Simple Bootstrap Routines

Simple bootstrap routines.

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) .

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.

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 Performance Remote File System, Database and 'Geospatial' Access Using 'duckdb'

Provides friendly wrappers for creating 'duckdb'-backed connections to tabular datasets ('csv', parquet, etc) on local or remote file systems. This mimics the behaviour of "open_dataset" in the 'arrow' package, but in addition to 'S3' file system also generalizes to any list of 'http' URLs.

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.

Predictive (Classification and Regression) Models Homologator

Methods to unify the different ways of creating predictive models and their different predictive formats for classification and regression. It includes methods such as K-Nearest Neighbors Schliep, K. P. (2004) , Decision Trees Leo Breiman, Jerome H. Friedman, Richard A. Olshen, Charles J. Stone (2017) , ADA Boosting Esteban Alfaro, Matias Gamez, Noelia García (2013) , Extreme Gradient Boosting Chen & Guestrin (2016) , Random Forest Breiman (2001) , Neural Networks Venables, W. N., & Ripley, B. D. (2002) , Support Vector Machines Bennett, K. P. & Campbell, C. (2000) , Bayesian Methods Gelman, A., Carlin, J. B., Stern, H. S., & Rubin, D. B. (1995) , Linear Discriminant Analysis Venables, W. N., & Ripley, B. D. (2002) , Quadratic Discriminant Analysis Venables, W. N., & Ripley, B. D. (2002) , Logistic Regression Dobson, A. J., & Barnett, A. G. (2018) and Penalized Logistic Regression Friedman, J. H., Hastie, T., & Tibshirani, R. (2010) .

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.

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) .

Pipe-Friendly Framework for Basic Statistical Tests

Provides a simple and intuitive pipe-friendly framework, coherent with the 'tidyverse' design philosophy, for performing basic statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and correlation analyses. The output of each test is automatically transformed into a tidy data frame to facilitate visualization. Additional functions are available for reshaping, reordering, manipulating and visualizing correlation matrix. Functions are also included to facilitate the analysis of factorial experiments, including purely 'within-Ss' designs (repeated measures), purely 'between-Ss' designs, and mixed 'within-and-between-Ss' designs. It's also possible to compute several effect size metrics, including "eta squared" for ANOVA, "Cohen's d" for t-test and 'Cramer V' for the association between categorical variables. The package contains helper functions for identifying univariate and multivariate outliers, assessing normality and homogeneity of variances.