Aggregates a set of trees with the same leaves to create a consensus tree. The trees are typically obtained via hierarchical clustering, hence the hclust format is used to encode both the aggregated trees and the final consensus tree. The method is exact and proven to be O(nqlog(n)), n being the individuals and q being the number of trees to aggregate.

The second version (0.2.0) contains implementation for exact matching which is an alternative to propensity score matching (see Glimm & Yau (2025)). The initial version (0.1.2) contains a collection of easy-to-implement tools for checking whether a MAIC can be conducted, as well as an alternative way of calculating weights (see Glimm & Yau (2021) <doi:10.1002/pst.2210>.).

Conduct a noncompartmental analysis with industrial strength. Some features are 1) Use of CDISC SDTM terms 2) Automatic or manual slope selection 3) Supporting both linear-up linear-down and linear-up log-down method 4) Interval(partial) AUCs with linear or log interpolation method * Reference: Gabrielsson J, Weiner D. Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and Applications. 5th ed. 2016. (ISBN:9198299107).

This package implements ordered beta regression models, which are for modeling continuous variables with upper and lower bounds, such as survey sliders, dose-response relationships and indexes. For more information, see Kubinec (2023) <doi:10.31235/osf.io/2sx6y>. The package is a front-end to the R package brms', which facilitates a range of regression specifications, including hierarchical, dynamic and multivariate modeling.

This package provides functions to make board game graphics with the ggplot2', grid', rayrender', rayvertex', and rgl packages. Specializes in game diagrams, animations, and "Print & Play" layouts for the piecepack <https://www.ludism.org/ppwiki> but can make graphics for other board game systems. Includes configurations for several public domain game systems such as checkers, (double-18) dominoes, go, piecepack', playing cards, etc.

This package implements statistical methods for estimating disease penetrance in family-based studies. Penetrance refers to the probability of disease§ manifestation in individuals carrying specific genetic variants. The package provides tools for age-specific penetrance estimation, handling missing data, and accounting for ascertainment bias in family studies. Cite as: Kubista, N., Braun, D. & Parmigiani, G. (2024) <doi:10.48550/arXiv.2411.18816>.

This package creates superpixels based on input spatial data. This package works on spatial data with one variable (e.g., continuous raster), many variables (e.g., RGB rasters), and spatial patterns (e.g., areas in categorical rasters). It is based on the SLIC algorithm (Achanta et al. (2012) <doi:10.1109/TPAMI.2012.120>), and readapts it to work with arbitrary dissimilarity measures.

Calculate Kernel Density Estimation (KDE) for spatial data. The algorithm is inspired by the tool Heatmap from QGIS'. The method is described by: Hart, T., Zandbergen, P. (2014) <doi:10.1108/PIJPSM-04-2013-0039>, Nelson, T. A., Boots, B. (2008) <doi:10.1111/j.0906-7590.2008.05548.x>, Chainey, S., Tompson, L., Uhlig, S.(2008) <doi:10.1057/palgrave.sj.8350066>.

Estimates split-half reliabilities for scoring algorithms of cognitive tasks and questionnaires. The splithalfr supports researcher-provided scoring algorithms, with six vignettes illustrating how on included datasets. The package provides four splitting methods (first-second, odd-even, permutated, Monte Carlo), the option to stratify splits by task design, a number of reliability coefficients, the option to sub-sample data, and bootstrapped confidence intervals.

This package provides a set of low-level utilities to retrieve data from the UCSC Genome Browser. Most functions in the package access the data via the UCSC REST API but some of them query the UCSC MySQL server directly. Note that the primary purpose of the package is to support higher-level functionalities implemented in downstream packages like GenomeInfoDb or txdbmaker.

This package provides supporting annotation and test data for SeSAMe package. This includes chip tango addresses, mapping information, performance annotation, and trained predictor for Infinium array data. This package provides user access to essential annotation data for working with many generations of the Infinium DNA methylation array. It currently supports human array (HM27, HM450, EPIC), mouse array (MM285) and the HorvathMethylChip40 (Mammal40) array.

This package provides tools for clustering and enhancing the resolution of spatial gene expression experiments. BayesSpace clusters a low-dimensional representation of the gene expression matrix, incorporating a spatial prior to encourage neighboring spots to cluster together. The method can enhance the resolution of the low-dimensional representation into "sub-spots", for which features such as gene expression or cell type composition can be imputed.

This package provides efficient routines for manipulation of date-time objects while accounting for time-zones and daylight saving times. The package includes utilities for updating of date-time components (year, month, day etc.), modification of time-zones, rounding of date-times, period addition and subtraction etc. Parts of the CCTZ source code, released under the Apache 2.0 License, are included in this package.

This package provides tools used by organizational researchers for the analysis of multilevel data. It includes four broad sets of tools.

1. functions for estimating within-group agreement and reliability indices.

2. functions for manipulating multilevel and longitudinal (panel) data.

3. simulations for estimating power and generating multilevel data.

4. miscellaneous functions for estimating reliability and performing simple calculations and data transformations.

This package provides a collection of functions to compute frequently used metrics for nutrition trials in aquaculture. Implementations include metrics to calculate growth, feed conversion, nutrient use efficiency, and feed digestibility. The package supports reproducible workflows for summarising experimental results and reduces manual calculation errors. For additional information see Machado e Silva, Karthikeyan and Tellbüscher (2025) <doi:10.13140/RG.2.2.27322.04808>.

Fits Cox model via stochastic gradient descent. This implementation avoids computational instability of the standard Cox Model when dealing large datasets. Furthermore, it scales up with large datasets that do not fit the memory. It also handles large sparse datasets using proximal stochastic gradient descent algorithm. For more details about the method, please see Aliasghar Tarkhan and Noah Simon (2020) <arXiv:2003.00116v2>.

This package provides a set of algorithms based on Quinn et al. (1991) <doi:10.1002/hyp.3360050106> for processing river network and digital elevation data to build implementations of Dynamic TOPMODEL, a semi-distributed hydrological model proposed in Beven and Freer (2001) <doi:10.1002/hyp.252>. The dynatop package implements simulation code for Dynamic TOPMODEL based on the output of dynatopGIS'.

This package provides a systematic biology tool was developed to repurpose drugs via a drug-drug functional similarity network. DrugSim2DR first predict drug-drug functional similarity in the context of specific disease, and then using the similarity constructed a weighted drug similarity network. Finally, it used a network propagation algorithm on the network to identify drugs with significant target abnormalities as candidate drugs.

Computes unidimensional and multidimensional Reciprocity and Inaccuracy indices. These indices are applicable to common heterostylous populations and to any other type of stylar dimorphic and trimorphic populations, such as in enantiostylous and three-dimensional heterostylous plants. Simón-Porcar, V., A. J. Muñoz-Pajares, J. Arroyo, and S. D. Johnson. (in press) "FlowerMate: multidimensional reciprocity and inaccuracy indices for style-polymorphic plant populations.".

This package performs a permutation test on the difference between two location parameters, a permutation correlation test, a permutation F-test, the Siegel-Tukey test, a ratio mean deviance test. Also performs some graphing techniques, such as for confidence intervals, vector addition, and Fourier analysis; and includes functions related to the Laplace (double exponential) and triangular distributions. Performs power calculations for the binomial test.

This package provides functionality for performing Nearest Centroid (NC) Sampling. The NC sampling procedure was developed for forestry applications and selects plots for ground measurement so as to maximize the efficiency of imputation estimates. It uses multiple auxiliary variables and multivariate clustering to search for an optimal sample. Further details are given in Melville G. & Stone C. (2016) <doi:10.1080/00049158.2016.1218265>.

This package provides a complete data set of historic GB trig points in British National Grid (OSGB36) coordinate reference system. Trig points (aka triangulation stations) are fixed survey points used to improve the accuracy of map making in Great Britain during the 20th Century. Trig points are typically located on hilltops so still serve as a useful navigational aid for walkers and hikers today.

The package detects extended diffuse and compact blemishes on microarray chips. Harshlight marks the areas in a collection of chips (affybatch objects). A corrected AffyBatch object will result. The package replaces the defected areas with N/As or the median of the values of the same probe. The new version handles the substitute value as a whole matrix to solve the memory problem.

This package was derived from Rsymphony. The package provides an R interface to SYMPHONY, a linear programming solver written in C++. The main difference between this package and Rsymphony is that it includes the solver source code, while Rsymphony expects to find header and library files on the users' system. Thus the intention of lpsymphony is to provide an easy to install interface to SYMPHONY.