|
r-sgmcmc
|
public |
Provides functions that performs popular stochastic gradient Markov chain Monte Carlo (SGMCMC) methods on user specified models. The required gradients are automatically calculated using 'TensorFlow' <https://www.tensorflow.org/>, an efficient library for numerical computation. This means only the log likelihood and log prior functions need to be specified. The methods implemented include stochastic gradient Langevin dynamics (SGLD), stochastic gradient Hamiltonian Monte Carlo (SGHMC), stochastic gradient Nose-Hoover thermostat (SGNHT) and their respective control variate versions for increased efficiency. References: M. Welling, Y. W. Teh (2011) <http://www.icml-2011.org/papers/398_icmlpaper.pdf>; T. Chen, E. B. Fox, C. E. Guestrin (2014) <arXiv:1402.4102>; N. Ding, Y. Fang, R. Babbush, C. Chen, R. D. Skeel, H. Neven (2014) <https://papers.nips.cc/paper/5592-bayesian-sampling-using-stochastic-gradient-thermostats>; J. Baker, P. Fearnhead, E. B. Fox, C. Nemeth (2017) <arXiv:1706.05439>. For more details see <doi:10.18637/jss.v091.i03>.
|
2025-03-25 |
|
r-sgee
|
public |
Stagewise techniques implemented with Generalized Estimating Equations to handle individual, group, bi-level, and interaction selection. Stagewise approaches start with an empty model and slowly build the model over several iterations, which yields a 'path' of candidate models from which model selection can be performed. This 'slow brewing' approach gives stagewise techniques a unique flexibility that allows simple incorporation of Generalized Estimating Equations; see Vaughan, G., Aseltine, R., Chen, K., Yan, J., (2017) <doi:10.1111/biom.12669> for details.
|
2025-03-25 |
|
r-sgb
|
public |
Main properties and regression procedures using a generalization of the Dirichlet distribution called Simplicial Generalized Beta distribution. It is a new distribution on the simplex (i.e. on the space of compositions or positive vectors with sum of components equal to 1). The Dirichlet distribution can be constructed from a random vector of independent Gamma variables divided by their sum. The SGB follows the same construction with generalized Gamma instead of Gamma variables. The Dirichlet exponents are supplemented by an overall shape parameter and a vector of scales. The scale vector is itself a composition and can be modeled with auxiliary variables through a log-ratio transformation. Graf, M. (2017, ISBN: 978-84-947240-0-8). See also the vignette enclosed in the package.
|
2025-03-25 |
|
r-sfinx
|
public |
The straightforward filtering index (SFINX) identifies true positive protein interactions in a fast, user-friendly, and highly accurate way. It is not only useful for the filtering of affinity purification - mass spectrometry (AP-MS) data, but also for similar types of data resulting from other co-complex interactomics technologies, such as TAP-MS, Virotrap and BioID. SFINX can also be used via the website interface at <http://sfinx.ugent.be>.
|
2025-03-25 |
|
r-sfa
|
public |
Stochastic Frontier Analysis introduced by Aigner, Lovell and Schmidt (1976) and Battese and Coelli (1992, 1995).
|
2025-03-25 |
|
r-severity
|
public |
This package contains functions for calculating severity and generating severity curves. Specifically, the simple case of the one-parameter Normal distribution (i.e., with known variance) is considered.
|
2025-03-25 |
|
r-settings
|
public |
Provides option settings management that goes beyond R's default 'options' function. With this package, users can define their own option settings manager holding option names, default values and (if so desired) ranges or sets of allowed option values that will be automatically checked. Settings can then be retrieved, altered and reset to defaults with ease. For R programmers and package developers it offers cloning and merging functionality which allows for conveniently defining global and local options, possibly in a multilevel options hierarchy. See the package vignette for some examples concerning functions, S4 classes, and reference classes. There are convenience functions to reset par() and options() to their 'factory defaults'.
|
2025-03-25 |
|
r-settest
|
public |
It provides cumulative distribution function (CDF), quantile, p-value, statistical power calculator and random number generator for a collection of group-testing procedures, including the Higher Criticism tests, the one-sided Kolmogorov-Smirnov tests, the one-sided Berk-Jones tests, the one-sided phi-divergence tests, etc. The input are a group of p-values. The null hypothesis is that they are i.i.d. Uniform(0,1). In the context of signal detection, the null hypothesis means no signals. In the context of the goodness-of-fit testing, which contrasts a group of i.i.d. random variables to a given continuous distribution, the input p-values can be obtained by the CDF transformation. The null hypothesis means that these random variables follow the given distribution. For reference, see Hong Zhang, Jiashun Jin and Zheyang Wu. "Distributions and Statistical Power of Optimal Signal-Detection Methods In Finite Cases", submitted.
|
2025-03-25 |
|
r-setter
|
public |
Mutators to set attributes of variables, that work well in a pipe (much like stats::setNames()).
|
2025-03-25 |
|
r-setrng
|
public |
Provides utilities to help set and record the setting of the seed and the uniform and normal generators used when a random experiment is run. The utilities can be used in other functions that do random experiments to simplify recording and/or setting all the necessary information for reproducibility. See the vignette and reference manual for examples.
|
2025-03-25 |
|
r-setrank
|
public |
Implements an algorithm to conduct advanced gene set enrichment analysis on the results of genomics experiments.
|
2025-03-25 |
|
r-setpath
|
public |
Tests gene expression data from a biological pathway for biologically meaningful differences in the eigenstructure between two classes. Specifically, it tests the null hypothesis that the two classes' leading eigenvalues and sums of eigenvalues are equal. A pathway's leading eigenvalue arguably represents the total variability due to variability in pathway activity, while the sum of all its eigenvalues represents the variability due to pathway activity and to other, unregulated causes. Implementation of the method described in Danaher (2015), "Covariance-based analyses of biological pathways".
|
2025-03-25 |
|
r-session
|
public |
Utility functions for interacting with R processes from external programs. This package includes functions to save and restore session information (including loaded packages, and attached data objects), as well as functions to evaluate strings containing R commands and return the printed results or an execution transcript.
|
2025-03-25 |
|
r-sesem
|
public |
Structural equation modeling is a powerful statistical approach for the testing of networks of direct and indirect theoretical causal relationships in complex data sets with inter-correlated dependent and independent variables. Here we implement a simple method for spatially explicit structural equation modeling based on the analysis of variance co-variance matrices calculated across a range of lag distances. This method provides readily interpreted plots of the change in path coefficients across scale.
|
2025-03-25 |
|
r-servr
|
public |
Start an HTTP server in R to serve static files, or dynamic documents that can be converted to HTML files (e.g., R Markdown) under a given directory.
|
2025-03-25 |
|
r-seroincidence
|
public |
Translates antibody levels measured in a (cross-sectional) population sample into an estimate of the frequency with which seroconversions (infections) occur in the sampled population.
|
2025-03-25 |
|
r-serieslcb
|
public |
Calculate and compare lower confidence bounds for binomial series system reliability. The R 'shiny' application, launched by the function launch_app(), weaves together a workflow of customized simulations and delta coverage calculations to output recommended lower confidence bound methods.
|
2025-03-25 |
|
r-serial
|
public |
Enables reading and writing binary and ASCII data to RS232/RS422/RS485 or any other virtual serial interface of the computer.
|
2025-03-25 |
|
r-sequential
|
public |
Functions to calculate exact critical values, statistical power, expected time to signal, and required sample sizes for performing exact sequential analysis. All these calculations can be done for either Poisson or binomial data, for continuous or group sequential analyses, and for different types of rejection boundaries. In case of group sequential analyses, the group sizes do not have to be specified in advance and the alpha spending can be arbitrarily settled.
|
2025-03-25 |
|
r-seqtest
|
public |
Sequential triangular test for the arithmetic mean in one- and two- samples, proportions in one- and two-samples, and the Pearson's correlation coefficient.
|
2025-03-25 |
|
r-seqrflp
|
public |
This package includes functions for handling DNA sequences, especially simulated RFLP and TRFLP pattern based on selected restriction enzyme and DNA sequences.
|
2025-03-25 |
|
r-seqmon
|
public |
S4 class object for creating and managing group sequential designs. It calculates the efficacy and futility boundaries at each look. It allows modifying the design and tracking the design update history.
|
2025-03-25 |
|
r-seqmade
|
public |
A network module-based generalized linear model for differential expression analysis with the count-based sequence data from RNA-Seq.
|
2025-03-25 |
|
r-seqicp
|
public |
Contains an implementation of invariant causal prediction for sequential data. The main function in the package is 'seqICP', which performs linear sequential invariant causal prediction and has guaranteed type I error control. For non-linear dependencies the package also contains a non-linear method 'seqICPnl', which allows to input any regression procedure and performs tests based on a permutation approach that is only approximately correct. In order to test whether an individual set S is invariant the package contains the subroutines 'seqICP.s' and 'seqICPnl.s' corresponding to the respective main methods.
|
2025-03-25 |
|
r-seqdesign
|
public |
A modification of the preventive vaccine efficacy trial design of Gilbert, Grove et al. (2011, Statistical Communications in Infectious Diseases) is implemented, with application generally to individual-randomized clinical trials with multiple active treatment groups and a shared control group, and a study endpoint that is a time-to-event endpoint subject to right-censoring. The design accounts for the issues that the efficacy of the treatment/vaccine groups may take time to accrue while the multiple treatment administrations/vaccinations are given; there is interest in assessing the durability of treatment efficacy over time; and group sequential monitoring of each treatment group for potential harm, non-efficacy/efficacy futility, and high efficacy is warranted. The design divides the trial into two stages of time periods, where each treatment is first evaluated for efficacy in the first stage of follow-up, and, if and only if it shows significant treatment efficacy in stage one, it is evaluated for longer-term durability of efficacy in stage two. The package produces plots and tables describing operating characteristics of a specified design including an unconditional power for intention-to-treat and per-protocol/as-treated analyses; trial duration; probabilities of the different possible trial monitoring outcomes (e.g., stopping early for non-efficacy); unconditional power for comparing treatment efficacies; and distributions of numbers of endpoint events occurring after the treatments/vaccinations are given, useful as input parameters for the design of studies of the association of biomarkers with a clinical outcome (surrogate endpoint problem). The code can be used for a single active treatment versus control design and for a single-stage design.
|
2025-03-25 |
|
r-seqalloc
|
public |
Potential randomization schemes are prospectively evaluated when units are assigned to treatment arms upon entry into the experiment. The schemes are evaluated for balance on covariates and on predictability (i.e., how well could a site worker guess the treatment of the next unit enrolled).
|
2025-03-25 |
|
r-separationplot
|
public |
Visual representations of model fit or predictive success in the form of "separation plots." See Greenhill, Brian, Michael D. Ward, and Audrey Sacks. "The separation plot: A new visual method for evaluating the fit of binary models." American Journal of Political Science 55.4 (2011): 991-1002.
|
2025-03-25 |
|
r-separate
|
public |
Maximum likelihood estimation of the parameters of matrix and 3rd-order tensor normal distributions with unstructured factor variance covariance matrices, two procedures, and for unbiased modified likelihood ratio testing of simple and double separability for variance-covariance structures, two procedures. References: Dutilleul P. (1999) <doi:10.1080/00949659908811970>, Manceur AM, Dutilleul P. (2013) <doi:10.1016/j.cam.2012.09.017>, and Manceur AM, Dutilleul P. (2013) <doi:10.1016/j.spl.2012.10.020>.
|
2025-03-25 |
|
r-senstrat
|
public |
Sensitivity analysis in unmatched observational studies, with or without strata. The main functions are sen2sample() and senstrat(). See Rosenbaum, P. R. and Krieger, A. M. (1990), JASA, 85, 493-498, <doi:10.1080/01621459.1990.10476226> and Gastwirth, Krieger and Rosenbaum (2000), JRSS-B, 62, 545–555 <doi:10.1111/1467-9868.00249> .
|
2025-03-25 |
|
r-sensrivastava
|
public |
Collection of datasets from Sen & Srivastava: "Regression Analysis, Theory, Methods and Applications", Springer. Sources for individual data files are more fully documented in the book.
|
2025-03-25 |
|
r-sensr
|
public |
Provides methods for sensory discrimination methods; duotrio, tetrad, triangle, 2-AFC, 3-AFC, A-not A, same-different, 2-AC and degree-of-difference. This enables the calculation of d-primes, standard errors of d-primes, sample size and power computations, and comparisons of different d-primes. Methods for profile likelihood confidence intervals and plotting are included.
|
2025-03-25 |
|
r-sensory
|
public |
Contains the function CUUimpute() which performs model-based clustering and imputation simultaneously.
|
2025-03-25 |
|
r-sensmediation
|
public |
We implement functions to estimate and perform sensitivity analysis to unobserved confounding of direct and indirect effects introduced in Lindmark, de Luna and Eriksson (2018) <doi:10.1002/sim.7620>. The estimation and sensitivity analysis are parametric, based on probit and/or linear regression models. Sensitivity analysis is implemented for unobserved confounding of the exposure-mediator, mediator-outcome and exposure-outcome relationships.
|
2025-03-25 |
|
r-sensitivitymw
|
public |
Sensitivity analysis for tests, confidence intervals and estimates in matched observational studies with one or more controls using weighted or unweighted Huber-Maritz M-tests (including the permutational t-test). The method is from Rosenbaum (2014) Weighted M-statistics with superior design sensitivity in matched observational studies with multiple controls JASA, 109(507), 1145-1158 <doi:10.1080/01621459.2013.879261>.
|
2025-03-25 |
|
r-sensitivitymv
|
public |
The package performs a sensitivity analysis in an observational study using an M-statistic, for instance, the mean. The main function in the package is senmv(), but amplify() and truncatedP() are also useful. The method is developed in Rosenbaum Biometrics, 2007, 63, 456-464, <doi:10.1111/j.1541-0420.2006.00717.x>.
|
2025-03-25 |
|
r-sensitivitymult
|
public |
Sensitivity analysis for multiple outcomes in observational studies. For instance, all linear combinations of several outcomes may be explored using Scheffe projections in the comparison() function; see Rosenbaum (2016, Annals of Applied Statistics) <doi:10.1214/16-AOAS942>. Alternatively, attention may focus on a few principal components in the principal() function. The package includes parallel methods for individual outcomes, including tests in the senm() function and confidence intervals in the senmCI() function.
|
2025-03-25 |
|
r-sensitivityfull
|
public |
Sensitivity to unmeasured biases in an observational study that is a full match. Function senfm() performs tests and function senfmCI() creates confidence intervals. The method uses Huber's M-statistics, including least squares, and is described in Rosenbaum (2007, Biometrics) <DOI:10.1111/j.1541-0420.2006.00717.x>.
|
2025-03-25 |
|
r-sensitivitycasecontrol
|
public |
Sensitivity analysis for case-control studies in which some cases may meet a more narrow definition of being a case compared to other cases which only meet a broad definition. The sensitivity analyses are described in Small, Cheng, Halloran and Rosenbaum (2013, "Case Definition and Sensitivity Analysis", Journal of the American Statistical Association, 1457-1468). The functions sens.analysis.mh and sens.analysis.aberrant.rank provide sensitivity analyses based on the Mantel-Haenszel test statistic and aberrant rank test statistic as described in Rosenbaum (1991, "Sensitivity Analysis for Matched Case Control Studies", Biometrics); see also Section 1 of Small et al. The function adaptive.case.test provides adaptive inferences as described in Section 5 of Small et al. The function adaptive.noether.brown provides a sensitivity analysis for a matched cohort study based on an adaptive test. The other functions in the package are internal functions.
|
2025-03-25 |
|
r-sensitivity2x2xk
|
public |
Performs exact or approximate adaptive or nonadaptive Cochran-Mantel-Haenszel-Birch tests and sensitivity analyses for one or two 2x2xk tables in observational studies.
|
2025-03-25 |
|
r-sensibo.sky
|
public |
Provides an interface to the 'Sensibo Sky' API which allows to remotely control non-smart air conditioning units. See <https://sensibo.com> for more informations.
|
2025-03-25 |
|
r-sensemakr
|
public |
Implements a suite of sensitivity analysis tools that extends the traditional omitted variable bias framework and makes it easier to understand the impact of omitted variables in regression models, as discussed in Cinelli, C. and Hazlett, C. (2020), "Making Sense of Sensitivity: Extending Omitted Variable Bias." Journal of the Royal Statistical Society, Series B (Statistical Methodology) <doi:10.1111/rssb.12348>.
|
2025-03-25 |
|
r-sendmailr
|
public |
Package contains a simple SMTP client with minimal dependencies which provides a portable solution for sending email, including file attachments and inline html reports, from within R. SMTP Authentication and SSL/STARTTLS is implemented using curl.
|
2025-03-25 |
|
r-sempower
|
public |
Provides a-priori, post-hoc, and compromise power-analyses for structural equation models (SEM).
|
2025-03-25 |
|
r-sempls
|
public |
Fits structural equation models using partial least squares (PLS). The PLS approach is referred to as 'soft-modeling' technique requiring no distributional assumptions on the observed data.
|
2025-03-25 |
|
r-semnetdictionaries
|
public |
Implements dictionaries that can be used in the 'SemNetCleaner' package. Also includes several functions aimed at facilitating the text cleaning analysis in the 'SemNetCleaner' package. This package is designed to integrate and update word lists and dictionaries based on each user's individual needs by allowing users to store and save their own dictionaries. Dictionaries can be added to the 'SemNetDictionaries' package by submitting user-defined dictionaries to <https://github.com/AlexChristensen/SemNetDictionaries>.
|
2025-03-25 |
|
r-semmodcomp
|
public |
Conduct tests of difference in fit for mean and covariance structure models as in structural equation modeling (SEM)
|
2025-03-25 |
|
r-semipar
|
public |
Functions for semiparametric regression analysis, to complement the book: Ruppert, D., Wand, M.P. and Carroll, R.J. (2003). Semiparametric Regression. Cambridge University Press.
|
2025-03-25 |
|
r-seminr
|
public |
A powerful, easy to syntax for specifying and estimating complex Structural Equation Models. Models can be estimated using Partial Least Squares Path Modeling or Covariance-Based Structural Equation Modeling or covariance based Confirmatory Factor Analysis. Methods described in Ray, Danks, and Valdez (2021).
|
2025-03-25 |
|
r-semid
|
public |
Provides routines to check identifiability or non-identifiability of linear structural equation models as described in Drton, Foygel, and Sullivant (2011) <doi:10.1214/10-AOS859>, Foygel, Draisma, and Drton (2012) <doi:10.1214/12-AOS1012>, and other works. The routines are based on the graphical representation of structural equation models.
|
2025-03-25 |
|
r-selfingtree
|
public |
A probability tree allows to compute probabilities of complex events, such as genotype probabilities in intermediate generations of inbreeding through recurrent self-fertilization (selfing). This package implements functionality to compute probability trees for two- and three-marker genotypes in the F2 to F7 selfing generations. The conditional probabilities are derived automatically and in symbolic form. The package also provides functionality to extract and evaluate the relevant probabilities.
|
2025-03-25 |
