Contains two functions that are intended to make
tuning supervised learning methods easy. The eztune function uses a
genetic algorithm or Hooke-Jeeves optimizer to find the best
set of tuning parameters. The user can choose the optimizer, the
learning method, and if optimization will be based on accuracy
obtained through validation error, cross validation, or resubstitution.
The function eztune.cv will compute a cross validated error rate. The purpose
of eztune_cv is to provide a cross validated accuracy or MSE when
resubstitution or validation data are used for optimization because
error measures from both approaches can be misleading.
knitr, rmarkdown, mlbench, doParallel, parallel

Tunes AdaBoost, Elastic Net, Support Vector Machines, and
Gradient Boosting Machines
ada, e1071, GA, gbm, optimx, rpart, glmnet, ROCR

ada, e1071, GA, gbm, optimx, rpart, glmnet, ROCR, BiocStyle
knitr, rmarkdown, mlbench, doParallel, parallel, dplyr,
yardstick, rsample

Multiple Locus Association Mapping on a Genome-Wide Scale
c(
person("Andrew", "George", role=c("aut", "cre"), email="andrew.george@csiro.au"),
person("Joshua", "Bowden", role="ctb"),
person("Ryan", "Stephenson", role="ctb"),
person("Hyun", "Kang", role="ctb"),
person("Noah", "Zaitlen", role="ctb"),
person("Claire", "Wade", role="ctb"),
person("Andrew", "Kirby", role="ctb"),
person("David", "Heckerman", role="ctb"),
person("Mark", "Daly", role="ctb"),
person("Eleazar", "Eskin", role="ctb") )
Andrew George [aut, cre],
Joshua Bowden [ctb],
Ryan Stephenson [ctb],
Hyun Kang [ctb],
Noah Zaitlen [ctb],
Claire Wade [ctb],
Andrew Kirby [ctb],
David Heckerman [ctb],
Mark Daly [ctb],
Eleazar Eskin [ctb]
An implementation of multiple-locus association mapping on a genome-wide scale. 'Eagle' can handle inbred or outbred study populations, populations of arbitrary unknown complexity, and data larger than the memory capacity of the computer. Since 'Eagle' is based on linear mixed models, it is best suited to the analysis of data on continuous traits. However, it can tolerate non-normal data. 'Eagle' reports, as its findings, the best set of snp in strongest association with a trait. To perform an analysis, run 'OpenGUI()'. This  opens a web browser to the menu-driven user interface for the input of data, and for performing genome-wide analysis.
matrixcalc, shiny, shinythemes, shinyBS, shinyjs, stats,
utils, parallel, data.table, tcltk