This package provides a method for prediction of environmental conditions based on transcriptome data linked with the environmental gradients. This package provides functions to overview gene-environment relationships, to construct the prediction model, and to predict environmental conditions where the transcriptomes were generated. This package can quest for candidate genes for the model construction even in non-model organisms transcriptomes without any genetic information.

Compile R functions annotated with type and shape declarations for extremely fast performance and robust runtime type checking. Supports both just-in-time (JIT) and ahead-of-time (AOT) compilation. Compilation is performed by lowering R code to Fortran.

The Ensemble Quadratic and Affine Invariant Markov chain Monte Carlo algorithms provide an efficient way to perform Bayesian inference in difficult parameter space geometries. The Ensemble Quadratic Monte Carlo algorithm was developed by Militzer (2023) <doi:10.3847/1538-4357/ace1f1>. The Ensemble Affine Invariant algorithm was developed by Goodman and Weare (2010) <doi:10.2140/camcos.2010.5.65> and it was implemented in Python by Foreman-Mackey et al (2013) <doi:10.48550/arXiv.1202.3665>. The Quadratic Monte Carlo method was shown to perform better than the Affine Invariant method in the paper by Militzer (2023) <doi:10.3847/1538-4357/ace1f1> and the Quadratic Monte Carlo method is the default method used. The Chen-Shao Highest Posterior Density Estimation algorithm is used for obtaining credible intervals and the potential scale reduction factor diagnostic is used for checking the convergence of the chains.

This package provides functions to Simultaneously Infer Causal Graphs and Genetic Architecture. Includes acyclic and cyclic graphs for data from an experimental cross with a modest number (<10) of phenotypes driven by a few genetic loci (QTL). Chaibub Neto E, Keller MP, Attie AD, Yandell BS (2010) Causal Graphical Models in Systems Genetics: a unified framework for joint inference of causal network and genetic architecture for correlated phenotypes. Annals of Applied Statistics 4: 320-339. <doi:10.1214/09-AOAS288>.

This package provides a range of quadratic forms are evaluated, using efficient methods. Unnecessary transposes are not performed. Complex values are handled consistently.

For QTL mapping, this package comprises several functions designed to execute diverse tasks, such as simulating or analyzing data, calculating significance thresholds, and visualizing QTL mapping results. The single-QTL or multiple-QTL method, which enables the fitting and comparison of various statistical models, is employed to analyze the data for estimating QTL parameters. The models encompass linear regression, permutation tests, normal mixture models, and truncated normal mixture models. The Gaussian stochastic process is utilized to compute significance thresholds for QTL detection on a genetic linkage map within experimental populations. Two types of data, complete genotyping, and selective genotyping data from various experimental populations, including backcross, F2, recombinant inbred (RI) populations, and advanced intercrossed (AI) populations, are considered in the QTL mapping analysis. For QTL hotspot detection, statistical methods can be developed based on either utilizing individual-level data or summarized data. We have proposed a statistical framework capable of handling both individual-level data and summarized QTL data for QTL hotspot detection. Our statistical framework can overcome the underestimation of thresholds resulting from ignoring the correlation structure among traits. Additionally, it can identify different types of hotspots with minimal computational cost during the detection process. Here, we endeavor to furnish the R codes for our QTL mapping and hotspot detection methods, intended for general use in genes, genomics, and genetics studies. The QTL mapping methods for the complete and selective genotyping designs are based on the multiple interval mapping (MIM) model proposed by Kao, C.-H. , Z.-B. Zeng and R. D. Teasdale (1999) <doi: 10.1534/genetics.103.021642> and H.-I Lee, H.-A. Ho and C.-H. Kao (2014) <doi: 10.1534/genetics.114.168385>, respectively. The QTL hotspot detection analysis is based on the method by Wu, P.-Y., M.-.H. Yang, and C.-H. Kao (2021) <doi: 10.1093/g3journal/jkab056>.

General purpose toolbox for simulating quantum versions of game theoretic models (Flitney and Abbott 2002) <arXiv:quant-ph/0208069>. Quantum (Nielsen and Chuang 2010, ISBN:978-1-107-00217-3) versions of models that have been handled are: Penny Flip Game (David A. Meyer 1998) <arXiv:quant-ph/9804010>, Prisoner's Dilemma (J. Orlin Grabbe 2005) <arXiv:quant-ph/0506219>, Two Person Duel (Flitney and Abbott 2004) <arXiv:quant-ph/0305058>, Battle of the Sexes (Nawaz and Toor 2004) <arXiv:quant-ph/0110096>, Hawk and Dove Game (Nawaz and Toor 2010) <arXiv:quant-ph/0108075>, Newcomb's Paradox (Piotrowski and Sladkowski 2002) <arXiv:quant-ph/0202074> and Monty Hall Problem (Flitney and Abbott 2002) <arXiv:quant-ph/0109035>.

Calculates the number of four-taxon subtrees consistent with a pair of cladograms, calculating the symmetric quartet distance of Bandelt & Dress (1986), Reconstructing the shape of a tree from observed dissimilarity data, Advances in Applied Mathematics, 7, 309-343 <doi:10.1016/0196-8858(86)90038-2>, and using the tqDist algorithm of Sand et al. (2014), tqDist: a library for computing the quartet and triplet distances between binary or general trees, Bioinformatics, 30, 2079â 2080 <doi:10.1093/bioinformatics/btu157> for pairs of binary trees.

Plotting functions for visualising textual data. Extends quanteda and related packages with plot methods designed specifically for text data, textual statistics, and models fit to textual data. Plot types include word clouds, lexical dispersion plots, scaling plots, network visualisations, and word keyness plots.

This package provides routines to create some quaternions splines: Barry-Goldman algorithm, De Casteljau algorithm, and Kochanek-Bartels algorithm. The implementations are based on the Python library splines'. Quaternions splines allow to construct spherical curves. References: Barry and Goldman <doi:10.1145/54852.378511>, Kochanek and Bartels <doi:10.1145/800031.808575>.

This package provides functions to convert data structures among the qtl2', qtl', and DOQTL packages for mapping quantitative trait loci (QTL).

Various data sets (stocks, stock indices, constituent data, FX, zero-coupon bond yield curves, volatility, commodities) for Quantitative Risk Management practice.

Developed to perform the estimation and inference for regression coefficient parameters in longitudinal marginal models using the method of quadratic inference functions. Like generalized estimating equations, this method is also a quasi-likelihood inference method. It has been showed that the method gives consistent estimators of the regression coefficients even if the correlation structure is misspecified, and it is more efficient than GEE when the correlation structure is misspecified. Based on Qu, A., Lindsay, B.G. and Li, B. (2000) <doi:10.1093/biomet/87.4.823>.

Converts R scripts (.R) into Quarto markdown documents (.qmd) with automatic formatting. Recognizes RStudio code sections, preserves comments as narrative text, extracts metadata from special comments, and provides both programmatic functions and an interactive RStudio add-in for easy conversion.

Grows a qualitative interaction tree. Quint is a tool for subgroup analysis, suitable for data from a two-arm randomized controlled trial. More information in Dusseldorp, E., Doove, L., & Van Mechelen, I. (2016) <doi:10.3758/s13428-015-0594-z>.

Based on Alan D. Hutson (1999) <doi:10.1080/02664769922458>, "Calculating nonparametric confidence intervals for quantiles using fractional order statistics", Journal of Applied Statistics, 26:3, 343-353.

This package implements Q-Learning, a model-free form of reinforcement learning, described in work by Strehl, Li, Wiewiora, Langford & Littman (2006) <doi:10.1145/1143844.1143955>.

Estimate quadratic vector autoregression models with the strong hierarchy using the Regularization Algorithm under Marginality Principle (RAMP) by Hao et al. (2018) <doi:10.1080/01621459.2016.1264956>, compare the performance with linear models, and construct networks with partial derivatives.

Function that implements the Quantum Genetic Algorithm, first proposed by Han and Kim in 2000. This is an R implementation of the python application developed by Lahoz-Beltra (<https://github.com/ResearchCodesHub/QuantumGeneticAlgorithms>). Each optimization problem is represented as a maximization one, where each solution is a sequence of (qu)bits. Following the quantum paradigm, these qubits are in a superposition state: when measuring them, they collapse in a 0 or 1 state. After measurement, the fitness of the solution is calculated as in usual genetic algorithms. The evolution at each iteration is oriented by the application of two quantum gates to the amplitudes of the qubits: (1) a rotation gate (always); (2) a Pauli-X gate (optionally). The rotation is based on the theta angle values: higher values allow a quicker evolution, and lower values avoid local maxima. The Pauli-X gate is equivalent to the classical mutation operator and determines the swap between alfa and beta amplitudes of a given qubit. The package has been developed in such a way as to permit a complete separation between the engine, and the particular problem subject to combinatorial optimization.

This package contains basic structures and operations used frequently in quantum computing. Intended to be a convenient tool to help learn quantum mechanics and algorithms. Can create arbitrarily sized kets and bras and implements quantum gates, inner products, and tensor products. Creates arbitrarily controlled versions of all gates and can simulate complete or partial measurements of kets. Has functionality to convert functions into equivalent quantum gates and model quantum noise. Includes larger applications, such as Steane error correction <DOI:10.1103/physrevlett.77.793>, Quantum Fourier Transform and Shor's algorithm (Shor 1999), Grover's algorithm (1996), Quantum Approximation Optimization Algorithm (QAOA) (Farhi, Goldstone, and Gutmann 2014) <arXiv:1411.4028>, and a variational quantum classifier (Schuld 2018) <arXiv:1804.00633>. Can be used with the gridsynth algorithm <arXiv:1212.6253> to perform decomposition into the Clifford+T set.

This package implements indices of qualitative variation proposed by Wilcox (1973).

Extensions of ggplot2 Q-Q plot functionalities.

This package implements the robust algorithm for fitting finite mixture models based on quantile regression proposed by Emir et al., 2017 (unpublished).

An implementation of Quantitative Fatty Acid Signature Analysis (QFASA) in R. QFASA is a method of estimating the diet composition of predators. The fundamental unit of information in QFASA is a fatty acid signature (signature), which is a vector of proportions describing the composition of fatty acids within lipids. Signature data from at least one predator and from samples of all potential prey types are required. Calibration coefficients, which adjust for the differential metabolism of individual fatty acids by predators, are also required. Given those data inputs, a predator signature is modeled as a mixture of prey signatures and its diet estimate is obtained as the mixture that minimizes a measure of distance between the observed and modeled signatures. A variety of estimation options and simulation capabilities are implemented. Please refer to the vignette for additional details and references.