This package provides some code to run simulations of state-space models, and then use these in the Approximate Bayesian Computation Sequential Monte Carlo (ABC-SMC) algorithm of Toni et al. (2009) <doi:10.1098/rsif.2008.0172> and a bootstrap particle filter based particle Markov chain Monte Carlo (PMCMC) algorithm (Andrieu et al., 2010 <doi:10.1111/j.1467-9868.2009.00736.x>). Also provides functions to plot and summarise the outputs.

The base tools union() intersect(), etc., follow the algebraic definition that each element of a set must be unique. Since it's often helpful to compare all elements of two vectors, this toolset treats every element as unique for counting purposes. For ease of use, all functions in vecsets have an argument multiple which, when set to FALSE, reverts them to the base::sets (alias for all the items) tools functionality.

An R interface for processing concentration-response datasets using Curvep, a response noise filtering algorithm. The algorithm was described in the publications (Sedykh A et al. (2011) <doi:10.1289/ehp.1002476> and Sedykh A (2016) <doi:10.1007/978-1-4939-6346-1_14>). Other parametric fitting approaches (e.g., Hill equation) are also adopted for ease of comparison. 3-parameter Hill equation from tcpl package (Filer D et al., <doi:10.1093/bioinformatics/btw680>) and 4-parameter Hill equation from Curve Class2 approach (Wang Y et al., <doi:10.2174/1875397301004010057>) are available. Also, methods for calculating the confidence interval around the activity metrics are also provided. The methods are based on the bootstrap approach to simulate the datasets (Hsieh J-H et al. <doi:10.1093/toxsci/kfy258>). The simulated datasets can be used to derive the baseline noise threshold in an assay endpoint. This threshold is critical in the toxicological studies to derive the point-of-departure (POD).

This package provides alternative statistical methods for meta-analysis, including:

1. bivariate generalized linear mixed models for synthesizing odds ratios, relative risks, and risk differences

2. heterogeneity tests and measures that are robust to outliers;

3. measures, tests, and visualization tools for publication bias or small-study effects;

4. meta-analysis of diagnostic tests for synthesizing sensitivities, specificities, etc.;

5. meta-analysis methods for synthesizing proportions;

6. models for multivariate meta-analysis.

The BioPlex package implements access to the BioPlex protein-protein interaction networks and related resources from within R. Besides protein-protein interaction networks for HEK293 and HCT116 cells, this includes access to CORUM protein complex data, and transcriptome and proteome data for the two cell lines. Functionality focuses on importing the various data resources and storing them in dedicated Bioconductor data structures, as a foundation for integrative downstream analysis of the data.

This package implements topological gene set analysis using a two-step empirical approach. It exploits graph decomposition theory to create a junction tree and reconstruct the most relevant signal path. In the first step clipper selects significant pathways according to statistical tests on the means and the concentration matrices of the graphs derived from pathway topologies. Then, it "clips" the whole pathway identifying the signal paths having the greatest association with a specific phenotype.

Statial is a suite of functions for identifying changes in cell state. The functionality provided by Statial provides robust quantification of cell type localisation which are invariant to changes in tissue structure. In addition to this Statial uncovers changes in marker expression associated with varying levels of localisation. These features can be used to explore how the structure and function of different cell types may be altered by the agents they are surrounded with.

Spaniel includes a series of tools to aid the quality control and analysis of Spatial Transcriptomics data. Spaniel can import data from either the original Spatial Transcriptomics system or 10X Visium technology. The package contains functions to create a SingleCellExperiment Seurat object and provides a method of loading a histologial image into R. The spanielPlot function allows visualisation of metrics contained within the S4 object overlaid onto the image of the tissue.

The number of bird or bat fatalities from collisions with buildings, towers or wind energy turbines can be estimated based on carcass searches and experimentally assessed carcass persistence times and searcher efficiency. Functions for estimating the probability that a bird or bat that died is found by a searcher are provided. Further functions calculate the posterior distribution of the number of fatalities based on the number of carcasses found and the estimated detection probability.

This package provides a collection of functions to calculate Composite Indicators methods, focusing, in particular, on the normalisation and weighting-aggregation steps, as described in OECD Handbook on constructing composite indicators: methodology and user guide, 2008, Vidoli and Fusco and Mazziotta <doi:10.1007/s11205-014-0710-y>, Mazziotta and Pareto (2016) <doi:10.1007/s11205-015-0998-2>, Van Puyenbroeck and Rogge <doi:10.1016/j.ejor.2016.07.038> and other authors.

This package provides automated methods for downloading, recoding, and merging selected years of the Current Population Survey's Voting and Registration Supplement, a large N national survey about registration, voting, and non-voting in United States federal elections. Provides documentation for appropriate use of sample weights to generate statistical estimates, drawing from Hur & Achen (2013) <doi:10.1093/poq/nft042> and McDonald (2018) <http://www.electproject.org/home/voter-turnout/voter-turnout-data>.

Orders a data-set consisting of an ensemble of probability density functions on the same x-grid. Visualizes a box-plot of these functions based on the notion of distance determined by the user. Reports outliers based on the distance chosen and the scaling factor for an interquartile range rule. For further details, see: Alexander C. Murph et al. (2023). "Visualization and Outlier Detection for Probability Density Function Ensembles." <https://sirmurphalot.github.io/publications>.

This package provides wrap functions to export and import graphics and data frames in R to microsoft office. And This package also provide write out figures with lots of different formats. Since people may work on the platform without GUI support, the package also provide function to easily write out figures to lots of different type of formats. Now this package provide function to extract colors from all types of figures and pdf files.

Execute Latent Class Analysis (LCA) and Latent Class Regression (LCR) by using Generalized Structured Component Analysis (GSCA). This is explained in Ryoo, Park, and Kim (2019) <doi:10.1007/s41237-019-00084-6>. It estimates the parameters of latent class prevalence and item response probability in LCA with a single line comment. It also provides graphs of item response probabilities. In addition, the package enables to estimate the relationship between the prevalence and covariates.

Automated model selection and model-averaging. Provides a wrapper for glm and other functions, automatically generating all possible models (under constraints set by the user) with the specified response and explanatory variables, and finding the best models in terms of some Information Criterion (AIC, AICc or BIC). Can handle very large numbers of candidate models. Features a Genetic Algorithm to find the best models when an exhaustive screening of the candidates is not feasible.

Cellular cooperation compromises the established method of calculating clonogenic activity from limiting dilution assay (LDA) data. This tool provides functions that enable robust analysis in presence or absence of cellular cooperation. The implemented method incorporates the same cooperativity module to model the non-linearity associated with cellular cooperation as known from the colony formation assay (Brix et al. (2021) <doi:10.1038/s41596-021-00615-0>: "Analysis of clonogenic growth in vitro." Nature protocols).

Interface to the Google Maps APIs: (1) routing directions based on the Directions API, returned as sf objects, either as single feature per alternative route, or a single feature per segment per alternative route; (2) travel distance or time matrices based on the Distance Matrix API; (3) geocoded locations based on the Geocode API, returned as sf objects, either points or bounds; (4) map images using the Maps Static API, returned as stars objects.

Regress network responses (both directed and undirected) onto covariates of interest that may be actor-, relation-, or network-valued. In addition, compute principled variance estimates of the coefficients assuming that the errors are jointly exchangeable. Missing data is accommodated. Additionally implements building and inversion of covariance matrices under joint exchangeability, and generates random covariance matrices from this class. For more detail on methods, see Marrs, Fosdick, and McCormick (2017) <arXiv:1701.05530>.

Applying the global sensitivity analysis workflow to investigate the parameter uncertainty and sensitivity in physiologically based kinetic (PK) models, especially the physiologically based pharmacokinetic/toxicokinetic model with multivariate outputs. The package also provides some functions to check the convergence and sensitivity of model parameters. The workflow was first mentioned in Hsieh et al., (2018) <doi:10.3389/fphar.2018.00588>, then further refined (Hsieh et al., 2020 <doi:10.1016/j.softx.2020.100609>).

This package provides functions for fitting abundance distributions over environmental gradients to the species in ecological communities, and tools for simulating the fossil assemblages from those abundance models for such communities, as well as simulating assemblages across various patterns of sedimentary history and sampling. These tools are for particular use with fossil records with detailed age models and abundance distributions used for calculating environmental gradients from ordinations or other indices based on fossil assemblages.

This package implements an iterative mean-variance panel regression estimator that allows both the mean and variance of the dependent variable to be functions of covariates. The method alternates between estimating a mean equation (using generalized linear models with Gaussian family) and a variance equation (using generalized linear models with Gamma family on squared within-group residuals) until convergence. Based on the methodology in Mooi-Reci and Liao (2025) <doi:10.1093/esr/jcae052>.

This tool proposes a new ranking algorithm that utilizes a "Y*WAASB" biplot generated by the metan'. The aim of the current package is to effectively distinguish the top-ranked genotypes in MET (Multi-Environmental Trials). For a detailed explanation of the process of obtaining "WAASB", "WAASBY" indices, and a "Y*WAASB" biplot, refer to the manual included in this package as well as the study by Olivoto & Lúcio (2020) <doi:10.1111/2041-210X.13384>. In this context, "WAASB" refers to the "Weighted Average of Absolute Scores" provided by Olivoto et al. (2019) <doi:10.2134/agronj2019.03.0220>, which quantifies the stability of genotypes across different environments using linear mixed-effect models. To run the package, you need to extract the "WAASB" and "WAASBY" coefficients using the metan and apply them. This tool utilizes PCA (Principal Component Analysis) and differentiates the entries which may be genotypes, hybrids, varieties, etc using "WAASB", "WAASBY", and a combination of the specified trait and WAASB index.

This package provides an R interface to Extreme Gradient Boosting, which is an efficient implementation of the gradient boosting framework from Chen and Guestrin (2016). The package includes efficient linear model solver and tree learning algorithms. The package can automatically do parallel computation on a single machine. It supports various objective functions, including regression, classification and ranking. The package is made to be extensible, so that users are also allowed to define their own objectives easily.

Archimax copulas are a mixture of Archimedean and EV copulas. This package provides definitions of several parametric families of generator and dependence function, computes CDF and PDF, estimates parameters, tests for goodness of fit, generates random sample and checks copula properties for custom constructs. In the 2-dimensional case explicit formulas for density are used, contrary to higher dimensions when all derivatives are linearly approximated. Several non-archimax families (normal, FGM, Plackett) are provided as well.