Decision Curve Analysis for Model Evaluation

Diagnostic and prognostic models are typically evaluated with measures of accuracy that do not address clinical consequences. Decision-analytic techniques allow assessment of clinical outcomes, but often require collection of additional information may be cumbersome to apply to models that yield a continuous result. Decision curve analysis is a method for evaluating and comparing prediction models that incorporates clinical consequences, requires only the data set on which the models are tested, and can be applied to models that have either continuous or dichotomous results. See the following references for details on the methods: Vickers (2006) , Vickers (2008) , and Pfeiffer (2020) .

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) .

Extending 'gt' for Beautiful HTML Tables

Provides additional functions for creating beautiful tables with 'gt'. The functions are generally wrappers around boilerplate or adding opinionated niche capabilities and helpers functions.

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.

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.

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) .

Tools for 'Box Geometry Model' (BGM) Files and Topology for the Atlantis Ecosystem Model

Facilities for working with Atlantis box-geometry model (BGM) files. Atlantis is a deterministic, biogeochemical, whole-of-ecosystem model. Functions are provided to read from BGM files directly, preserving their internal topology, as well as helper functions to generate spatial data from these mesh forms. This functionality aims to simplify the creation and modification of box and geometry as well as the ability to integrate with other data sources.