Given a set of data points, a clustering is defined as a disjoint partition where each pair of sets in a partition has no overlapping elements. This package provides 25 methods that play a role somewhat similar to distance or metric that measures similarity of two clusterings - or partitions. For a more detailed description, see Meila, M. (2005) <doi:10.1145/1102351.1102424>.

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 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 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 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>.

Build complex HTML or LaTeX tables using kable() from knitr and the piping syntax from magrittr. The function kable() is a light weight table generator coming from knitr. This package simplifies the way to manipulate the HTML or LaTeX codes generated by kable() and allows users to construct complex tables and customize styles using a readable syntax.

This package provides exploratory data analysis methods to summarize, visualize and describe datasets. The main principal component methods are available, those with the largest potential in terms of applications: principal component analysis (PCA) when variables are quantitative, correspondence analysis (CA) and multiple correspondence analysis (MCA) when variables are categorical, Multiple Factor Analysis when variables are structured in groups, etc. and hierarchical cluster analysis.

Rxvt-unicode (urxvt) is a colour vt102 terminal emulator intended as an xterm replacement for users who do not require features such as Tektronix 4014 emulation and toolkit-style configurability. It supports unicode, XFT and may be extended with Perl plugins. It also comes with a client/daemon pair that lets you open any number of terminal windows from within a single process.

Ranked set sampling (RSS) is introduced as an advanced method for data collection which is substantial for the statistical and methodological analysis in scientific studies by McIntyre (1952) (reprinted in 2005) <doi:10.1198/000313005X54180>. This package introduces the first package that implements the RSS and its modified versions for sampling. With RSSampling', the researchers can sample with basic RSS and the modified versions, namely, Median RSS, Extreme RSS, Percentile RSS, Balanced groups RSS, Double RSS, L-RSS, Truncation-based RSS, Robust extreme RSS. The RSSampling also allows imperfect ranking using an auxiliary variable (concomitant) which is widely used in the real life applications. Applicants can also use this package for parametric and nonparametric inference such as mean, median and variance estimation, regression analysis and some distribution-free tests where the the samples are obtained via basic RSS.

Implementation of a Metropolis-within-Gibbs MCMC algorithm to flexibly estimate the spectral density of a stationary time series. The algorithm updates a nonparametric B-spline prior using the Whittle likelihood to produce pseudo-posterior samples and is based on the work presented in Edwards, M.C., Meyer, R. and Christensen, N., Statistics and Computing (2018). <doi.org/10.1007/s11222-017-9796-9>.

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 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.

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'.

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.

granulator is an R package for the cell type deconvolution of heterogeneous tissues based on bulk RNA-seq data or single cell RNA-seq expression profiles. The package provides a unified testing interface to rapidly run and benchmark multiple state-of-the-art deconvolution methods. Data for the deconvolution of peripheral blood mononuclear cells (PBMCs) into individual immune cell types is provided as well.

Many complex plots are actually composite plots, such as oncoplot', funkyheatmap', upsetplot', etc. We can produce subplots using ggplot2 and combine them to create composite plots using aplot'. In this way, it is easy to customize these complex plots, by adding, deleting or modifying subplots in the final plot. This package provides a set of utilities to help users to create subplots and complex plots.

Generates different posterior distributions of adjusted odds ratio under different priors of sensitivity and specificity, and plots the models for comparison. It also provides estimations for the specifications of the models using diagnostics of exposure status with a non-linear mixed effects model. It implements the methods that are first proposed in <doi:10.1016/j.annepidem.2006.04.001> and <doi:10.1177/0272989X09353452>.

Predicts anticancer peptides using random forests trained on the n-gram encoded peptides. The implemented algorithm can be accessed from both the command line and shiny-based GUI. The CancerGram model is too large for CRAN and it has to be downloaded separately from the repository: <https://github.com/BioGenies/CancerGramModel>. For more information see: Burdukiewicz et al. (2020) <doi:10.3390/pharmaceutics12111045>.

Functionality for analyzing dose-volume histograms (DVH) in radiation oncology: Read DVH text files, calculate DVH metrics as well as generalized equivalent uniform dose (gEUD), biologically effective dose (BED), equivalent dose in 2 Gy fractions (EQD2), normal tissue complication probability (NTCP), and tumor control probability (TCP). Show DVH diagrams, check and visualize quality assurance constraints for the DVH. Includes web-based graphical user interface.