Uses a novel rank-based nonparametric approach to evaluate a surrogate marker in a small sample size setting. Details are described in Parast et al (2024) <doi:10.1093/biomtc/ujad035>, in Hughes A et al (2025) <doi:10.1002/sim.70241>, and in Hughes A et al (2026) <doi:10.48550/arXiv.2605.03819>. A tutorial for this package can be found at <https://www.laylaparast.com/surrogaterank> and a Shiny App implementing the package can be found at <https://parastlab.shinyapps.io/SurrogateRankApp/>.

Code for describing and manipulating scuba diving profiles (depth-time curves) and decompression models, for calculating the predictions of decompression models, for calculating maximum no-decompression time and decompression tables, and for performing mixed gas calculations.

This package provides functions for (1) soil water retention (SWC) and unsaturated hydraulic conductivity (Ku) (van Genuchten-Mualem (vGM or vG) [1, 2], Peters-Durner-Iden (PDI) [3, 4, 5], Brooks and Corey (bc) [8]), (2) fitting of parameter for SWC and/or Ku using Shuffled Complex Evolution (SCE) optimisation and (3) calculation of soil hydraulic properties (Ku and soil water contents) based on the simplified evaporation method (SEM) [6, 7]. Main references: [1] van Genuchten (1980) <doi:10.2136/sssaj1980.03615995004400050002x>, [2] Mualem (1976) <doi:10.1029/WR012i003p00513>, [3] Peters (2013) <doi:10.1002/wrcr.20548>, [4] Iden and Durner (2013) <doi:10.1002/2014WR015937>, [5] Peters (2014) <doi:10.1002/2014WR015937>, [6] Wind G. P. (1966), [7] Peters and Durner (2008) <doi:10.1016/j.jhydrol.2008.04.016> and [8] Brooks and Corey (1964).

This package provides a flexible framework for fitting generalized linear models (GLMs) with slab and shrinkage estimators. Methods include the Stein estimator (St), Diagonal Shrinkage (DSh), Simple Slab Regression (SR), Generalized Slab Regression (GSR), Ledoit-Wolf Linear Shrinkage (LW), Quadratic-Inverse Shrinkage (QIS), and Shrinkage (Sh), all integrated into the iteratively reweighted least squares (IRLS) algorithm. This approach enhances estimation accuracy, convergence, and robustness in the presence of multicollinearity. The best-fitting model is selected based on the Akaike Information Criterion (AIC). Methods are related to methods described in Marschner (2011) <doi:10.32614/RJ-2011-012>, Asimit et al. (2025) <https://openaccess.city.ac.uk/id/eprint/35005/>, Ledoit and Wolf (2004) <doi:10.1016/S0047-259X(03)00096-4>, and Ledoit and Wolf (2022) <doi:10.3150/20-BEJ1315>.

This package provides a fast implementation with additional experimental features for testing, monitoring and dating structural changes in (linear) regression models. strucchangeRcpp features tests/methods from the generalized fluctuation test framework as well as from the F test (Chow test) framework. This includes methods to fit, plot and test fluctuation processes (e.g. cumulative/moving sum, recursive/moving estimates) and F statistics, respectively. These methods are described in Zeileis et al. (2002) <doi:10.18637/jss.v007.i02>. Finally, the breakpoints in regression models with structural changes can be estimated together with confidence intervals, and their magnitude as well as the model fit can be evaluated using a variety of statistical measures.

Two versions of sample variance plots, Sv-plot1 and Sv-plot2, will be provided illustrating the squared deviations from sample variance. Besides indicating the contribution of squared deviations for the sample variability, these plots are capable of detecting characteristics of the distribution such as symmetry, skewness and outliers. A remarkable graphical method based on Sv-plot2 can determine the decision on testing hypotheses over one or two population means. In sum, Sv-plots will be appealing visualization tools. Complete description of this methodology can be found in the article, Wijesuriya (2020) <doi:10.1080/03610918.2020.1851716>.

Takes a list of character strings and forms an adjacency matrix for the times the specified characters appear together in the strings provided. For use in social network analysis and data wrangling. Simple package, comprised of three functions.

Specifying lavaan models manually can be time consuming when multiple similar models are required. The semFromKeys package streamlines the process of running lavaan models by generating model code from simple keys lists and running entire collections of models at once. The package was inspired by the process used in the code for Bainbridge, T. F., Ludeke, S. G., & Smillie, L. D. (2022) <doi:10.1037/pspp0000395>. The package also optionally checks that identical models have not been run on the same data, which saves time when code needs to be run again.

Apply the spectral residual algorithm to data, such as a time series, to detect anomalies. Anomaly scores can be used to determine outliers based upon a threshold or fed into more sophisticated prediction models. Methods are based upon "Time-Series Anomaly Detection Service at Microsoft", Ren, H., Xu, B., Wang, Y., et al., (2019) <doi:10.48550/arXiv.1906.03821>.

Bio-Layer Interferometry (BLI) is a technology to determine the binding kinetics between biomolecules. BLI signals are small and noisy when small molecules are investigated as ligands (analytes). We develop this package to process and analyze the BLI data acquired on Octet Red96 from Fortebio more accurately. Sun Q., Li X., et al (2020) <doi:10.1038/s41467-019-14238-3>. In this new version, we organize the BLI experiment data and analysis methods into a S4 class with self-explaining structure.

This package provides an S4 class for representing and interacting with sparse plus rank matrices. At the moment the implementation is quite spare, but the plan is eventually subclass Matrix objects.

High dimensional survival data analysis with Markov Chain Monte Carlo(MCMC). Currently supports frailty data analysis. Allows for Weibull and Exponential distribution. Includes function for interval censored data.

This package implements the Segment Profile Extraction via Pattern Analysis method for row-mean-centered multivariate data. Core capabilities include SVD-based row-isometric biplot construction, bias-corrected and accelerated, and percentile bootstrap confidence intervals for domain coordinates and per-person direction cosines, Procrustes alignment of bootstrap replicates across planes, parallel analysis for dimensionality selection, and segment profile reconstruction in planes defined by pairs of singular dimensions. A synthetic Woodcock-Johnson IV look-alike dataset is provided for examples and testing. The method is described in Kim and Grochowalski (2019) <doi:10.1007/s00357-018-9277-7>.

Perform spatial temporal analysis of moving polygons; a longstanding analysis problem in Geographic Information Systems. Facilitates directional analysis, distance analysis, and some other simple functionality for examining spatial-temporal patterns of moving polygons.

This package provides functions implementing Single Source of Error state space models for purposes of time series analysis and forecasting. The package includes ADAM (Svetunkov, 2023, <https://openforecast.org/adam/>), Exponential Smoothing (Hyndman et al., 2008, <doi:10.1007/978-3-540-71918-2>), SARIMA (Svetunkov & Boylan, 2019 <doi: 10.1080/00207543.2019.1600764>), Complex Exponential Smoothing (Svetunkov & Kourentzes, 2018, <doi:10.13140/RG.2.2.24986.29123>), Simple Moving Average (Svetunkov & Petropoulos, 2018 <doi:10.1080/00207543.2017.1380326>) and several simulation functions. It also allows dealing with intermittent demand based on the iETS framework (Svetunkov & Boylan, 2019, <doi:10.13140/RG.2.2.35897.06242>).

This package provides ggplot2 graphics for analysing time series data. It aims to fit into the tidyverse and grammar of graphics framework for handling temporal data.

Use R and SAS within reproducible multilingual quarto documents. Run SAS code blocks interactively, send data back and forth between SAS and R, and render SAS output within quarto documents. SAS connections are established through a combination of SASPy and reticulate'.

This package provides a widget for shiny apps to handle schedule expression input, using the cron-expression-input JavaScript component. Note that this does not edit the crontab file, it is just an input element for the schedules. See <https://github.com/DatalabFabriek/shinycroneditor/blob/main/inst/examples/shiny-app.R> for an example implementation.

Variable selection techniques are essential tools for model selection and estimation in high-dimensional statistical models. Through this publicly available package, we provide a unified environment to carry out variable selection using iterative sure independence screening (SIS) (Fan and Lv (2008)<doi:10.1111/j.1467-9868.2008.00674.x>) and all of its variants in generalized linear models (Fan and Song (2009)<doi:10.1214/10-AOS798>) and the Cox proportional hazards model (Fan, Feng and Wu (2010)<doi:10.1214/10-IMSCOLL606>).

It computes Relative survival, AER and SMR based on French death rates.

It helps in determination of sample size for estimation of population mean and proportion based upon the availability of prior information on coefficient of variation (CV) of the population under Simple Random Sampling (SRS) with or without replacement sampling design. If there is no prior information on the population CV, then a small preliminary sample of size is selected to estimate the population CV which is then used for determination of final sample size. If the final sample size is more than the preliminary sample size, then the preliminary sample is augmented by drawing additional units from the remaining population units so that the size of the augmented sample is equal to the final sample size. On the other hand, if the preliminary sample size is larger than the final sample size, then the preliminary sample is considered as the final sample.

This package provides functionalities for performing stability analysis of genotype by environment interaction (GEI) to identify superior and stable genotypes across diverse environments. It implements Eberhart and Russellâ s ANOVA method (1966)(<doi:10.2135/cropsci1966.0011183X000600010011x>), Finlay and Wilkinsonâ s Joint Linear Regression method (1963) (<doi:10.1071/AR9630742>), Wrickeâ s Ecovalence (1962, 1964), Shuklaâ s stability variance parameter (1972) (<doi:10.1038/hdy.1972.87>), Kangâ s simultaneous selection for high yield and stability (1991) (<doi:10.2134/agronj1991.00021962008300010037x>), Additive Main Effects and Multiplicative Interaction (AMMI) method and Genotype plus Genotypes by Environment (GGE) Interaction methods.

This package provides a template dashboard system with AI agent integrated. Comes with default themes that can be customized. Developers can upload modified templates on Github', and users can easily download templates with RStudio project wizard. The key features of the default template include light and dark theme switcher, resizing graphs, synchronizing inputs across sessions, new notification system, fancy progress bars, and card-like flip panels with back sides, as well as various of HTML tool widgets.

Data in multidimensional systems is obtained from operational systems and is transformed to adapt it to the new structure. Frequently, the operations to be performed aim to transform a flat table into a star schema. Transformations can be carried out using professional extract, transform and load tools or tools intended for data transformation for end users. With the tools mentioned, this transformation can be carried out, but it requires a lot of work. The main objective of this package is to define transformations that allow obtaining stars from flat tables easily. In addition, it includes basic data cleaning, dimension enrichment, incremental data refresh and query operations, adapted to this context.