Compute Contributional Diversity Metrics

Compute alpha and beta contributional diversity metrics, which is intended for linking taxonomic and functional microbiome data. See 'GitHub' repository for the tutorial: < https://github.com/gavinmdouglas/FuncDiv/wiki>. Citation: Gavin M. Douglas, Sunu Kim, Morgan G. I. Langille, B. Jesse Shapiro (2023) .

Tool for Unbiased Literature Searching and Gene List Curation

Designed for genomic and proteomic data analysis, enabling unbiased PubMed searching, protein interaction network visualization, and comprehensive data summarization. This package aims to help users identify novel targets within their data sets based on protein network interactions and publication precedence of target's association with research context based on literature precedence. Methods in this package are described in detail in: Douglas (Year) . Key functionalities of this package also leverage methodologies from previous works, such as: - Szklarczyk et al. (2023) - Winter (2017) .

Benchmark the Performance of 'shiny' Applications

Compare performance between different versions of a 'shiny' application based on 'git' references.

'R' 'Markdown' Format for 'shower' Presentations

'R' 'Markdown' format for 'shower' presentations, see < https://github.com/shower/shower>.

Quick Multivariate Graphs

Functions used for graphing in multivariate contexts. These functions are designed to support produce reasonable graphs with minimal input of graphing parameters. The motivation for these functions was to support students learning multivariate concepts and R - there may be other functions and packages better-suited to practical data analysis. For details about the ellipse methods see Johnson and Wichern (2007, ISBN:9780131877153).

Approximate Marginal Inference for Regression-Scale Models

Implements likelihood inference based on higher order approximations for linear nonnormal regression models.

Probability of Sporulation Potential in MAGs

Implements an ensemble machine learning approach to predict the sporulation potential of metagenome-assembled genomes (MAGs) from uncultivated Firmicutes based on the presence/absence of sporulation-associated genes.

Collection of Household Survey Packages Conducted by IBGE

Provides access to packages developed for downloading, reading and analyzing microdata from household surveys in Integrated System of Household Surveys - SIPD conducted by Brazilian Institute of Geography and Statistics - IBGE. More information can be obtained from the official website < https://www.ibge.gov.br/>.

Estimating Causal Dose Response Functions

Functions and data to estimate causal dose response functions given continuous, ordinal, or binary treatments. A description of the methods is given in Galagate (2016) < https://drum.lib.umd.edu/handle/1903/18170>.

Microeconomic Analysis and Modelling

Various tools for microeconomic analysis and microeconomic modelling, e.g. estimating quadratic, Cobb-Douglas and Translog functions, calculating partial derivatives and elasticities of these functions, and calculating Hessian matrices, checking curvature and preparing restrictions for imposing monotonicity of Translog functions.