Conservation Indicators using Spatial Information

Supports the assessment of the degree of conservation of taxa in conservation systems, both in ex situ [in genebanks, botanical gardens, and other repositories] and in situ [in protected natural areas]. Methods are described in Carver et al. [2021] , building on Khoury et al. [2020] , Khoury et al. [2019] , Khoury et al. [2019] , Castaneda-Alvarez et al. [2016] , and Ramirez-Villegas et al. [2010] .

'Dang' Associated New Goodies

A collection of utility functions.

Easily Download Data and Metadata from 'DataONE'

A set of tools to foster the development of reproducible analytical workflow by simplifying the download of data and metadata from 'DataONE' (< https://www.dataone.org>) and easily importing this information into R.

Simple Process-Led Algorithms for Simulating Habitats

This program calculates bioclimatic indices and fluxes (radiation, evapotranspiration, soil moisture) for use in studies of ecosystem function, species distribution, and vegetation dynamics under changing climate scenarios. Predictions are based on a minimum of required inputs: latitude, precipitation, air temperature, and cloudiness. Davis et al. (2017) .

A Tuning-Free Robust and Efficient Approach to High-Dimensional Regression

Provide functions to estimate the coefficients in high-dimensional linear regressions via a tuning-free and robust approach. The method was published in Wang, L., Peng, B., Bradic, J., Li, R. and Wu, Y. (2020), "A Tuning-free Robust and Efficient Approach to High-dimensional Regression", Journal of the American Statistical Association, 115:532, 1700-1714(JASA’s discussion paper), . See also Wang, L., Peng, B., Bradic, J., Li, R. and Wu, Y. (2020), "Rejoinder to “A tuning-free robust and efficient approach to high-dimensional regression". Journal of the American Statistical Association, 115, 1726-1729, ; Peng, B. and Wang, L. (2015), "An Iterative Coordinate Descent Algorithm for High-Dimensional Nonconvex Penalized Quantile Regression", Journal of Computational and Graphical Statistics, 24:3, 676-694, ; Clémençon, S., Colin, I., and Bellet, A. (2016), "Scaling-up empirical risk minimization: optimization of incomplete u-statistics", The Journal of Machine Learning Research, 17(1):2682–2717; Fan, J. and Li, R. (2001), "Variable Selection via Nonconcave Penalized Likelihood and its Oracle Properties", Journal of the American Statistical Association, 96:456, 1348-1360, .

Exploring Portfolio-Based Conjectures About Financial Instruments

The backtest package provides facilities for exploring portfolio-based conjectures about financial instruments (stocks, bonds, swaps, options, et cetera).

High-Throughput Toxicokinetics

Pre-made models that can be rapidly tailored to various chemicals and species using chemical-specific in vitro data and physiological information. These tools allow incorporation of chemical toxicokinetics ("TK") and in vitro-in vivo extrapolation ("IVIVE") into bioinformatics, as described by Pearce et al. (2017) (). Chemical-specific in vitro data characterizing toxicokinetics have been obtained from relatively high-throughput experiments. The chemical-independent ("generic") physiologically-based ("PBTK") and empirical (for example, one compartment) "TK" models included here can be parameterized with in vitro data or in silico predictions which are provided for thousands of chemicals, multiple exposure routes, and various species. High throughput toxicokinetics ("HTTK") is the combination of in vitro data and generic models. We establish the expected accuracy of HTTK for chemicals without in vivo data through statistical evaluation of HTTK predictions for chemicals where in vivo data do exist. The models are systems of ordinary differential equations that are developed in MCSim and solved using compiled (C-based) code for speed. A Monte Carlo sampler is included for simulating human biological variability (Ring et al., 2017 ) and propagating parameter uncertainty (Wambaugh et al., 2019 ). Empirically calibrated methods are included for predicting tissue:plasma partition coefficients and volume of distribution (Pearce et al., 2017 ). These functions and data provide a set of tools for using IVIVE to convert concentrations from high-throughput screening experiments (for example, Tox21, ToxCast) to real-world exposures via reverse dosimetry (also known as "RTK") (Wetmore et al., 2015 ).

A Collection of Small Text Corpora of Interesting Data

A collection of small text corpora of interesting data. It contains all data sets from 'dariusk/corpora'. Some examples: names of animals: birds, dinosaurs, dogs; foods: beer categories, pizza toppings; geography: English towns, rivers, oceans; humans: authors, US presidents, occupations; science: elements, planets; words: adjectives, verbs, proverbs, US president quotes.