Aims at detecting single nucleotide variation (SNV) and insertion/deletion (INDEL) in circulating tumor DNA (ctDNA), used as a surrogate marker for tumor, at each base position of an Next Generation Sequencing (NGS) analysis. Mutations are assessed by comparing the minor-allele frequency at each position to the measured PER in control samples.

An implementation of a formal grammar and parser for R Markdown documents using the Boost Spirit X3 library. It also includes a collection of high level functions for working with the resulting abstract syntax tree.

Download and generate summaries for the rodent, plant, ant, and weather data from the Portal Project. Portal is a long-term (and ongoing) experimental monitoring site in the Chihuahuan desert. The raw data files can be found at <https://github.com/weecology/portaldata>.

This package provides tools for retrieving and analyzing air quality data from PurpleAir sensors through their API. Functions enable downloading historical measurements, accessing sensor metadata, and managing API request limitations through chunked data retrieval. For more information about the PurpleAir API, see <https://api.purpleair.com/>.

Projection Pursuit (PP) algorithm for dimension reduction based on Gaussian Mixture Models (GMMs) for density estimation using Genetic Algorithms (GAs) to maximise an approximated negentropy index. For more details see Scrucca and Serafini (2019) <doi:10.1080/10618600.2019.1598871>.

This package provides a suite of statistical tools for post-linkage data analysis (PLDA), designed to account for record linkage errors in downstream modeling. The package implements a familiar, formula-based regression interface that adjusts for linkage uncertainty, accommodating workflows where direct access to unlinked primary files is restricted. It consolidates diverse adjustment methodologies, all of which support generalized linear models (linear, logistic, Poisson, and Gamma). These methodologies include weighting approaches (Chambers (2009) <https://hdl.handle.net/10779/uow.27788247>; Chambers et al. (2023) <doi:10.1002/wics.1596>), mixture modeling (Slawski et al. (2025) <doi:10.1093/jrsssa/qnae083>), and Bayesian mixture modeling (Gutman et al. (2016) <doi:10.1002/sim.6586>). For time-to-event data, both the weighting (Vo et al. (2024) <doi:10.1002/sim.9960>) and mixture modeling approaches accommodate Cox proportional hazards models, while the Bayesian approaches extend to parametric survival analysis. Additionally, the package leverages mixture modeling for contingency table analyses and Bayesian methods to enable the multiple imputation of latent match status.

Estimate commonly used population genomic statistics and generate publication quality figures. PopGenHelpR uses vcf, geno (012), and csv files to generate output.

Automate specification search for identifying noninvariant items in factorial invariance analyses, as described in Yoon & Millsap (2007) <doi:10.1080/10705510701301677>. Models are specified in lavaan syntax. Supports continuous indicators with loadings, intercepts, residuals (uniqueness), and residual covariances invariance, and ordered categorical indicators with loadings, thresholds, and residual covariances invariance.

This package provides functions for generating progressively Type-II censored data in a mixture structure and fitting models using a constrained EM algorithm. It can also create a progressive Type-II censored version of a given real dataset to be considered for model fitting.

Perform classic chi-squared tests and Ripol et al(1999) binomial confidence interval approach for autopolyploid dominant markers. Also, dominant markers may be generated for families of offspring where either one or both of the parents possess the marker. Missing values and misclassified markers may be generated at random.

Person fit statistics based on Quality Control measures are provided for questionnaires and tests given a specified IRT model. Statistics based on Cumulative Sum (CUSUM) charts are provided. Options are given for banks with polytomous and dichotomous data.

This package provides tools for fitting piecewise-constant hazard models for survival and competing risks data, including ensemble hazard estimation via the Super Learner framework. The package supports estimation of survival functions and absolute risk predictions from fitted cause-specific hazard models. For the Super Learner framework see van der Laan, Polley and Hubbard (2007) <doi:10.2202/1544-6115.1309>.

Generate Mermaid syntax for a pedigree flowchart from a pedigree data frame. Mermaid syntax is commonly used to generate plots, charts, diagrams, and flowcharts. It is a textual syntax for creating reproducible illustrations. This package generates Mermaid syntax from a pedigree data frame to visualize a pedigree flowchart. The Mermaid syntax can be embedded in a Markdown or R Markdown file, or viewed on Mermaid editors and renderers. Links shape, style, and orientation can be customized via function arguments, and nodes shapes and styles can be customized via optional columns in the pedigree data frame.

Psychometric mixture models based on flexmix infrastructure. At the moment Rasch mixture models with different parameterizations of the score distribution (saturated vs. mean/variance specification), Bradley-Terry mixture models, and MPT mixture models are implemented. These mixture models can be estimated with or without concomitant variables. See Frick et al. (2012) <doi:10.18637/jss.v048.i07> and Frick et al. (2015) <doi:10.1177/0013164414536183> for details on the Rasch mixture models.

This package contains logic for computing the statistical association of variable groups, i.e., gene sets, with respect to the principal components of genomic data.

This package provides tools for transforming, a posteriori time-scaling, and modifying phylogenies containing extinct (i.e. fossil) lineages. In particular, most users are interested in the functions timePaleoPhy, bin_timePaleoPhy, cal3TimePaleoPhy and bin_cal3TimePaleoPhy, which date cladograms of fossil taxa using stratigraphic data. This package also contains a large number of likelihood functions for estimating sampling and diversification rates from different types of data available from the fossil record (e.g. range data, occurrence data, etc). paleotree users can also simulate diversification and sampling in the fossil record using the function simFossilRecord, which is a detailed simulator for branching birth-death-sampling processes composed of discrete taxonomic units arranged in ancestor-descendant relationships. Users can use simFossilRecord to simulate diversification in incompletely sampled fossil records, under various models of morphological differentiation (i.e. the various patterns by which morphotaxa originate from one another), and with time-dependent, longevity-dependent and/or diversity-dependent rates of diversification, extinction and sampling. Additional functions allow users to translate simulated ancestor-descendant data from simFossilRecord into standard time-scaled phylogenies or unscaled cladograms that reflect the relationships among taxon units.

Implementation of the pattern recognition technique Principal Component Pursuit tailored to environmental health data, as described in Gibson et al (2022) <doi:10.1289/EHP10479>.

Gene-level variant association tests with disease status for pedigree data: kernel and burden association statistics.

Spearman's rank correlation test with precomputed exact null distribution for n <= 22.

Computes profile extrema functions for arbitrary functions. If the function is expensive-to-evaluate it computes profile extrema by emulating the function with a Gaussian process (using package DiceKriging'). In this case uncertainty quantification on the profile extrema can also be computed. The different plotting functions for profile extrema give the user a tool to better locate excursion sets.

This package provides a set of Study Data Tabulation Model (SDTM) datasets constructed by modifying the pharmaversesdtm package to meet J&J Innovative Medicine's standard data structure for Clinical and Statistical Programming.

This package provides functions for creating color palettes, visualizing palettes, modifying colors, and assigning colors for plotting.

Design, backtest, and analyze portfolio strategies using simple, English-like function chains. Includes technical indicators, flexible stock selection, portfolio construction methods (equal weighting, signal weighting, inverse volatility, hierarchical risk parity), and a compact backtesting engine for portfolio returns, drawdowns, and summary metrics.

Download press freedom index data from Reporters Without Borders (RSF) with period-aware encoding handling. Data are downloaded from the RSF website (<https://rsf.org/en/index>). Provides infrastructure for data cleaning and ISO 3166 standardization in downstream phases.