Helps fisheries scientists collect measurements from calcified structures and back-calculate estimated lengths at previous ages using standard procedures and models. This is intended to replace much of the functionality provided by the now out-dated fishBC software (<https://fisheries.org/bookstore/all-titles/software/70317/>).

Fast tools for unequal probability sampling in multi-dimensional spaces, implemented in Rust for high performance. The package offers a wide range of methods, including Sampford (Sampford, 1967, <doi:10.1093/biomet/54.3-4.499>) and correlated Poisson sampling (Bondesson and Thorburn, 2008, <doi:10.1111/j.1467-9469.2008.00596.x>), pivotal sampling (Deville and Tillé, 1998, <doi:10.1093/biomet/91.4.893>), and balanced sampling such as the cube method (Deville and Tillé, 2004, <doi:10.1093/biomet/91.4.893>) to ensure auxiliary totals are respected. Spatially balanced approaches, including the local pivotal method (Grafström et al., 2012, <doi:10.1111/j.1541-0420.2011.01699.x>), spatially correlated Poisson sampling (Grafström, 2012, <doi:10.1016/j.jspi.2011.07.003>), and locally correlated Poisson sampling (Prentius, 2024, <doi:10.1002/env.2832>), provide efficient designs when the target variable is linked to auxiliary information.

This package implements the regularized exponentially tilted empirical likelihood method. Details of the method are given in Kim, MacEachern, and Peruggia (2023) <doi:10.48550/arXiv.2312.17015>. This work was supported by the U.S. National Science Foundation under Grants No. SES-1921523 and DMS-2015552.

Generates pseudo-random vectors that follow an arbitrary von Mises-Fisher distribution on a sphere. This method is fast and efficient when generating a large number of pseudo-random vectors. Functions to generate random variates and compute density for the distribution of an inner product between von Mises-Fisher random vector and its mean direction are also provided. Details are in Kang and Oh (2024) <doi:10.1007/s11222-024-10419-3>.

Truncated Newton function minimization with bounds constraints based on the Matlab'/'Octave codes of Stephen Nash.

Enhances the R Optimization Infrastructure ('ROI') package with the Embedded Conic Solver ('ECOS') for solving conic optimization problems.

The r4sub package is a meta-package that installs and loads core packages of the R4SUB (R for Regulatory Submission) clinical submission readiness ecosystem. Loading r4sub attaches r4subcore', r4subtrace', r4subscore', r4subrisk', r4subdata', and r4subprofile'.

Read Statistical Data and Metadata Exchange (SDMX) XML data. This the main transmission format used in official statistics. Data can be imported from local SDMX-ML files or a SDMX web-service and will be read in as is into a dataframe object. The RapidXML C++ library <https://rapidxml.sourceforge.net/> is used to parse the XML data.

This package provides a toolkit for making antigenic maps from immunological assay data, in order to quantify and visualize antigenic differences between different pathogen strains as described in Smith et al. (2004) <doi:10.1126/science.1097211> and used in the World Health Organization influenza vaccine strain selection process. Additional functions allow for the diagnostic evaluation of antigenic maps and an interactive viewer is provided to explore antigenic relationships amongst several strains and incorporate the visualization of associated genetic information.

Access the Refuge API, a web-application for locating trans and intersex-friendly restrooms, including unisex and accessible restrooms. Includes data on the location of restrooms, along with directions, comments, user ratings and amenities. Coverage is global, but data is most comprehensive in the United States. See <https://www.refugerestrooms.org/api/docs/> for full API documentation.

This package provides a model agnostic tool for white-box model trained on features extracted from a black-box model. For more information see: Gosiewska et al. (2020) <doi:10.1016/j.dss.2021.113556>.

This package provides a quantile regression method for multivariate data to find linear combinations of explanatory and response variables generalizing canonical correlation. The package consists of functions, rqcan() for fitting the coefficients, and summary.rqcan(), which calls a bootstrap function. For details, see the help files for rqcan() and summary.rqcan(), and the reference: Portnoy (2022) <doi:10.1016/j.jmva.2022.105071>.

This function conducts variation partitioning and hierarchical partitioning to calculate the unique, shared (referred as to "common") and individual contributions of each predictor (or matrix) towards explained variation (R-square and adjusted R-square) on canonical analysis (RDA,CCA and db-RDA), applying the algorithm of Lai J.,Zou Y., Zhang J.,Peres-Neto P.(2022) Generalizing hierarchical and variation partitioning in multiple regression and canonical analyses using the rdacca.hp R package.Methods in Ecology and Evolution,13: 782-788 <DOI:10.1111/2041-210X.13800>.

Robust Location and Scatter Estimation and Robust Multivariate Analysis with High Breakdown Point for Incomplete Data (missing values) (Todorov et al. (2010) <doi:10.1007/s11634-010-0075-2>).

This package produces Shiny applications for different types of popular functional data analyses. The functional data analyses are implemented in the refund package, then refund.shiny reads in the refund object and implements an object-specific set of plots based on the object class using S3.

This package provides a random-effects stochastic model that allows quick detection of clonal dominance events from clonal tracking data collected in gene therapy studies. Starting from the Ito-type equation describing the dynamics of cells duplication, death and differentiation at clonal level, we first considered its local linear approximation as the base model. The parameters of the base model, which are inferred using a maximum likelihood approach, are assumed to be shared across the clones. Although this assumption makes inference easier, in some cases it can be too restrictive and does not take into account possible scenarios of clonal dominance. Therefore we extended the base model by introducing random effects for the clones. In this extended formulation the dynamic parameters are estimated using a tailor-made expectation maximization algorithm. Further details on the methods can be found in L. Del Core et al., (2022) <doi:10.1101/2022.05.31.494100>.

Implemented fast and memory-efficient Notch-filter, Welch-periodogram, discrete wavelet spectrogram for minutes of high-resolution signals, fast 3D convolution, image registration, 3D mesh manipulation; providing fundamental toolbox for intracranial Electroencephalography (iEEG) pipelines. Documentation and examples about RAVE project are provided at <https://rave.wiki>, and the paper by John F. Magnotti, Zhengjia Wang, Michael S. Beauchamp (2020) <doi:10.1016/j.neuroimage.2020.117341>; see citation("ravetools") for details.

The evaluation criteria of rangeland health, condition and landscape function analysis based on species diversity and functional diversity of rangeland plant communities.

This package provides a programmatic interface to web-services of YouTheria. YouTheria is an online database of mammalian trait data <http://www.utheria.org/>.

This package provides a collection of randomization tests, data sets and examples. The current version focuses on five testing problems and their implementation in empirical work. First, it facilitates the empirical researcher to test for particular hypotheses, such as comparisons of means, medians, and variances from k populations using robust permutation tests, which asymptotic validity holds under very weak assumptions, while retaining the exact rejection probability in finite samples when the underlying distributions are identical. Second, the description and implementation of a permutation test for testing the continuity assumption of the baseline covariates in the sharp regression discontinuity design (RDD) as in Canay and Kamat (2018) <https://goo.gl/UZFqt7>. More specifically, it allows the user to select a set of covariates and test the aforementioned hypothesis using a permutation test based on the Cramer-von Misses test statistic. Graphical inspection of the empirical CDF and histograms for the variables of interest is also supported in the package. Third, it provides the practitioner with an effortless implementation of a permutation test based on the martingale decomposition of the empirical process for testing for heterogeneous treatment effects in the presence of an estimated nuisance parameter as in Chung and Olivares (2021) <doi:10.1016/j.jeconom.2020.09.015>. Fourth, this version considers the two-sample goodness-of-fit testing problem under covariate adaptive randomization and implements a permutation test based on a prepivoted Kolmogorov-Smirnov test statistic. Lastly, it implements an asymptotically valid permutation test based on the quantile process for the hypothesis of constant quantile treatment effects in the presence of an estimated nuisance parameter.

Yandex Clickhouse (<https://clickhouse.com/>) is a high-performance relational column-store database to enable big data exploration and analytics scaling to petabytes of data. Methods are provided that enable working with Yandex Clickhouse databases via DBI methods and using dplyr'/'dbplyr idioms.

This package provides a fast implementation of the greedy algorithm for the set cover problem using Rcpp'.

Standardized methods for calculating common important derived physical features of lakes including water density based based on temperature, thermal layers, thermocline depth, lake number, Wedderburn number, Schmidt stability and others.

Mass rollup for a Bill of Materials is an example of a class of computations in which elements are arranged in a tree structure and some property of each element is a computed function of the corresponding values of its child elements. Leaf elements, i.e., those with no children, have values assigned. In many cases, the combining function is simple arithmetic sum; in other cases (e.g., mass properties), the combiner may involve other information such as the geometric relationship between parent and child, or statistical relations such as root-sum-of-squares (RSS). This package implements a general function for such problems. It is adapted to specific recursive computations by functional programming techniques; the caller passes a function as the update parameter to rollup() (or, at a lower level, passes functions as the get, set, combine, and override parameters to update_prop()) at runtime to specify the desired operations. The implementation relies on graph-theoretic algorithms from the igraph package of Csárdi, et al. (2006 <doi:10.5281/zenodo.7682609>).