Title: Functions to analyze and visualize likert type items
Author: Jason Bryer <jason@bryer.org>, Kimberly Speerschneider
Description: Functions to analyze and visualize likert type itemss

Description: Functions to analyze and visualize likert type items

Title: Functions to Analyze and Visualize Likert Type Items
Description: Functions to analyze and visualize likert type items.

Title: Analysis and Visualization Likert Items
Description: An approach to analyzing Likert response items, with an emphasis on visualizations.
The stacked bar plot is the preferred method for presenting Likert results. Tabular results
are also implemented along with density plots to assist researchers in determining whether
Likert responses can be used quantitatively instead of qualitatively. See the likert(),
summary.likert(), and plot.likert() functions to get started.

Title: Metabolomics Personalized Pathway Analysis Tool
person("Fadhl", "Alakwaa", email = "falakwaa@hawaii.edu", role = c("aut", "cre")),
person("Sijia", "Huang", email = "scarlettcanny@gmail.com", role = c( "aut")))
Description: Computes the pathway deregulation score for a given set of metabolites, selects the pathways with the highest mutual information and then uses them to build a classifier. F. Alakwaa, S. Huang, and L. Garmire (2018) <doi:10.1101/283408>.
Imports: caret, corrplot, devtools, dplyr, e1071, gbm, ggplot2, glmnet,
hash, Hmisc, infotheo, Matrix, pamr, R.oo, princurve, pROC,

person("Xinying", "Fang", email = "xinyingf@umich.edu", role = c("aut")),
person("Yu", "Liu", email = "uiluy@umich.edu", role = "aut"),
person("Zhijie", "Ren", email = "rzj@umich.edu", role = "aut"),
person("Fadhl", "Alakwaa", email = "falakwaa@hawaii.edu", role = "aut"),
person("Sijia", "Huang", email = "scarlettcanny@gmail.com", role = "aut"),
person("Lana", "Garmire", email = "lgarmire@med.umich.edu", role = c("aut","cre")))
Description: A personalized metabolites and pathway analysis tool. With the metabolites data provided by users, lilikoi maps the metabolites data into pathways and calculates pathway deregulation scores. It enables users to perform exploratory analysis, classification and prognosis analysis on both metabolites and pathways. References: Fadhl M AlAkwaa, Breck Yunits, Sijia Huang, Hassam Alhajaji, Lana X Garmire <doi.org/10.1093/gigascience/giy136> H. Paul Benton <http://www.metabolomics-forum.com/index.php?topic=281.0> Jeff Xia <https://github.com/cangfengzhe/Metabo/blob/master/MetaboAnalyst/website/name_match.R> Travers Ching, Xun Zhu, Lana X. Garmire (2018) <doi:10.1371/journal.pcbi.1006076>.
Imports: car, caret, dplyr, gbm, ggplot2, glmnet, h2o, impute,
infotheo, limma, M3C, Metrics, MLmetrics, parallel, pathifier,
pathview, plyr, preprocessCore, pROC, RCy3, reticulate,
reshape, RWeka, scales, stringr, survminer, survival