Likelihood based population viability analysis in the presence of observation error and missing data. The package can be used to fit, compare, predict, and forecast various growth model types using data cloning.

This package provides functions and data sets for reproducing selected results from the book "Quantitative Risk Management: Concepts, Techniques and Tools". Furthermore, new developments and auxiliary functions for Quantitative Risk Management practice.

This package creates a contextual menu that can be triggered with keyboard shortcuts or programmatically. This can replace traditional sidebars or navigation bars, thereby enhancing the user experience with lighter user interfaces.

Implementation of the SAM prior and generation of its operating characteristics for dynamically borrowing information from historical data. For details, please refer to Yang et al. (2023) <doi:10.1111/biom.13927>.

Generates a game of 2048 that can be played in the console. Supports grids of arbitrary sizes, undoing the last move, and resuming a game that was exited during the current session.

Converts pathways from WikiPathways GPML format or KEGG KGML format into igraph objects. Includes tools to find all cycles in the resulting graphs and determine which ones involve negative feedback (inhibition).

Conducts single coefficient tests and multiple-contrast hypothesis tests of meta-regression models using cluster wild bootstrapping, based on methods examined in Joshi, Pustejovsky, and Beretvas (2022) <DOI:10.1002/jrsm.1554>.

Selected Affymetrix and Illlumina SNP data for HapMap subjects. Data provided by the Center for Inherited Disease Research at Johns Hopkins University and the Broad Institute of MIT and Harvard University.

Implemented temporal PageRank analysis as defined by Rozenshtein and Gionis. Implemented multiplex PageRank as defined by Halu et al. Applied temporal and multiplex PageRank in gene regulatory network analysis.

Hidden Markov model to segment and predict regions of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH), and estimate cellular prevalence of clonal clusters in tumour whole genome sequencing data.

This package contains data which are used by functions of the abc package which implements several Approximate Bayesian Computation (ABC) algorithms for performing parameter estimation, model selection, and goodness-of-fit.

This package provides tools for the maximum likelihood estimation of the parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and Raftery, Appl.Statistics, 1989); it includes inference and basic methods.

This package is an R wrapper around the cubature C library for adaptive multivariate integration over hypercubes. This version provides both hcubature and pcubature routines in addition to a vector interface.

Namae (名前) is a parser for human names. It recognizes personal names of various cultural backgrounds and tries to split them into their component parts (e.g., given and family names, honorifics etc.).

This package provides a header-only C++ library is provided with support for dates, time zones, ISO weeks, Julian dates, and Islamic dates. date offers extensive date and time functionality for the C++11, C++14 and C++17 standards. A slightly modified version has been accepted (along with tz.h) as part of C++20. This package regroups all header files from the upstream repository so that other R packages can use them in their C++ code.

The basic algorithm to perform the folding test of unimodality. Given a dataset X (d dimensional, n samples), the test checks whether the distribution of the data are rather unimodal or rather multimodal. This package stems from the following research publication: Siffer Alban, Pierre-Alain Fouque, Alexandre Termier, and Christine Largouët. "Are your data gathered?" In Proceedings of the 24th ACM SIGKDD International Conference on Knowledge Discovery Data Mining, pp. 2210-2218. ACM, 2018. <doi:10.1145/3219819.3219994>.

The SPRITE algorithm creates possible distributions of discrete responses based on reported sample parameters, such as mean, standard deviation and range (Heathers et al., 2018, <doi:10.7287/peerj.preprints.26968v1>). This package implements it, drawing heavily on the code for Nick Brown's rSPRITE Shiny app <https://shiny.ieis.tue.nl/sprite/>. In addition, it supports the modeling of distributions based on multi-item (Likert-type) scales and the use of restrictions on the frequency of particular responses.

RETROFIT is a Bayesian non-negative matrix factorization framework to decompose cell type mixtures in ST data without using external single-cell expression references. RETROFIT outperforms existing reference-based methods in estimating cell type proportions and reconstructing gene expressions in simulations with varying spot size and sample heterogeneity, irrespective of the quality or availability of the single-cell reference. RETROFIT recapitulates known cell-type localization patterns in a Slide-seq dataset of mouse cerebellum without using any single-cell data.

Parsing R code is key to build tools such as linters and stylers. This package provides a binding to the Rust crate ast-grep so that one can parse and explore R code.

This package provides functions to compute pair-wise dissimilarities (distance matrices) and multiple-site dissimilarities, separating the turnover and nestedness-resultant components of taxonomic (incidence and abundance based), functional and phylogenetic beta diversity.

Tree- and rule-based models can be bagged (<doi:10.1007/BF00058655>) using this package and their predictions equations are stored in an efficient format to reduce the model objects size and speed.

The Codemeta Project defines a JSON-LD format for describing software metadata, as detailed at <https://codemeta.github.io>. This package provides core utilities to generate this metadata with a minimum of dependencies.

The cystiSim package provides an agent-based model for Taenia solium transmission and control. cystiSim was developed within the framework of CYSTINET, the European Network on taeniosis/cysticercosis, COST ACTION TD1302.

This package provides a drop-in replacement for dplyr', powered by DuckDB for performance. Offers convenient utilities for working with in-memory and larger-than-memory data while retaining full dplyr compatibility.