This is a core implementation of SAS procedures for linear models - GLM, REG, ANOVA, TTEST, FREQ, and UNIVARIATE. Some R packages provide Type II and Type III SS. However, the results of nested and complex designs are often different from those of SAS'. Different results do not necessarily mean incorrectness. However, many want the same results as SAS'. This package aims to achieve that. Reference: Littell RC, Stroup WW, Freund RJ (2002, ISBN:0-471-22174-0).

Simple tabulation should be dead simple. This package is an opinionated approach to easy tabulations while also providing exact numbers and allowing for re-usability. This is achieved by providing tabulations as data.frames with columns for values, optional variable names, frequency counts including and excluding NAs and percentages for counts including and excluding NAs. Also values are automatically sorted by in decreasing order of frequency counts to allow for fast skimming of the most important information.

This package implements the recursively detrended panel unit root tests proposed by Westerlund (2015) <doi:10.1016/j.jeconom.2014.09.013>. Two variants are provided: the basic t-REC test assuming iid errors, and the robust t-RREC test that accounts for serial correlation, cross-sectional dependence, and heteroskedasticity via defactoring and BIC-selected lag augmentation. Both tests have a standard normal null distribution requiring no mean or variance correction. The panel must be strongly balanced.

Random generation of survival data from a wide range of regression models, including accelerated failure time (AFT), proportional hazards (PH), proportional odds (PO), accelerated hazard (AH), Yang and Prentice (YP), and extended hazard (EH) models. The package rsurv also stands out by its ability to generate survival data from an unlimited number of baseline distributions provided that an implementation of the quantile function of the chosen baseline distribution is available in R. Another nice feature of the package rsurv lies in the fact that linear predictors are specified via a formula-based approach, facilitating the inclusion of categorical variables and interaction terms. The functions implemented in the package rsurv can also be employed to simulate survival data with more complex structures, such as survival data with different types of censoring mechanisms, survival data with cure fraction, survival data with random effects (frailties), multivariate survival data, and competing risks survival data. Details about the R package rsurv can be found in Demarqui (2024) <doi:10.48550/arXiv.2406.01750>.

Expression levels of mRNA molecules are regulated by different processes, comprising inhibition or activation by transcription factors and post-transcriptional degradation by microRNAs. birta (Bayesian Inference of Regulation of Transcriptional Activity) uses the regulatory networks of transcription factors and miRNAs together with mRNA and miRNA expression data to predict switches in regulatory activity between two conditions. A Bayesian network is used to model the regulatory structure and Markov-Chain-Monte-Carlo is applied to sample the activity states.

This package provides a high-level R interface to data files written using Unidata's netCDF library (version 4 or earlier), which are binary data files that are portable across platforms and include metadata information in addition to the data sets. Using this package, netCDF files can be opened and data sets read in easily. It is also easy to create new netCDF dimensions, variables, and files, in either version 3 or 4 format, and manipulate existing netCDF files.

RocksDB is a library that forms the core building block for a fast key-value server, especially suited for storing data on flash drives. It has a Log-Structured-Merge-Database (LSM) design with flexible tradeoffs between Write-Amplification-Factor (WAF), Read-Amplification-Factor (RAF) and Space-Amplification-Factor (SAF). It has multi-threaded compactions, making it specially suitable for storing multiple terabytes of data in a single database. RocksDB is partially based on LevelDB.

An R package that offers a workflow to predict condition-specific enhancers from ChIP-seq data. The prediction of regulatory units is done in four main steps: Step 1 - the normalization of the ChIP-seq counts. Step 2 - the prediction of active enhancers binwise on the whole genome. Step 3 - the condition-specific clustering of the putative active enhancers. Step 4 - the detection of possible target genes of the condition-specific clusters using RNA-seq counts.

An implementation of the model in Steorts (2015) <DOI:10.1214/15-BA965SI>, which performs Bayesian entity resolution for categorical and text data, for any distance function defined by the user. In addition, the precision and recall are in the package to allow one to compare to any other comparable method such as logistic regression, Bayesian additive regression trees (BART), or random forests. The experiments are reproducible and illustrated using a simple vignette. LICENSE: GPL-3 + file license.

Estimates the Concordance Correlation Coefficient to assess agreement. The scenarios considered are non-repeated measures, non-longitudinal repeated measures (replicates) and longitudinal repeated measures. It also includes the estimation of the one-way intraclass correlation coefficient also known as reliability index. The estimation approaches implemented are variance components and U-statistics approaches. Description of methods can be found in Fleiss (1986) <doi:10.1002/9781118032923> and Carrasco et al. (2013) <doi:10.1016/j.cmpb.2012.09.002>.

This package contains functions for the MCMC simulation of (multilevel) dyadic network models j2 (Zijlstra, 2017, <doi:10.1080/0022250X.2017.1387858>) and p2 (Van Duijn, Snijders & Zijlstra, 2004, <doi: 10.1046/j.0039-0402.2003.00258.x>), the multilevel p2 model (Zijlstra, Van Duijn & Snijders (2009) <doi: 10.1348/000711007X255336>), and the bidirectional (multilevel) counterpart of the the multilevel p2 model as described in Zijlstra, Van Duijn & Snijders (2009) <doi: 10.1348/000711007X255336>, the (multilevel) b2 model.

Diagnostic plots for optimisation, with a focus on projection pursuit. These show paths the optimiser takes in the high-dimensional space in multiple ways: by reducing the dimension using principal component analysis, and also using the tour to show the path on the high-dimensional space. Several botanical colour palettes are included, reflecting the name of the package. A paper describing the methodology can be found at <https://journal.r-project.org/articles/RJ-2021-105/index.html>.

Analysis of Fluorescence Recovery After Photobleaching (FRAP) experiments using nonlinear mixed-effects regression models and analysis of the results. FRApp is not limited to the analysis of FRAP experiments only. Any nonlinear mixed-effects models with an asymptotic exponential functional relationship to hierarchical data in various domains can be fitted. The analysis of data available in the package is presented in Di Credico, G., Pelucchi, S., Pauli, F. et al. (2025) <doi:10.1038/s41598-025-87154-w>.

This is a C++ mutual information (MI) library based on the k-nearest neighbor (KNN) algorithm. There are three functions provided for computing MI for continuous values, mixed continuous and discrete values, and conditional MI for continuous values. They are based on algorithms by A. Kraskov, et. al. (2004) <doi:10.1103/PhysRevE.69.066138>, BC Ross (2014)<doi:10.1371/journal.pone.0087357>, and A. Tsimpiris (2012) <doi:10.1016/j.eswa.2012.05.014>, respectively.

We implement a surrogate modeling algorithm to guide simulation-based sample size planning. The method is described in detail in our paper (Zimmer & Debelak (2023) <doi:10.1037/met0000611>). It supports multiple study design parameters and optimization with respect to a cost function. It can find optimal designs that correspond to a desired statistical power or that fulfill a cost constraint. We also provide a tutorial paper (Zimmer et al. (2023) <doi:10.3758/s13428-023-02269-0>).

Estimates the sample size needed to detect microbial contamination in a lot with a user-specified detection probability and user-specified analytical sensitivity. Various patterns of microbial contamination are accounted for: homogeneous (Poisson), heterogeneous (Poisson-Gamma) or localized(Zero-inflated Poisson). Ida Jongenburger et al. (2010) <doi:10.1016/j.foodcont.2012.02.004> "Impact of microbial distributions on food safety". Leroy Simon (1963) <doi:10.1017/S0515036100001975> "Casualty Actuarial Society - The Negative Binomial and Poisson Distributions Compared".

An n-gram is a sequence of n "words" taken, in order, from a body of text. This is a collection of utilities for creating, displaying, summarizing, and "babbling" n-grams. The tokenization and "babbling" are handled by very efficient C code, which can even be built as its own standalone library. The babbler is a simple Markov chain. The package also offers a vignette with complete example workflows and information about the utilities offered in the package.

This package provides native access to the Open Neural Network Exchange (ONNX) Runtime <https://onnxruntime.ai/>, which is a performant engine for running machine learning models that are saved to a standardized format. Rather than interfacing with ONNX via Python', as in the official onnx package, onnxr directly interfaces with the runtime's C++ API via cpp11'. Models saved to .onnx files can be loaded and run on various backends, including CPUs and Apple's CoreML library.

This package provides tools for penalised maximum likelihood estimation of hidden semi-Markov models (HSMMs) with flexible state dwell-time distributions. These include functions for model fitting, model checking and state-decoding. The package considers HSMMs for univariate time series with state-dependent gamma, normal, Poisson or Bernoulli distributions. For details, see Pohle, J., Adam, T. and Beumer, L.T. (2021): Flexible estimation of the state dwell-time distribution in hidden semi-Markov models. <arXiv:2101.09197>.

In causal mediation analysis with multiple causally ordered mediators, a set of path-specific effects are identified under standard ignorability assumptions. This package implements an imputation approach to estimating these effects along with a set of bias formulas for conducting sensitivity analysis (Zhou and Yamamoto <doi:10.31235/osf.io/2rx6p>). It contains two main functions: paths() for estimating path-specific effects and sens() for conducting sensitivity analysis. Estimation uncertainty is quantified using the nonparametric bootstrap.

Computes noncompartmental pharmacokinetic parameters for drug concentration profiles. For each profile, data imputations and adjustments are made as necessary and basic parameters are estimated. Supports single dose, multi-dose, and multi-subject data. Supports steady-state calculations and various routes of drug administration. See ?qpNCA and vignettes. Methodology follows Rowland and Tozer (2011, ISBN:978-0-683-07404-8), Gabrielsson and Weiner (1997, ISBN:978-91-9765-100-4), and Gibaldi and Perrier (1982, ISBN:978-0824710422).

Supports the calculation of meteorological characteristics in evapotranspiration research and reference crop evapotranspiration, and offers three models to simulate crop evapotranspiration and soil water balance in the field, including single crop coefficient and dual crop coefficient, as well as the Shuttleworth-Wallace model. These calculations main refer to Allen et al.(1998, ISBN:92-5-104219-5), Teh (2006, ISBN:1-58-112-998-X), and Liu et al.(2006) <doi:10.1016/j.agwat.2006.01.018>.

This package provides a system contains easy-to-use tools as a support for time series analysis courses. In particular, it incorporates a technique called Generalized Method of Wavelet Moments (GMWM) as well as its robust implementation for fast and robust parameter estimation of time series models which is described, for example, in Guerrier et al. (2013) <doi: 10.1080/01621459.2013.799920>. More details can also be found in the paper linked to via the URL below.

Holds functions developed by the University of Ottawa's SAiVE (Spatio-temporal Analysis of isotope Variations in the Environment) research group with the intention of facilitating the re-use of code, foster good code writing practices, and to allow others to benefit from the work done by the SAiVE group. Contributions are welcome via the GitHub repository <https://github.com/UO-SAiVE/SAiVE> by group members as well as non-members.