Extract Shared Variation in Collections of Data Sets Using Regression Models

The algorithm extracts shared variation from a collection of data sets using regression models.



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cocoreg is an R-package for extracting shared variation in collections of datasets using regression models. The current stable release is available in CRAN:

http://cran.r-project.org/package=cocoreg

The algorithm is described in the paper:

Using regression makes extraction of shared variation in multiple datasets easy: Jussi Korpela, Andreas Henelius, Lauri Ahonen, Arto Klami, Kai Puolamäki, Data Mining and Knowledge Discovery, 2016. URL: http://dx.doi.org/10.1007/s10618-016-0465-y

The authors' version is available in this repository as cocoreg_plain.pdf. The final publication will be available at link.springer.com.

Usage

A minimal usage example:

library(cocoreg)
dc <- create_syn_data_toy()
ccr <- cocoreg(dc$data)
shared.by.all.df <- variation_shared_by(dc, 'all') #only on synthetic datasets
ggplot_dclst(list(observed = dc$data, shared = shared.by.all.df, cocoreg = ccr$data))

 
library(reshape) #importing from namespace does not work as expected
ggcompare_dclst(list(shared = shared.by.all.df, cocoreg = ccr$data))

Overview

The most important functions in cocoreg are:

  • cocoreg() which extracts shared variation from a collection of datasets

  • Functions to visualize output such as ggplot_dclst() and ggcompare_dclst() for lists of data collections, ggplot_dflst() for lists of data.frames (i.e. one data collection) and ggplot_df() for a single data.frame (a dataset)

Installation

Install the release version from CRAN:

install.packages("cocoreg")

Or the development version from GitHub:

# library(devtools)
devtools::install_github("bwrc/cocoreg-r")

News

cocoreg 0.1.1

Fixed documentation (NAMESPACE exports, spell check) and added README.md figures as part of the package in "man/figures".

cocoreg 0.1.0

Initial CRAN release upon article publication.

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("cocoreg")

0.1.1 by Jussi Korpela, a year ago


Browse source code at https://github.com/cran/cocoreg


Authors: Jussi Korpela [aut, cre], Andreas Henelius [aut], Finnish Institute of Occupational Health [cph]


Documentation:   PDF Manual  


MIT + file LICENSE license


Imports ggplot2, gridExtra, CCAGFA, RGCCA, combinat, abind, MASS, glmnet, pls, e1071, multiway, reshape

Suggests knitr, rmarkdown


See at CRAN