This package implements a semiparametric estimator for the odds ratio model with censored, time-lagged, ordered categorical outcome in a randomized clinical trial that incorporates baseline and time-dependent information. Tsiatis AA, Davidian M, Holloway ST (2023) <doi:10.1111/biom.13603>.

This package provides a versatile range of functions, including exploratory data analysis, time-series analysis, organizational network analysis, and data validation, whilst at the same time implements a set of best practices in analyzing and visualizing data specific to Microsoft Viva Insights'.

This package performs two-sample comparisons using the restricted mean survival time (RMST) when survival curves end at different time points between groups. This package implements a sensitivity approach that allows the threshold timepoint tau to be specified after the longest survival time in the shorter survival group. Two kinds of between-group contrast estimators (the difference in RMST and the ratio of RMST) are computed: Uno et al(2014)<doi:10.1200/JCO.2014.55.2208>, Uno et al(2022)<https://CRAN.R-project.org/package=survRM2>, Ueno and Morita(2023)<doi:10.1007/s43441-022-00484-z>.

RegLog system provides a set of shiny modules to handle register procedure for your users, alongside with login, edit credentials and password reset functionality. It provides support for popular SQL databases and optionally googlesheet-based database for easy setup. For email sending it provides support for emayili and gmailr backends. Architecture makes customizing usability pretty straightforward. The authentication system created with shiny.reglog is designed to be optional: user don't need to be logged-in to access your application, but when logged-in the user data can be used to read from and write to relational databases.

This package lets you fit generalized linear mixed models for a single grouping factor under maximum likelihood approximating the integrals over the random effects with an adaptive Gaussian quadrature rule; Jose C. Pinheiro and Douglas M. Bates (1995) <doi:10.1080/10618600.1995.10474663>.

The ChromHeatMap package can be used to plot genome-wide data (e.g. expression, CGH, SNP) along each strand of a given chromosome as a heat map. The generated heat map can be used to interactively identify probes and genes of interest.

Frequentist statistical inference for cluster randomised trials with multiple outcomes that controls the family-wise error rate and provides nominal coverage of confidence sets. A full description of the methods can be found in Watson et al. (2023) <doi:10.1002/sim.9831>.

This package contains functions that check for formatting of the Subject Phenotype data set and data dictionary as specified by the National Center for Biotechnology Information (NCBI) Database of Genotypes and Phenotypes (dbGaP) <https://www.ncbi.nlm.nih.gov/gap/docs/submissionguide/>.

This package provides a fast C++ implementation for computing various graph kernels including (1) simple kernels between vertex and/or edge label histograms, (2) graphlet kernels, (3) random walk kernels (popular baselines), and (4) the Weisfeiler-Lehman graph kernel (state-of-the-art).

This package provides functions to justify alpha levels for statistical hypothesis tests by avoiding Lindley's paradox, or by minimizing or balancing error rates. For more information about the package please read the following: Maier & Lakens (2021) <doi:10.31234/osf.io/ts4r6>).

Efficient way to design and conduct psychological experiments for testing the performance of large language models. It simplifies the process of setting up experiments and data collection via language modelsâ API, facilitating a smooth workflow for researchers in the field of machine behaviour.

This package provides convenience functions and pre-programmed Stan models related to the paired comparison factor model. Its purpose is to make fitting paired comparison data using Stan easy. This package is described in Pritikin (2020) <doi:10.1016/j.heliyon.2020.e04821>.

Free UK geocoding using data from Office for National Statistics. It is using several functions to get information about post codes, outward codes, reverse geocoding, nearest post codes/outward codes, validation, or randomly generate a post code. API wrapper around <https://postcodes.io>.

Providing functions to diagnose and make inferences from various linear models, such as those obtained from aov', lm', glm', gls', lme', lmer', glmmTMB and semireg'. Inferences include predicted means and standard errors, contrasts, multiple comparisons, permutation tests, adjusted R-square and graphs.

Transforms or simulates data with a target empirical covariance matrix supplied by the user. The method to obtain the data with the target empirical covariance matrix is described in Section 5.1 of Christidis, Van Aelst and Zamar (2019) <arXiv:1812.05678>.

This package provides delayed computation of a matrix of scaled and centered values. The result is equivalent to using the scale function but avoids explicit realization of a dense matrix during block processing. This permits greater efficiency in common operations, most notably matrix multiplication.

mlr3learners extends mlr3 and mlr3proba with interfaces to essential machine learning packages on CRAN. This includes, but is not limited to: (penalized) linear and logistic regression, linear and quadratic discriminant analysis, k-nearest neighbors, naive Bayes, support vector machines, and gradient boosting.

This package defines S4 classes for single-cell genomic data and associated information, such as dimensionality reduction embeddings, nearest-neighbor graphs, and spatially-resolved coordinates. It provides data access methods and R-native hooks to ensure the Seurat object is familiar to other R users.

GSALightning provides a fast implementation of permutation-based gene set analysis for two-sample problem. This package is particularly useful when testing simultaneously a large number of gene sets, or when a large number of permutations is necessary for more accurate p-values estimation.

This package provides a set of tools built around updateObject() to work with old serialized S4 instances. The package is primarily useful to package maintainers who want to update the serialized S4 instances included in their package. This is still work-in-progress.

The COVID Symptom Study is a non-commercial project that uses a free mobile app to facilitate real-time data collection of symptoms, exposures, and risk factors related to COVID19. The package allows easy access to summary statistics data from COVID Symptom Study Sweden.

Helper functions for descriptive tasks such as making print-friendly bivariate tables, sample size flow counts, and visualizing sample distributions. Also contains R approximations of some common SAS and Stata functions such as PROC MEANS from SAS and ladder', gladder', and pwcorr from Stata'.

Flexible implementation of a structural change point detection algorithm for multivariate time series. It authorizes inclusion of trends, exogenous variables, and break test on the intercept or on the full vector autoregression system. Bai, Lumsdaine, and Stock (1998) <doi:10.1111/1467-937X.00051>.

This package provides a suite of tools to allow you to download all publicly available parasite rate survey points, mosquito occurrence points and raster surfaces from the Malaria Atlas Project <https://malariaatlas.org/> servers as well as utility functions for plotting the downloaded data.