Simulation of random vectors from truncated multivariate normal and t distributions based on the algorithms proposed by Yifang Li and Sujit K. Ghosh (2015) <doi:10.1080/15598608.2014.996690>.

This package provides functions that compute predictions from Generalised Additive Models (GAMs) fitted with mgcv and return them as a tibble. These can be plotted with a generic plot()-method that uses ggplot2 or plotted as any other data frame. The main function is predict_gam().

Estimation of group-based trajectory models, including finite mixture models for longitudinal data, supporting censored normal, zero-inflated Poisson, logit, and beta distributions, using expectation-maximization and quasi-Newton methods, with tools for model selection, diagnostics, and visualization of latent trajectory groups, <doi:10.4159/9780674041318>, Nagin, D. (2005). Group-Based Modeling of Development. Cambridge, MA: Harvard University Press. and Noel (2022), <https://orbilu.uni.lu/>, thesis.

Attain excellent covariate balance by matching two treated units and one control unit or vice versa within strata. Using such triples, as opposed to also allowing pairs of treated and control units, allows easier interpretation of the two possible weights of observations and better insensitivity to unmeasured bias in the test statistic. Using triples instead of matching in a fixed 1:2 or 2:1 ratio allows for the match to be feasible in more situations. The rrelaxiv package, which provides an alternative solver for the underlying network flow problems, carries an academic license and is not available on CRAN, but may be downloaded from GitHub at <https://github.com/josherrickson/rrelaxiv/>. The Gurobi commercial optimization software is required to use the two functions [infsentrip()] and [triplesIP()]. These functions are not essential to the main purpose of this package. A free academic license can be obtained at <https://www.gurobi.com/features/academic-named-user-license/>. The gurobi R package can then be installed following the instructions at <https://www.gurobi.com/documentation/9.1/refman/ins_the_r_package.html>.

Swift and seamless Single Sign-On (SSO) integration. Designed for effortless compatibility with popular Single Sign-On providers like Google and Microsoft, it streamlines authentication, enhancing both user experience and application security. Elevate your shiny applications for a simplified, unified, and secure authentication process.

U.S. Department of the Treasury, Alcohol and Tobacco Tax and Trade Bureau (TTB) collects data and reports on monthly beer industry production and operations. This data package includes a collection of 10 years (2006 - 2015) worth of data on materials used at U.S. breweries in pounds reported by the Brewer's Report of Operations and the Quarterly Brewer's Report of Operations forms, ready for data analysis. This package also includes historical tax rates on distilled spirits, wine, beer, champagne, and tobacco products as individual data sets.

Goodness of Fit and Forecast Evaluation Tests for timeseries models. Includes, among others, the Generalized Method of Moments (GMM) Orthogonality Test of Hansen (1982), the Nyblom (1989) parameter constancy test, the sign-bias test of Engle and Ng (1993), and a range of tests for value at risk and expected shortfall evaluation.

Plot official statistics time series conveniently: automatic legends, highlight windows, stacked bar chars with positive and negative contributions, sum-as-line option, two y-axes with automatic horizontal grids that fit both axes and other popular chart types. tstools comes with a plethora of defaults to let you plot without setting an abundance of parameters first, but gives you the flexibility to tweak the defaults. In addition to charts, tstools provides a super fast, data.table backed time series I/O that allows the user to export / import long format, wide format and transposed wide format data to various file types.

Miscellaneous utility functions for data manipulation, data tidying, and working with gene expression data.

Implementation of target-controlled infusion algorithms for compartmental pharmacokinetic and pharmacokinetic-pharmacodynamic models. Jacobs (1990) <doi:10.1109/10.43622>; Marsh et al. (1991) <doi:10.1093/bja/67.1.41>; Shafer and Gregg (1993) <doi:10.1007/BF01070999>; Schnider et al. (1998) <doi:10.1097/00000542-199805000-00006>; Abuhelwa, Foster, and Upton (2015) <doi:10.1016/j.vascn.2015.03.004>; Eleveld et al. (2018) <doi:10.1016/j.bja.2018.01.018>.

This package provides a simple approach for constructing dynamic materials modeling suggested by Prasad and Gegel (1984) <doi:10.1007/BF02664902>. It can easily generate various processing-maps based on this model as well. The calculation result in this package contains full materials constants, information about power dissipation efficiency factor, and rheological properties, can be exported completely also, through which further analysis and customized plots will be applicable as well.

Collection of ancillary functions and utilities to be used in conjunction with the TraMineR package for sequence data exploration. Includes, among others, specific functions such as state survival plots, position-wise group-typical states, dynamic sequence indicators, and dissimilarities between event sequences. Also includes contributions by non-members of the TraMineR team such as methods for polyadic data and for the comparison of groups of sequences.

Extends invariant causal prediction (Peters et al., 2016, <doi:10.1111/rssb.12167>) to generalized linear and transformation models (Hothorn et al., 2018, <doi:10.1111/sjos.12291>). The methodology is described in Kook et al. (2023, <doi:10.1080/01621459.2024.2395588>).

The best ANN structure for time series data analysis is a demanding need in the present era. This package will find the best-fitted ANN model based on forecasting accuracy. The optimum size of the hidden layers was also determined after determining the number of lags to be included. This package has been developed using the algorithm of Paul and Garai (2021) <doi:10.1007/s00500-021-06087-4>.

This package provides a plug-in for the text mining framework tm to support text mining in a distributed way. The package provides a convenient interface for handling distributed corpus objects based on distributed list objects.

Interacts with a suite of web application programming interfaces (API) for taxonomic tasks, such as getting database specific taxonomic identifiers, verifying species names, getting taxonomic hierarchies, fetching downstream and upstream taxonomic names, getting taxonomic synonyms, converting scientific to common names and vice versa, and more. Some of the services supported include NCBI E-utilities (<https://www.ncbi.nlm.nih.gov/books/NBK25501/>), Encyclopedia of Life (<https://eol.org/docs/what-is-eol/data-services>), Global Biodiversity Information Facility (<https://techdocs.gbif.org/en/openapi/>), and many more. Links to the API documentation for other supported services are available in the documentation for their respective functions in this package.

This package provides tools that stem and lemmatize text. Stemming is a process that removes endings such as affixes. Lemmatization is the process of grouping inflected forms together as a single base form.

Identifies clusters of individual longitudinal trajectories. In the spirit of Leffondre et al. (2004), the procedure involves identifying each trajectory to a point in the space of measures. In this context, a measure is a quantity meant to capture a certain characteristic feature of the trajectory. The points in the space of measures are then clustered using a version of spectral clustering.

Ports the Stata ado package tost which provides a suite of commands to perform two one-sided tests for equivalence following the approach by Schuirman (1987) <doi:10.1007/BF01068419>. Commands are provided for t tests on means, z tests on proportions, McNemar's test (1947) <doi:10.1007/BF02295996> on proportions and related tests, tests on the regression coefficients from OLS linear regression (not yet implementing all of the current regression options from the Stata tostregress command, e.g., survey regression options, estimation options, etc.), Wilcoxon's (1945) <doi:10.2307/3001968> signed rank tests, Wilcoxon-Mann-Whitney (1947) <doi:10.1214/aoms/1177730491> rank sum tests, supporting inference about equivalence for a number of paired and unpaired, parametric and nonparametric study designs and data types. Each command tests a null hypothesis that samples were drawn from populations different by at least plus or minus some researcher-defined level of tolerance, which can be defined in terms of units of the data or rank units (Delta), or in units of the test statistic's distribution (epsilon) except for tost.rrp() and tost.rrpi(). Enough evidence rejects this null hypothesis in favor of equivalence within the tolerance. Equivalence intervals for all tests may be defined symmetrically or asymmetrically.

Algorithms for accelerating the convergence of slow, monotone sequences from smooth, contraction mapping such as the EM and MM algorithms. It can be used to accelerate any smooth, linearly convergent acceleration scheme. A tutorial style introduction to this package is available in a vignette on the CRAN download page or, when the package is loaded in an R session, with vignette("turboEM").

This package provides a Tcl/Tk Graphical User Interface (GUI) to display images than can be zoomed and panned using the mouse and keyboard shortcuts. tkImgR read and write different image formats (PPM/PGM, PNG and GIF) using the standard Tcl/Tk distribution (>=8.6), but other formats (JPEG, TIFF, CR2) can be handled using the tkImg package for Tcl/Tk'.

Testing for trajectory presence and heterogeneity on multivariate data. Two statistical methods (Tenha & Song 2022) <doi:10.1371/journal.pcbi.1009829> are implemented. The tree dimension test quantifies the statistical evidence for trajectory presence. The subset specificity measure summarizes pattern heterogeneity using the minimum subtree cover. There is no user tunable parameters for either method. Examples are included to illustrate how to use the methods on single-cell data for studying gene and pathway expression dynamics and pathway expression specificity.

This package provides Apache Spark style window aggregation for R dataframes and remote dbplyr tables via mutate in dplyr flavour.

This package implements inverse and augmented inverse probability weighted estimators for common treatment effect parameters at an interim analysis with time-lagged outcome that may not be available for all enrolled subjects. Produces estimators, standard errors, and information that can be used to compute stopping boundaries using software that assumes that the estimators/test statistics have independent increments. Tsiatis, A. A. and Davidian, M., (2022) <doi:10.1002/sim.9580> .