The graphical approach is proposed as a general framework for clinical trial designs involving multiple hypotheses, where decisions are made only based on the observed marginal p-values. A reverse graphical approach starts from a set of singleton graphs, and gradually add vertices into graphs until rejection of a set of hypotheses is made. See Gou, J. (2020). Reverse graphical approaches for multiple test procedures. Technical Report.
Additional matrix functionality for R including: (1) wrappers for the base matrix function that allow matrices to be created from character strings and lists (the former is especially useful for creating block matrices), (2) better printing of large matrices via the generic "pretty" print function, and (3) a number of convenience functions for users more familiar with other scientific languages like Julia', Matlab'/'Octave', or Python'+'NumPy'.
R interface to CPLEX solvers for linear, quadratic, and (linear and quadratic) mixed integer programs. Support for quadratically constrained programming is available. See the file "INSTALL" for details on how to install the Rcplex package in Linux/Unix-like and Windows systems. Support for sparse matrices is provided by an S3-style class "simple_triplet_matrix" from package slam and by objects from the Matrix package class hierarchy.
This package provides a dataset with an uneven number of cases in each class is said to be unbalanced. Many models produce a subpar performance on unbalanced datasets.
Functions and examples are provided for transmission/disequilibrium tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999) "Transmission/disequilibrium tests for extended marker haplotypes".
This package provides functions for numerical analysis and linear algebra, numerical optimization, differential equations, plus some special functions. It uses Matlab function names where appropriate to simplify porting.
Look up the username and full name of the current user, the current user's email address and GitHub username, using various sources of system and configuration information.
This package is an extension to the testthat package that makes it easy to add graphical unit tests. It provides a Shiny application to manage the test cases.
This package provides functionality for creating Quantile-Quantile (QQ) and Probability-Probability (PP) plots with simultaneous testing bands to asses significance of sample deviation from a reference distribution.
Per-channel variance stabilization from a collection of flow cytometry samples by Bertlett test for homogeneity of variances. The approach is applicable to microarrays data as well.
The miaViz package implements functions to visualize TreeSummarizedExperiment objects especially in the context of microbiome analysis. Part of the mia family of R/Bioconductor packages.
Package performs summarization of replicates, filtering by frequency, several different options for imputing missing data, and a variety of options for transforming, batch correcting, and normalizing data.
The pRoloc package implements machine learning and visualisation methods for the analysis and interogation of quantitiative mass spectrometry data to reliably infer protein sub-cellular localisation.
traseR performs GWAS trait-associated SNP enrichment analyses in genomic intervals using different hypothesis testing approaches, also provides various functionalities to explore and visualize the results.
Create Tables for Reporting Clinical Trials. Calculates descriptive statistics and hypothesis tests, arranges the results in a table ready for reporting with LaTeX, HTML or Word.
This package contains functions to perform copula estimation by the non-parametric Bayesian method, Dirichlet-based Polya Tree. See Ning (2018) <doi:10.1080/00949655.2017.1421194>.
Fast functions for effective sample size, weighted multivariate mean, variance, and quantile computation, and weight diagnostic plot for generic importance sampling type or other probability weighted samples.
Package for Genetic Epidemiologic Methods Developed at MSKCC. It contains functions to calculate haplotype specific odds ratio and the power of two stage design for GWAS studies.
This package provides functions to compute generalized eigenvalues and eigenvectors, the generalized Schur decomposition and the generalized Singular Value Decomposition of a matrix pair, using Lapack routines.
This package provides methods to perform and analyse I-prior regression models. Estimation is done either via direct optimisation of the log-likelihood or an EM algorithm.
One-way and two-way analysis of variance for replicated point patterns, grouped by one or two classification factors, on the basis of the corresponding K-functions.
Interact with LaminDB'. LaminDB is an open-source data framework for biology. This package allows you to query and download data from LaminDB instances.
This package contains functions for performing Mokken scale analysis on test and questionnaire data. It includes an automated item selection algorithm, and various checks of model assumptions.