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

This package provides functions for estimating ploidy levels and detecting aneuploidy in individuals using allele intensities or allele count data from high-throughput genotyping platforms, including single nucleotide polymorphism (SNP) arrays and sequencing-based technologies. Implements method described in Taniguti et al. (2025) <doi:10.1002/tpg2.70044> an extended version of the PennCNV signal standardization method by Wang et al. (2007) <doi:10.1101/gr.6861907> for higher ploidy levels. Computes B-allele frequencies (BAF), z-scores, and identifies copy number variation patterns.

This package provides a set of functions for taking qualitative GIS data, hand drawn on a map, and converting it to a simple features object. These tools are focused on data that are drawn on a map that contains some type of polygon features. For each area identified on the map, the id numbers of these polygons can be entered as vectors and transformed using qualmap.

This package provides several methods for computing the Quantile Treatment Effect (QTE) and Quantile Treatment Effect on the Treated (QTT). The main cases covered are (i) treatment is randomly assigned, (ii) treatment is as good as randomly assigned after conditioning on covariates (selection on observables) using the methods of Firpo (2007) <doi:10.1111/j.1468-0262.2007.00738.x>, and (iii) identification is based on a Difference in Differences assumption, with support for several varieties including Athey and Imbens (2006) <doi:10.1111/j.1468-0262.2006.00668.x>, Callaway and Li (2019) <doi:10.3982/QE935>, and Callaway, Li, and Oka (2018) <doi:10.1016/j.jeconom.2018.06.008>. Version 2.0 adds a unified staggered treatment adoption API (built on ptetools') for all DiD-based estimators, as well as a new lagged-outcome unconfoundedness estimator ('lou_qtt').

Web-based interactive charts (using D3.js) for the analysis of experimental crosses to identify genetic loci (quantitative trait loci, QTL) contributing to variation in quantitative traits. Broman (2015) <doi:10.1534/genetics.114.172742>.

This package provides functions to manipulate dates and count days for quantitative finance analysis. The quantdates package considers leap, holidays and business days for relevant calendars in a financial context to simplify quantitative finance calculations, consistent with International Swaps and Derivatives Association (ISDA) (2006) <https://www.isda.org/book/2006-isda-definitions/> regulations.

Construct message-passing style objects with types and features. Q7 types uses composition instead of inheritance in creating derived types, allowing defining any code segment as feature and associating any feature to any object. Compared to R6, Q7 is simpler and more flexible, and is more friendly in syntax.

Molecular descriptors and outcomes for several public domain data sets.

This package provides a high-level plotting system, compatible with `ggplot2` objects, maps from `sf`, `terra`, `raster`, `sp`. It is built primarily on the grid package. The objective of the package is to provide a plotting system that is built for speed and modularity. This is useful for quick visualizations when testing code and for plotting multiple figures to the same device from independent sources that may be independent of one another (i.e., different function or modules the create the visualizations).

This package provides tools for (automated and manual) quality control of the results of Epigenome-Wide Association Studies.

This package provides a high-level pipeline that simplifies text classification into three streamlined steps: preprocessing, model training, and standardized prediction. It unifies the interface for multiple algorithms (including glmnet', ranger', xgboost', and naivebayes') and memory-efficient sparse matrix vectorization methods (Bag-of-Words, Term Frequency, TF-IDF, and Binary). Users can go from raw text to a fully evaluated sentiment model, complete with ROC-optimized thresholds, in just a few function calls. The resulting model artifact automatically aligns the vocabulary of new datasets during the prediction phase, safely appending predicted classes and probability matrices directly to the user's original dataframe to preserve metadata.

This package provides statistical components, tables, and graphs that are useful in Quarto and RMarkdown reports and that produce Quarto elements for special formatting such as tabs and marginal notes and graphs. Some of the functions produce entire report sections with tabs, e.g., the missing data report created by missChk(). Functions for inserting variables and tables inside graphviz and mermaid diagrams are included, and so are special clinical trial graphics for adverse event reporting.

This function produces both the numerical and graphical summaries of the QTL hotspot detection in the genomes that are available on the worldwide web including the flanking markers of QTLs.

This package implements Quantile-on-Quantile Kernel-Based Regularized Least Squares (QQKRLS) as in Adebayo, Ozkan and Eweade (2024) <doi:10.1016/j.jclepro.2024.140832>. Combines Kernel-Based Regularized Least Squares (KRLS) of Hainmueller and Hazlett (2014) <doi:10.1093/pan/mpt019> with the Quantile-on-Quantile regression of Sim and Zhou (2015) <doi:10.1016/j.jbankfin.2015.01.013>: for each quantile theta of the independent variable the response is fit by KRLS on the corresponding sub-sample and the tau-quantile of the resulting pointwise marginal effects yields beta(theta, tau). Standard errors come from a paired bootstrap. Visualisations use the MATLAB Parula colour map by default.

Mortality rates are typically provided in an abridged format, i.e., by age groups 0, [1, 5], [5, 10]', [10, 15]', and so on. Some applications necessitate a detailed (single) age description. Despite the large number of proposed approaches in the literature, only a few methods ensure great performance at both younger and higher ages. For example, the 6-term Lagrange interpolation function is well suited to mortality interpolation at younger ages (with irregular intervals), but not at older ages. The Karup-King method, on the other hand, performs well at older ages but is not suitable for younger ones. Interested readers can find a full discussion of the two stated methods in the book Shryock, Siegel, and Associates (1993).The Q2q package combines the two methods to allow for the interpolation of mortality rates across all age groups. It begins by implementing each method independently, and then the resulting curves are linked using a 5-age averaged error between the two partial curves.

Textual statistics functions formerly in the quanteda package. Textual statistics for characterizing and comparing textual data. Includes functions for measuring term and document frequency, the co-occurrence of words, similarity and distance between features and documents, feature entropy, keyword occurrence, readability, and lexical diversity. These functions extend the quanteda package and are specially designed for sparse textual data.

Integration of the units and errors packages for a complete quantity calculus system for R vectors, matrices and arrays, with automatic propagation, conversion, derivation and simplification of magnitudes and uncertainties. Documentation about units and errors is provided in the papers by Pebesma, Mailund & Hiebert (2016, <doi:10.32614/RJ-2016-061>) and by Ucar, Pebesma & Azcorra (2018, <doi:10.32614/RJ-2018-075>), included in those packages as vignettes; see citation("quantities") for details.

This package provides a collection of tools associated with the qdap package that may be useful outside of the context of text analysis.

This package provides functions for assigning treatments in randomized experiments using near-optimal threshold blocking. The package is made with large data sets in mind and derives blocks more than an order of magnitude quicker than other methods.

This package provides a toolkit for analysis and visualization of data from fluorophore-assisted seed amplification assays, such as Real-Time Quaking-Induced Conversion (RT-QuIC) and Fluorophore-Assisted Protein Misfolding Cyclic Amplification (PMCA). QuICSeedR addresses limitations in existing software by automating data processing, supporting large-scale analysis, and enabling comparative studies of analysis methods. It incorporates methods described in Henderson et al. (2015) <doi:10.1099/vir.0.069906-0>, Li et al. (2020) <doi:10.1038/s41598-021-96127-8>, Rowden et al. (2023) <doi:10.3390/pathogens12020309>, Haley et al. (2013) <doi:10.1371/journal.pone.0081488>, and Mair and Wilcox (2020) <doi:10.3758/s13428-019-01246-w>. Please refer to the original publications for details.

Joint estimation of quantile specific intercept and slope parameters in a linear regression setting.

This package provides a tool that can be customized to aid in the clean up of ecological data collected using quadrats and can crop quadrats to ensure comparability between quadrats collected under different methodologies.

This package provides tools for AI-assisted qualitative data coding using large language models ('LLMs') via the ellmer package, supporting providers including OpenAI', Anthropic', Google', Azure', and local models via Ollama'. Provides a codebook'-based workflow for defining coding instructions and applying them to texts, images, audio recordings, and other data. Includes built-in codebooks for common applications such as sentiment analysis and policy coding, and functions for creating custom codebooks for specific research questions. Supports systematic replication across models and settings, computing inter-coder reliability statistics including Krippendorff's alpha (Krippendorff 2019, <doi:10.4135/9781071878781>) and Fleiss kappa (Fleiss 1971, <doi:10.1037/h0031619>), as well as gold-standard validation metrics including accuracy, precision, recall, and F1 scores following Sokolova and Lapalme (2009, <doi:10.1016/j.ipm.2009.03.002>). Provides audit trail functionality for documenting coding workflows following Lincoln and Guba's (1985, ISBN:0803924313) framework for establishing trustworthiness in qualitative research.

This package provides a copula-based measure for quantifying asymmetry in dependence and associations. Documentation and theory about qad is provided by the paper by Junker, Griessenberger & Trutschnig (2021, <doi:10.1016/j.csda.2020.107058>), and the paper by Trutschnig (2011, <doi:10.1016/j.jmaa.2011.06.013>).