Calculates an acceptance sampling plan, (sample size and acceptance number) based in MIL STD 105E, Dodge Romig and MIL STD 414 tables and procedures. The arguments for each function are related to lot size, inspection level and quality level. The specific plan operating curve (OC), is calculated by the binomial distribution.

This package provides a C++ backend for multivariate phylogenetic comparative models implemented in the R-package PCMBase'. Can be used in combination with PCMBase to enable fast and parallel likelihood calculation. Implements the pruning likelihood calculation algorithm described in Mitov et al. (2020) <doi:10.1016/j.tpb.2019.11.005>. Uses the SPLITT C++ library for parallel tree traversal described in Mitov and Stadler (2018) <doi:10.1111/2041-210X.13136>.

Small self-contained plots for use in larger plots or to delegate plotting in other functions. Also contains a number of alternative color palettes and HSL color space based tools to modify colors or palettes.

Conducts hierarchical partitioning to calculate individual contributions of phylogenetic tree and predictors (groups) towards total R2 for phylogenetic linear regression models.

Gene-based association tests using the actual impurity reduction (AIR) variable importance. The function aggregates AIR importance measures from a group of SNPs or probes and outputs a p-value for each gene. The procedures builds upon the method described in <doi:10.1093/Bioinformatics/Bty373> and will be published soon.

Uses provenance collected by rdtLite package or comparable tool to display information about input files, output files, and exchanged files for a single R script or a series of R scripts.

Pattern causality is a novel approach for detecting the hidden causality in the complex system.

Efficient implementations of multiple exact and approximate methods as described in Hong (2013) <doi:10.1016/j.csda.2012.10.006>, Biscarri, Zhao & Brunner (2018) <doi:10.1016/j.csda.2018.01.007> and Zhang, Hong & Balakrishnan (2018) <doi:10.1080/00949655.2018.1440294> for computing the probability mass, cumulative distribution and quantile functions, as well as generating random numbers for both the ordinary and generalized Poisson binomial distribution.

NOTE: PARAMLINK HAS BEEN SUPERSEDED BY THE PEDSUITE PACKAGES (<https://magnusdv.github.io/pedsuite/>). PARAMLINK IS MAINTAINED ONLY FOR LEGACY PURPOSES AND SHOULD NOT BE USED IN NEW PROJECTS. A suite of tools for analysing pedigrees with marker data, including parametric linkage analysis, forensic computations, relatedness analysis and marker simulations. The core of the package is an implementation of the Elston-Stewart algorithm for pedigree likelihoods, extended to allow mutations as well as complex inbreeding. Features for linkage analysis include singlepoint LOD scores, power analysis, and multipoint analysis (the latter through a wrapper to the MERLIN software). Forensic applications include exclusion probabilities, genotype distributions and conditional simulations. Data from the Familias software can be imported and analysed in paramlink'. Finally, paramlink offers many utility functions for creating, manipulating and plotting pedigrees with or without marker data (the actual plotting is done by the kinship2 package).

Runs generalized and multinominal logistic (GLM and MLM) models, as well as random forest (RF), Bagging (BAG), and Boosting (BOOST). This package prints out to predictive outcomes easy for the selected data and data splits.

This package provides functions for the computation of F-, f- and D-statistics (e.g., Fst, hierarchical F-statistics, Patterson's F2, F3, F3*, F4 and D parameters) in population genomics studies from allele count or Pool-Seq read count data and for the fitting, building and visualization of admixture graphs. The package also includes several utilities to manipulate Pool-Seq data stored in standard format (e.g., such as vcf files or rsync files generated by the the PoPoolation software) and perform conversion to alternative format (as used in the BayPass and SelEstim software). As of version 2.0, the package also includes utilities to manipulate standard allele count data (e.g., stored in TreeMix, BayPass and SelEstim format).

Compilation and digitalization of the official registry of victims of state terrorism in Argentina during the last military coup. The original data comes from RUVTE-ILID (2019) <https://www.argentina.gob.ar/sitiosdememoria/ruvte/informe> and <http://basededatos.parquedelamemoria.org.ar/registros/>. The title, presentes, comes from present in spanish.

This package implements the Phylogeny-Guided Microbiome OTU-Specific Association Test method, which boosts the testing power by adaptively borrowing information from phylogenetically close OTUs (operational taxonomic units) of the target OTU. This method is built on a kernel machine regression framework and allows for flexible modeling of complex microbiome effects, adjustments for covariates, and can accommodate both continuous and binary outcomes.

Estimation, prediction, thresholding, transformation, and plotting for partially linear additive quantile regression. Intuitive functions for fitting and plotting partially linear additive quantile regression models. Uses and works with functions from the quantreg package.

This package provides a collection of utilities and ggplot2 extensions to assist with visualisations in genomic epidemiology. This includes the phylepic chart, a visual combination of a phylogenetic tree and a matched epidemic curve. The included ggplot2 extensions such as date axes binned by week are relevant for other applications in epidemiology and beyond. The approach is described in Suster et al. (2024) <doi:10.1101/2024.04.02.24305229>.

This package provides functions for conventionally formatting descriptive stats, reshaping data frames and formatting R output as HTML.

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

Test-based Image structural similarity measure and test of independence. This package implements the key functions of two tasks: (1) computing image structural similarity measure PSSIM of Wang, Maldonado and Silwal (2011) <DOI:10.1016/j.csda.2011.04.021>; and (2) test of independence between a response and a covariate in presence of heteroscedastic treatment effects proposed by Wang, Tolos, and Wang (2010) <DOI:10.1002/cjs.10068>.

Offers tools to estimate and visualize levels of major pollutants (CO, NO2, SO2, Ozone, PM2.5 and PM10) across the conterminous United States for user-defined time ranges. Provides functions to retrieve pollutant data from the U.S. Environmental Protection Agencyâ s Air Quality System (AQS) API service <https://aqs.epa.gov/aqsweb/documents/data_api.html> for interactive visualization through a shiny application, allowing users to explore pollutant levels for a given location over time relative to the National Ambient Air Quality Standards (NAAQS).

This package provides functionality for quality control processing and statistical analysis of mass spectrometry (MS) omics data, in particular proteomic (either at the peptide or the protein level), lipidomic, and metabolomic data, as well as RNA-seq based count data and nuclear magnetic resonance (NMR) data. This includes data transformation, specification of groups that are to be compared against each other, filtering of features and/or samples, data normalization, data summarization (correlation, PCA), and statistical comparisons between defined groups. Implements methods described in: Webb-Robertson et al. (2014) <doi:10.1074/mcp.M113.030932>. Webb-Robertson et al. (2011) <doi:10.1002/pmic.201100078>. Matzke et al. (2011) <doi:10.1093/bioinformatics/btr479>. Matzke et al. (2013) <doi:10.1002/pmic.201200269>. Polpitiya et al. (2008) <doi:10.1093/bioinformatics/btn217>. Webb-Robertson et al. (2010) <doi:10.1021/pr1005247>.

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

References and cites R and R packages on the fly in R Markdown and Quarto'. pakret provides a minimalistic API that generates preformatted citations of R and R packages, and adds their reference to a .bib file directly from within your document.

Presentation of a new goodness-of-fit normality test based on the Lilliefors method. For details on this method see: Sulewski (2019) <doi:10.1080/03610918.2019.1664580>.

This package provides an interface to access public economic and financial data for economic research and quantitative analysis. The data sources including NBS, FRED, Sina, Eastmoney and etc. It also provides quantitative functions for trading strategies based on the data.table', TTR', PerformanceAnalytics and etc packages.