Advanced Processing and Chart Generation from activPAL Events Files

Contains functions to generate pre-defined summary statistics from activPAL events files . The package also contains functions to produce informative graphics that visualise physical activity behaviour and trends. This includes generating graphs that align physical activity behaviour with additional time based observations described by other data sets, such as sleep diaries and continuous glucose monitoring data.

Data sets from "Introductory Statistics for Engineering Experimentation"

Datasets from Nelson, Coffin and Copeland "Introductory Statistics for Engineering Experimentation" (Elsevier, 2003) with sample code.

Inferring Differentially Expressed Genes using Generalized Linear Mixed Models

Genes that are differentially expressed between two or more experimental conditions can be detected in RNA-Seq. A high biological variability may impact the discovery of these genes once it may be divergent between the fixed effects. However, this variability can be covered by the random effects. 'DEGRE' was designed to identify the differentially expressed genes considering fixed and random effects on individuals. These effects are identified earlier in the experimental design matrix. 'DEGRE' has the implementation of preprocessing procedures to clean the near zero gene reads in the count matrix, normalize by 'RLE' published in the 'DESeq2' package, 'Love et al. (2014)' and it fits a regression for each gene using the Generalized Linear Mixed Model with the negative binomial distribution, followed by a Wald test to assess the regression coefficients.

Downloading, Reading and Analyzing POF Microdata - Package in Development

Provides tools for downloading, reading and analyzing the POF, a household survey from Brazilian Institute of Geography and Statistics - IBGE. The data must be downloaded from the official website < https://www.ibge.gov.br/>. Further analysis must be made using package 'survey'.

Lightweight Reproducible Reporting

Order, create and store reports from R. By defining a lightweight interface around the inputs and outputs of an analysis, a lot of the repetitive work for reproducible research can be automated. We define a simple format for organising and describing work that facilitates collaborative reproducible research and acknowledges that all analyses are run multiple times over their lifespans.

Analysis Functions of Respiratory Data

Provides functions for the complete analysis of respiratory data. Consists of a set of functions that allow to preprocessing respiratory data, calculate both regular statistics and nonlinear statistics, conduct group comparison and visualize the results. Especially, Power Spectral Density ('PSD') (A. Eke (2000) ), 'MultiScale Entropy(MSE)' ('Madalena Costa(2002)' ) and 'MultiFractal Detrended Fluctuation Analysis(MFDFA)' ('Jan W.Kantelhardt' (2002) ) were applied for the analysis of respiratory data.

Portfolio Analysis, Including Numerical Methods for Optimization of Portfolios

Portfolio optimization and analysis routines and graphics.

Data Sets from Mixed-Effects Models in S

Data sets and sample analyses from Pinheiro and Bates, "Mixed-effects Models in S and S-PLUS" (Springer, 2000).

Data Sets for Psychometric Modeling

Collection of data sets from various assessments that can be used to evaluate psychometric models. These data sets have been analyzed in the following papers that introduced new methodology as part of the application section: Jimenez, A., Balamuta, J. J., & Culpepper, S. A. (2023) , Culpepper, S. A., & Balamuta, J. J. (2021) , Yinghan Chen et al. (2021) , Yinyin Chen et al. (2020) , Culpepper, S. A. (2019a) , Culpepper, S. A. (2019b) , Culpepper, S. A., & Chen, Y. (2019) , Culpepper, S. A., & Balamuta, J. J. (2017) , and Culpepper, S. A. (2015) .

Forest Structure Extrapolation with R

Set of tools to streamline the modeling of the relationship between satellite imagery time series or any other environmental information, such as terrain elevation, with forest structural attributes derived from 3D point cloud data and their subsequent imputation over the broader landscape.