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r-simtimer
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public |
Handles datetimes as integers for the usage inside Discrete-Event Simulations (DES). The conversion is made using the internally generic function as.numeric() of the base package. DES is described in Simulation Modeling and Analysis by Averill Law and David Kelton (1999) <doi:10.2307/2288169>.
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2025-03-25 |
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r-simsurv
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Simulate survival times from standard parametric survival distributions (exponential, Weibull, Gompertz), 2-component mixture distributions, or a user-defined hazard, log hazard, cumulative hazard, or log cumulative hazard function. Baseline covariates can be included under a proportional hazards assumption. Time dependent effects (i.e. non-proportional hazards) can be included by interacting covariates with linear time or a user-defined function of time. Clustered event times are also accommodated. The 2-component mixture distributions can allow for a variety of flexible baseline hazard functions reflecting those seen in practice. If the user wishes to provide a user-defined hazard or log hazard function then this is possible, and the resulting cumulative hazard function does not need to have a closed-form solution. Note that this package is modelled on the 'survsim' package available in the 'Stata' software (see Crowther and Lambert (2012) <http://www.stata-journal.com/sjpdf.html?articlenum=st0275> or Crowther and Lambert (2013) <doi:10.1002/sim.5823>).
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2025-03-25 |
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r-simsem
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public |
Provides an easy framework for Monte Carlo simulation in structural equation modeling, which can be used for various purposes, such as such as model fit evaluation, power analysis, or missing data handling and planning.
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2025-03-25 |
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r-simscrpiecewise
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Contains two functions for simulating survival data from piecewise exponential hazards with a proportional hazards adjustment for covariates. The first function SimUNIVPiecewise simulates univariate survival data based on a piecewise exponential hazard, covariate matrix and true regression vector. The second function SimSCRPiecewise semi-competing risks data based on three piecewise exponential hazards, three true regression vectors and three matrices of patient covariates (which can be different or the same). This simulates from the Semi-Markov model of Lee et al (2015) given patient covariates, regression parameters, patient frailties and baseline hazard functions.
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2025-03-25 |
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r-simsalapar
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public |
Tools for setting up ("design"), conducting, and evaluating large-scale simulation studies with graphics and tables, including parallel computations.
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2025-03-25 |
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r-simplicialcubature
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public |
Provides methods to integrate functions over m-dimensional simplices in n-dimensional Euclidean space. There are exact methods for polynomials and adaptive methods for integrating an arbitrary function. Dirichlet probabilities are calculated in certain cases.
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2025-03-25 |
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r-simplesetup
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public |
When working across multiple machines and, similarly for reproducible research, it can be time consuming to ensure that you have all of the needed packages installed and loaded and that the correct working directory is set. 'simpleSetup' provides simple functions for making these tasks more straightforward.
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2025-03-25 |
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r-simplercache
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Simple result caching in R based on R.cache. The global environment is not considered when caching results simplifying moving files between multiple instances of R. Relies on more base functions than R.cache (e.g. cached results are saved using saveRDS() and readRDS()).
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2025-03-25 |
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r-simpleneural
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public |
Trains neural networks (multilayer perceptrons with one hidden layer) for bi- or multi-class classification.
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2025-03-25 |
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r-simplegraph
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public |
Simple classic graph algorithms for simple graph classes. Graphs may possess vertex and edge attributes. 'simplegraph' has so dependencies and it is written entirely in R, so it is easy to install.
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2025-03-25 |
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r-simplecache
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public |
Provides intuitive functions for caching R objects, encouraging reproducible, restartable, and distributed R analysis. The user selects a location to store caches, and then provides nothing more than a cache name and instructions (R code) for how to produce the R object. Also provides some advanced options like environment assignments, recreating or reloading caches, and cluster compute bindings (using the 'batchtools' package) making it flexible enough for use in large-scale data analysis projects.
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2025-03-25 |
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r-simpleboot
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public |
Simple bootstrap routines.
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2025-03-25 |
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r-simphe
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public |
Provides functions to simulate single or multiple, independent or correlated phenotype(s) with additive, dominance effects and their interactions. Also includes functions to generate phenotype(s) with specific heritability. Flexible and user-friendly options for simulation.
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2025-03-25 |
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r-simms
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public |
Algorithms to create prognostic biomarkers using biological genesets or networks.
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2025-03-25 |
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r-simml
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public |
A major challenge in estimating treatment decision rules from a randomized clinical trial dataset with covariates measured at baseline lies in detecting relatively small treatment effect modification-related variability (i.e., the treatment-by-covariates interaction effects on treatment outcomes) against a relatively large non-treatment-related variability (i.e., the main effects of covariates on treatment outcomes). The class of Single-Index Models with Multiple-Links is a novel single-index model specifically designed to estimate a single-index (a linear combination) of the covariates associated with the treatment effect modification-related variability, while allowing a nonlinear association with the treatment outcomes via flexible link functions. The models provide a flexible regression approach to developing treatment decision rules based on patients' data measured at baseline. We refer to Petkova, Tarpey, Su, and Ogden (2017) <doi: 10.1093/biostatistics/kxw035> and "A constrained single-index model for estimating interactions between a treatment and covariates" (under review, 2019) for detail. The main function of this package is simml().
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2025-03-25 |
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r-simile
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public |
Allows a Simile model saved as a compiled binary to be loaded, parameterized, executed and interrogated. This version works with Simile v5.97 on.
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2025-03-25 |
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r-similaritymeasures
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public |
Functions to run and assist four different similarity measures. The similarity measures included are: longest common subsequence (LCSS), Frechet distance, edit distance and dynamic time warping (DTW). Each of these similarity measures can be calculated from two n-dimensional trajectories, both in matrix form.
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2025-03-25 |
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r-simhaz
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public |
Generate power for the Cox proportional hazards model by simulating survival events data with time dependent exposure status for subjects. A dichotomous exposure variable is considered with a single transition from unexposed to exposed status during the subject's time on study.
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2025-03-25 |
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r-simexaft
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Implement of the Simulation-Extrapolation (SIMEX) algorithm for the accelerated failure time (AFT) with covariates subject to measurement error.
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2025-03-25 |
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r-simex
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public |
Implementation of the SIMEX-Algorithm by Cook & Stefanski (1994) <doi:10.1080/01621459.1994.10476871> and MCSIMEX by Küchenhoff, Mwalili & Lesaffre (2006) <doi:10.1111/j.1541-0420.2005.00396.x>.
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2025-03-25 |
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r-simdistr
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public |
Assessment of the distributions of baseline continuous and categorical variables in randomised trials. This method is based on the Carlisle-Stouffer method with Monte Carlo simulations. It calculates p-values for each trial baseline variable, as well as combined p-values for each trial - these p-values measure how compatible are distributions of trials baseline variables with random sampling. This package also allows for graphically plotting the cumulative frequencies of computed p-values. Please note that code was partly adapted from Carlisle JB, Loadsman JA. (2017) <doi:10.1111/anae.13650>.
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2025-03-25 |
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r-simcop
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Provides a framework to generating random variates from arbitrary multivariate copulae, while concentrating on (bivariate) extreme value copulae. Particularly useful if the multivariate copulae are not available in closed form.
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2025-03-25 |
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r-simcausal
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A flexible tool for simulating complex longitudinal data using structural equations, with emphasis on problems in causal inference. Specify interventions and simulate from intervened data generating distributions. Define and evaluate treatment-specific means, the average treatment effects and coefficients from working marginal structural models. User interface designed to facilitate the conduct of transparent and reproducible simulation studies, and allows concise expression of complex functional dependencies for a large number of time-varying nodes. See the package vignette for more information, documentation and examples.
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2025-03-25 |
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r-simboot
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Provides estimation of simultaneous bootstrap and asymptotic confidence intervals for diversity indices, namely the Shannon and the Simpson index. Several pre--specified multiple comparison types are available to choose. Further user--defined contrast matrices are applicable. In addition, simboot estimates adjusted as well as unadjusted p--values for two of the three proposed bootstrap methods. Further simboot allows for comparing biological diversities of two or more groups while simultaneously testing a user-defined selection of Hill numbers of orders q, which are considered as appropriate and useful indices for measuring diversity.
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2025-03-25 |
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r-sii
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This package calculates ANSI S3.5-1997 Speech Intelligibility Index (SII), a standard method for computing the intelligibility of speech from acoustical measurements of speech, noise, and hearing thresholds. This package includes data frames corresponding to Tables 1 - 4 in the ANSI standard as well as a function utilizing these tables and user-provided hearing threshold and noise level measurements to compute the SII score. The methods implemented here extend the standard computations to allow calculation of SII when the measured frequencies do not match those required by the standard by applying interpolation to obtain values for the required frequencies -- Development of this package was funded by the Center for Bioscience Education and Technology (CBET) of the Rochester Institute of Technology (RIT).
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2025-03-25 |
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r-sigora
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Pathway Analysis is the process of statistically linking observations on the molecular level to biological processes or pathways on the systems(i.e. organism, organ, tissue, cell) level. Traditionally, pathway analysis methods regard pathways as collections of single genes and treat all genes in a pathway as equally informative. This can lead to identification of spurious pathways as statistically significant, since components are often shared amongst pathways. SIGORA seeks to avoid this pitfall by focusing on genes or gene-pairs that are (as a combination) specific to a single pathway. In relying on such pathway gene-pair signatures (Pathway-GPS), SIGORA inherently uses the status of other genes in the experimental context to identify the most relevant pathways. The current version allows for pathway analysis of human and mouse datasets and contains pre-computed Pathway-GPS data for pathways in the KEGG and Reactome pathway repositories as well as mechanisms for extracting GPS for user supplied repositories.
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2025-03-25 |
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r-sigoptr
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Interfaces with the 'SigOpt' API. More info at <https://sigopt.com>.
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2025-03-25 |
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r-signmedian.test
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public |
Perform sign test on one-sample data, which is one of the oldest non-parametric statistical methods. Assume that X comes from a continuous distribution with median = v ( unknown ). Test the null hypothesis H0: median of X v = mu ( mu is the location parameter and is given in the test ) v.s. the alternative hypothesis H1: v > mu ( or v < mu or v != mu ) and calculate the p-value. When the sample size is large, perform the asymptotic sign test. In both ways, calculate the R-estimate of location of X and the distribution free confidence interval for mu.
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2025-03-25 |
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r-signifreg
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Provide consistent significance controlled variable selection procedure with different directions (forward, backward, stepwise) based on diverse criteria (AIC, BIC, adjusted r-square, and p-value). The algorithm selects a final model with only significant variables based on a correction choice of False Discovery Rate, Bonferroni, or no correction.
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2025-03-25 |
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r-sigmoid
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public |
Several different sigmoid functions are implemented, including a wrapper function, SoftMax preprocessing and inverse functions.
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2025-03-25 |
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r-sigmanet
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public |
Create interactive graph visualizations using 'Sigma.js' <http://sigmajs.org/>. This package is meant to be used in conjunction with 'igraph', replacing the (somewhat underwhelming) plotting features of the package. The idea is to quickly render graphs, regardless of their size, in a way that allows for easy, iterative modification of aesthetics. Because 'Sigma.js' is a 'javascript' library, the visualizations are inherently interactive and are well suited for integration with 'Shiny' apps. While there are several 'htmlwidgets' focused on network visualization, they tend to underperform on medium to large sized graphs. 'Sigma.js' was designed for larger network visualizations and this package aims to make those strengths available to 'R' users.
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2025-03-25 |
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r-sightabilitymodel
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Uses logistic regression to model the probability of detection as a function of covariates. This model is then used with observational survey data to estimate population size, while accounting for uncertain detection. See Steinhorst and Samuel (1989).
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2025-03-25 |
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r-sigclust
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public |
SigClust is a statistical method for testing the significance of clustering results. SigClust can be applied to assess the statistical significance of splitting a data set into two clusters. For more than two clusters, SigClust can be used iteratively.
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2025-03-25 |
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r-sig
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public |
Print function signatures and find overly complicated code.
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2025-03-25 |
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r-sievetest
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public |
Functions for making particle-size analysis. Sieve tests are widely used to obtain particle-size distribution of powders or granular materials.
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2025-03-25 |
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r-sieveph
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public |
Implements semiparametric estimation and testing procedures for a continuous, possibly multivariate, mark-specific hazard ratio (treatment/placebo) of an event of interest in a randomized treatment efficacy trial with a time-to-event endpoint, as described in Juraska M and Gilbert PB (2013), Mark-specific hazard ratio model with multivariate continuous marks: an application to vaccine efficacy. Biometrics 69(2):328 337, and in Juraska M and Gilbert PB (2015), Mark-specific hazard ratio model with missing multivariate marks. Lifetime Data Analysis 22(4): 606-25. The former considers continuous multivariate marks fully observed in all subjects who experience the event of interest, whereas the latter extends the previous work to allow multivariate marks that are subject to missingness-at-random. For models with missing marks, two estimators are implemented based on (i) inverse probability weighting (IPW) of complete cases, and (ii) augmentation of the IPW estimating functions by leveraging correlations between the mark and auxiliary data to 'impute' the expected profile score vectors for subjects with missing marks. The augmented IPW estimator is doubly robust and recommended for use with incomplete mark data. The methods make two key assumptions: (i) the time-to-event is assumed to be conditionally independent of the mark given treatment, and (ii) the weight function in the semiparametric density ratio/biased sampling model is assumed to be exponential. Diagnostic testing procedures for evaluating validity of both assumptions are implemented. Summary and plotting functions are provided for estimation and inferential results.
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2025-03-25 |
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r-sier
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public |
Methods for regression with high-dimensional predictors and univariate or maltivariate response variables. It considers the decomposition of the coefficient matrix that leads to the best approximation to the signal part in the response given any rank, and estimates the decomposition by solving a penalized generalized eigenvalue problem followed by a least squares procedure. Ruiyan Luo and Xin Qi (2017) <doi:10.1016/j.jmva.2016.09.005>.
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2025-03-25 |
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r-siebanxicor
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public |
Allows to retrieve time series of all indicators available in the Bank of Mexico's Economic Information System (<http://www.banxico.org.mx/SieInternet/>).
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2025-03-25 |
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r-si
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public |
An implementation of four stochastic methods of integrating in R, including: 1. Stochastic Point Method (or Monte Carlo Method); 2. Mean Value Method; 3. Important Sampling Method; 4. Stratified Sampling Method. It can be used to estimate one-dimension or multi-dimension integration by Monte Carlo methods. And the estimated variance (precision) is given. Reference: Caflisch, R. E. (1998) <doi:10.1017/S0962492900002804>.
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2025-03-25 |
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r-shutterstock
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public |
Access 'Shutterstock' API from R. The 'Shutterstock' API presents access to search, view, license and download the media and information from the 'Shutterstock's library <https://api-reference.shutterstock.com/>.
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2025-03-25 |
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r-shuffle
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public |
Implementation of the shuffle estimator, a non-parametric estimator for signal and noise variance under mild noise correlations.
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2025-03-25 |
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r-showimage
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public |
Sometimes it is handy to be able to view an image file on an 'R' graphics device. This package just does that. Currently it supports 'PNG' files.
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2025-03-25 |
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r-shotgroups
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public |
Analyzes shooting data with respect to group shape, precision, and accuracy. This includes graphical methods, descriptive statistics, and inference tests using standard, but also non-parametric and robust statistical methods. Implements distributions for radial error in bivariate normal variables. Works with files exported by 'OnTarget PC/TDS', 'Silver Mountain' e-target, 'ShotMarker' e-target, or 'Taran', as well as with custom data files in text format. Supports inference from range statistics like extreme spread. Includes a set of web-based graphical user interfaces.
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2025-03-25 |
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r-shopifyr
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public |
An interface to the Admin API of the E-commerce service Shopify, (<https://help.shopify.com/en/api/reference>).
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2025-03-25 |
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r-shipunov
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public |
A collection of functions for data manipulation, plotting and statistical computing, to use separately or with the book "Visual Statistics. Use R!": Shipunov (2019) <http://ashipunov.info/shipunov/software/r/r-en.htm>. Most useful functions are probably Bclust(), Jclust() and BootA() which bootstrap hierarchical clustering; Recode...() which multiple recode in a fast, flexible and simple way; Misclass() which outputs confusion matrix even if classes are not concerted; Overlap() which calculates overlaps of convex hulls from any projection; and Pleiad() which is fast and flexible correlogram. In fact, there are much more useful functions, please see documentation.
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2025-03-25 |
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r-ship
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public |
The SHIP-package allows the estimation of various types of shrinkage covariance matrices. These types differ in terms of the so-called covariance target (to be chosen by the user), the highly structured matrix which the standard unbiased sample covariance matrix is shrunken towards and which optionally incorporates prior biological knowledge extracted from the database KEGG. The shrinkage intensity is obtained via an analytical procedure.
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2025-03-25 |
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r-shinywidgets
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public |
Collection of custom input controls and user interface components for 'Shiny' applications. Give your applications a unique and colorful style !
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2025-03-25 |
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r-shinytree
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public |
Exposes bindings to jsTree -- a JavaScript library that supports interactive trees -- to enable a rich, editable trees in Shiny.
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2025-03-25 |
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r-shinytoastr
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Browser notifications in 'Shiny' apps, using 'toastr': <https://github.com/CodeSeven/toastr#readme>.
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2025-03-25 |
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r-shinytime
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public |
Provides a time input widget for Shiny. This widget allows intuitive time input in the '[hh]:[mm]:[ss]' or '[hh]:[mm]' (24H) format by using a separate numeric input for each time component. The interface with R uses date-time objects. See the project page for more information and examples.
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2025-03-25 |
