t5 research

8/7/2019 T5 RESEARCH

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Henrik [email protected]

(MSc Computer Science, PhD candidate in Statistics)

Mathematical Statistics

Centre forMathematical Sciences

Lund University, Sweden

ObjectObject--oriented programming andoriented programming and

programming style guidelines for Rprogramming style guidelines for R


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Outline

Objects and Classes

Concepts of object-oriented programming

A comp

lete ex

amp

le in [R] Sh

apes

References in [R]

[R] Programming Style Guidelines with a

few coding conventions.


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Part I:

Object-oriented programming in [R]


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Objects and Classes

MicroarrayData

layout: Layout

R: double[][]G: double[][]

Rb: double[][]

Gb: double[][]

nbrOfSlides(): int

nbrOfSpots(): intswapDyes(...)

append()

as.data.frame(): data.frame

getLayout(): LayoutsetLayout(layout)

subtractBackground(...)normalizeWithinSlide(...)

normalizeAcrossSlides(...)plot(...)

plotSpatial(...)boxplot(...)

hist(...)

static read(...):MicroarrayData

write(...)

Class name

Fields

Methods

MicroarrayData

Layout

MicroarrayData

MicroarrayData

a class is a data type -

an object is an instance of a class

Objects of different classes

A class is the recipe for a certain cake...

...and the objects are the actual cakes of that kind.


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Encapsulation, Inheritance, and Polymorphism

Encapsulation means that a group of related properties,methods, and other members are treated as a single unit orobject. Objects can control how properties are changed andmethods are executed.

Why: Makes it easier to change your implementation at alater date by letting you hide implementation details of yourobjects, a practice called data hiding.


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Encapsulation, Inheritance, and Polymorphism

Polymorphism means that you can have multiple classesthat can be used interchangeably, even though each classimplements the same properties or methods in differentways. Polymorphism is essential to object-oriented

programming because it allows you to use items with thesame names, no matter what type of object is in use at themoment.

Why: Inheritance becomes more flexible. Subclasses can

keep some methods inherited from their super classes andoverride others.


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Overloading and Overriding

Overloaded members are used to provide different versionsof a property or method that have the same name, but thataccept a different number of parameters, or parameters withdifferent data types. Currently not supported in [R].

Overridden properties and methods are used to replace aninherited property or method that is not appropriate in aderived class. Overridden members must accept the samedata type and number of arguments (not enforced in [R]).

Derived classes inherit overridden members.


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Unified Modeling Language (UML) class diagram

10..*

abstractstatic

private

association

(using)

inheritance

(is a)


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# Create different Shape objects and store them in alist

allShapes


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setClassS3("Point", function(x=0, y=0) {

extend(Object(), "Point",.x = x, # private

.y = y # private

);

})

setMethodS3("getX", "Point", function(this) {

this$.x;

})

setMethodS3("getY", "Point", function(this) {

this$.y;})

setMethodS3("getXY", "Point", function(this) {

c(this$.x, this$.y);

})

setMethodS3("setX", "Point", function(this, newX) {

this$.x


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References, how?

References are notsupported by [R] since everything iscopy-by-value. Have to return new instance:

setValue


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Part II:

[R] Programming Style Guidelines


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Programming Style Guidelines

80% of the lifetime cost ofa piece of softwaregoes to maintenance.

Hardly any software is maintained for itswhole life by the originalauthor.

Code conventions improve the readability ofthe software, allowing programmers tounderstand new code more quickly andthoroughly.

If you ship your source code as a product, youneed to make sure it is as well packaged andclean as any other product you create.


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[R] Coding Convention

Currently there is no RCC and people

invent their own conventions or not at

all.

We suggest to adapt a modified version

of the Java coding convention, which

has proved to be successfuland is ade

facto stand

ard.


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Class names

Names representing classes must be nouns and

written in mixed case starting with upper case.

Shape, Rectangle, Point,MicroarrayData, Layout

Avoid . (period) in class names, because it might lead toambiguities. , e.g. my.very.own.class is nota good

name.


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Field and variable names

Variables and fields names must be in mixed

case starting with lower case.

x, y, nbrOfSlides, locus

To maintain readability of the code, do notshorten variablenames, e.g. nbrOfGrids (orngrids) is much better than

ngr.

Avoid using . (period) in variable names to make names

more consistent with other naming conventions. However,private fields, e.g. layout., may contain periods for

improving readability.


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Method names

Names representing methods (functions) must

be verbs and written in mixed case starting with

lower case.

getLayout(), normalize(method, slides)

To maintain readability of the code, do notshorten methodnames, e.g. normalizeWithinSlides() is much better

than normWSl().

For same reasons as before avoid using . (period) in methodnames, e.g. get.layout() is notgood.


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File names

Classes should be declared in individual files

with the file name matching the class name.

Point.R, GenePixData.R

Results in well organized file structure and also gives quick

access to the source code, Listing all *.R files in a source

directory will give you an overview of all the classes.

For stand-alone functions one may adapt the same policy;intToHex.R, col2rgb.R


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Where to start

Tutorials and source code:

R Programming Style Guidelines

Programming with References in R

Implementing support for references in R

http://www.maths.lth.se/help/R/

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