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How to learn Hacking Part 2

Now that you have read the basics here at http://www.decisionstats.com/how-to-learn-to-be-a-hacker-easily/ (please do read this before reading the below)

 

Here is a list of tutorials that you should study (in order of ease)

1) LEARN BASICS – enough to get you a job maybe if that’s all you wanted.

http://www.offensive-security.com/metasploit-unleashed/Main_Page

2) READ SOME MORE-

Lena’s Reverse Engineering Tutorial-“Use Google.com  for finding the Tutorial

Lena’s Reverse Engineering tutorial. It includes 36 parts of individual cracking techniques and will teach you the basics of protection bypassing

01. Olly + assembler + patching a basic reverseme
02. Keyfiling the reverseme + assembler
03. Basic nag removal + header problems
04. Basic + aesthetic patching
05. Comparing on changes in cond jumps, animate over/in, breakpoints
06. “The plain stupid patching method”, searching for textstrings
07. Intermediate level patching, Kanal in PEiD
08. Debugging with W32Dasm, RVA, VA and offset, using LordPE as a hexeditor
09. Explaining the Visual Basic concept, introduction to SmartCheck and configuration
10. Continued reversing techniques in VB, use of decompilers and a basic anti-anti-trick
11. Intermediate patching using Olly’s “pane window”
12. Guiding a program by multiple patching.
13. The use of API’s in software, avoiding doublechecking tricks
14. More difficult schemes and an introduction to inline patching
15. How to study behaviour in the code, continued inlining using a pointer
16. Reversing using resources
17. Insights and practice in basic (self)keygenning
18. Diversion code, encryption/decryption, selfmodifying code and polymorphism
19. Debugger detected and anti-anti-techniques
20. Packers and protectors : an introduction
21. Imports rebuilding
22. API Redirection
23. Stolen bytes
24. Patching at runtime using loaders from lena151 original
25. Continued patching at runtime & unpacking armadillo standard protection
26. Machine specific loaders, unpacking & debugging armadillo
27. tElock + advanced patching
28. Bypassing & killing server checks
29. Killing & inlining a more difficult server check
30. SFX, Run Trace & more advanced string searching
31. Delphi in Olly & DeDe
32. Author tricks, HIEW & approaches in inline patching
33. The FPU, integrity checks & loader versus patcher
34. Reversing techniques in packed software & a S&R loader for ASProtect
35. Inlining inside polymorphic code
36. Keygenning

If you want more free training – hang around this website

http://www.owasp.org/index.php/Cheat_Sheets

OWASP Cheat Sheet Series

Draft OWASP Cheat Sheets

3) SPEND SOME MONEY on TRAINING

http://www.corelan-training.com/index.php/training/corelan-live/

Course overview

Module 1 – The x86 environment

  • System Architecture
  • Windows Memory Management
  • Registers
  • Introduction to Assembly
  • The stack

Module 2 – The exploit developer environment

  • Setting up the exploit developer lab
  • Using debuggers and debugger plugins to gather primitives

Module 3 – Saved Return Pointer Overwrite

  • Functions
  • Saved return pointer overwrites
  • Stack cookies

Module 4 – Abusing Structured Exception Handlers

  • Abusing exception handler overwrites
  • Bypassing Safeseh

Module 5 – Pointer smashing

  • Function pointers
  • Data/object pointers
  • vtable/virtual functions

Module 6 – Off-by-one and integer overflows

  • Off-by-one
  • Integer overflows

Module 7 – Limited buffers

  • Limited buffers, shellcode splitting

Module 8 – Reliability++ & reusability++

  • Finding and avoiding bad characters
  • Creative ways to deal with character set limitations

Module 9 – Fun with Unicode

  • Exploiting Unicode based overflows
  • Writing venetian alignment code
  • Creating and Using venetian shellcode

Module 10 – Heap Spraying Fundamentals

  • Heap Management and behaviour
  • Heap Spraying for Internet Explorer 6 and 7

Module 11 – Egg Hunters

  • Using and tweaking Egg hunters
  • Custom egghunters
  • Using Omelet egghunters
  • Egghunters in a WoW64 environment

Module 12 – Shellcoding

  • Building custom shellcode from scratch
  • Understanding existing shellcode
  • Writing portable shellcode
  • Bypassing Antivirus

Module 13 – Metasploit Exploit Modules

  • Writing exploits for the Metasploit Framework
  • Porting exploits to the Metasploit Framework

Module 14 – ASLR

  • Bypassing ASLR

Module 15 – W^X

  • Bypassing NX/DEP
  • Return Oriented Programming / Code Reuse (ROP) )

Module 16 – Advanced Heap Spraying

  • Heap Feng Shui & heaplib
  • Precise heap spraying in modern browsers (IE8 & IE9, Firefox 13)

Module 17 – Use After Free

  • Exploiting Use-After-Free conditions

Module 18 – Windows 8

  • Windows 8 Memory Protections and Bypass
TRAINING SCHEDULES AT

ALSO GET CERTIFIED http://www.offensive-security.com/information-security-training/penetration-testing-with-backtrack/ ($950 cost)

the syllabus is here at

http://www.offensive-security.com/documentation/penetration-testing-with-backtrack.pdf

4) HANG AROUND OTHER HACKERS

At http://attrition.org/attrition/

or The Noir  Hat Conferences-

http://blackhat.com/html/bh-us-12/training/bh-us-12-training_complete.html

or read this website

http://software-security.sans.org/developer-how-to/

5) GET A DEGREE

Yes it is possible

 

See http://web.jhu.edu/jhuisi/

The Johns Hopkins University Information Security Institute (JHUISI) is the University’s focal point for research and education in information security, assurance and privacy.

Scholarship Information

 

The Information Security Institute is now accepting applications for the Department of Defense’s Information Assurance Scholarship Program (IASP).  This scholarship includes full tuition, a living stipend, books and health insurance. In return each student recipient must work for a DoD agency at a competitive salary for six months for every semester funded. The scholarship is open to American citizens only.

http://web.jhu.edu/jhuisi/mssi/index.html

MASTER OF SCIENCE IN SECURITY INFORMATICS PROGRAM

The flagship educational experience offered by Johns Hopkins University in the area of information security and assurance is represented by the Master of Science in Security Informatics degree.  Over thirty courses are available in support of this unique and innovative graduate program.

———————————————————–

Disclaimer- I havent done any of these things- This is just a curated list from Quora  so I am open to feedback.

You use this at your own risk of conscience ,local legal jurisdictions and your own legal liability.

 

 

 

 

 

 

Book Review- Machine Learning for Hackers

This is review of the fashionably named book Machine Learning for Hackers by Drew Conway and John Myles White (O’Reilly ). The book is about hacking code in R.

 

The preface introduces the reader to the authors conception of what machine learning and hacking is all about. If the name of the book was machine learning for business analytsts or data miners, I am sure the content would have been unchanged though the popularity (and ambiguity) of the word hacker can often substitute for its usefulness. Indeed the many wise and learned Professors of statistics departments through out the civilized world would be mildly surprised and bemused by their day to day activities as hacking or teaching hackers. The book follows a case study and example based approach and uses the GGPLOT2 package within R programming almost to the point of ignoring any other native graphics system based in R. It can be quite useful for the aspiring reader who wishes to understand and join the booming market for skilled talent in statistical computing.

Chapter 1 has a very useful set of functions for data cleansing and formatting. It walks you through the basics of formatting based on dates and conditions, missing value and outlier treatment and using ggplot package in R for graphical analysis. The case study used is an Infochimps dataset with 60,000 recordings of UFO sightings. The case study is lucid, and done at a extremely helpful pace illustrating the powerful and flexible nature of R functions that can be used for data cleansing.The chapter mentions text editors and IDEs but fails to list them in a tabular format, while listing several other tables like Packages used in the book. It also jumps straight from installation instructions to functions in R without getting into the various kinds of data types within R or specifying where these can be referenced from. It thus assumes a higher level of basic programming understanding for the reader than the average R book.

Chapter 2 discusses data exploration, and has a very clear set of diagrams that explain the various data summary operations that are performed routinely. This is an innovative approach and will help students or newcomers to the field of data analysis. It introduces the reader to type determination functions, as well different kinds of encoding. The introduction to creating functions is quite elegant and simple , and numerical summary methods are explained adequately. While the chapter explains data exploration with the help of various histogram options in ggplot2 , it fails to create a more generic framework for data exploration or rules to assist the reader in visual data exploration in non standard data situations. While the examples are very helpful for a reader , there needs to be slightly more depth to step out of the example and into a framework for visual data exploration (or references for the same). A couple of case studies however elaborately explained cannot do justice to the vast field of data exploration and especially visual data exploration.

Chapter 3 discussed binary classification for the specific purpose for spam filtering using a dataset from SpamAssassin. It introduces the reader to the naïve Bayes classifier and the principles of text mining suing the tm package in R. Some of the example codes could have been better commented for easier readability in the book. Overall it is quite a easy tutorial for creating a naïve Bayes classifier even for beginners.

Chapter 4 discusses the issues in importance ranking and creating recommendation systems specifically in the case of ordering email messages into important and not important. It introduces the useful grepl, gsub, strsplit, strptime ,difftime and strtrim functions for parsing data. The chapter further introduces the reader to the concept of log (and affine) transformations in a lucid and clear way that can help even beginners learn this powerful transformation concept. Again the coding within this chapter is sparsely commented which can cause difficulties to people not used to learn reams of code. ( it may have been part of the code attached with the book, but I am reading an electronic book and I did not find an easy way to go back and forth between the code and the book). The readability of the chapters would be further enhanced by the use of flow charts explaining the path and process followed than overtly verbose textual descriptions running into multiple pages. The chapters are quite clearly written, but a helpful visual summary can help in both revising the concepts and elucidate the approach taken further.A suggestion for the authors could be to compile the list of useful functions they introduce in this book as a sort of reference card (or Ref Card) for R Hackers or atleast have a chapter wise summary of functions, datasets and packages used.

Chapter 5 discusses linear regression , and it is a surprising and not very good explanation of regression theory in the introduction to regression. However the chapter makes up in practical example what it oversimplifies in theory. The chapter on regression is not the finest chapter written in this otherwise excellent book. Part of this is because of relative lack of organization- correlation is explained after linear regression is explained. Once again the lack of a function summary and a process flow diagram hinders readability and a separate section on regression metrics that help make a regression result good or not so good could be a welcome addition. Functions introduced include lm.

Chapter 6 showcases Generalized Additive Model (GAM) and Polynomial Regression, including an introduction to singularity and of over-fitting. Functions included in this chapter are transform, and poly while the package glmnet is also used here. The chapter also introduces the reader formally to the concept of cross validation (though examples of cross validation had been introduced in earlier chapters) and regularization. Logistic regression is also introduced at the end in this chapter.

Chapter 7 is about optimization. It describes error metric in a very easy to understand way. It creates a grid by using nested loops for various values of intercept and slope of a regression equation and computing the sum of square of errors. It then describes the optim function in detail including how it works and it’s various parameters. It introduces the curve function. The chapter then describes ridge regression including definition and hyperparameter lamda. The use of optim function to optimize the error in regression is useful learning for the aspiring hacker. Lastly it describes a case study of breaking codes using the simplistic Caesar cipher, a lexical database and the Metropolis method. Functions introduced in this chapter include .Machine$double.eps .

Chapter 8 deals with Principal Component Analysis and unsupervised learning. It uses the ymd function from lubridate package to convert string to date objects, and the cast function from reshape package to further manipulate the structure of data. Using the princomp functions enables PCA in R.The case study creates a stock market index and compares the results with the Dow Jones index.

Chapter 9 deals with Multidimensional Scaling as well as clustering US senators on the basis of similarity in voting records on legislation .It showcases matrix multiplication using %*% and also the dist function to compute distance matrix.

Chapter 10 has the subject of K Nearest Neighbors for recommendation systems. Packages used include class ,reshape and and functions used include cor, function and log. It also demonstrates creating a custom kNN function for calculating Euclidean distance between center of centroids and data. The case study used is the R package recommendation contest on Kaggle. Overall a simplistic introduction to creating a recommendation system using K nearest neighbors, without getting into any of the prepackaged packages within R that deal with association analysis , clustering or recommendation systems.

Chapter 11 introduces the reader to social network analysis (and elements of graph theory) using the example of Erdos Number as an interesting example of social networks of mathematicians. The example of Social Graph API by Google for hacking are quite new and intriguing (though a bit obsolete by changes, and should be rectified in either the errata or next edition) . However there exists packages within R that should be atleast referenced or used within this chapter (like TwitteR package that use the Twitter API and ROauth package for other social networks). Packages used within this chapter include Rcurl, RJSONIO, and igraph packages of R and functions used include rbind and ifelse. It also introduces the reader to the advanced software Gephi. The last example is to build a recommendation engine for whom to follow in Twitter using R.

Chapter 12 is about model comparison and introduces the concept of Support Vector Machines. It uses the package e1071 and shows the svm function. It also introduces the concept of tuning hyper parameters within default algorithms . A small problem in understanding the concepts is the misalignment of diagram pages with the relevant code. It lastly concludes with using mean square error as a method for comparing models built with different algorithms.

 

Overall the book is a welcome addition in the library of books based on R programming language, and the refreshing nature of the flow of material and the practicality of it’s case studies make this a recommended addition to both academic and corporate business analysts trying to derive insights by hacking lots of heterogeneous data.

Have a look for yourself at-
http://shop.oreilly.com/product/0636920018483.do

Business Metrics

Business Metrics (a partial extract from my upcoming book “R for Business Analytics”

Business Metrics are important variables that are collected on a periodic basis to assess the health and sustainability of a business. They should have the following properties-

1) What is a Business Metric-The absence of collection of regular update of the business metric could cause business disruption by incorrect and incomplete decision making.

2) Cost of Business Metrics- The costs of collection, storage and updating of the business metric is less than the opportunity costs of wrong decision making cause by lack of information of that business metric.

3) Continuity in your Business Metrics- The business metrics are continuous in comparing across time periods and business units- if necessary the assumptions for smoothing the comparisons should be listed in the business metric presentation itself.

4) Simplify your Business Metrics- Business metrics can be derived as well from other business metrics. If necessary and to avoid clutter only the most important business metrics should be presented, or the metrics with the biggest deviation from past trends should be mentioned.

5) Normalize your Business Metrics- Scale of the business metric units should be comparable to other business metrics as well as significant to emphasize the difference in numbers.

6) Standardize your Business Metrics- Dimension of business metrics should be increased to enhance comparison and contrasts without enhancing complexity. This means adding an extra dimension for analysis rather than a 2 by 2 comparison, to add time /geography/ employee/business owner as a dimension .

Analytics 2011 Conference

From http://www.sas.com/events/analytics/us/

The Analytics 2011 Conference Series combines the power of SAS’s M2010 Data Mining Conference and F2010 Business Forecasting Conference into one conference covering the latest trends and techniques in the field of analytics. Analytics 2011 Conference Series brings the brightest minds in the field of analytics together with hundreds of analytics practitioners. Join us as these leading conferences change names and locations. At Analytics 2011, you’ll learn through a series of case studies, technical presentations and hands-on training. If you are in the field of analytics, this is one conference you can’t afford to miss.

Conference Details

October 24-25, 2011
Grande Lakes Resort
Orlando, FL

Analytics 2011 topic areas include:

  • Data Mining
  • Forecasting
  • Text Analytics
  • Fraud Detection
  • Data Visualization (more…)

Updated Interview Elissa Fink -VP Tableau Software

Here is an interview with Elissa Fink, VP Marketing of that new wonderful software called Tableau that makes data visualization so nice and easy to learn and work with.

Elissa Fink, VP, Marketing

Ajay-  Describe your career journey from high school to over 20 plus years in marketing. What are the various trends that you have seen come and go in marketing.

Elissa- I studied literature and linguistics in college and didn’t discover analytics until my first job selling advertising for the Wall Street Journal. Oddly enough, the study of linguistics is not that far from decision analytics: they both are about taking a structured view of information and trying to see and understand common patterns. At the Journal, I was completely captivated analyzing and comparing readership data. At the same time, the idea of using computers in marketing was becoming more common. I knew that the intersection of technology and marketing was going to radically change things – how we understand consumers, how we market and sell products, and how we engage with customers. So from that point on, I’ve always been focused on technology and marketing, whether it’s working as a marketer at technology companies or applying technology to marketing problems for other types of companies.  There have been so many interesting trends. Taking a long view, a key trend I’ve noticed is how marketers work to understand, influence and motivate consumer behavior. We’ve moved marketing from where it was primarily unpredictable, qualitative and aimed at talking to mass audiences, where the advertising agency was king. Now it’s a discipline that is more data-driven, quantitative and aimed at conversations with individuals, where the best analytics wins. As with any trend, the pendulum swings far too much to either side causing backlashes but overall, I think we are in a great place now. We are using data-driven analytics to understand consumer behavior. But pure analytics is not the be-all, end-all; good marketing has to rely on understanding human emotions, intuition and gut feel – consumers are far from rational so taking only a rational or analytical view of them will never explain everything we need to know.

Ajay- Do you think technology companies are still predominantly dominated by men . How have you seen diversity evolve over the years. What initiatives has Tableau taken for both hiring and retaining great talent.

Elissa- The thing I love about the technology industry is that its key success metrics – inventing new products that rapidly gain mass adoption in pursuit of making profit – are fairly objective. There’s little subjective nature to the counting of dollars collected selling a product and dollars spent building a product. So if a female can deliver a better product and bigger profits faster and better, then that female is going to get the resources, jobs, power and authority to do exactly that. That’s not to say that the technology industry is gender-blind, race-blind, etc. It isn’t – technology is far from perfect. For example, the industry doesn’t have enough diversity in positions of power. But I think overall, in comparison to a lot of other industries, it’s pretty darn good at giving people with great ideas the opportunities to realize their visions regardless of their backgrounds or characteristics.

At Tableau, we are very serious about bringing in and developing talented people – they are the key to our growth and success. Hiring is our #1 initiative so we’ve spent a lot of time and energy both on finding great candidates and on making Tableau a place that they want to work. This includes things like special recruiting events, employee referral programs, a flexible work environment, fun social events, and the rewards of working for a start-up. Probably our biggest advantage is the company itself – working with people you respect on amazing, cutting-edge products that delight customers and are changing the world is all too rare in the industry but a reality at Tableau. One of our senior software developers put it best when he wrote “The emphasis is on working smarter rather than longer: family and friends are why we work, not the other way around. Tableau is all about happy, energized employees executing at the highest level and delivering a highly usable, high quality, useful product to our customers.” People who want to be at a place like that should check out our openings at http://www.tableausoftware.com/jobs.

Ajay- What are most notable features in tableau’s latest edition. What are the principal software that competes with Tableau Software products and how would you say Tableau compares with them.

Elissa- Tableau 6.1 will be out in July and we are really excited about it for 3 reasons.

First, we’re introducing our mobile business intelligence capabilities. Our customers can have Tableau anywhere they need it. When someone creates an interactive dashboard or analytical application with Tableau and it’s viewed on a mobile device, an iPad in particular, the viewer will have a native, touch-optimized experience. No trying to get your fingertips to act like a mouse. And the author didn’t have to create anything special for the iPad; she just creates her analytics the usual way in Tableau. Tableau knows the dashboard is being viewed on an iPad and presents an optimized experience.

Second, we’ve take our in-memory analytics engine up yet another level. Speed and performance are faster and now people can update data incrementally rapidly. Introduced in 6.0, our data engine makes any data fast in just a few clicks. We don’t run out of memory like other applications. So if I build an incredible dashboard on my 8-gig RAM PC and you try to use it on your 2-gig RAM laptop, no problem.

And, third, we’re introducing more features for the international markets – including French and German versions of Tableau Desktop along with more international mapping options.  It’s because we are constantly innovating particularly around user experience that we can compete so well in the market despite our relatively small size. Gartner’s seminal research study about the Business Intelligence market reported a massive market shift earlier this year: for the first time, the ease-of-use of a business intelligence platform was more important than depth of functionality. In other words, functionality that lots of people can actually use is more important than having sophisticated functionality that only specialists can use. Since we focus so heavily on making easy-to-use products that help people rapidly see and understand their data, this is good news for our customers and for us.

Ajay-  Cloud computing is the next big thing with everyone having a cloud version of their software. So how would you run Cloud versions of Tableau Server (say deploying it on an Amazon Ec2  or a private cloud)

Elissa- In addition to the usual benefits espoused about Cloud computing, the thing I love best is that it makes data and information more easily accessible to more people. Easy accessibility and scalability are completely aligned with Tableau’s mission. Our free product Tableau Public and our product for commercial websites Tableau Digital are two Cloud-based products that deliver data and interactive analytics anywhere. People often talk about large business intelligence deployments as having thousands of users. With Tableau Public and Tableau Digital, we literally have millions of users. We’re serving up tens of thousands of visualizations simultaneously – talk about accessibility and scalability!  We have lots of customers connecting to databases in the Cloud and running Tableau Server in the Cloud. It’s actually not complex to set up. In fact, we focus a lot of resources on making installation and deployment easy and fast, whether it’s in the cloud, on premise or what have you. We don’t want people to have spend weeks or months on massive roll-out projects. We want it to be minutes, hours, maybe a day or 2. With the Cloud, we see that people can get started and get results faster and easier than ever before. And that’s what we’re about.

Ajay- Describe some of the latest awards that Tableau has been wining. Also how is Tableau helping universities help address the shortage of Business Intelligence and Big Data professionals.

Elissa-Tableau has been very fortunate. Lately, we’ve been acknowledged by both Gartner and IDC as the fastest growing business intelligence software vendor in the world. In addition, our customers and Tableau have won multiple distinctions including InfoWorld Technology Leadership awards, Inc 500, Deloitte Fast 500, SQL Server Magazine Editors’ Choice and Community Choice awards, Data Hero awards, CODiEs, American Business Awards among others. One area we’re very passionate about is academia, participating with professors, students and universities to help build a new generation of professionals who understand how to use data. Data analysis should not be exclusively for specialists. Everyone should be able to see and understand data, whatever their background. We come from academic roots, having been spun out of a Stanford research project. Consequently, we strongly believe in supporting universities worldwide and offer 2 academic programs. The first is Tableau For Teaching, where any professor can request free term-length licenses of Tableau for academic instruction during his or her courses. And, we offer a low-cost Student Edition of Tableau so that students can choose to use Tableau in any of their courses at any time.

Elissa Fink, VP Marketing,Tableau Software

 

Elissa Fink is Tableau Software’s Vice President of Marketing. With 20+ years helping companies improve their marketing operations through applied data analysis, Elissa has held executive positions in marketing, business strategy, product management, and product development. Prior to Tableau, Elissa was EVP Marketing at IXI Corporation, now owned by Equifax. She has also served in executive positions at Tele Atlas (acquired by TomTom), TopTier Software (acquired by SAP), and Nielsen/Claritas. Elissa also sold national advertising for the Wall Street Journal. She’s a frequent speaker and has spoken at conferences including the DMA, the NCDM, Location Intelligence, the AIR National Forum and others. Elissa is a graduate of Santa Clara University and holds an MBA in Marketing and Decision Systems from the University of Southern California.

Elissa first discovered Tableau late one afternoon at her previous company. Three hours later, she was still “at play” with her data. “After just a few minutes using the product, I was getting answers to questions that were taking my company’s programmers weeks to create. It was instantly obvious that Tableau was on a special mission with something unique to offer the world. I just had to be a part of it.”

To know more – read at http://www.tableausoftware.com/

and existing data viz at http://www.tableausoftware.com/learn/gallery

Storm seasons: measuring and tracking key indicators
What’s happening with local real estate prices?
How are sales opportunities shaping up?
Identify your best performing products
Applying user-defined parameters to provide context
Not all tech companies are rocket ships
What’s really driving the economy?
Considering factors and industry influencers
The complete orbit along the inside, or around a fixed circle
How early do you have to be at the airport?
What happens if sales grow but so does customer churn?
What are the trends for new retail locations?
How have student choices changed?
Do patients who disclose their HIV status recover better?
Closer look at where gas prices swing in areas of the U.S.
U.S. Census data shows more women of greater age
Where do students come from and how does it affect their grades?
Tracking customer service effectiveness
Comparing national and local test scores
What factors correlate with high overall satisfaction ratings?
Fund inflows largely outweighed outflows well after the bubble
Which programs are competing for federal stimulus dollars?
Oil prices and volatility
A classic candlestick chart
How do oil, gold and CPI relate to the GDP growth rate?

 

Top Ten Graphs for Business Analytics -Pie Charts (1/10)

I have not been really posting or writing worthwhile on the website for some time, as I am still busy writing ” R for Business Analytics” which I hope to get out before year end. However while doing research for that, I came across many types of graphs and what struck me is the actual usage of some kinds of graphs is very different in business analytics as compared to statistical computing.

The criterion of top ten graphs is as follows-

1) Usage-The order in which they appear is not strictly in terms of desirability but actual frequency of usage. So a frequently used graph like box plot would be recommended above say a violin plot.

2) Adequacy- Data Visualization paradigms change over time- but the need for accurate conveying of maximum information in a minium space without overwhelming reader or misleading data perceptions.

3) Ease of creation- A simpler graph created by a single function is more preferrable to writing 4-5 lines of code to create an elaborate graph.

4) Aesthetics- Aesthetics is relative and  in addition studies have shown visual perception varies across cultures and geographies. However , beauty is universally appreciated and a pretty graph is sometimes and often preferred over a not so pretty graph. Here being pretty is in both visual appeal without compromising perceptual inference from graphical analysis.

 

so When do we use a bar chart versus a line graph versus a pie chart? When is a mosaic plot more handy and when should histograms be used with density plots? The list tries to capture most of these practicalities.

Let me elaborate on some specific graphs-

1) Pie Chart- While Pie Chart is not really used much in stats computing, and indeed it is considered a misleading example of data visualization especially the skewed or two dimensional charts. However when it comes to evaluating market share at a particular instance, a pie chart is simple to understand. At the most two pie charts are needed for comparing two different snapshots, but three or more pie charts on same data at different points of time is definitely a bad case.

In R you can create piechart, by just using pie(dataset$variable)

As per official documentation, pie charts are not  recommended at all.

http://stat.ethz.ch/R-manual/R-patched/library/graphics/html/pie.html

Pie charts are a very bad way of displaying information. The eye is good at judging linear measures and bad at judging relative areas. A bar chart or dot chart is a preferable way of displaying this type of data.

Cleveland (1985), page 264: “Data that can be shown by pie charts always can be shown by a dot chart. This means that judgements of position along a common scale can be made instead of the less accurate angle judgements.” This statement is based on the empirical investigations of Cleveland and McGill as well as investigations by perceptual psychologists.

—-

Despite this, pie charts are frequently used as an important metric they inevitably convey is market share. Market share remains an important analytical metric for business.

The pie3D( ) function in the plotrix package provides 3D exploded pie charts.An exploded pie chart remains a very commonly used (or misused) chart.

From http://lilt.ilstu.edu/jpda/charts/chart%20tips/Chartstip%202.htm#Rules

we see some rules for using Pie charts.

 

  1. Avoid using pie charts.
  2. Use pie charts only for data that add up to some meaningful total.
  3. Never ever use three-dimensional pie charts; they are even worse than two-dimensional pies.
  4. Avoid forcing comparisons across more than one pie chart

 

From the R Graph Gallery (a slightly outdated but still very comprehensive graphical repository)

http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=4

par(bg="gray")
pie(rep(1,24), col=rainbow(24), radius=0.9)
title(main="Color Wheel", cex.main=1.4, font.main=3)
title(xlab="(test)", cex.lab=0.8, font.lab=3)
(Note adding a grey background is quite easy in the basic graphics device as well without using an advanced graphical package)

 

Using Views in R and comparing functions across multiple packages

Some RDF hacking relating to updating probabil...

Image via Wikipedia

R has almost 2923 available packages

This makes the task of searching among these packages and comparing functions for the same analytical task across different packages a bit tedious and prone to manual searching (of reading multiple Pdfs of help /vignette of packages) or sending an email to the R help list.

However using R Views is a slightly better way of managing all your analytical requirements for software rather than the large number of packages (see Graphics view below).

CRAN Task Views allow you to browse packages by topic and provide tools to automatically install all packages for special areas of interest. Currently, 28 views are available. http://cran.r-project.org/web/views/

Bayesian Bayesian Inference
ChemPhys Chemometrics and Computational Physics
ClinicalTrials Clinical Trial Design, Monitoring, and Analysis
Cluster Cluster Analysis & Finite Mixture Models
Distributions Probability Distributions
Econometrics Computational Econometrics
Environmetrics Analysis of Ecological and Environmental Data
ExperimentalDesign Design of Experiments (DoE) & Analysis of Experimental Data
Finance Empirical Finance
Genetics Statistical Genetics
Graphics Graphic Displays & Dynamic Graphics & Graphic Devices & Visualization
gR gRaphical Models in R
HighPerformanceComputing High-Performance and Parallel Computing with R
MachineLearning Machine Learning & Statistical Learning
MedicalImaging Medical Image Analysis
Multivariate Multivariate Statistics
NaturalLanguageProcessing Natural Language Processing
OfficialStatistics Official Statistics & Survey Methodology
Optimization Optimization and Mathematical Programming
Pharmacokinetics Analysis of Pharmacokinetic Data
Phylogenetics Phylogenetics, Especially Comparative Methods
Psychometrics Psychometric Models and Methods
ReproducibleResearch Reproducible Research
Robust Robust Statistical Methods
SocialSciences Statistics for the Social Sciences
Spatial Analysis of Spatial Data
Survival Survival Analysis
TimeSeries Time Series Analysis

To automatically install these views, the ctv package needs to be installed, e.g., via

install.packages("ctv")
library("ctv")
Created by Pretty R at inside-R.org


and then the views can be installed via install.views or update.views (which first assesses which of the packages are already installed and up-to-date), e.g.,

install.views("Econometrics")
 update.views("Econometrics")
 Created by Pretty R at inside-R.org

CRAN Task View: Graphic Displays & Dynamic Graphics & Graphic Devices & Visualization

Maintainer: Nicholas Lewin-Koh
Contact: nikko at hailmail.net
Version: 2009-10-28

R is rich with facilities for creating and developing interesting graphics. Base R contains functionality for many plot types including coplots, mosaic plots, biplots, and the list goes on. There are devices such as postscript, png, jpeg and pdf for outputting graphics as well as device drivers for all platforms running R. lattice and grid are supplied with R’s recommended packages and are included in every binary distribution. lattice is an R implementation of William Cleveland’s trellis graphics, while grid defines a much more flexible graphics environment than the base R graphics.

R’s base graphics are implemented in the same way as in the S3 system developed by Becker, Chambers, and Wilks. There is a static device, which is treated as a static canvas and objects are drawn on the device through R plotting commands. The device has a set of global parameters such as margins and layouts which can be manipulated by the user using par() commands. The R graphics engine does not maintain a user visible graphics list, and there is no system of double buffering, so objects cannot be easily edited without redrawing a whole plot. This situation may change in R 2.7.x, where developers are working on double buffering for R devices. Even so, the base R graphics can produce many plots with extremely fine graphics in many specialized instances.

One can quickly run into trouble with R’s base graphic system if one wants to design complex layouts where scaling is maintained properly on resizing, nested graphs are desired or more interactivity is needed. grid was designed by Paul Murrell to overcome some of these limitations and as a result packages like latticeggplot2vcd or hexbin (on Bioconductor ) use grid for the underlying primitives. When using plots designed with grid one needs to keep in mind that grid is based on a system of viewports and graphic objects. To add objects one needs to use grid commands, e.g., grid.polygon() rather than polygon(). Also grid maintains a stack of viewports from the device and one needs to make sure the desired viewport is at the top of the stack. There is a great deal of explanatory documentation included with grid as vignettes.

The graphics packages in R can be organized roughly into the following topics, which range from the more user oriented at the top to the more developer oriented at the bottom. The categories are not mutually exclusive but are for the convenience of presentation:

  • Plotting : Enhancements for specialized plots can be found in plotrix, for polar plotting, vcd for categorical data, hexbin (on Bioconductor ) for hexagon binning, gclus for ordering plots and gplots for some plotting enhancements. Some specialized graphs, like Chernoff faces are implemented in aplpack, which also has a nice implementation of Tukey’s bag plot. For 3D plots latticescatterplot3d and misc3d provide a selection of plots for different kinds of 3D plotting. scatterplot3d is based on R’s base graphics system, while misc3d is based on rgl. The package onion for visualizing quaternions and octonions is well suited to display 3D graphics based on derived meshes.
  • Graphic Applications : This area is not much different from the plotting section except that these packages have tools that may not for display, but can aid in creating effective displays. Also included are packages with more esoteric plotting methods. For specific subject areas, like maps, or clustering the excellent task views contributed by other dedicated useRs is an excellent place to start.
    • Effect ordering : The gclus package focuses on the ordering of graphs to accentuate cluster structure or natural ordering in the data. While not for graphics directly cba and seriation have functions for creating 1 dimensional orderings from higher dimensional criteria. For ordering an array of displays, biclust can be useful.
    • Large Data Sets : Large data sets can present very different challenges from moderate and small datasets. Aside from overplotting, rendering 1,000,000 points can tax even modern GPU’s. For univariate datalvplot produces letter value boxplots which alleviate some of the problems that standard boxplots exhibit for large data sets. For bivariate data ash can produce a bivariate smoothed histogram very quickly, and hexbin, on Bioconductor , can bin bivariate data onto a hexagonal lattice, the advantage being that the irregular lines and orientation of hexagons do not create linear artifacts. For multivariate data, hexbin can be used to create a scatterplot matrix, combined with lattice. An alternative is to use scagnostics to produce a scaterplot matrix of “data about the data”, and look for interesting combinations of variables.
    • Trees and Graphs ape and ade4 have functions for plotting phylogenetic trees, which can be used for plotting dendrograms from clustering procedures. While these packages produce decent graphics, they do not use sophisticated algorithms for node placement, so may not be useful for very large trees. igraph has the Tilford-Rheingold algorithm implementead and is useful for plotting larger trees. diagram as facilities for flow diagrams and simple graphs. For more sophisticated graphs Rgraphviz and igraph have functions for plotting and layout, especially useful for representing large networks.
  • Graphics Systems lattice is built on top of the grid graphics system and is an R implementation of William Cleveland’s trellis system for S-PLUS. lattice allows for building many types of plots with sophisticated layouts based on conditioning. ggplot2 is an R implementation of the system described in “A Grammar of Graphics” by Leland Wilkinson. Like latticeggplot (also built on top of grid) assists in trellis-like graphics, but allows for much more. Since it is built on the idea of a semantics for graphics there is much more emphasis on reshaping data, transformation, and assembling the elements of a plot.
  • Devices : Whereas grid is built on top of the R graphics engine, many in the R community have found the R graphics engine somewhat inflexible and have written separate device drivers that either emphasize interactivity or plotting in various graphics formats. R base supplies devices for PostScript, PDF, JPEG and other formats. Devices on CRAN include cairoDevice which is a device based libcairo, which can actually render to many device types. The cairo device is desgned to work with RGTK2, which is an interface to the Gimp Tool Kit, similar to pyGTK2. GDD provides device drivers for several bitmap formats, including GIF and BMP. RSvgDevice is an SVG device driver and interfaces well with with vector drawing programs, or R web development packages, such as Rpad. When SVG devices are for web display developers should be aware that internet explorer does not support SVG, but has their own standard. Trust Microsoft. rgl provides a device driver based on OpenGL, and is good for 3D and interactive development. Lastly, the Augsburg group supplies a set of packages that includes a Java-based device, JavaGD.
  • Colors : The package colorspace provides a set of functions for transforming between color spaces and mixcolor() for mixing colors within a color space. Based on the HCL colors provided in colorspacevcdprovides a set of functions for choosing color palettes suitable for coding categorical variables ( rainbow_hcl()) and numerical information ( sequential_hcl()diverge_hcl()). Similar types of palettes are provided in RColorBrewer and dichromat is focused on palettes for color-impaired viewers.
  • Interactive Graphics : There are several efforts to implement interactive graphics systems that interface well with R. In an interactive system the user can interactively query the graphics on the screen with the mouse, or a moveable brush to zoom, pan and query on the device as well as link with other views of the data. rggobi embeds the GGobi interactive graphics system within R, so that one can display a data frame or several in GGobi directly from R. The package has functions to support longitudinal data, and graphs using GGobi’s edge set functionality. The RoSuDA repository maintained and developed by the University of Augsburg group has two packages, iplots and iwidgets as well as their Java development environment including a Java device, JavaGD. Their interactive graphics tools contain functions for alpha blending, which produces darker shading around areas with more data. This is exceptionally useful for parallel coordinate plots where many lines can quickly obscure patterns. playwith has facilities for building interactive versions of R graphics using the cairoDevice and RGtk2. Lastly, the rgl package has mechanisms for interactive manipulation of plots, especially 3D rotations and surfaces.
  • Development : For development of specialized graphics packages in R, grid should probably be the first consideration for any new plot type. rgl has better tools for 3D graphics, since the device is interactive, though it can be slow. An alternative is to use Java and the Java device in the RoSuDA packages, though Java has its own drawbacks. For porting plotting code to grid, using the package gridBase presents a nice intermediate step to embed base graphics in grid graphics and vice versa.
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