Computes likelihood ratio test (LRT) p-values for free parameters in a structural equation model. Currently supports models fitted by the lavaan package by Rosseel (2012) <doi:10.18637/jss.v048.i02>.

This package creates a data specification that describes the columns of a table (data.frame). Provides methods to read, write, and update the specification. Checks whether a table matches its specification. See specification.data.frame(),read.spec(), write.spec(), as.csv.spec(), respecify.character(), and %matches%.data.frame().

An input controller for R Shiny: a matrix with radio buttons, where only one option per row can be selected.

An easy to use implementation of routine structural missing data diagnostics with functions to visualize the proportions of missing observations, investigate missing data patterns and conduct various empirical missing data diagnostic tests. Reference: Weberpals J, Raman SR, Shaw PA, Lee H, Hammill BG, Toh S, Connolly JG, Dandreo KJ, Tian F, Liu W, Li J, Hernández-Muñoz JJ, Glynn RJ, Desai RJ. smdi: an R package to perform structural missing data investigations on partially observed confounders in real-world evidence studies. JAMIA Open. 2024 Jan 31;7(1):ooae008. <doi:10.1093/jamiaopen/ooae008>.

This package provides a canonical correlation based framework ('SmCCNet') designed for the construction of phenotype-specific multi-omics networks. This framework adeptly integrates single or multiple omics data types along with a quantitative or binary phenotype of interest. It offers a streamlined setup process that can be tailored manually or configured automatically, ensuring a flexible and user-friendly experience. Methods are described in Shi et al. (2019) "Unsupervised discovery of phenotype-specific multi-omics networks" <doi:10.1093/bioinformatics/btz226>.

Build a project framework for users with access to only the most basic of automation tools.

This package provides a function that behaves nearly as base::source() but implements a caching mechanism on disk, project based. It allows to quasi source() R scripts that gather data but can fail or consume to much time to respond even if nothing new is expected. It comes with tools to check and execute on demand or when cache is invalid the script.

An implementation of image processing effects that convert a photo into a line drawing image. For details, please refer to Tsuda, H. (2020). sketcher: An R package for converting a photo into a sketch style image. <doi:10.31234/osf.io/svmw5>.

This package provides functions to retrieve the location of R scripts loaded through the source() function or run from the command line using the Rscript command. This functionality is analogous to the Bash shell's $BASH_SOURCE[0]. Users can first set the project root's path relative to the script path and then all subsequent paths relative to the root. This system ensures that all paths lead to the same location regardless of where any script is executed/loaded from without resorting to the use of setwd() at the top of the scripts.

Data sets and code blocks for the book Statistical Analysis of Network Data with R, 2nd Edition'.

This package provides a way to call the functions in SUNDIALS C ODE solving library (<https://computing.llnl.gov/projects/sundials>). Currently the serial version of ODE solver, CVODE', sensitivity calculator CVODES and differential algebraic solver IDA from the SUNDIALS library are implemented. The package requires ODE to be written as an R or Rcpp function and does not require the SUNDIALS library to be installed on the local machine.

Tidy snapshot of every episode of the public-television travel series Rick Steves Europe (2000-2025), enriched with IMDB ratings, geocoded destinations, ISO country codes, episode thumbnails, and descriptive summaries. Designed as a companion dataset for introductory data analysis and visualization in the spirit of the moderndive textbook: every row is an episode, every column is a candidate for a plot or a join. Compiled from public sources for teaching purposes; not an official or verified Rick Steves Europe dataset, and shared with the permission of the Rick Steves Europe team.

Handles both vector and matrices, using a flexible S4 class for automatic differentiation. The method used is forward automatic differentiation. Many functions and methods have been defined, so that in most cases, functions written without automatic differentiation in mind can be used without change.

Performance of functional kriging, cokriging, optimal sampling and simulation for spatial prediction of functional data. The framework of spatial prediction, optimal sampling and simulation are extended from scalar to functional data. SpatFD is based on the Karhunen-Loève expansion that allows to represent the observed functions in terms of its empirical functional principal components. Based on this approach, the functional auto-covariances and cross-covariances required for spatial functional predictions and optimal sampling, are completely determined by the sum of the spatial auto-covariances and cross-covariances of the respective score components. The package provides new classes of data and functions for modeling spatial dependence structure among curves. The spatial prediction of curves at unsampled locations can be carried out using two types of predictors, and both of them report, the respective variances of the prediction error. In addition, there is a function for the determination of spatial locations sampling configuration that ensures minimum variance of spatial functional prediction. There are also two functions for plotting predicted curves at each location and mapping the surface at each time point, respectively. References Bohorquez, M., Giraldo, R., and Mateu, J. (2016) <doi:10.1007/s10260-015-0340-9>, Bohorquez, M., Giraldo, R., and Mateu, J. (2016) <doi:10.1007/s00477-016-1266-y>, Bohorquez M., Giraldo R. and Mateu J. (2021) <doi:10.1002/9781119387916>.

The sparseMatEst package provides functions for estimating sparse covariance and precision matrices with error control. A false positive rate is fixed corresponding to the probability of falsely including a matrix entry in the support of the estimator. It uses the binary search method outlined in Kashlak and Kong (2019) <arXiv:1705.02679> and in Kashlak (2019) <arXiv:1903.10988>.

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.

This package provides a set of functions used in teaching STATS 201/208 Data Analysis at the University of Auckland. The functions are designed to make parts of R more accessible to a large undergraduate population who are mostly not statistics majors.

Testing the mediation effect of multiple SNPs on an outcome through a mediator.

An interactive framework for simulating blockchain protocols using a hybrid R-Shiny and Python architecture. The package provides tools to visualize peer-to-peer network maps, manage supply chain logistics on-chain, and execute cross-border settlements via smart contract logic. It leverages the reticulate package to perform standardized cryptographic operations, including SHA-256 hashing, Merkle Tree construction, and ECDSA (Elliptic Curve Digital Signature Algorithm) key generation. This tool is designed for pedagogical demonstration and rapid prototyping of distributed ledger requirements.

To automated functional annotation of genetic variants and linked proxies. Linked SNPs in moderate to high linkage disequilibrium (e.g. r2>0.50) with the corresponding index SNPs will be selected for further analysis.

Computes and integrates surface energy balance components of evapotranspiration (ET), sensible heat (H), soil heat flux (G) and net radiation (Rn) into the Food and Agriculture Organization (FAO) Irrigation and Drainage Paper 56 (FAO-56) water balance model. The package can perform single crop coefficient (Kc), dual Kc and the integration of thermal-based evaporative fractions in a water balance model. The surface energy balance models include Two-Source Surface Energy Balance (TSEB) models, namely the Priestley-Taylor TSEB (TSEB-PT), the Penman-Monteith TSEB (TSEB-PM) and TSEB-Parallel, as well as One-Source Surface Energy Balance (OSEB) models, namely the Surface Energy Balance Algorithm for Land (SEBAL), Mapping Evapotranspiration at high Resolution with Internalized Calibration (METRIC), Surface Energy Balance Index (SEBI), Simplified Surface Energy Balance (SSEB) and Surface Energy Balance System (SEBS). Methods are described in Allen et al. (2007) <doi:10.1061/(ASCE)0733-9437(2007)133:4(380)> and Bastiaanssen et al. (1998) <doi:10.1016/S0022-1694(98)00253-4>.

Full text, in data frames containing one row per verse, of the Standard Works of The Church of Jesus Christ of Latter-day Saints (LDS). These are the Old Testament, (KJV), the New Testament (KJV), the Book of Mormon, the Doctrine and Covenants, and the Pearl of Great Price.

Transcribe audio files using the Speechmatics speech-to-text API <https://www.speechmatics.com/>. Supports custom vocabulary, speaker diarization, punctuation control, and audio filtering.

Analysis of field trial experiments by modelling spatial trends using two-dimensional Penalised spline (P-spline) models.