Selection Threshold Optimized Empirically via Splitting

Implements variable selection procedures for low to moderate size generalized linear regressions models. It includes the STOPES functions for linear regression (Capanu M, Giurcanu M, Begg C, Gonen M, Optimized variable selection via repeated data splitting, Statistics in Medicine, 2020, 19(6):2167-2184) as well as subsampling based optimization methods for generalized linear regression models (Marinela Capanu, Mihai Giurcanu, Colin B Begg, Mithat Gonen, Subsampling based variable selection for generalized linear models).

Reliably Return the Source and Call Location of a Command

Robust and reliable functions to return informative outputs to console with the run or source location of a command. This can be from the 'RScript'/R terminal commands or 'RStudio' console, source editor, 'Rmarkdown' document and a Shiny application.

Tools for Managing Classes on GitHub

Interface for the GitHub API that enables efficient management of courses on GitHub. It has a functionality for managing organizations, teams, repositories, and users on GitHub and helps automate most of the tedious and repetitive tasks around creating and distributing assignments.

Interface to Geometry Engine - Open Source ('GEOS')

Interface to Geometry Engine - Open Source ('GEOS') using the C 'API' for topology operations on geometries. Please note that 'rgeos' will be retired during October 2023, plan transition to 'sf' or 'terra' functions using 'GEOS', or the 'geos' package, at your earliest convenience (see < https://r-spatial.org/r/2023/05/15/evolution4.html> and earlier blogs for guidance). The 'GEOS' library is external to the package, and, when installing the package from source, must be correctly installed first. Windows and Mac Intel OS X binaries are provided on 'CRAN'. ('rgeos' >= 0.5-1): Up to and including 'GEOS' 3.7.1, topological operations succeeded with some invalid geometries for which the same operations fail from and including 'GEOS' 3.7.2. The 'checkValidity=' argument defaults and structure have been changed, from default FALSE to integer default '0L' for 'GEOS' < 3.7.2 (no check), '1L' 'GEOS' >= 3.7.2 (check and warn). A value of '2L' is also provided that may be used, assigned globally using 'set_RGEOS_CheckValidity(2L)', or locally using the 'checkValidity=2L' argument, to attempt zero-width buffer repair if invalid geometries are found. The previous default (FALSE, now '0L') is fastest and used for 'GEOS' < 3.7.2, but will not warn users of possible problems before the failure of topological operations that previously succeeded. From 'GEOS' 3.8.0, repair of geometries may also be attempted using 'gMakeValid()', which may, however, return a collection of geometries of different types.

Generate Personality Insights Sunburst Diagrams

Generates Personality Insights sunburst diagrams based on 'IBM Watson' Personality Insights service output.

Pain Assessment at Withdrawal Speeds (PAWS)

Automated pain scoring from paw withdrawal tracking data. Based on Jones et al. (2020) "A machine-vision approach for automated pain measurement at millisecond timescales" .

Loewe's Additivity

Estimate model parameters to determine whether two compounds have synergy, antagonism, or Loewe's Additivity.

Exact Rate Ratio Test

Performs exact rate ratio tests.

Small-Sample Adjustments for Wald Tests Using Sandwich Estimators

Tests coefficients with sandwich estimator of variance and with small samples. Regression types supported are gee, linear regression, and conditional logistic regression.

An R Interface to the JBrowse 2 Genome Browser

Provides an R interface to the JBrowse 2 genome browser. Enables embedding a JB2 genome browser in a Shiny app or R Markdown document. The browser can also be launched from an interactive R console. The browser can be loaded with a variety of common genomics data types, and can be used with a custom theme.