.dk>. The development of this package is completely independent from the government agency, Klimadatastyrelsen, who maintains the API.
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archivedpackagesr-universe
4.35 score 5 stars 1 dependents 495 downloads
Stat2Data - Datasets for Stat2
Datasets for the textbook Stat2: Modeling with Regression and ANOVA (second edition). The package also includes data for the first edition, Stat2: Building Models for a World of Data and a few functions for plotting diagnostics.
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archivedpackagesr-universe
4.34 score 5 stars 944 scripts 4.6k downloadsBIGDAWG - Case-Cotrol Analysis of Multi-Allelic Loci
Data sets and functions for chi-squared Hardy-Weinberg and case-control association tests of highly polymorphic genetic data [e.g., human leukocyte antigen (HLA) data]. Performs association tests at multiple levels of polymorphism (haplotype, locus and HLA amino-acids) as described in Pappas DJ, Marin W, Hollenbach JA, Mack SJ (2016) <doi:10.1016/j.humimm.2015.12.006>. Combines rare variants to a common class to account for sparse cells in tables as described by Hollenbach JA, Mack SJ, Thomson G, Gourraud PA (2012) <doi:10.1007/978-1-61779-842-9_14>.
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archivedpackagesr-universe
4.32 score 5 stars 1 dependents 621 downloads
tidyfit - Regularized Linear Modeling with Tidy Data
An extension to the 'R' tidy data environment for automated machine learning. The package allows fitting and cross validation of linear regression and classification algorithms on grouped data.
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archivedpackagesr-universe
4.30 score 5 stars 275 downloadsTSrepr - Time Series Representations
Methods for representations (i.e. dimensionality reduction, preprocessing, feature extraction) of time series to help more accurate and effective time series data mining. Non-data adaptive, data adaptive, model-based and data dictated (clipped) representation methods are implemented. Also various normalisation methods (min-max, z-score, Box-Cox, Yeo-Johnson), and forecasting accuracy measures are implemented.
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archivedpackagesr-universecpp
4.27 score 5 stars 124 scripts 436 downloadsimaginarycss - Tools for Studying Imaginary Cognitive Social Structure
Provides functions to measure and test imaginary cognitive social structure (CSS) motifs, which are patterns of perceived relationships among individuals in a social network. Includes tools for calculating motif frequencies, comparing observed motifs to expected distributions, and visualizing motif structures. Implements methods described in Tanaka and Vega Yon (2023) <doi:10.1016/j.socnet.2023.11.005>.
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archivedpackagesr-universequartocpp
4.23 score 5 stars 17 scripts 72 downloadsmombf - Model Selection with Bayesian Methods and Information Criteria
Model selection and averaging for regression and mixtures, inclusing Bayesian model selection and information criteria (BIC, EBIC, AIC, GIC).
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archivedpackagesr-universeopenblascpp
4.18 score 5 stars 2 dependents 609 downloadsiterors - Fast, Compact Iterators and Tools
A fresh take on iterators in R. Designed to be cross-compatible with the 'iterators' package, but using the 'nextOr' method will offer better performance as well as more compact code. With batteries included: includes a collection of iterator constructors and combinators ported and refined from the 'iterators', 'itertools', and 'itertools2' packages.
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archivedpackagesr-universe
4.10 score 5 stars 326 downloadsearlyR - Estimation of Transmissibility in the Early Stages of a Disease Outbreak
Implements a simple, likelihood-based estimation of the reproduction number (R0) using a branching process with a Poisson likelihood. This model requires knowledge of the serial interval distribution, and dates of symptom onsets. Infectiousness is determined by weighting R0 by the probability mass function of the serial interval on the corresponding day. It is a simplified version of the model introduced by Cori et al. (2013) <doi:10.1093/aje/kwt133>.
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archivedpackagesr-universe
4.07 score 5 stars 79 scripts 544 downloadssensiPhy - Sensitivity Analysis for Comparative Methods
An implementation of sensitivity analysis for phylogenetic comparative methods. The package is an umbrella of statistical and graphical methods that estimate and report different types of uncertainty in PCM: (i) Species Sampling uncertainty (sample size; influential species and clades). (ii) Phylogenetic uncertainty (different topologies and/or branch lengths). (iii) Data uncertainty (intraspecific variation and measurement error).
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archivedpackagesr-universe
4.00 score 5 stars 67 scripts 317 downloadsrepfdr - Replicability Analysis for Multiple Studies of High Dimension
Estimation of Bayes and local Bayes false discovery rates for replicability analysis (Heller & Yekutieli, 2014 <doi:10.1214/13-AOAS697> ; Heller at al., 2015 <doi: 10.1093/bioinformatics/btu434>).
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archivedpackagesr-universecpp
3.98 score 5 stars 19 scripts 370 downloadsplotluck - 'ggplot2' Version of "I'm Feeling Lucky!"
Examines the characteristics of a data frame and a formula to automatically choose the most suitable type of plot out of the following supported options: scatter, violin, box, bar, density, hexagon bin, spine plot, and heat map. The aim of the package is to let the user focus on what to plot, rather than on the "how" during exploratory data analysis. It also automates handling of observation weights, logarithmic axis scaling, reordering of factor levels, and overlaying smoothing curves and median lines. Plots are drawn using 'ggplot2'.
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archivedpackagesr-universe
3.94 score 5 stars 35 scripts 272 downloadsocp - Bayesian Online Changepoint Detection
Implements the Bayesian online changepoint detection method by Adams and MacKay (2007) <arXiv:0710.3742> for univariate or multivariate data. Gaussian and Poisson probability models are implemented. Provides post-processing functions with alternative ways to extract changepoints.
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archivedpackagesr-universe
3.86 score 5 stars 29 scripts 439 downloadstfaddons - Interface to 'TensorFlow SIG Addons'
'TensorFlow SIG Addons' <https://www.tensorflow.org/addons> is a repository of community contributions that conform to well-established API patterns, but implement new functionality not available in core 'TensorFlow'. 'TensorFlow' natively supports a large number of operators, layers, metrics, losses, optimizers, and more. However, in a fast moving field like Machine Learning, there are many interesting new developments that cannot be integrated into core 'TensorFlow' (because their broad applicability is not yet clear, or it is mostly used by a smaller subset of the community).
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archivedpackagesr-universe
3.85 score 5 stars 28 scripts 243 downloadsRHPCBenchmark - Benchmarks for High-Performance Computing Environments
Microbenchmarks for determining the run time performance of aspects of the R programming environment and packages relevant to high-performance computation. The benchmarks are divided into three categories: dense matrix linear algebra kernels, sparse matrix linear algebra kernels, and machine learning functionality.
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archivedpackagesr-universe
3.72 score 5 stars 21 scripts 239 downloadsEZFragility - Compute Neural Fragility for Ictal iEEG Time Series
Provides tools to compute the neural fragility matrix from intracranial electrocorticographic (iEEG) recordings, enabling the analysis of brain dynamics during seizures. The package implements the method described by Li et al. (2017) <doi:10.23919/ACC.2017.7963378> and includes functions for data preprocessing ('Epoch'), fragility computation ('calcAdjFrag'), and visualization.
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archivedpackagesr-universe
3.70 score 5 stars 10 scripts 505 downloadswebreadr - Tools for Reading Formatted Access Log Files
R is used by a vast array of people for a vast array of purposes - including web analytics. This package contains functions for consuming and munging various common forms of request log, including the Common and Combined Web Log formats and various Amazon access logs.
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archivedpackagesr-universecpp
3.65 score 5 stars 18 scripts 239 downloadsPolyPatEx - Paternity Exclusion in Autopolyploid Species
Functions to perform paternity exclusion via allele matching, in autopolyploid species having ploidy 4, 6, or 8. The marker data used can be genotype data (copy numbers known) or 'allelic phenotype data' (copy numbers not known).
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archivedpackagesr-universe
3.63 score 5 stars 17 scripts 214 downloadsarenar - Arena for the Exploration and Comparison of any ML Models
Generates data for challenging machine learning models in 'Arena' <https://arena.drwhy.ai> - an interactive web application. You can start the server with XAI (Explainable Artificial Intelligence) plots to be generated on-demand or precalculate and auto-upload data file beside shareable 'Arena' URL.
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3.53 score 5 stars 17 scripts 388 downloadsRdice - A Collection of Functions to Experiment Dice Rolls
A collection of functions to simulate dice rolls and the like. In particular, experiments and exercises can be performed looking at combinations and permutations of values in dice rolls and coin flips, together with the corresponding frequencies of occurrences. When applying each function, the user has to input the number of times (rolls, flips) to toss the dice. Needless to say, the more the tosses, the more the frequencies approximate the actual probabilities. Moreover, the package provides functions to generate non-transitive sets of dice (like Efron's) and to check whether a given set of dice is non-transitive with given probability.
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archivedpackagesr-universe
3.51 score 5 stars 13 scripts 216 downloadsfuzzyRankTests - Fuzzy Rank Tests and Confidence Intervals
Does fuzzy tests and confidence intervals (following Geyer and Meeden, Statistical Science, 2005, <doi:10.1214/088342305000000340>) for sign test and Wilcoxon signed rank and rank sum tests.
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archivedpackagesr-universe
3.48 score 5 stars 1 dependents 426 downloadsMapGAM - Mapping Smoothed Effect Estimates from Individual-Level Data
Contains functions for mapping odds ratios, hazard ratios, or other effect estimates using individual-level data such as case-control study data, using generalized additive models (GAMs) or Cox models for smoothing with a two-dimensional predictor (e.g., geolocation or exposure to chemical mixtures) while adjusting linearly for confounding variables, using methods described by Kelsall and Diggle (1998), Webster at al. (2006), and Bai et al. (2020). Includes convenient functions for mapping point estimates and confidence intervals, efficient control sampling, and permutation tests for the null hypothesis that the two-dimensional predictor is not associated with the outcome variable (adjusting for confounders).
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archivedpackagesr-universe
3.45 score 5 stars 1 dependents 62 scripts 215 downloadsMangrove - Risk Prediction on Trees
Methods for performing genetic risk prediction from genotype data. You can use it to perform risk prediction for individuals, or for families with missing data.
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archivedpackagesr-universe
3.41 score 5 stars 17 scripts 385 downloadslater2 - Utilities for Scheduling Functions to Execute Later with Event Loops
Executes arbitrary R or C functions some time after the current time, after the R execution stack has emptied. The functions are scheduled in an event loop. This is a derived work from the 'later' package aiming to reduce the number of dependencies.
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archivedpackagesr-universecpp
3.40 score 5 stars 243 downloadstabulog - Parsing Semi-Structured Log Files into Tabular Format
Convert semi-structured log files (such as 'Apache' access.log files) into a tabular format (data.frame) using a standard template system.
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archivedpackagesr-universe
3.40 score 5 stars 7 scripts 191 downloadsloewesadditivity - Loewe's Additivity
Estimate model parameters to determine whether two compounds have synergy, antagonism, or Loewe's Additivity.
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archivedpackagesr-universe
3.40 score 5 stars 8 scripts 293 downloadsincidental - Implements Empirical Bayes Incidence Curves
Make empirical Bayes incidence curves from reported case data using a specified delay distribution.
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archivedpackagesr-universe
3.40 score 5 stars 10 scripts 298 downloads
incubate - Parametric Time-to-Event Analysis with Variable Incubation Phases
Fit parametric models for time-to-event data that show an initial 'incubation period', i.e. a variable delay phase where no events occur. The delayed Weibull distribution serves as the foundational data model. For parameter estimation, different flavours of maximum likelihood estimation ('MLE') and the method of maximum product of spacings estimation ('MPSE') are implemented. Bootstrap confidence intervals for parameters and significance tests in a two group setting are provided.
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archivedpackagesr-universecpp
3.40 score 5 stars 409 downloads
shinyreprex - Reproducible Code for 'Shiny' Objects
Provides functionality to extract reactive expressions from a 'shiny' application and convert them into stand-alone R scripts. This enables users to reproduce tables and visualisations outside the interactive UI, facilitating integration into static reports or automated workflows without requiring access to the original application source code.
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archivedpackagesr-universe
3.40 score 5 stars 467 downloadsmathml - Translate R Expressions to 'MathML' and 'LaTeX'/'MathJax'
Translate R expressions to 'MathML' or 'MathJax'/'LaTeX' so that they can be rendered in R markdown documents and shiny apps.
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archivedpackagesr-universe
3.40 score 5 stars 373 downloadsdsdp - Density Estimation with Semidefinite Programming
The models of probability density functions are Gaussian or exponential distributions with polynomial correction terms. Using a maximum likelihood method, 'dsdp' computes parameters of Gaussian or exponential distributions together with degrees of polynomials by a grid search, and coefficient of polynomials by a variant of semidefinite programming. It adopts Akaike Information Criterion for model selection. See a vignette for a tutorial and more on our 'Github' repository <https://github.com/tsuchiya-lab/dsdp/>.
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archivedpackagesr-universeopenblasfortran
3.40 score 5 stars 6 scripts 105 downloadsgeesmv - Modified Variance Estimators for Generalized Estimating Equations
Generalized estimating equations with the original sandwich variance estimator proposed by Liang and Zeger (1986), and eight types of more recent modified variance estimators for improving the finite small-sample performance.
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archivedpackagesr-universe
3.13 score 5 stars 45 scripts 404 downloadsPROSPER - Simulation of Weed Population Dynamics
An environment to simulate the development of annual plant populations with regard to population dynamics and genetics, especially herbicide resistance. It combines genetics on the individual level (Renton et al. 2011) with a stochastic development on the population level (Daedlow, 2015). Renton, M, Diggle, A, Manalil, S and Powles, S (2011) <doi:10.1016/j.jtbi.2011.05.010> Daedlow, Daniel (2015, doctoral dissertation: University of Rostock, Faculty of Agriculture and Environmental Sciences.)
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archivedpackagesr-universe
3.11 score 5 stars 26 scripts 248 downloadsvietnamcode - Convert Vietnam Provincial Codes
Converts Vietnam's provinces' names and ID across different formats. Handles diacritics and different spellings.
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archivedpackagesr-universe
3.11 score 5 stars 51 scripts 207 downloadsMASSTIMATE - Body Mass Estimation Equations for Vertebrates
Estimation equations are from a variety of sources and associated error estimation.
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archivedpackagesr-universe
3.10 score 5 stars 7 scripts 238 downloadsHDclust - Clustering High Dimensional Data with Hidden Markov Model on Variable Blocks
Clustering of high dimensional data with Hidden Markov Model on Variable Blocks (HMM-VB) fitted via Baum-Welch algorithm. Clustering is performed by the Modal Baum-Welch algorithm (MBW), which finds modes of the density function. Lin Lin and Jia Li (2017) <https://jmlr.org/papers/v18/16-342.html>.
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archivedpackagesr-universecppopenmp
3.00 score 5 stars 20 scripts 106 downloadsextrasteps - 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.
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archivedpackagesr-universe
2.98 score 5 stars 38 scripts 369 downloadsNetMix - Dynamic Mixed-Membership Network Regression Model
Stochastic collapsed variational inference on mixed-membership stochastic blockmodel for networks, incorporating node-level predictors of mixed-membership vectors, as well as dyad-level predictors. For networks observed over time, the model defines a hidden Markov process that allows the effects of node-level predictors to evolve in discrete, historical periods. In addition, the package offers a variety of utilities for exploring results of estimation, including tools for conducting posterior predictive checks of goodness-of-fit and several plotting functions. The package implements methods described in Olivella, Pratt and Imai (2019) 'Dynamic Stochastic Blockmodel Regression for Social Networks: Application to International Conflicts', available at <https://www.santiagoolivella.info/pdfs/socnet.pdf>.
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archivedpackagesr-universeopenblascppopenmp
2.97 score 5 stars 37 scripts 84 downloadsDDM - Death Registration Coverage Estimation
A set of three two-census methods to the estimate the degree of death registration coverage for a population. Implemented methods include the Generalized Growth Balance method (GGB), the Synthetic Extinct Generation method (SEG), and a hybrid of the two, GGB-SEG. Each method offers automatic estimation, but users may also specify exact parameters or use a graphical interface to guess parameters in the traditional way if desired.
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archivedpackagesr-universe
2.88 score 5 stars 15 scripts 304 downloadsMDFS - MultiDimensional Feature Selection
Functions for MultiDimensional Feature Selection (MDFS): calculating multidimensional information gains, scoring variables, finding important variables, plotting selection results. This package includes an optional CUDA implementation that speeds up information gain calculation using NVIDIA GPGPUs. R. Piliszek et al. (2019) <doi:10.32614/RJ-2019-019>.
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archivedpackagesr-universecppopenmp
2.88 score 5 stars 1 dependents 310 downloadsPNDSIBGE - Downloading, Reading and Analyzing PNDS Microdata - Package in Development
Provides tools for downloading, reading and analyzing the National Survey of Demographic and Health - PNDS, a household survey from Brazilian Institute of Geography and Statistics - IBGE. The data must be downloaded from the official website <https://www.ibge.gov.br/>. Further analysis must be made using package 'survey'.
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archivedpackagesr-universe
2.88 score 5 stars 1 dependents 250 downloadsLearnClust - Learning Hierarchical Clustering Algorithms
Classical hierarchical clustering algorithms, agglomerative and divisive clustering. Algorithms are implemented as a theoretical way, step by step. It includes some detailed functions that explain each step. Every function allows options to get different results using different techniques. The package explains non expert users how hierarchical clustering algorithms work.
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archivedpackagesr-universe
2.85 score 5 stars 14 scripts 239 downloadsdineq - Decomposition of (Income) Inequality
Decomposition of (income) inequality by population sub groups. For a decomposition on a single variable the mean log deviation can be used (see Mookherjee Shorrocks (1982) <DOI:10.2307/2232673>). For a decomposition on multiple variables a regression based technique can be used (see Fields (2003) <DOI:10.1016/s0147-9121(03)22001-x>). Recentered influence function regression for marginal effects of the (income or wealth) distribution (see Firpo et al. (2009) <DOI:10.3982/ECTA6822>). Some extensions to inequality functions to handle weights and/or missings.
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archivedpackagesr-universe
2.80 score 5 stars 126 scripts 433 downloadsvarband - 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>.
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archivedpackagesr-universeopenblascpp
2.78 score 5 stars 12 scripts 231 downloadsunitedR - Assessment and Evaluation of Formations in United
United is a software tool which can be downloaded at the following website <http://www.schroepl.net/pbm/software/united/>. In general, it is a virtual manager game for football teams. This package contains helpful functions for determining an optimal formation for a virtual match in United. E.g. knowing that the opponent has a strong defensive it is advisable to beat him in the midfield. Furthermore, this package contains functions for computing the optimal usage of hardness in a game.
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archivedpackagesr-universe
2.70 score 5 stars 10 scripts 227 downloadsSparseMDC - Implementation of SparseMDC Algorithm
Implements the algorithm described in Barron, M., and Li, J. (Not yet published). This algorithm clusters samples from multiple ordered populations, links the clusters across the conditions and identifies marker genes for these changes. The package was designed for scRNA-Seq data but is also applicable to many other data types, just replace cells with samples and genes with variables. The package also contains functions for estimating the parameters for SparseMDC as outlined in the paper. We recommend that users further select their marker genes using the magnitude of the cluster centers.
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archivedpackagesr-universe
2.70 score 5 stars 7 scripts 260 downloadsTMDb - Access to TMDb API
Provides an R-interface to the TMDb API (see TMDb API on <https://developers.themoviedb.org/3/getting-started/introduction>). The Movie Database (TMDb) is a popular user editable database for movies and TV shows (see <https://www.themoviedb.org>).
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archivedpackagesr-universe
2.70 score 5 stars 100 scripts 212 downloadsMED - Mediation by Tilted Balancing
Nonparametric estimation and inference for natural direct and indirect effects by Chan, Imai, Yam and Zhang (2016) <arXiv:1601.03501>.
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archivedpackagesr-universe
2.70 score 5 stars 8 scripts 223 downloadsPAS - Polygenic Analysis System (PAS)
An R package for polygenic trait analysis.
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archivedpackagesr-universe
2.70 score 5 stars 7 scripts 224 downloadsdrda - Dose-Response Data Analysis
Fit logistic functions to observed dose-response continuous data and evaluate goodness-of-fit measures. See Malyutina A., Tang J., and Pessia A. (2023) <doi:10.18637/jss.v106.i04>.
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archivedpackagesr-universe
2.70 score 5 stars 470 downloadsCausalMBSTS - MBSTS Models for Causal Inference and Forecasting
Infers the causal effect of an intervention on a multivariate response through the use of Multivariate Bayesian Structural Time Series models (MBSTS) as described in Menchetti & Bojinov (2020) <arXiv:2006.12269>. The package also includes functions for model building and forecasting.
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archivedpackagesr-universe
2.70 score 5 stars 461 downloadsLLM - Logit Leaf Model Classifier for Binary Classification
Fits the Logit Leaf Model, makes predictions and visualizes the output. (De Caigny et al., (2018) <DOI:10.1016/j.ejor.2018.02.009>).
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archivedpackagesr-universeopenjdk
2.70 score 5 stars 217 downloadsFahrmeir - Data from the Book "Multivariate Statistical Modelling Based on Generalized Linear Models", First Edition, by Ludwig Fahrmeir and Gerhard Tutz
Data and functions for the book "Multivariate Statistical Modelling Based on Generalized Linear Models", first edition, by Ludwig Fahrmeir and Gerhard Tutz. Useful when using the book.
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archivedpackagesr-universe
2.54 score 5 stars 42 scripts 1.7k downloadspreference - 2-Stage Preference Trial Design and Analysis
Design and analyze two-stage randomized trials with a continuous outcome measure. The package contains functions to compute the required sample size needed to detect a given preference, treatment, and selection effect; alternatively, the package contains functions that can report the study power given a fixed sample size. Finally, analysis functions are provided to test each effect using either summary data (i.e. means, variances) or raw study data <doi:10.18637/jss.v094.c02>.
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2.48 score 5 stars 12 scripts 276 downloadsFMP - Filtered Monotonic Polynomial IRT Models
Estimates Filtered Monotonic Polynomial IRT Models as described by Liang and Browne (2015) <DOI:10.3102/1076998614556816>.
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archivedpackagesr-universe
2.44 score 5 stars 11 scripts 191 downloadssignalHsmm - Predict Presence of Signal Peptides
Predicts the presence of signal peptides in eukaryotic protein using hidden semi-Markov models. The implemented algorithm can be accessed from both the command line and GUI.
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archivedpackagesr-universecpp
2.40 score 5 stars 9 scripts 291 downloadsmarkdownInput - Shiny Module for a Markdown Input with Result Preview
An R-Shiny module containing a "markdownInput". This input allows the user to write some markdown code and to preview the result. This input has been inspired by the "comment" window of <https://github.com/>.
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archivedpackagesr-universe
2.40 score 5 stars 9 scripts 273 downloadsnbconvertR - Vignette Engine Wrapping Jupyter Notebooks
Calls the 'Jupyter' script 'nbconvert' to create vignettes from notebooks. Those notebooks ('.ipynb' files) are files containing rich text, code, and its output. Code cells can be edited and evaluated interactively. See <https://jupyter.org/> for more information.
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2.40 score 5 stars 8 scripts 227 downloadsrecombinator - Recombinate Nested Lists to Dataframes
Turns nested lists into data.frames in an orderly manner.
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archivedpackagesr-universe
2.40 score 5 stars 3 scripts 216 downloadskdist - K-Distribution and Weibull Paper
Density, distribution function, quantile function and random generation for the K-distribution. A plotting function that plots data on Weibull paper and another function to draw additional lines. See results from package in T Lamont-Smith (2018), submitted J. R. Stat. Soc.
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archivedpackagesr-universe
2.40 score 5 stars 3 scripts 240 downloadslifx - Control 'LIFX' Smart Light Bulbs
Allows you to read and change the state of 'LIFX' smart light bulbs via the 'LIFX' developer api <https://api.developer.lifx.com/>. Covers most 'LIFX' api endpoints, including changing light color and brightness, selecting lights by id, group or location as well as activating effects.
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archivedpackagesr-universe
2.40 score 5 stars 1 scripts 245 downloadsfermicatsR - Fermi Large Area Telescope Catalogs
Data from various catalogs of astrophysical gamma-ray sources detected by NASA's Large Area Telescope (The Astrophysical Journal, 697, 1071, 2009 June 1), on board the Fermi gamma-ray satellite. More information on Fermi and its data products is available from the Fermi Science Support Center (http://fermi.gsfc.nasa.gov/ssc/).
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archivedpackagesr-universe
2.40 score 5 stars 1 scripts 418 downloadsgclm - Graphical Continuous Lyapunov Models
Estimation of covariance matrices as solutions of continuous time Lyapunov equations. Sparse coefficient matrix and diagonal noise are estimated with a proximal gradient method for an l1-penalized loss minimization problem. Varando G, Hansen NR (2020) <arXiv:2005.10483>.
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archivedpackagesr-universeopenblas
2.40 score 5 stars 7 scripts 274 downloadsWeibullFit - Fits and Plots a Dataset to the Weibull Probability Distribution Function
Provides a single function to fit data of an input data frame into one of the selected Weibull functions (w2, w3 and it's truncated versions), calculating the scale, location and shape parameters accordingly. The resulting plots and files are saved into the 'folder' parameter provided by the user. References: a) John C. Nash, Ravi Varadhan (2011). "Unifying Optimization Algorithms to Aid Software System Users: optimx for R" <doi:10.18637/jss.v043.i09>.
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2.40 score 5 stars 1 scripts 310 downloadscalcUnique - Simple Wrapper for Computationally Expensive Functions
This is a one-function package that will pass only unique values to a computationally-expensive function that returns an output of the same length as the input. In importing and working with tidy data, it is common to have index columns, often including time stamps that are far from unique. Some functions to work with these such as text conversion to other variable types (e.g. as.POSIXct()), various grep()-based functions, and often the cut() function are relatively slow when working with tens of millions of rows or more.
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archivedpackagesr-universe
2.40 score 5 stars 2 scripts 315 downloadsaffinitymatrix - Estimation of Affinity Matrix
Tools to study sorting patterns in matching markets and to estimate the affinity matrix of both the bipartite one-to-one matching model without frictions and with Transferable Utility by 'Dupuy' and 'Galichon' (2014) <doi:10.1086/677191> and its 'unipartite' variant by 'Ciscato', 'Galichon' and 'Gousse' (2020) <doi:10.1086/704611>. It also contains all the necessary tools to implement the 'saliency' analysis, to run rank tests of the affinity matrix and to build tables and plots summarizing the findings.
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archivedpackagesr-universe
2.40 score 5 stars 2 scripts 364 downloadsaimPlot - Create Pie Like Plot for Completeness
Create a pie like plot to visualise if the aim or several aims of a project is achieved or close to be achieved i.e the aim is achieved when the point is at the center of the pie plot. Imagine it's like a dartboard and the center means 100% completeness/achievement. Achievement can also be understood as 100% coverage. The standard distribution of completeness allocated in the pie plot is 50%, 80% and 100% completeness.
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archivedpackagesr-universe
2.40 score 5 stars 2 scripts 366 downloadschartql - Simplified Language for Plots and Charts
Provides a very simple syntax for the user to generate custom plot(s) without having to remember complicated 'ggplot2' syntax. The 'chartql' package uses 'ggplot2' and manages all the syntax complexities internally. As an example, to generate a bar chart of company sales faceted by product category further faceted by season of the year, we simply write: "CHART bar X category, season Y sales".
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archivedpackagesr-universe
2.40 score 5 stars 329 downloadsPakPMICS2014HH - Multiple Indicator Cluster Survey (MICS) 2014 Household Questionnaire Data for Punjab, Pakistan
Provides data set and function for exploration of Multiple Indicator Cluster Survey (MICS) 2014 Household questionnaire data for Punjab, Pakistan (<http://www.mics.unicef.org/surveys>).
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archivedpackagesr-universe
2.40 score 5 stars 1 scripts 346 downloadsPakPMICS2014Ch - Multiple Indicator Cluster Survey (MICS) 2014 Child Questionnaire Data for Punjab, Pakistan
Provides data set and functions for exploration of Multiple Indicator Cluster Survey (MICS) 2014 Child questionnaire data for Punjab, Pakistan (<http://www.mics.unicef.org/surveys>).
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archivedpackagesr-universe
2.40 score 5 stars 1 scripts 326 downloadsArCo - Artificial Counterfactual Package
Set of functions to analyse and estimate Artificial Counterfactual models from Carvalho, Masini and Medeiros (2016) <DOI:10.2139/ssrn.2823687>.
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2.40 score 5 stars 6 scripts 512 downloadsLZeroSpikeInference - Exact Spike Train Inference via L0 Optimization
An implementation of algorithms described in Jewell and Witten (2017) <arXiv:1703.08644>.
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2.40 score 5 stars 9 scripts 228 downloadsCIplot - Functions to Plot Confidence Interval
Plot confidence interval from the objects of statistical tests such as t.test(), var.test(), cor.test(), prop.test() and fisher.test() ('htest' class), Tukey test [TukeyHSD()], Dunnett test [glht() in 'multcomp' package], logistic regression [glm()], and Tukey or Games-Howell test [posthocTGH() in 'userfriendlyscience' package]. Users are able to set the styles of lines and points. This package contains the function to calculate odds ratios and their confidence intervals from the result of logistic regression.
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2.40 score 5 stars 5 scripts 370 downloadsRegDDM - Generalized Linear Regression with DDM
Drift-Diffusion Model (DDM) has been widely used to model binary decision-making tasks, and many research studies the relationship between DDM parameters and other characteristics of the subject. This package uses 'RStan' to perform generalized liner regression analysis over DDM parameters via a single Bayesian Hierarchical model. Compared to estimating DDM parameters followed by a separate regression model, 'RegDDM' reduces bias and improves statistical power.
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2.40 score 5 stars 4 scripts 235 downloadsbcRP - Access 'BCRPDATA' API
Search and access more than ten thousand datasets included in 'BCRPDATA' (see <https://estadisticas.bcrp.gob.pe/estadisticas/series/ayuda/bcrpdata> for more information).
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archivedpackagesr-universe
2.40 score 5 stars 335 downloads
surveytidy - Tidy 'dplyr'/'tidyr' Verbs for Survey Design Objects
Provides 'dplyr' and 'tidyr' verbs, survey-aware recoding helpers, and row-wise statistics for survey design objects created with the 'surveycore' package. filter() uses domain estimation to preserve variance estimation validity; other verbs preserve design variables and metadata automatically. Also supports survey_collection objects for applying the same operation across a list of surveys.
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2.40 score 5 stars 368 downloadsbunsen - Marginal Survival Estimation with Covariate Adjustment
Provides an efficient and robust implementation for estimating marginal Hazard Ratio (HR) and Restricted Mean Survival Time (RMST) with covariate adjustment using Daniel et al. (2021) <doi:10.1002/bimj.201900297> and Karrison et al. (2018) <doi:10.1177/1740774518759281>.
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archivedpackagesr-universecpp
2.40 score 5 stars 413 downloadsMVTests - Multivariate Hypothesis Tests
Multivariate hypothesis tests and confidence intervals...
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2.40 score 5 stars 830 downloadscomorbidPGS - Assessing Predisposition Between Phenotypes using Polygenic Scores
Using polygenic scores (PGS, or PRS/GRS for binary outcomes), this package allows to investigate shared predisposition between different conditions, and do fast association analysis, export plots and views of the PGS distribution using 'ggplot2' object.
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archivedpackagesr-universe
2.40 score 5 stars 231 downloadsCEC - Cross-Entropy Clustering
Splits data into Gaussian type clusters using the Cross-Entropy Clustering ('CEC') method. This method allows for the simultaneous use of various types of Gaussian mixture models, for performing the reduction of unnecessary clusters, and for discovering new clusters by splitting them. 'CEC' is based on the work of Spurek, P. and Tabor, J. (2014) <doi:10.1016/j.patcog.2014.03.006>.
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archivedpackagesr-universeopenblascpp
2.40 score 5 stars 420 downloadshint - Tools for Hypothesis Testing Based on Hypergeometric Intersection Distributions
Hypergeometric Intersection distributions are a broad group of distributions that describe the probability of picking intersections when drawing independently from two (or more) urns containing variable numbers of balls belonging to the same n categories. <arXiv:1305.0717>.
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archivedpackagesr-universecpp
2.40 score 5 stars 220 downloadsagghoo - Aggregated Hold-Out Cross Validation
The 'agghoo' procedure is an alternative to usual cross-validation. Instead of choosing the best model trained on V subsamples, it determines a winner model for each subsample, and then aggregates the V outputs. For the details, see "Aggregated hold-out" by Guillaume Maillard, Sylvain Arlot, Matthieu Lerasle (2021) <arXiv:1909.04890> published in Journal of Machine Learning Research 22(20):1--55.
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2.40 score 5 stars 1 scripts 312 downloadsdtGAP - Supervised Generalized Association Plots Based on Decision Trees
Enhances decision tree visualization by incorporating Generalized Association Plots (GAP) through matrix-based visualizations including confusion matrix maps, decision tree matrix maps, and predicted class membership maps based on supervised correlation and distance metrics.
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archivedpackagesr-universe
2.40 score 5 stars 1 scripts 255 downloadszenstats - Statistics from 'Zenodo' Deposits
Fetch statistics about views, downloads and data volume from 'Zenodo' deposits. The package collects a 'Zenodo' (<https://zenodo.org>) deposit file information, respecting the website scrapping policies.
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archivedpackagesr-universe
2.40 score 5 stars 4 scripts 375 downloads
defm - Estimation and Simulation of Multi-Binary Response Models
Multi-binary response models are a class of models that allow for the estimation of multiple binary outcomes simultaneously. This package provides functions to estimate and simulate these models using the Discrete Exponential-Family Models [DEFM] framework. In it, we implement the models described in Vega Yon, Valente, and Pugh (2023) <doi:10.48550/arXiv.2211.00627>. DEFMs include Exponential-Family Random Graph Models [ERGMs], which characterize graphs using sufficient statistics, which is also the core of DEFMs. Using sufficient statistics, we can describe the data through meaningful motifs, for example, transitions between different states, joint distribution of the outcomes, etc.
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archivedpackagesr-universecppopenmp
2.40 score 5 stars 4 scripts 59 downloadsioanalysis - Input Output Analysis
Calculates fundamental IO matrices (Leontief, Wassily W. (1951) <doi:10.1038/scientificamerican1051-15>); within period analysis via various rankings and coefficients (Sonis and Hewings (2006) <doi:10.1080/09535319200000013>, Blair and Miller (2009) <ISBN:978-0-521-73902-3>, Antras et al (2012) <doi:10.3386/w17819>, Hummels, Ishii, and Yi (2001) <doi:10.1016/S0022-1996(00)00093-3>); across period analysis with impact analysis (Dietzenbacher, van der Linden, and Steenge (2006) <doi:10.1080/09535319300000017>, Sonis, Hewings, and Guo (2006) <doi:10.1080/09535319600000002>); and a variety of table operators.
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2.31 score 5 stars 41 scripts 485 downloadsCompR - Paired Comparison Data Analysis
Different tools for describing and analysing paired comparison data are presented. Main methods are estimation of products scores according Bradley Terry Luce model. A segmentation of the individual could be conducted on the basis of a mixture distribution approach. The number of classes can be tested by the use of Monte Carlo simulations. This package deals also with multi-criteria paired comparison data.
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2.31 score 5 stars 41 scripts 307 downloadsDTDA.cif - Doubly Truncated Data Analysis, Cumulative Incidence Functions
Nonparametric estimator of the cumulative incidences of competing risks under double truncation. The estimator generalizes the Efron-Petrosian NPMLE (Non-Parametric Maximun Likelihood Estimator) to the competing risks setting. Efron, B. and Petrosian, V. (1999) <doi:10.2307/2669997>.
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archivedpackagesr-universecpp
2.30 score 5 stars 317 downloadsPOCRE - Penalized Orthogonal-Components Regression
Penalized orthogonal-components regression (POCRE) is a supervised dimension reduction method for high-dimensional data. It sequentially constructs orthogonal components (with selected features) which are maximally correlated to the response residuals. POCRE can also construct common components for multiple responses and thus build up latent-variable models.
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archivedpackagesr-universe
2.30 score 5 stars 255 downloadsforestr - Ecosystem and Canopy Structural Complexity Metrics from LiDAR
Provides a toolkit for calculating forest and canopy structural complexity metrics from terrestrial LiDAR (light detection and ranging). References: Atkins et al. 2018 <doi:10.1111/2041-210X.13061>; Hardiman et al. 2013 <doi:10.3390/f4030537>; Parker et al. 2004 <doi:10.1111/j.0021-8901.2004.00925.x>.
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2.20 score 5 stars 32 scripts 333 downloadsEnsCat - Clustering of Categorical Data
An implementation of the clustering methods of categorical data discussed in Amiri, S., Clarke, B., and Clarke, J. (2015). Clustering categorical data via ensembling dissimilarity matrices. Preprint <arXiv:1506.07930>.
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2.04 score 5 stars 22 scripts 334 downloadssdPrior - Scale-Dependent Hyperpriors in Structured Additive Distributional Regression
Utility functions for scale-dependent and alternative hyperpriors. The distribution parameters may capture location, scale, shape, etc. and every parameter may depend on complex additive terms (fixed, random, smooth, spatial, etc.) similar to a generalized additive model. Hyperpriors for all effects can be elicitated within the package. Including complex tensor product interaction terms and variable selection priors. The basic model is explained in in Klein and Kneib (2016) <doi:10.1214/15-BA983>.
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2.02 score 5 stars 15 scripts 1.4k downloadschords - Estimation in Respondent Driven Samples
Maximum likelihood estimation in respondent driven samples.
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2.00 score 5 stars 20 scripts 350 downloadsAntAngioCOOL - Anti-Angiogenic Peptide Prediction
Machine learning based package to predict anti-angiogenic peptides using heterogeneous sequence descriptors. 'AntAngioCOOL' exploits five descriptor types of a peptide of interest to do prediction including: pseudo amino acid composition, k-mer composition, k-mer composition (reduced alphabet), physico-chemical profile and atomic profile. According to the obtained results, 'AntAngioCOOL' reached to a satisfactory performance in anti-angiogenic peptide prediction on a benchmark non-redundant independent test dataset.
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archivedpackagesr-universeopenjdk
2.00 score 5 stars 1 scripts 389 downloadswtest - The W-Test for Genetic Interactions Testing
Perform the calculation of W-test, diagnostic checking, calculate minor allele frequency (MAF) and odds ratio.
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1.90 score 5 stars 16 scripts 211 downloadsStrainRanking - Ranking of Pathogen Strains
Regression-based ranking of pathogen strains with respect to their contributions to natural epidemics, using demographic and genetic data sampled in the curse of the epidemics. This package also includes the GMCPIC test.
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1.88 score 5 stars 15 scripts 179 downloadsParetoPosStable - Computing, Fitting and Validating the PPS Distribution
Statistical functions to describe a Pareto Positive Stable (PPS) distribution and fit it to real data. Graphical and statistical tools to validate the fits are included.
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1.85 score 5 stars 14 scripts 287 downloadsflam - Fits Piecewise Constant Models with Data-Adaptive Knots
Implements the fused lasso additive model as proposed in Petersen, A., Witten, D., and Simon, N. (2016). Fused Lasso Additive Model. Journal of Computational and Graphical Statistics, 25(4): 1005-1025.
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archivedpackagesr-universecpp
1.81 score 5 stars 13 scripts 302 downloadskriens - Continuation Passing Style Development
Provides basic functions for Continuation-Passing Style development.
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archivedpackagesr-universe
1.81 score 5 stars 13 scripts 224 downloadslongROC - Time-Dependent Prognostic Accuracy with Multiply Evaluated Bio Markers or Scores
Time-dependent Receiver Operating Characteristic curves, Area Under the Curve, and Net Reclassification Indexes for repeated measures. It is based on methods in Barbati and Farcomeni (2017) <doi:10.1007/s10260-017-0410-2>.
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1.78 score 5 stars 12 scripts 226 downloadsstepPenal - Stepwise Forward Variable Selection in Penalized Regression
Model Selection Based on Combined Penalties. This package implements a stepwise forward variable selection algorithm based on a penalized likelihood criterion that combines the L0 with L2 or L1 norms.
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1.74 score 5 stars 11 scripts 242 downloadsBayesTreePrior - Bayesian Tree Prior Simulation
Provides a way to simulate from the prior distribution of Bayesian trees by Chipman et al. (1998) <DOI:10.2307/2669832>. The prior distribution of Bayesian trees is highly dependent on the design matrix X, therefore using the suggested hyperparameters by Chipman et al. (1998) <DOI:10.2307/2669832> is not recommended and could lead to unexpected prior distribution. This work is part of my master thesis (expected 2016).
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1.74 score 5 stars 11 scripts 305 downloadssym.arma - Autoregressive and Moving Average Symmetric Models
Functions for fitting the Autoregressive and Moving Average Symmetric Model for univariate time series introduced by Maior and Cysneiros (2018), <doi:10.1007/s00362-016-0753-z>. Fitting method: conditional maximum likelihood estimation. For details see: Wei (2006), Time Series Analysis: Univariate and Multivariate Methods, Section 7.2.
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1.70 score 5 stars 9 scripts 234 downloadssodavis - SODA: Main and Interaction Effects Selection for Logistic Regression, Quadratic Discriminant and General Index Models
Variable and interaction selection are essential to classification in high-dimensional setting. In this package, we provide the implementation of SODA procedure, which is a forward-backward algorithm that selects both main and interaction effects under logistic regression and quadratic discriminant analysis. We also provide an extension, S-SODA, for dealing with the variable selection problem for semi-parametric models with continuous responses.
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1.70 score 5 stars 3 scripts 255 downloadsmetafuse - Fused Lasso Approach in Regression Coefficient Clustering
Fused lasso method to cluster and estimate regression coefficients of the same covariate across different data sets when a large number of independent data sets are combined. Package supports Gaussian, binomial, Poisson and Cox PH models.
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1.70 score 5 stars 4 scripts 267 downloadsplotprotein - Development of Visualization Tools for Protein Sequence
The image of the amino acid transform on the protein level is drawn, and the automatic routing of the functional elements such as the domain and the mutation site is completed.
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1.70 score 5 stars 8 scripts 335 downloadsmulticmp - Flexible Modeling of Multivariate Count Data via the Multivariate Conway-Maxwell-Poisson Distribution
A toolkit containing statistical analysis models motivated by multivariate forms of the Conway-Maxwell-Poisson (COM-Poisson) distribution for flexible modeling of multivariate count data, especially in the presence of data dispersion. Currently the package only supports bivariate data, via the bivariate COM-Poisson distribution described in Sellers et al. (2016) <doi:10.1016/j.jmva.2016.04.007>. Future development will extend the package to higher-dimensional data.
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1.70 score 5 stars 6 scripts 232 downloadsrreg - Visualization for Norwegian Health Quality Registries
Assists for presentation and visualization of data from the Norwegian Health Quality Registries following the standardization based on the requirement specified by the National Service for Health Quality Registries. This requirement can be accessed from (<https://www.kvalitetsregistre.no/resultater-til-publisering-pa-nett>). Unfortunately the website is only available in Norwegian.
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archivedpackagesr-universe
1.70 score 5 stars 10 scripts 261 downloadsgarray - Generalized Array Arithmetic for Ragged Arrays with Named Margins
Organize a so-called ragged array as generalized arrays, which is simply an array with sub-dimensions denoting the subdivision of dimensions (grouping of members within dimensions). By the margins (names of dimensions and sub-dimensions) in generalized arrays, operators and utility functions provided in this package automatically match the margins, doing map-reduce style parallel computation along margins. Generalized arrays are also cooperative to R's native functions that work on simple arrays.
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1.70 score 5 stars 8 scripts 254 downloadsdtp - Dynamic Panel Threshold Model
Compute the dynamic threshold panel model suggested by (Stephanie Kremer, Alexander Bick and Dieter Nautz (2013) <doi:10.1007/s00181-012-0553-9>) in which they extended the (Hansen (1999) <doi: 10.1016/S0304-4076(99)00025-1>) original static panel threshold estimation and the Caner and (Hansen (2004) <doi:10.1017/S0266466604205011>) cross-sectional instrumental variable threshold model, where generalized methods of moments type estimators are used.
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1.70 score 5 stars 1 scripts 300 downloadsenvoutliers - Methods for Identification of Outliers in Environmental Data
Three semi-parametric methods for detection of outliers in environmental data based on kernel regression and subsequent analysis of smoothing residuals. The first method (Campulova, Michalek, Mikuska and Bokal (2018) <DOI: 10.1002/cem.2997>) analyzes the residuals using changepoint analysis, the second method is based on control charts (Campulova, Veselik and Michalek (2017) <DOI: 10.1016/j.apr.2017.01.004>) and the third method (Holesovsky, Campulova and Michalek (2018) <DOI: 10.1016/j.apr.2017.06.005>) analyzes the residuals using extreme value theory (Holesovsky, Campulova and Michalek (2018) <DOI: 10.1016/j.apr.2017.06.005>).
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1.70 score 5 stars 4 scripts 416 downloadskernelFactory - Kernel Factory: An Ensemble of Kernel Machines
Binary classification based on an ensemble of kernel machines ("Ballings, M. and Van den Poel, D. (2013), Kernel Factory: An Ensemble of Kernel Machines. Expert Systems With Applications, 40(8), 2904-2913"). Kernel factory is an ensemble method where each base classifier (random forest) is fit on the kernel matrix of a subset of the training data.
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1.70 score 5 stars 4 scripts 325 downloadsdynpanel - Dynamic Panel Data Models
Computes the first stage GMM estimate of a dynamic linear model with p lags of the dependent variables.
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1.70 score 5 stars 7 scripts 371 downloadsclinsig - Clinical Significance Functions
Functions for calculating clinical significance.
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1.70 score 5 stars 2 scripts 364 downloadsRZigZag - Zig-Zag Sampler
Implements the Zig-Zag algorithm (Bierkens, Fearnhead, Roberts, 2016) <arXiv:1607.03188> applied and Bouncy Particle Sampler <arXiv:1510.02451> for a Gaussian target and Student distribution.
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archivedpackagesr-universecpp
1.70 score 5 stars 5 scripts 247 downloadsRRI - Residual Randomization Inference for Regression Models
Testing and inference for regression models using residual randomization methods. The basis of inference is an invariance assumption on the regression errors, e.g., clustered errors, or doubly-clustered errors.
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archivedpackagesr-universeopenblascpp
1.70 score 5 stars 203 downloadscope - Coverage Probability Excursion (CoPE) Sets
Provides functions to compute and plot Coverage Probability Excursion (CoPE) sets for real valued functions on a 2-dimensional domain. CoPE sets are obtained from repeated noisy observations of the function on the entire domain. They are designed to bound the excursion set of the target function at a given level from above and below with a predefined probability. The target function can be a parameter in spatially-indexed linear regression. Support by NIH grant R01 CA157528 is gratefully acknowledged.
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1.70 score 5 stars 6 scripts 361 downloadsMixSAL - Mixtures of Multivariate Shifted Asymmetric Laplace (SAL) Distributions
The current version of the 'MixSAL' package allows users to generate data from a multivariate SAL distribution or a mixture of multivariate SAL distributions, evaluate the probability density function of a multivariate SAL distribution or a mixture of multivariate SAL distributions, and fit a mixture of multivariate SAL distributions using the Expectation-Maximization (EM) algorithm (see Franczak et. al, 2014, <doi:10.1109/TPAMI.2013.216>, for details).
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1.70 score 5 stars 7 scripts 205 downloadsMDimNormn - Multi-Dimensional MA Normalization for Plate Effect
Normalize data to minimize the difference between sample plates (batch effects). For given data in a matrix and grouping variable (or plate), the function 'normn_MA' normalizes the data on MA coordinates. More details are in the citation. The primary method is 'Multi-MA'. Other fitting functions on MA coordinates can also be employed e.g. loess.
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1.70 score 5 stars 3 scripts 215 downloadsOBMbpkg - Estimate the Population Size for the Mb Capture-Recapture Model
Applies an objective Bayesian method to the Mb capture-recapture model to estimate the population size N. The Mb model is a class of capture-recapture methods used to account for variations in capture probability due to animal behavior. Under the Mb formulation, the initial capture of an animal may effect the probability of subsequent captures due to their becoming "trap happy" or "trap shy."
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1.70 score 5 stars 1 scripts 318 downloadsCopCTS - Copula-Based Semiparametric Analysis for Time Series Data with Detection Limits
Semiparametric estimation for censored time series with lower detection limit. The latent response is a sequence of stationary process with Markov property of order one. Estimation of copula parameter(COPC) and Conditional quantile estimation are included for five available copula functions. Copula selection methods based on L2 distance from empirical copula function are also included.
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archivedpackagesr-universe
1.70 score 5 stars 4 scripts 329 downloadsAutoplotprotein - Development of Visualization Tools for Protein Sequence
The image of the amino acid transform on the protein level is drawn, and the automatic routing of the functional elements such as the domain and the mutation site is completed.
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archivedpackagesr-universe
1.70 score 5 stars 9 scripts 367 downloadsFourgameteP - FourGamete Test
The four-gamete test is based on the infinite-sites model which assumes that the probability of the same mutation occurring twice (recurrent or parallel mutations) and the probability of a mutation back to the original state (reverse mutations) are close to zero. Without these types of mutations, the only explanation for observing the four dilocus genotypes (example below) is recombination (Hudson and Kaplan 1985, Genetics 111:147-164). Thus, the presence of all four gametes is also called phylogenetic incompatibility.
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archivedpackagesr-universe
1.70 score 5 stars 1 scripts 259 downloadsGSparO - Group Sparse Optimization
Approaches a group sparse solution of an underdetermined linear system. It implements the proximal gradient algorithm to solve a lower regularization model of group sparse learning. For details, please refer to the paper "Y. Hu, C. Li, K. Meng, J. Qin and X. Yang. Group sparse optimization via l_{p,q} regularization. Journal of Machine Learning Research, to appear, 2017".
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1.70 score 5 stars 2 scripts 277 downloadsGWASbyCluster - Identifying Significant SNPs in Genome Wide Association Studies (GWAS) via Clustering
Identifying disease-associated significant SNPs using clustering approach. This package is implementation of method proposed in Xu et al (2019) <DOI:10.1038/s41598-019-50229-6>.
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archivedpackagesr-universe
1.70 score 5 stars 286 downloadswelo - Weighted and Standard Elo Rates
Estimates the standard and weighted Elo (WElo, Angelini et al., 2022 <doi:10.1016/j.ejor.2021.04.011>) rates. The current version provides Elo and WElo rates for tennis, according to different systems of weights (games or sets) and scale factors (constant, proportional to the number of matches, with more weight on Grand Slam matches or matches played on a specific surface). Moreover, the package gives the possibility of estimating the (bootstrap) standard errors for the rates. Finally, the package includes betting functions that automatically select the matches on which place a bet.
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archivedpackagesr-universe
1.70 score 5 stars 356 downloadsHydroMe - Estimating Water Retention and Infiltration Model Parameters using Experimental Data
Estimates the parameters of infiltration and water retention models using the curve-fitting methods as shown in Omuto and Gumbe (2009) <doi:10.1016/j.cageo.2008.08.011>. The models considered are those that are commonly used in soil science. Version 2 of the package has new models for water retention characteristic curves.
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1.70 score 5 stars 313 downloadsThomasJeffersonUniv - Handy Tools for TJU/TJUH Employees
Functions for admin needs of employees of Thomas Jefferson University and Thomas Jefferson University Hospital, Philadelphia, PA.
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archivedpackagesr-universe
1.70 score 5 stars 229 downloadscompetitiontoolbox - A Graphical User Interface for Antitrust and Trade Practitioners
A graphical user interface for simulating the effects of mergers, tariffs, and quotas under an assortment of different economic models. The interface is powered by the 'Shiny' web application framework from 'RStudio'.
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archivedpackagesr-universe
1.70 score 5 stars 313 downloadsRAFS - Robust Aggregative Feature Selection
A cross-validated minimal-optimal feature selection algorithm. It utilises popularity counting, hierarchical clustering with feature dissimilarity measures, and prefiltering with all-relevant feature selection method to obtain the minimal-optimal set of features.
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archivedpackagesr-universe
1.70 score 5 stars 351 downloadsfpop - Segmentation using Optimal Partitioning and Function Pruning
A dynamic programming algorithm for the fast segmentation of univariate signals into piecewise constant profiles. The 'fpop' package is a wrapper to a C++ implementation of the fpop (Functional Pruning Optimal Partioning) algorithm described in Maidstone et al. 2017 <doi:10.1007/s11222-016-9636-3>. The problem of detecting changepoints in an univariate sequence is formulated in terms of minimising the mean squared error over segmentations. The fpop algorithm exactly minimizes the mean squared error for a penalty linear in the number of changepoints.
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archivedpackagesr-universecpp
1.70 score 5 stars 6 scripts 329 downloadssimgof - Simultaneous Goodness-of-Fits Tests
Routine that allows the user to run several goodness-of-fit tests. It also combines the tests and returns a properly adjusted family-wise p value. Details can be found in <arXiv:2007.04727>.
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archivedpackagesr-universe
1.70 score 5 stars 1 scripts 73 downloads