Fast and very memory-efficient calculation of isotope patterns, subsequent convolution to theoretical envelopes (profiles) plus valley detection and centroidization or intensoid calculation. Batch processing, resolution interpolation, wrapper, adduct calculations and molecular formula parsing. Loos, M., Gerber, C., Corona, F., Hollender, J., Singer, H. (2015) <doi:10.1021/acs.analchem.5b00941>.

Statistical tool set for population genetics. The package provides following functions: 1) empirical Bayes estimator of Fst and other measures of genetic differentiation, 2) regression analysis of environmental effects on genetic differentiation using bootstrap method, 3) interfaces to read and manipulate GENEPOP format data files and allele/haplotype frequency format files.

Extends the capabilities for flexible partitioning and model-based clustering available in the packages flexclust and flexmix to handle ordinal and mixed-with-ordinal data types via new distance, centroid and driver functions that make various assumptions regarding ordinality. Using them within the flex-scheme allows for easy comparisons across methods.

High-order functions for data manipulation : sort or group data, given one or more auxiliary functions. Functions are inspired by other pure functional programming languages ('Haskell mainly). The package also provides built-in function operators for creating compact anonymous functions, as well as the possibility to use the purrr package syntax.

Function factories are functions that make functions. They can be confusing to construct. Straightforward techniques can produce functions that are fragile or hard to understand. While more robust techniques exist to construct function factories, those techniques can be confusing. This package is designed to make it easier to construct function factories.

Calculates Agresti's generalized odds ratios. For a randomly selected pair of observations from two groups, calculates the odds that the second group will have a higher scoring outcome than that of the first group. Package provides hypothesis testing for if this odds ratio is significantly different to 1 (equal chance).

Estimate risk caused by two extreme and dependent forcing variables using bivariate extreme value models as described in Zheng, Westra, and Sisson (2013) <doi:10.1016/j.jhydrol.2013.09.054>; Zheng, Westra and Leonard (2014) <doi:10.1002/2013WR014616>; Zheng, Leonard and Westra (2015) <doi:10.2166/hydro.2015.052>.

This package creates HTML strings to embed tables, images or graphs in pop-ups of interactive maps created with packages like leaflet or mapview'. Handles local images located on the file system or via remote URL. Handles graphs created with lattice or ggplot2 as well as interactive plots created with htmlwidgets'.

Access and Analyze Official Development Assistance (ODA) data using the OECD API <https://gitlab.algobank.oecd.org/public-documentation/dotstat-migration/-/raw/main/OECD_Data_API_documentation.pdf>. ODA data includes sovereign-level aid data such as key aggregates (DAC1), geographical distributions (DAC2A), project-level data (CRS), and multilateral contributions (Multisystem).

This package provides tools to analyse, interpret and understand air pollution data. Data are typically regular time series and air quality measurement, meteorological data and dispersion model output can be analysed. The package is described in Carslaw and Ropkins (2012, <doi:10.1016/j.envsoft.2011.09.008>) and subsequent papers.

Designed to enhance data validation and management processes by employing a set of functions that read a set of rules from a CSV or Excel file and apply them to a dataset. Funded by the National Renewable Energy Laboratory and Possibility Lab, maintained by the Moore Institute for Plastic Pollution Research.

Improving graphics by ameliorating order effects, using Eulerian tours and Hamiltonian decompositions of graphs. References for the methods presented here are C.B. Hurley and R.W. Oldford (2010) <doi:10.1198/jcgs.2010.09136> and C.B. Hurley and R.W. Oldford (2011) <doi:10.1007/s00180-011-0229-5>.

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.

Function for the computation of fractal dimension based on mass of soil particle size distribution by Tyler & Wheatcraft (1992) <doi:10.2136/sssaj1992.03615995005600020005x>. It also provides functions for calculation of mean weight and geometric mean diameter of particle size distribution by Perfect et al. (1992) <doi:10.2136/sssaj1992.03615995005600050012x>.

An implementation of a computationally efficient method to fit large-scale interaction models based on the reluctant interaction selection principle. The method and its properties are described in greater depth in Yu, G., Bien, J., and Tibshirani, R.J. (2019) "Reluctant interaction modeling", which is available at <arXiv:1907.08414>.

Does prediction in the case of a censored survival outcome, or a regression outcome, using the "supervised principal component" approach. Superpc is especially useful for high-dimensional data when the number of features p dominates the number of samples n (p >> n paradigm), as generated, for instance, by high-throughput technologies.

Fits, spatially predicts and temporally forecasts large amounts of space-time data using [1] Bayesian Gaussian Process (GP) Models, [2] Bayesian Auto-Regressive (AR) Models, and [3] Bayesian Gaussian Predictive Processes (GPP) based AR Models for spatio-temporal big-n problems. Bakar and Sahu (2015) <doi:10.18637/jss.v063.i15>.

Get sun position, sunlight phases (times for sunrise, sunset, dusk, etc.), moon position and lunar phase for the given location and time. Most calculations are based on the formulas given in Astronomy Answers articles about position of the sun and the planets : <https://www.aa.quae.nl/en/reken/zonpositie.html>.

This package provides a set of measures of dissimilarity between time series to perform time series clustering. Metrics based on raw data, on generating models and on the forecast behavior are implemented. Some additional utilities related to time series clustering are also provided, such as clustering algorithms and cluster evaluation metrics.

The goal of vetiver is to provide fluent tooling to version, share, deploy, and monitor a trained model. Functions handle both recording and checking the model's input data prototype, and predicting from a remote API endpoint. The vetiver package is extensible, with generics that can support many kinds of models.

The PSMatch package helps proteomics practitioners to load, handle and manage peptide spectrum matches. It provides functions to model peptide-protein relations as adjacency matrices and connected components, visualise these as graphs and make informed decision about shared peptide filtering. The package also provides functions to calculate and visualise MS2 fragment ions.

This package provides a function to format R source code. Spaces and indent will be added to the code automatically, and comments will be preserved under certain conditions, so that R code will be more human-readable and tidy. There is also a Shiny app as a user interface in this package.

This package offers features plots for mlr3 objects such as tasks, learners, predictions, benchmark results, tuning instances and filters via the autoplot() generic of ggplot2. The mlr3viz package draws plots with the viridis color palette and applies the minimal theme. Visualizations include barplots, boxplots, histograms, ROC curves, and precision-recall curves.

This package provides tools to identify global ("unknown" or "free") objects in R expressions by code inspection using various strategies, e.g. conservative or liberal. The objective of this package is to make it as simple as possible to identify global objects for the purpose of exporting them in distributed compute environments.