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r-survmisc
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A collection of functions to help in the analysis of right-censored survival data. These extend the methods available in package:survival.
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2024-01-16 |
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r-survregcenscov
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The function SurvRegCens() of this package allows estimation of a Weibull Regression for a right-censored endpoint, one interval-censored covariate, and an arbitrary number of non-censored covariates. Additional functions allow to switch between different parametrizations of Weibull regression used by different R functions, inference for the mean difference of two arbitrarily censored Normal samples, and estimation of canonical parameters from censored samples for several distributional assumptions. Hubeaux, S. and Rufibach, K. (2014) <arXiv:1402.0432>.
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2024-01-16 |
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r-survtrunc
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Package performs Cox regression and survival distribution function estimation when the survival times are subject to double truncation. In case that the survival and truncation times are quasi-independent, the estimation procedure for each method involves inverse probability weighting, where the weights correspond to the inverse of the selection probabilities and are estimated using the survival times and truncation times only. A test for checking this independence assumption is also included in this package. The functions available in this package for Cox regression, survival distribution function estimation, and testing independence under double truncation are based on the following methods, respectively: Rennert and Xie (2018) <doi:10.1111/biom.12809>, Shen (2010) <doi:10.1007/s10463-008-0192-2>, Martin and Betensky (2005) <doi:10.1198/016214504000001538>. When the survival times are dependent on at least one of the truncation times, an EM algorithm is employed to obtain point estimates for the regression coefficients. The standard errors are calculated using the bootstrap method. See Rennert and Xie (2022) <doi:10.1111/biom.13451>. Both the independent and dependent cases assume no censoring is present in the data. Please contact Lior Rennert <[email protected]> for questions regarding function coxDT and Yidan Shi <[email protected]> for questions regarding function coxDTdep.
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2024-01-16 |
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r-survrm2adapt
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Estimates the restricted mean survival time (RMST) with the time window [0, tau], where tau is adaptively selected from the procedure, proposed by Horiguchi et al. (2018) <doi:10.1002/sim.7661>. It also estimates the RMST with the time window [tau1, tau2], where tau1 is adaptively selected from the procedure, proposed by Horiguchi et al. (2023) <doi:10.1002/sim.9662>.
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2024-01-16 |
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r-survrm2
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Performs two-sample comparisons using the restricted mean survival time (RMST) as a summary measure of the survival time distribution. Three kinds of between-group contrast metrics (i.e., the difference in RMST, the ratio of RMST and the ratio of the restricted mean time lost (RMTL)) are computed. It performs an ANCOVA-type covariate adjustment as well as unadjusted analyses for those measures.
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2024-01-16 |
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r-support.ces
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Provides basic functions that support an implementation of (discrete) choice experiments (CEs). CEs is a question-based survey method measuring people's preferences for goods/services and their characteristics. Refer to Louviere et al. (2000) <doi:10.1017/CBO9780511753831> for details on CEs, and Aizaki (2012) <doi:10.18637/jss.v050.c02> for the package.
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2024-01-16 |
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r-sur
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Access to the datasets and many of the functions used in "Statistics Using R: An Integrative Approach". These datasets include a subset of the National Education Longitudinal Study, the Framingham Heart Study, as well as several simulated datasets used in the examples throughout the textbook. The functions included in the package reproduce some of the functionality of 'Stata' that is not directly available in 'R'. The package also contains a tutorial on basic data frame management, including how to handle missing data.
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2024-01-16 |
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r-survjamda.data
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Three breast cancer gene expression data sets that can be used for package 'survJamda'. This package contains the gene expression and phenotype data of GSE1992, GSE3143 and GSE4335.
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2024-01-16 |
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r-survlong
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Provides kernel weighting methods for estimation of proportional hazards models with intermittently observed longitudinal covariates. Cao H., Churpek M. M., Zeng D., and Fine J. P. (2015) <doi:10.1080/01621459.2014.957289>.
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2024-01-16 |
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r-survey
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Summary statistics, two-sample tests, rank tests, generalised linear models, cumulative link models, Cox models, loglinear models, and general maximum pseudolikelihood estimation for multistage stratified, cluster-sampled, unequally weighted survey samples. Variances by Taylor series linearisation or replicate weights. Post-stratification, calibration, and raking. Two-phase subsampling designs. Graphics. PPS sampling without replacement.
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2024-01-16 |
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r-survivalmpl
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Estimate the regression coefficients and the baseline hazard of proportional hazard Cox models with left, right or interval censored survival data using maximum penalised likelihood. A 'non-parametric' smooth estimate of the baseline hazard function is provided.
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2024-01-16 |
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r-survexp.fr
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It computes Relative survival, AER and SMR based on French death rates.
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2024-01-16 |
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r-survbootoutliers
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Three new methods to perform outlier detection in a survival context. In total there are six methods provided, the first three methods are traditional residual-based outlier detection methods, the second three are the concordance-based. Package developed during the work on the two following publications: Pinto J., Carvalho A. and Vinga S. (2015) <doi:10.5220/0005225300750082>; Pinto J.D., Carvalho A.M., Vinga S. (2015) <doi:10.1007/978-3-319-27926-8_22>.
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2024-01-16 |
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r-survawkmt2
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Tests for equality of two survival functions based on integrated weighted differences of two Kaplan-Meier curves.
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2024-01-16 |
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r-surtex
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suRtex was designed for easy descriptive statistic reporting of categorical survey data (e.g., Likert scales) in LaTeX. suRtex takes a matrix or data frame and produces the LaTeX code necessary for a sideways table creation. Mean, median, standard deviation, and sample size are optional.
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2024-01-16 |
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r-surrosurvroc
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Nonparametric and semiparametric estimations of the time-dependent ROC curve for an incomplete failure time data with surrogate failure time endpoints.
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2024-01-16 |
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r-surrogatetest
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Provides functions to test for a treatment effect in terms of the difference in survival between a treatment group and a control group using surrogate marker information obtained at some early time point in a time-to-event outcome setting. Nonparametric kernel estimation is used to estimate the test statistic and perturbation resampling is used for variance estimation. More details will be available in the future in: Parast L, Cai T, Tian L (2019) ``Using a Surrogate Marker for Early Testing of a Treatment Effect" Biometrics, 75(4):1253-1263. <doi:10.1111/biom.13067>.
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2024-01-16 |
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r-surrogateoutcome
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Provides functions to estimate the proportion of treatment effect on a censored primary outcome that is explained by the treatment effect on a censored surrogate outcome/event. All methods are described in detail in Parast, Tian, Cai (2020) "Assessing the Value of a Censored Surrogate Outcome" <doi:10.1007/s10985-019-09473-1>. The main functions are (1) R.q.event() which calculates the proportion of the treatment effect (the difference in restricted mean survival time at time t) explained by surrogate outcome information observed up to a selected landmark time, (2) R.t.estimate() which calculates the proportion of the treatment effect explained by primary outcome information only observed up to a selected landmark time, and (3) IV.event() which calculates the incremental value of the surrogate outcome information.
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2024-01-16 |
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r-superheat
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A system for generating extendable and customizable heatmaps for exploring complex datasets, including big data and data with multiple data types.
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2024-01-16 |
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r-superlearner
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Implements the super learner prediction method and contains a library of prediction algorithms to be used in the super learner.
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2024-01-16 |
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r-support.bws
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Provides basic functions that support an implementation of object case (Case 1) best-worst scaling: a function for converting a two-level orthogonal main-effect design/balanced incomplete block design into questions; two functions for creating a data set suitable for analysis; a function for calculating count-based scores; a function for calculating shares of preference; and a function for generating artificial responses to questions. See Louviere et al. (2015) <doi:10.1017/CBO9781107337855> for details on best-worst scaling, and Aizaki and Fogarty (2023) <doi:10.1016/j.jocm.2022.100394> for the package.
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2024-01-16 |
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r-support.bws2
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Provides three basic functions that support an implementation of Case 2 (profile case) best-worst scaling. The first is to convert an orthogonal main-effect design into questions, the second is to create a dataset suitable for analysis, and the third is to calculate count-based scores. For details, see Aizaki and Fogarty (2019) <doi:10.1016/j.jocm.2019.100171>.
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2024-01-16 |
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r-superpc
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Does prediction in the case of a censored survival outcome, or a regression outcome, using the "supervised principal component" approach. 'Superpc' is especially useful for high-dimensional data when the number of features p dominates the number of samples n (p >> n paradigm), as generated, for instance, by high-throughput technologies.
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2024-01-16 |
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r-supernova
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Produces ANOVA tables in the format used by Judd, McClelland, and Ryan (2017, ISBN: 978-1138819832) in their introductory textbook, Data Analysis. This includes proportional reduction in error and formatting to improve ease the transition between the book and R.
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2024-01-16 |
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r-sungeo
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Tools for integrating spatially-misaligned GIS datasets. Part of the Sub-National Geospatial Data Archive System.
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2024-01-16 |
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r-suntools
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Provides a set of convenient functions for calculating sun-related information, including the sun's position (elevation and azimuth), and the times of sunrise, sunset, solar noon, and twilight for any given geographical location on Earth. These calculations are based on equations provided by the National Oceanic & Atmospheric Administration (NOAA) <https://gml.noaa.gov/grad/solcalc/calcdetails.html> as described in "Astronomical Algorithms" by Jean Meeus (1991, ISBN: 978-0-943396-35-4). A resource for researchers and professionals working in fields such as climatology, biology, and renewable energy.
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2024-01-16 |
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r-superdiag
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The 'superdiag' package provides a comprehensive test suite for testing Markov Chain nonconvergence. It integrates five standard empirical MCMC convergence diagnostics (Gelman-Rubin, Geweke, Heidelberger-Welch, Raftery-Lewis, and Hellinger distance) and plotting functions for trace plots and density histograms. The functions of the package can be used to present all diagnostic statistics and graphs at once for conveniently checking MCMC nonconvergence.
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2024-01-16 |
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r-supcluster
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Clusters features under the assumption that each cluster has a random effect and there is an outcome variable that is related to the random effects by a linear regression. In this way the cluster analysis is ``supervised'' by the outcome variable. An alternate specification is that features in each cluster have the same compound symmetric normal distribution, and the conditional distribution of the outcome given the features has the same coefficient for each feature in a cluster.
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2024-01-16 |
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r-sunburstr
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Make interactive 'd3.js' sequence sunburst diagrams in R with the convenience and infrastructure of an 'htmlwidget'.
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2024-01-16 |
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r-summclust
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Module to compute cluster specific information for regression models with clustered errors, including leverage and influence statistics. Models of type 'lm' and 'fixest'(from the 'stats' and 'fixest' packages) are supported. 'summclust' implements similar features as the user-written 'summclust.ado' Stata module (MacKinnon, Nielsen & Webb, 2022; <arXiv:2205.03288v1>).
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2024-01-16 |
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r-stylo
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Supervised and unsupervised multivariate methods, supplemented by GUI and some visualizations, to perform various analyses in the field of computational stylistics, authorship attribution, etc. For further reference, see Eder et al. (2016), <https://journal.r-project.org/archive/2016/RJ-2016-007/index.html>. You are also encouraged to visit the Computational Stylistics Group's website <https://computationalstylistics.github.io/>, where a reasonable amount of information about the package and related projects are provided.
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2024-01-16 |
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r-sunclarco
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Survival analysis for unbalanced clusters using Archimedean copulas (Prenen et al. (2016) <DOI:10.1111/rssb.12174>).
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2024-01-16 |
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r-suncalc
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Get sun position, sunlight phases (times for sunrise, sunset, dusk, etc.), moon position and lunar phase for the given location and time. Most calculations are based on the formulas given in Astronomy Answers articles about position of the sun and the planets : <https://www.aa.quae.nl/en/reken/zonpositie.html>.
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2024-01-16 |
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r-styler
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Pretty-prints R code without changing the user's formatting intent.
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2024-01-16 |
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r-sudokualt
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Tools for making, retrieving, displaying and solving sudoku games. This package is an alternative to the earlier sudoku-solver package, 'sudoku'. The present package uses a slightly different algorithm, has a simpler coding and presents a few more sugar tools, such as plot and print methods. Solved sudoku games are of some interest in Experimental Design as examples of Latin Square designs with additional balance constraints.
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2024-01-16 |
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r-sudoku
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Generates, plays, and solves Sudoku puzzles. The GUI playSudoku() needs package "tkrplot" if you are not on Windows.
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2024-01-16 |
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r-subsamp
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This subsample winner algorithm (SWA) for regression with a large-p data (X, Y) selects the important variables (or features) among the p features X in explaining the response Y. The SWA first uses a base procedure, here a linear regression, on each of subsamples randomly drawn from the p variables, and then computes the scores of all features, i.e., the p variables, according to the performance of these features collected in each of the subsample analyses. It then obtains the 'semifinalist' of the features based on the resulting scores and determines the 'finalists', i.e., the important features, from the 'semifinalist'. Fan, Sun and Qiao (2017) <http://sr2c.case.edu/swa-reg/>.
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2024-01-16 |
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r-subgxe
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Classical methods for combining summary data from genome-wide association studies (GWAS) only use marginal genetic effects and power can be compromised in the presence of heterogeneity. 'subgxe' is a R package that implements p-value assisted subset testing for association (pASTA), a method developed by Yu et al. (2019) <doi:10.1159/000496867>. pASTA generalizes association analysis based on subsets by incorporating gene-environment interactions into the testing procedure.
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2024-01-16 |
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r-subgroup
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Produces various measures of expected treatment effect heterogeneity under an assumption of homogeneity across subgroups. Graphical presentations are created to compare these expected differences with the observed differences.
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2024-01-16 |
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r-subdetect
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A test for the existence of a subgroup with enhanced treatment effect. And, a sample size calculation procedure for the subgroup detection test.
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2024-01-16 |
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r-streamr
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Functions to access Twitter's filter, sample, and user streams, and to parse the output into data frames.
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2024-01-16 |
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r-subcopem2d
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Calculate empirical subcopula and dependence measures from a given bivariate sample, and Bernstein copula approximations.
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2024-01-16 |
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r-stv
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Implementations of the Single Transferable Vote counting system. By default, it uses the Cambridge method for surplus allocation and Droop method for quota calculation. Fractional surplus allocation and the Hare quota are available as options.
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2024-01-16 |
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r-stuart
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Construct subtests from a pool of items by using ant-colony-optimization, genetic algorithms, brute force, or random sampling. Schultze (2017) <doi:10.17169/refubium-622>.
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2024-01-16 |
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r-structfdr
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Perform more powerful false discovery control (FDR) for microbiome data, taking into account the prior phylogenetic relationship among bacteria species. As a general methodology, it is applicable to any type of (genomic) data with prior structure information.
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2024-01-16 |
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r-stripless
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For making Trellis-type conditioning plots without strip labels. This is useful for displaying the structure of results from factorial designs and other studies when many conditioning variables would clutter the display with layers of redundant strip labels. Settings of the variables are encoded by layout and spacing in the trellis array and decoded by a separate legend. The functionality is implemented by a single S3 generic strucplot() function that is a wrapper for the Lattice package's xyplot() function. This allows access to all Lattice graphics capabilities in the usual way.
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2024-01-16 |
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r-strip
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The strip function deletes components of R model outputs that are useless for specific purposes, such as predict[ing], print[ing], summary[izing], etc.
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2024-01-16 |
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r-stringr
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A consistent, simple and easy to use set of wrappers around the fantastic 'stringi' package. All function and argument names (and positions) are consistent, all functions deal with "NA"'s and zero length vectors in the same way, and the output from one function is easy to feed into the input of another.
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2024-01-16 |
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r-stringb
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Base R already ships with string handling capabilities 'out- of-the-box' but lacks streamlined function names and workflow. The 'stringi' ('stringr') package on the other hand has well named functions, extensive Unicode support and allows for a streamlined workflow. On the other hand it adds dependencies and regular expression interpretation between base R functions and 'stringi' functions might differ. This packages aims at providing a solution to the use case of unwanted dependencies on the one hand but the need for streamlined text processing on the other. The packages' functions are solely based on wrapping base R functions into 'stringr'/'stringi' like function names. Along the way it adds one or two extra functions and last but not least provides all functions as generics, therefore allowing for adding methods for other text structures besides plain character vectors.
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2024-01-16 |
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r-stringformattr
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Pass named and unnamed character vectors into specified positions in strings. This represents an attempt to replicate some of python's string formatting.
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2024-01-16 |
