Perform gene set enrichment analyses using the Gene set Ordinal Association Test (GOAT) algorithm and visualize your results. Koopmans, F. (2024) <doi:10.1038/s42003-024-06454-5>.

This package provides a native R implementation of grammatical evolution (GE). GE facilitates the discovery of programs that can achieve a desired goal. This is done by performing an evolutionary optimisation over a population of R expressions generated via a user-defined context-free grammar (CFG) and cost function.

Data-driven approach for arriving at person-specific time series models from within a Graphical Vector Autoregression (VAR) framework. The method first identifies which relations replicate across the majority of individuals to detect signal from noise. These group-level relations are then used as a foundation for starting the search for person-specific (or individual-level) relations. All estimates are obtained uniquely for each individual in the final models. The method for the graphicalVAR approach is found in Epskamp, Waldorp, Mottus & Borsboom (2018) <doi:10.1080/00273171.2018.1454823>.

Computes Gregory weights for a given number nodes and function order. Anthony Ralston and Philip Rabinowitz (2001) <ISBN:9780486414546>.

An implementation of the generalized graded unfolding model (GGUM) in R, see Roberts, Donoghue, and Laughlin (2000) <doi:10.1177/01466216000241001>). It allows to simulate data sets based on the GGUM. It fits the GGUM and the GUM, and it retrieves item and person parameter estimates. Several plotting functions are available (item and test information functions; item and test characteristic curves; item category response curves). Additionally, there are some functions that facilitate the communication between R and GGUM2004'. Finally, a model-fit checking utility, MODFIT(), is also available.

This package provides a ggplot2 extension for visualising uncertainty with the goal of signal suppression. Usually, uncertainty visualisation focuses on expressing uncertainty as a distribution or probability, whereas ggdibbler differentiates itself by viewing an uncertainty visualisation as an adjustment to an existing graphic that incorporates the inherent uncertainty in the estimates. You provide the code for an existing plot, but replace any of the variables with a vector of distributions, and it will convert the visualisation into it's signal suppression counterpart.

This package implements the five-parameter Generalized Kumaraswamy ('gkw') distribution proposed by Carrasco, Ferrari and Cordeiro (2010) <doi:10.48550/arXiv.1004.0911> and its seven nested sub-families for modeling bounded continuous data on the unit interval (0,1). The gkw distribution extends the Kumaraswamy distribution described by Jones (2009) <doi:10.1016/j.stamet.2008.04.001>. Provides density, distribution, quantile, and random generation functions, along with analytical log-likelihood, gradient, and Hessian functions implemented in C++ via RcppArmadillo for maximum computational efficiency. Suitable for modeling proportions, rates, percentages, and indices exhibiting complex features such as asymmetry, or heavy tails and other shapes not adequately captured by standard distributions like simple Beta or Kumaraswamy.

Using simple input, this package creates plots of gene models. Users can create plots of alternatively spliced gene variants and the positions of mutations and other gene features.

Automatically performs desired statistical tests (e.g. wilcox.test(), t.test()) to compare between groups, and adds the resulting p-values to the plot with an annotation bar. Visualizing group differences are frequently performed by boxplots, bar plots, etc. Statistical test results are often needed to be annotated on these plots. This package provides a convenient function that works on ggplot2 objects, performs the desired statistical test between groups of interest and annotates the test results on the plot.

An implementation of Gini-based weighting approaches in constructing composite indicators, providing functionalities for normalization, aggregation, and ranking comparison.

An R interface to the GPTZero API (<https://gptzero.me/docs>). Allows users to classify text into human and computer written with probabilities. Formats the data into data frames where each sentence is an observation. Paragraph-level and document-level predictions are organized to align with the sentences.

This package provides tools for using genetic markers, stable isotope data, and habitat suitability data to calculate posterior probabilities of breeding origin of migrating birds.

Compute standard and generalized Nash Equilibria of non-cooperative games. Optimization methods available are nonsmooth reformulation, fixed-point formulation, minimization problem and constrained-equation reformulation. See e.g. Kanzow and Facchinei (2010), <doi:10.1007/s10479-009-0653-x>.

Analysis of multivariate data using generalized linear latent variable models (gllvm). Estimation is performed using either the Laplace method, variational approximations, or extended variational approximations, implemented via TMB (Kristensen et al. (2016), <doi:10.18637/jss.v070.i05>).

This package provides a plain Rcpp wrapper for MeCab that can segment Chinese, Japanese, and Korean text into tokens. The main goal of this package is to provide an alternative to tidytext using morphological analysis.

This package provides a statistical hypothesis test for conditional independence. It performs nonlinear regressions on the conditioning variable and then tests for a vanishing covariance between the resulting residuals. It can be applied to both univariate random variables and multivariate random vectors. Details of the method can be found in Rajen D. Shah and Jonas Peters: The Hardness of Conditional Independence Testing and the Generalised Covariance Measure, Annals of Statistics 48(3), 1514--1538, 2020.

Data sets used in the book "R Graphics Cookbook" by Winston Chang, published by O'Reilly Media.

This package implements iterative conditional expectation (ICE) estimators of the plug-in g-formula (Wen, Young, Robins, and Hernán (2020) <doi: 10.1111/biom.13321>). Both singly robust and doubly robust ICE estimators based on parametric models are available. The package can be used to estimate survival curves under sustained treatment strategies (interventions) using longitudinal data with time-varying treatments, time-varying confounders, censoring, and competing events. The interventions can be static or dynamic, and deterministic or stochastic (including threshold interventions). Both prespecified and user-defined interventions are available.

The Geocoordinate Validation Service (GVS) runs checks of coordinates in latitude/longitude format. It returns annotated coordinates with additional flags and metadata that can be used in data cleaning. Additionally, the package has functions related to attribution and metadata information. More information can be found at <https://github.com/ojalaquellueva/gvs/tree/master/api>.

This package provides methods from the paper: Pena, EA and Slate, EH, "Global Validation of Linear Model Assumptions," J. American Statistical Association, 101(473):341-354, 2006.

This package provides basic graphing functions to fully demonstrate point-to-point connections in a polar coordinate space.

This package implements various Gifi methods in a user-friendly way: categorical principal component analysis (princals), multiple correspondence analysis (homals), monotone regression analysis (morals).

Computes the sample probability value (p-value) for the estimated coefficient from a standard genome-wide univariate regression. It computes the exact finite-sample p-value under the assumption that the measured phenotype (the dependent variable in the regression) has a known Bernoulli-normal mixture distribution. Finite-sample genome-wide regression p-values (Gwrpv) with a non-normally distributed phenotype (Gregory Connor and Michael O'Neill, bioRxiv 204727 <doi:10.1101/204727>).

This package provides functions for model fitting and selection of generalised hypergeometric ensembles of random graphs (gHypEG). To learn how to use it, check the vignettes for a quick tutorial. Please reference its use as Casiraghi, G., Nanumyan, V. (2019) <doi:10.5281/zenodo.2555300> together with those relevant references from the one listed below. The package is based on the research developed at the Chair of Systems Design, ETH Zurich. Casiraghi, G., Nanumyan, V., Scholtes, I., Schweitzer, F. (2016) <arXiv:1607.02441>. Casiraghi, G., Nanumyan, V., Scholtes, I., Schweitzer, F. (2017) <doi:10.1007/978-3-319-67256-4_11>. Casiraghi, G., (2017) <arXiv:1702.02048> Brandenberger, L., Casiraghi, G., Nanumyan, V., Schweitzer, F. (2019) <doi:10.1145/3341161.3342926> Casiraghi, G. (2019) <doi:10.1007/s41109-019-0241-1>. Casiraghi, G., Nanumyan, V. (2021) <doi:10.1038/s41598-021-92519-y>. Casiraghi, G. (2021) <doi:10.1088/2632-072X/ac0493>.