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constructs the graph of class relationships, including slots of S4 classes

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packagestructure's Introduction

packagestructure

Create a graph of the structure of an R package.

May be useful in reducing the cognitive load when writing R packages with any more than a few S4 classes.

Currently only supports S4 classes and slots. See TODO list below.

Installation

devtools::install_github("rmflight/packagestructure")

Examples

A Source Package on Your Local Machine

library(packagestructure)
example_package <- system.file("exampledata", package = "packagestructure")
e_g <- class_graph(example_package)
plot(e_g)

In this example, classes class_B, class_C directly inherit from class_A, while class_D inherits from class_B. Each of these has particular slots of particular classes. You can see the set of class definitions here.

An Installed Package

# not run
library(Matrix)
m_g <- class_graph("package:Matrix")
plot(m_g)

History

Another package, classGraph is available on Cran, and was created by Martin Maechler based on code originally done by Robert Gentleman. However, that package uses Bioconductor's graph package (which does not handle graph unions nicely), and Rgraphviz, which can be a pain to install on Windows machines, and does not handle slots and their relationships.

Therefore I used some of the relevant code from Martin's package (licensed as GPL, which is why this package is GPL-2 and why he is listed as an author), converted it to use igraph, and did some of my own thing.

TODO

improve test coverage (classunion and no-classes)
add travis-ci and coveralls
allow specification of classes to show and classes to exclude
add methods?
add function call dependency?

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packagestructure's Issues

need package with classUnion classes

convert classTree algorithm to use igraph

convert the classTree function from MM to use igraph instead of graphNEL

put slot -> class code into own function

should have the code that makes the links between the slot and classes of slots into it's own function

travis-ci

coveralls

add slots to classtree

Given a merged class tree, add slots and slot class edges to the class tree.

need package with no classes

expect_equal_to_reference

Change to using expect_equal_to_reference for the graphs, instead of saving them

switch to igraph

Should we be using the igraph packge instead of graph? It provides automatic plotting, and if we need the graphNEL for viewing in Cytoscape, etc, we should be able to convert w/out too much trouble.

put duplicate slots code into it's own function

In the interest of being able to test, and change it if need be, we should put the duplicate slots code into it's own function

use changed envir to test package:pkgname

Check if getting the package environment modifies the search(), and is stable between tests so that we can just use the changed envir to do the package:pkgname test instead of actually doing load_all()

multiclass version of classtree

classGraph package has class tree function to generate tree for one class. We should be able to generate multiple trees and merge them

custom join function

Need a custom join function that handles nodes with no edges, and duplicate edges.

The current join will choke on duplicate edges and nodes with no edges.

remove inherited slots

With the full slot class tree in #2, there may be redundancy in the slots. We should only keep slots that are unique to a class when we have class inheritance.

I think only way to do this is for each leaf, generate list of slots:classes, and for each parent of leaf, remove slots:classes that exist in the leaves. May be difficult to keep list of slot:classes updated correctly so that wrong slots don't get removed on the wrong parent. Will take work to design the right test cases.

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