Fast 'Rcpp' Implementation of Gauss-Hermite Quadrature

Fast, numerically-stable Gauss-Hermite quadrature rules and utility functions for adaptive GH quadrature. See Liu, Q. and Pierce, D. A. (1994) for a reference on these methods.

Models for Data from Unmarked Animals

Fits hierarchical models of animal abundance and occurrence to data collected using survey methods such as point counts, site occupancy sampling, distance sampling, removal sampling, and double observer sampling. Parameters governing the state and observation processes can be modeled as functions of covariates. References: Kellner et al. (2023) , Fiske and Chandler (2011) .

Perform Inference on Algorithm-Agnostic Variable Importance

Calculate point estimates of and valid confidence intervals for nonparametric, algorithm-agnostic variable importance measures in high and low dimensions, using flexible estimators of the underlying regression functions. For more information about the methods, please see Williamson et al. (Biometrics, 2020), Williamson et al. (JASA, 2021), and Williamson and Feng (ICML, 2020).

Integrating Phylogenies and Ecology

Functions for phylocom integration, community analyses, null-models, traits and evolution. Implements numerous ecophylogenetic approaches including measures of community phylogenetic and trait diversity, phylogenetic signal, estimation of trait values for unobserved taxa, null models for community and phylogeny randomizations, and utility functions for data input/output and phylogeny plotting. A full description of package functionality and methods are provided by Kembel et al. (2010) .

Smoothing Methods for Nonparametric Regression and Density Estimation

This is software linked to the book 'Applied Smoothing Techniques for Data Analysis - The Kernel Approach with S-Plus Illustrations' Oxford University Press.

Useful Tools for Structural Equation Modeling

Provides miscellaneous tools for structural equation modeling, many of which extend the 'lavaan' package. For example, latent interactions can be estimated using product indicators (Lin et al., 2010, ) and simple effects probed; analytical power analyses can be conducted (Jak et al., 2021, ); and scale reliability can be estimated based on estimated factor-model parameters.

High-Throughput Screening for Plate Based Essays

Can be used to carry out extraction, normalization, quality control (QC), candidate hits identification and visualization for plate based assays, in drug discovery. The package methods were applied in H. W. Choi et al. "Identification of Novel Mast Cell Activators Using Cell-Based High-Throughput Screening", SLAS Discovery 24(6), 2019. This project was funded by the Division of Allergy, Immunology, and Transplantation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under contract No. HHSN272201400054C entitled "Adjuvant Discovery For Vaccines Against West Nile Virus and Influenza", awarded to Duke University and lead by Drs. Herman Staats and Soman Abraham.

Visualizations of Distributions and Uncertainty

Provides primitives for visualizing distributions using 'ggplot2' that are particularly tuned for visualizing uncertainty in either a frequentist or Bayesian mode. Both analytical distributions (such as frequentist confidence distributions or Bayesian priors) and distributions represented as samples (such as bootstrap distributions or Bayesian posterior samples) are easily visualized. Visualization primitives include but are not limited to: points with multiple uncertainty intervals, eye plots (Spiegelhalter D., 1999) < https://ideas.repec.org/a/bla/jorssa/v162y1999i1p45-58.html>, density plots, gradient plots, dot plots (Wilkinson L., 1999) , quantile dot plots (Kay M., Kola T., Hullman J., Munson S., 2016) , complementary cumulative distribution function barplots (Fernandes M., Walls L., Munson S., Hullman J., Kay M., 2018) , and fit curves with multiple uncertainty ribbons.

Gravitational and Magnetic Attraction of 3-D Vertical Rectangular Prisms

Computes the gravitational and magnetic anomalies generated by 3-D vertical rectangular prisms at specific observation points using the method of Plouff (1976) .

Graphical Analysis of Structural Causal Models

A port of the web-based software 'DAGitty', available at < https://dagitty.net>, for analyzing structural causal models (also known as directed acyclic graphs or DAGs). This package computes covariate adjustment sets for estimating causal effects, enumerates instrumental variables, derives testable implications (d-separation and vanishing tetrads), generates equivalent models, and includes a simple facility for data simulation.