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R Package for Normalizing and Transforming Numerical Data
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README.md

R Package for Normalizing and Transforming Numerical Data

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Introduction

When we fit models to data, we often do not want to use the raw data as-is. Instead, we usually want to fit models to normalized or log-scaled versions of the data. If all data elements are in [0,1], this makes it easier to pick initial parameter values for models. If there are exponential relationships present in data sets, we may want to get rid of them by log-scaling the data. This means that, after the models have been fitted, we need to transform the model back by applying the inverse of the data transformation to the model.

This package uses our functionComposeR package to construct and apply such bijective transformations. The core of this package are the Transformation and TransformedData S4 classes and the routines to construct instances of them.

Transformation allows us to specify a bijection, i.e., foward and backward function for which backward(forward(x)) = x holds (at least within the prescribed domain). Such transformations can be constructed and composed with this package. For instance, Transformation.mapIntervals(a, b, c, d) creates a Transformation whose forward function maps the elements from interval [a, b] to interval [c, d] (whereas the backward function maps [c, d] back to [a, b]). Transformation.andThen1(first, after) creates a new Transformation whose forward function corresponds to after@forward(before@forward(x)) and whose backward function corresponds to before@backward(after@backward(x)).

Instances of TransformedData hold a transformed data vector along with the Transformation that was used to create it. Several functions are defined which create such transformed dataset. For example, Transformation.normalize(d) creates a TransformedData where the data vector is a version of d normalized into [0,1]. Transformation.log(d), on the other hand, will first log-scale all elements of d and then normalize the result. If some elements in d are less or equal to zero, d is shifted into the positive domain first, by using the Transformation created by Transformation.makePositive(d).

Using Transformation.applyAll(data, transformations) you can apply a list transformations of transformations to a data set and obtain a list of resulting TransformedData instances. This list is automatically pruned to not contain two identical transformed data vectors. Transformation.applyDefault(data) will apply a set of default transformations, including plain normalization to [0,1], the negated normalization (the smallest data value maps to 1, the largest to 0), a normalized logarithmic scaling, and a negated-normalized logarithmic scaling. Both Transformation.applyAll and Transformation.applyDefault can add a TransformedData instance corresponding to the orginal data (using the identity Transformation) and do so by default.

The goal is to provide a toolbox which will allow you to automatically obtain normalized and scaled versions of data vectors along with functions to convert back and forth between the original and transformed data representation.

A transformation is furthermore accompanied by a positive complexity. Only Transformation.identity has complexity 0L. All other transformations should have a larger complexity. If we simply log-scale some data (e.g., via Transformation.log) by just applying the log function, this could have complexity 1L. If we have a transformation involving n variables whose values we decide upon, then we should pick complexity n+1L: If we first move the data by 3 units and then divide it by 2, i.e., apply something like (x+3)/}, this transformation should have a complexity of 3 - we chose two values and applied them in a function.

Motivating Example

Assume that you have the data vector

data <- c(-1, 0, 2, 6, 14, 30)

You can obtain a log-scaled and normalized version of this data by doing

Transformation.log(data)
# An object of class "TransformedData"
# Slot "transformation":
# An object of class "Transformation"
# Slot "forward":
# function (x)
# log(x + 2) * 0.288539008177793
# <environment: 0x3b5cc18>
# 
# Slot "complexity":
# [1] 5
#
# Slot "backward":
# function (x)
# exp(x = x * 3.46573590279973) - 2
# <environment: 0x3c19460>
#
# Slot "data":
# [1] 0.0 0.2 0.4 0.6 0.8 1.0

The resulting data vector shown above has a lot of nice properties. First, you know that all elements are in [0, 1], which will help when looking for initial values when fitting models. Second, in this example, the data became beautifully linear. If you were fitting a linear model to this, you can then translate this model back into the original data space easily using the backward and forward functions. Furthermore, we also get some measure of the complexity that the log scaling has involved. We may then decide to apply a model fitting approach to both the raw and the transformed data. When deciding which of the two resulting models to choose, we may not just consider the model performance, but also that the model on the transformed data is actually more complex than the one of the raw data.

By the way, did you notice the beautiful readble bodies of the transformation functions? They do not contain any unresolved variables or nested, opaque functions (apart from the system functions log and exp). They are constructed with the support of our functionComposeR package.

Installation

You can install the package directl from GitHub by using the package devtools as follows:

library(devtools)
install_github("thomasWeise/dataTransformeR")

If devtools is not yet installed on your machine, you need to FIRST do

install.packages("devtools")

License

The copyright holder of this package is Prof. Dr. Thomas Weise (see Contact). The package is licensed under the GNU LESSER GENERAL PUBLIC LICENSE Version 3, 29 June 2007.

Contact

For more information, see our correspondingblog post.

If you have any questions or suggestions, please contact Prof. Dr. Thomas Weise of the Institute of Applied Optimization at Hefei University in Hefei, Anhui, China via email to tweise@hfuu.edu.cn.

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