Tag: manipulation

Funny Stuff on Book Resellers and Dynamic Pricing at Amazon

I have been keeping an eye on the pricing figure of R for Business Analytics at Amazon.com and have watched it fluctuate between 49$ to 59$ while it is currently at 50$. (Incidentally- Per Capita GDP of India is 3700$ per year or ~$10 per day)

My point is

  1. why should a used book reseller offer to sell the same book at a HIGHER price,
  2. while a new book reseller offers to sell the same book that Amazon is selling (in stock) at a higher price.
  3. On top of that, these resellers have hundreds of thousands of ratings from delighted book buyers (of other books) who were very happy at buying the same book (used or new) at higher prices including upto twice the price.

Funny Stuff , huh!

Continue reading “Funny Stuff on Book Resellers and Dynamic Pricing at Amazon”

Data Frame in Python

Exploring some Python Packages and R packages to move /work with both Python and R without melting your brain or exceeding your project deadline

—————————————

If you liked the data.frame structure in R, you have some way to work with them at a faster processing speed in Python.

Here are three packages that enable you to do so-

(1) pydataframe http://code.google.com/p/pydataframe/

An implemention of an almost R like DataFrame object. (install via Pypi/Pip: “pip install pydataframe”)

Usage:

        u = DataFrame( { "Field1": [1, 2, 3],
                        "Field2": ['abc', 'def', 'hgi']},
                        optional:
                         ['Field1', 'Field2']
                         ["rowOne", "rowTwo", "thirdRow"])

A DataFrame is basically a table with rows and columns.

Columns are named, rows are numbered (but can be named) and can be easily selected and calculated upon. Internally, columns are stored as 1d numpy arrays. If you set row names, they’re converted into a dictionary for fast access. There is a rich subselection/slicing API, see help(DataFrame.get_item) (it also works for setting values). Please note that any slice get’s you another DataFrame, to access individual entries use get_row(), get_column(), get_value().

DataFrames also understand basic arithmetic and you can either add (multiply,…) a constant value, or another DataFrame of the same size / with the same column names, like this:

#multiply every value in ColumnA that is smaller than 5 by 6.
my_df[my_df[:,'ColumnA'] < 5, 'ColumnA'] *= 6

#you always need to specify both row and column selectors, use : to mean everything
my_df[:, 'ColumnB'] = my_df[:,'ColumnA'] + my_df[:, 'ColumnC']

#let's take every row that starts with Shu in ColumnA and replace it with a new list (comprehension)
select = my_df.where(lambda row: row['ColumnA'].startswith('Shu'))
my_df[select, 'ColumnA'] = [row['ColumnA'].replace('Shu', 'Sha') for row in my_df[select,:].iter_rows()]

Dataframes talk directly to R via rpy2 (rpy2 is not a prerequiste for the library!)

 

(2) pandas http://pandas.pydata.org/

Library Highlights

  • A fast and efficient DataFrame object for data manipulation with integrated indexing;
  • Tools for reading and writing data between in-memory data structures and different formats: CSV and text files, Microsoft Excel, SQL databases, and the fast HDF5 format;
  • Intelligent data alignment and integrated handling of missing data: gain automatic label-based alignment in computations and easily manipulate messy data into an orderly form;
  • Flexible reshaping and pivoting of data sets;
  • Intelligent label-based slicing, fancy indexing, and subsetting of large data sets;
  • Columns can be inserted and deleted from data structures for size mutability;
  • Aggregating or transforming data with a powerful group by engine allowing split-apply-combine operations on data sets;
  • High performance merging and joining of data sets;
  • Hierarchical axis indexing provides an intuitive way of working with high-dimensional data in a lower-dimensional data structure;
  • Time series-functionality: date range generation and frequency conversion, moving window statistics, moving window linear regressions, date shifting and lagging. Even create domain-specific time offsets and join time series without losing data;
  • The library has been ruthlessly optimized for performance, with critical code paths compiled to C;
  • Python with pandas is in use in a wide variety of academic and commercial domains, including Finance, Neuroscience, Economics, Statistics, Advertising, Web Analytics, and more.

Why not R?

First of all, we love open source R! It is the most widely-used open source environment for statistical modeling and graphics, and it provided some early inspiration for pandas features. R users will be pleased to find this library adopts some of the best concepts of R, like the foundational DataFrame (one user familiar with R has described pandas as “R data.frame on steroids”). But pandas also seeks to solve some frustrations common to R users:

  • R has barebones data alignment and indexing functionality, leaving much work to the user. pandas makes it easy and intuitive to work with messy, irregularly indexed data, like time series data. pandas also provides rich tools, like hierarchical indexing, not found in R;
  • R is not well-suited to general purpose programming and system development. pandas enables you to do large-scale data processing seamlessly when developing your production applications;
  • Hybrid systems connecting R to a low-productivity systems language like Java, C++, or C# suffer from significantly reduced agility and maintainability, and you’re still stuck developing the system components in a low-productivity language;
  • The “copyleft” GPL license of R can create concerns for commercial software vendors who want to distribute R with their software under another license. Python and pandas use more permissive licenses.

(3) datamatrix http://pypi.python.org/pypi/datamatrix/0.8

datamatrix 0.8

A Pythonic implementation of R’s data.frame structure.

Latest Version: 0.9

This module allows access to comma- or other delimiter separated files as if they were tables, using a dictionary-like syntax. DataMatrix objects can be manipulated, rows and columns added and removed, or even transposed

—————————————————————–

Modeling in Python

Continue reading “Data Frame in Python”

Possible Digital Disruptions by Cyber Actors in USA Electoral Cycle

Some possible electronic disruptions  that threaten to disrupt the electoral cycle in United States of America currently underway is-

1) Limited Denial of Service Attacks (like for 5-8 minutes) on fund raising websites, trying to fly under the radar of network administrators to deny the targeted  fundraising website for a small percentage of funds . Money remains critical to the world’s most expensive political market. Even a 5% dropdown in online fund-raising capacity can cripple a candidate.

2)  Limited Man of the Middle  Attacks on ground volunteers to disrupt ,intercept and manipulate communication flows. Basically cyber attacks at vulnerable ground volunteers in critical counties /battleground /swing states (like Florida)

3) Electro-Magnetic Disruptions of Electronic Voting Machines in critical counties /swing states (like Florida) to either disrupt, manipulate or create an impression that some manipulation has been done.

4) Use search engine flooding (for search engine de-optimization of rival candidates keywords), and social media flooding for disrupting the listening capabilities of sentiment analysis.

5) Selected leaks (including using digital means to create authetntic, fake or edited collateral) timed to embarrass rivals or influence voters , this can be geo-coded and mass deployed.

6) using Internet communications to selectively spam or influence independent or opinionated voters through emails, short messaging service , chat channels, social media.

7) Disrupt the Hillary for President 2016 campaign by Anonymous-Wikileak sympathetic hacktivists.

 

 

Interview Kelci Miclaus, SAS Institute Using #rstats with JMP

Here is an interview with Kelci Miclaus, a researcher working with the JMP division of the SAS Institute, in which she demonstrates examples of how the R programming language is a great hit with JMP customers who like to be flexible.

 

Ajay- How has JMP been using integration with R? What has been the feedback from customers so far? Is there a single case study you can point out where the combination of JMP and R was better than any one of them alone?

Kelci- Feedback from customers has been very positive. Some customers are using JMP to foster collaboration between SAS and R modelers within their organizations. Many are using JMP’s interactive visualization to complement their use of R. Many SAS and JMP users are using JMP’s integration with R to experiment with more bleeding-edge methods not yet available in commercial software. It can be used simply to smooth the transition with regard to sending data between the two tools, or used to build complete custom applications that take advantage of both JMP and R.

One customer has been using JMP and R together for Bayesian analysis. He uses R to create MCMC chains and has found that JMP is a great tool for preparing the data for analysis, as well as displaying the results of the MCMC simulation. For example, the Control Chart platform and the Bubble Plot platform in JMP can be used to quickly verify convergence of the algorithm. The use of both tools together can increase productivity since the results of an analysis can be achieved faster than through scripting and static graphics alone.

I, along with a few other JMP developers, have written applications that use JMP scripting to call out to R packages and perform analyses like multidimensional scaling, bootstrapping, support vector machines, and modern variable selection methods. These really show the benefit of interactive visual analysis of coupled with modern statistical algorithms. We’ve packaged these scripts as JMP add-ins and made them freely available on our JMP User Community file exchange. Customers can download them and now employ these methods as they would a regular JMP platform. We hope that our customers familiar with scripting will also begin to contribute their own add-ins so a wider audience can take advantage of these new tools.

(see http://www.decisionstats.com/jmp-and-r-rstats/)

Ajay- Are there plans to extend JMP integration with other languages like Python?

Kelci- We do have plans to integrate with other languages and are considering integrating with more based on customer requests. Python has certainly come up and we are looking into possibilities there.

 Ajay- How is R a complimentary fit to JMP’s technical capabilities?

Kelci- R has an incredible breadth of capabilities. JMP has extensive interactive, dynamic visualization intrinsic to its largely visual analysis paradigm, in addition to a strong core of statistical platforms. Since our brains are designed to visually process pictures and animated graphs more efficiently than numbers and text, this environment is all about supporting faster discovery. Of course, JMP also has a scripting language (JSL) allowing you to incorporate SAS code, R code, build analytical applications for others to leverage SAS, R and other applications for users who don’t code or who don’t want to code.

JSL is a powerful scripting language on its own. It can be used for dialog creation, automation of JMP statistical platforms, and custom graphic scripting. In other ways, JSL is very similar to the R language. It can also be used for data and matrix manipulation and to create new analysis functions. With the scripting capabilities of JMP, you can create custom applications that provide both a user interface and an interactive visual back-end to R functionality. Alternatively, you could create a dashboard using statistical and/or graphical platforms in JMP to explore the data and with the click of a button, send a portion of the data to R for further analysis.

Another JMP feature that complements R is the add-in architecture, which is similar to how R packages work. If you’ve written a cool script or analysis workflow, you can package it into a JMP add-in file and send it to your colleagues so they can easily use it.

Ajay- What is the official view on R from your organization? Do you think it is a threat, or a complimentary product or another statistical platform that coexists with your offerings?

Kelci- Most definitely, we view R as complimentary. R contributors are providing a tremendous service to practitioners, allowing them to try a wide variety of methods in the pursuit of more insight and better results. The R community as a whole is providing a valued role to the greater analytical community by focusing attention on newer methods that hold the most promise in so many application areas. Data analysts should be encouraged to use the tools available to them in order to drive discovery and JMP can help with that by providing an analytic hub that supports both SAS and R integration.

Ajay-  While you do use R, are there any plans to give back something to the R community in terms of your involvement and participation (say at useR events) or sponsoring contests.

 Kelci- We are certainly open to participating in useR groups. At Predictive Analytics World in NY last October, they didn’t have a local useR group, but they did have a Predictive Analytics Meet-up group comprised of many R users. We were happy to sponsor this. Some of us within the JMP division have joined local R user groups, myself included.  Given that some local R user groups have entertained topics like Excel and R, Python and R, databases and R, we would be happy to participate more fully here. I also hope to attend the useR! annual meeting later this year to gain more insight on how we can continue to provide tools to help both the JMP and R communities with their work.

We are also exploring options to sponsor contests and would invite participants to use their favorite tools, languages, etc. in pursuit of the best model. Statistics is about learning from data and this is how we make the world a better place.

About- Kelci Miclaus

Kelci is a research statistician developer for JMP Life Sciences at SAS Institute. She has a PhD in Statistics from North Carolina State University and has been using SAS products and R for several years. In addition to research interests in statistical genetics, clinical trials analysis, and multivariate analysis/visualization methods, Kelci works extensively with JMP, SAS, and R integration.

.

 

#rstats -Basic Data Manipulation using R

Continuing my series of basic data manipulation using R. For people knowing analytics and
new to R.
1 Keeping only some variables

Using subset we can keep only the variables we want-

Sitka89 <- subset(Sitka89, select=c(size,Time,treat))

Will keep only the variables we have selected (size,Time,treat).

2 Dropping some variables

Harman23.cor$cov.arm.span <- NULL
This deletes the variable named cov.arm.span in the dataset Harman23.cor

3 Keeping records based on character condition

Titanic.sub1<-subset(Titanic,Sex=="Male")

Note the double equal-to sign
4 Keeping records based on date/time condition

subset(DF, as.Date(Date) >= '2009-09-02' & as.Date(Date) <= '2009-09-04')

5 Converting Date Time Formats into other formats

if the variable dob is “01/04/1977) then following will convert into a date object

z=strptime(dob,”%d/%m/%Y”)

and if the same date is 01Apr1977

z=strptime(dob,"%d%b%Y")

6 Difference in Date Time Values and Using Current Time

The difftime function helps in creating differences in two date time variables.

difftime(time1, time2, units='secs')

or

difftime(time1, time2, tz = "", units = c("auto", "secs", "mins", "hours", "days", "weeks"))

For current system date time values you can use

Sys.time()

Sys.Date()

This value can be put in the difftime function shown above to calculate age or time elapsed.

7 Keeping records based on numerical condition

Titanic.sub1<-subset(Titanic,Freq >37)

For enhanced usage-
you can also use the R Commander GUI with the sub menu Data > Active Dataset

8 Sorting Data

Sorting A Data Frame in Ascending Order by a variable

AggregatedData<- sort(AggregatedData, by=~ Package)

Sorting a Data Frame in Descending Order by a variable

AggregatedData<- sort(AggregatedData, by=~ -Installed)

9 Transforming a Dataset Structure around a single variable

Using the Reshape2 Package we can use melt and acast functions

library("reshape2")

tDat.m<- melt(tDat)

tDatCast<- acast(tDat.m,Subject~Item)

If we choose not to use Reshape package, we can use the default reshape method in R. Please do note this takes longer processing time for bigger datasets.

df.wide <- reshape(df, idvar="Subject", timevar="Item", direction="wide")

10 Type in Data

Using scan() function we can type in data in a list

11 Using Diff for lags and Cum Sum function forCumulative Sums

We can use the diff function to calculate difference between two successive values of a variable.

Diff(Dataset$X)

Cumsum function helps to give cumulative sum

Cumsum(Dataset$X)

> x=rnorm(10,20) #This gives 10 Randomly distributed numbers with Mean 20

> x

[1] 20.76078 19.21374 18.28483 20.18920 21.65696 19.54178 18.90592 20.67585

[9] 20.02222 18.99311

> diff(x)

[1] -1.5470415 -0.9289122 1.9043664 1.4677589 -2.1151783 -0.6358585 1.7699296

[8] -0.6536232 -1.0291181 >

cumsum(x)

[1] 20.76078 39.97453 58.25936 78.44855 100.10551 119.64728 138.55320

[8] 159.22905 179.25128 198.24438

> diff(x,2) # The diff function can be used as diff(x, lag = 1, differences = 1, ...) where differences is the order of differencing

[1] -2.4759536 0.9754542 3.3721252 -0.6474195 -2.7510368 1.1340711 1.1163064

[8] -1.6827413

Becker, R. A., Chambers, J. M. and Wilks, A. R. (1988) The New S Language. Wadsworth & Brooks/Cole.

12 Merging Data

Deducer GUI makes it much simpler to merge datasets. The simplest syntax for a merge statement is

totalDataframeZ <- merge(dataframeX,dataframeY,by=c("AccountId","Region"))

13 Aggregating and group processing of a variable

We can use multiple methods for aggregating and by group processing of variables.
Two functions we explore here are aggregate and Tapply.

Refering to the R Online Manual at
[http://stat.ethz.ch/R-manual/R-patched/library/stats/html/aggregate.html]

## Compute the averages for the variables in 'state.x77', grouped

## according to the region (Northeast, South, North Central, West) that

## each state belongs to

aggregate(state.x77, list(Region = state.region), mean)

Using TApply

## tapply(Summary Variable, Group Variable, Function)

Reference

[http://www.ats.ucla.edu/stat/r/library/advanced_function_r.htm#tapply]

We can also use specialized packages for data manipulation.

For additional By-group processing you can see the doBy package as well as Plyr package
 for data manipulation.Doby contains a variety of utilities including:
 1) Facilities for groupwise computations of summary statistics and other facilities for working with grouped data.
 2) General linear contrasts and LSMEANS (least-squares-means also known as population means),
 3) HTMLreport for autmatic generation of HTML file from R-script with a minimum of markup, 4) various other utilities and is available at[ http://cran.r-project.org/web/packages/doBy/index.html]
Also Available at [http://cran.r-project.org/web/packages/plyr/index.html],
Plyr is a set of tools that solves a common set of problems:
you need to break a big problem down into manageable pieces,
operate on each pieces and then put all the pieces back together.
 For example, you might want to fit a model to each spatial location or
 time point in your study, summarise data by panels or collapse high-dimensional arrays
 to simpler summary statistics.

Ten steps to analysis using R

I am just listing down a set of basic R functions that allow you to start the task of business analytics, or analyzing a dataset(data.frame). I am doing this both as a reference for myself as well as anyone who wants to learn R- quickly.

I am not putting in data import functions, because data manipulation is a seperate baby altogether. Instead I assume you have a dataset ready for analysis and what are the top R commands you would need to analyze it.

 

For anyone who thought R was too hard to learn- here is ten functions to learning R

1) str(dataset) helps you with the structure of dataset

2) names(dataset) gives you the names of variables

3)mean(dataset) returns the mean of numeric variables

4)sd(dataset) returns the standard deviation of numeric variables

5)summary(variables) gives the summary quartile distributions and median of variables

That about gives me the basic stats I need for a dataset.

> data(faithful)
> names(faithful)
[1] "eruptions" "waiting"
> str(faithful)
'data.frame':   272 obs. of  2 variables:
 $ eruptions: num  3.6 1.8 3.33 2.28 4.53 ...
 $ waiting  : num  79 54 74 62 85 55 88 85 51 85 ...
> summary(faithful)
   eruptions        waiting
 Min.   :1.600   Min.   :43.0
 1st Qu.:2.163   1st Qu.:58.0
 Median :4.000   Median :76.0
 Mean   :3.488   Mean   :70.9
 3rd Qu.:4.454   3rd Qu.:82.0
 Max.   :5.100   Max.   :96.0

> mean(faithful)
eruptions   waiting
 3.487783 70.897059
> sd(faithful)
eruptions   waiting
 1.141371 13.594974

6) I can do a basic frequency analysis of a particular variable using the table command and $ operator (similar to dataset.variable name in other statistical languages)

> table(faithful$waiting)

43 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 62 63 64 65 66 67 68 69 70
 1  3  5  4  3  5  5  6  5  7  9  6  4  3  4  7  6  4  3  4  3  2  1  1  2  4
71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 96
 5  1  7  6  8  9 12 15 10  8 13 12 14 10  6  6  2  6  3  6  1  1  2  1  1
or I can do frequency analysis of the whole dataset using
> table(faithful)
         waiting
eruptions 43 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 62 63 64 65 66 67
    1.6    0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0
    1.667  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0
    1.7    0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0
    1.733  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0
.....output truncated
7) plot(dataset)
It helps plot the dataset

8) hist(dataset$variable) is better at looking at histograms

hist(faithful$waiting)

9) boxplot(dataset)

10) The tenth function for a beginner would be cor(dataset$var1,dataset$var2)

> cor(faithful)
          eruptions   waiting
eruptions 1.0000000 0.9008112
waiting   0.9008112 1.0000000

 

I am assuming that as a beginner you would use the list of GUI at http://rforanalytics.wordpress.com/graphical-user-interfaces-for-r/  to import and export Data. I would deal with ten steps to data manipulation in R another post.

 

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 lattice, ggplot2, vcd 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 lattice, scatterplot3d 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 lattice, ggplot (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 colorspace, vcdprovides 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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