Metabolomics Data Analysis Functions

A collection of functions for processing and analyzing metabolite data. The namesake function mrbin() converts 1D or 2D Nuclear Magnetic Resonance data into a matrix of values suitable for further data analysis and performs basic processing steps in a reproducible way. Negative values, a common issue in such data, can be replaced by positive values (). All used parameters are stored in a readable text file and can be restored from that file to enable exact reproduction of the data at a later time. The function fia() ranks features according to their impact on classifier models, especially artificial neural network models.

DicePlot Visualization for 'ggplot2'

Provides 'ggplot2' extensions for creating dice-based visualizations where each dot position represents a specific categorical variable. The package includes 'geom_dice()' for displaying presence/absence of categorical variables using traditional dice patterns. Each dice position (1-6) represents a different category, with dots shown only when that category is present. This allows intuitive visualization of up to 6 categorical variables simultaneously.

Display and Analyze ROC Curves

Tools for visualizing, smoothing and comparing receiver operating characteristic (ROC curves). (Partial) area under the curve (AUC) can be compared with statistical tests based on U-statistics or bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.

JIRA REST API Wrapper for R

Allows to interact with the 'JIRA SERVER REST API' to analyze the retrieved data in R. For further information about the API visit < https://docs.atlassian.com/software/jira/docs/api/REST/8.9.1/>.

Extrapolate Gender, Age and Nationality of a Name

Connects to the < https://genderize.io/>, < https://agify.io/> and < https://nationalize.io/> APIs to estimate gender, age and nationality of a first name.

Run the 'Open-WBO' MaxSAT Solver

Provides a wrapper for running the bundled 'Open-WBO' Maximum Satisfiability (MaxSAT) solver (< https://github.com/sat-group/open-wbo>). Users can pass command-line arguments to the solver and capture its output as a character string or file.

PARAFAC Analysis of EEMs from DOM

'This is a user-friendly way to run a parallel factor (PARAFAC) analysis (Harshman, 1971) on excitation emission matrix (EEM) data from dissolved organic matter (DOM) samples (Murphy et al., 2013) . The analysis includes profound methods for model validation. Some additional functions allow the calculation of absorbance slope parameters and create beautiful plots.'

Query 'SWI'-'Prolog' from R

This R package connects to SWI-Prolog, < https://www.swi-prolog.org/>, so that R can send deterministic and non-deterministic queries to prolog (consult, query/submit, once, findall).

Easy Computation of Functional Diversity Indices

Computes six functional diversity indices. These are namely, Functional Divergence (FDiv), Function Evenness (FEve), Functional Richness (FRic), Functional Richness intersections (FRic_intersect), Functional Dispersion (FDis), and Rao's entropy (Q) (reviewed in Villéger et al. 2008 ). Provides efficient, modular, and parallel functions to compute functional diversity indices (preprint: ).

Translate R Expressions to 'MathML' and 'LaTeX'/'MathJax'

Translate R expressions to 'MathML' or 'MathJax'/'LaTeX' so that they can be rendered in R markdown documents and shiny apps.