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Using a Linux only package in Windows #rstats

April 26, 2013 9:57 am / 1 Comment

Here is some R code for using a R package that has only a tar.gz file available (used to load R packages in Linux) and no Zip file available (used to load R packages in Windows).

Step 1- Download the tar.gz file.

Step 2 Unzip it (twice) using 7zip

Step 3 Change the path variable below to your unzipped, downloaded location for the R sub folder within the package folder .

Step 4 Copy and Paste this in R

Step 5 Start using the R package in Windows (where 75% of the money and clients and businesses still are)

Caveat Emptor- No X Dependencies (ok!)

path="C:\\Users\\KUs\\Desktop\\segue\\R"
b=dir(path)
c=length(b)
for (i in 1:c){source(gsub(" ","",paste(path,"\\",b[i])))}
ls()

 

R2D2

Using R for Cricket Analysis #rstats #IPL

April 25, 2013 7:58 am / Leave a Comment 

#Downloading the Data for batting across all formats of cricket
library(XML)
url="http://stats.espncricinfo.com/ci/engine/stats/index.html?class=11;template=results;type=batting"
tables=readHTMLTable(url,stringsAsFactors = F)
#Note we wrote stringsAsFactors=F in this to avoid getting factor variables, 
#since we will need to convert these variables to numeric variables
table2=tables$"Overall figures"
rm(tables)
#Creating new variables from Span
table2$Debut=as.numeric(substr(table2$Span,1,4))
table2$LastYr=as.numeric(substr(table2$Span,6,10))
table2$YrsPlayed=table2$LastYr-table2$Debut
#Creating New Variables. In cricket a not out score is denoted by * which can cause data quality error. 
#This is treated by grepl for finding and gsub for removing the *. 
#Note the double \ to escape regex charachter
table2$HSNotOut=grepl("\\*",table2$HS)
table2$HS2=gsub("\\*","",table2$HS)
#Creating a FOR Loop (!) to convert variables to numeric variables
for (i in 3:17) {
+     table2[, i] <- as.numeric(table2[, i])
+ }

and we see why Sachin Tendulkar is the best (by using ggplot via Deducer)

dmancasestudy5

Also see 


  • Freaknomics Challenge-
    1. Prove match fixing does not and cannot exist in IPL
    2. Create an ideal fantasy team
    

    • 







 

		







	
Using R for Cricket Analysis #rstats

	

		April 14, 2013 5:03 am / 1 Comment	

	
ESPN Crincinfo is the best site for cricket data (you can see an earlier detailed post on the database  here http://decisionstats.com/2012/04/07/cricinfo-statsguru-database-for-statistical-and-graphical-analysis/  ), and using the XML package in R we can easily scrape and manipulate data


Here is the code.






library(XML)
url="http://stats.espncricinfo.com/ci/engine/stats/index.html?class=1;team=6;template=results;type=batting"
#Note I can also break the url string and use paste command to modify this url with parameters
tables=readHTMLTable(url)
tables$"Overall figures"

#Now see this- since I only got 50 results in each page, I look at the url of next page

table1=tables$"Overall figures"
url="http://stats.espncricinfo.com/ci/engine/stats/index.html?class=1;page=2;team=6;template=results;type=batting"
tables=readHTMLTable(url)
table2=tables$"Overall figures"

#Now I need to join these two tables vertically

table3=rbind(table1,table2)

Note-I can also automate the web scraping .
Now the data is within R, we can use something like Deducer to visualize.






Created by Pretty R at inside-R.org

		







	
R 3.0 launched #rstats

	

		April 3, 2013 10:15 pm / Leave a Comment	

	
The 3.0 Era for R starts today! Changes include  better Big Data support.


Read the NEWS here


    

  • install.packages() has a new argument quiet to reduce the amount of output shown.
    • 

  • New functions cite() and citeNatbib() have been added, to allow generation of in-text citations from "bibentry" objects. A cite() function may be added to bibstyle() environments.
    • 

  • merge() works in more cases where the data frames include matrices. (Wish of PR#14974.)
    • 

  • sample.int() has some support for n >= 2^31: see its help for the limitations.A different algorithm is used for (n, size, replace = FALSE, prob = NULL) for n > 1e7 and size <= n/2. This is much faster and uses less memory, but does give different results.
    • 

  • list.files() (aka dir()) gains a new optional argument no.. which allows to exclude "." and ".." from listings.
    • 

  • Profiling via Rprof() now optionally records information at the statement level, not just the function level.
    • 

  • available.packages() gains a "license/restricts_use" filter which retains only packages for which installation can proceed solely based on packages which are guaranteed not to restrict use.
    • 

  • File ‘share/licenses/licenses.db’ has some clarifications, especially as to which variants of ‘BSD’ and ‘MIT’ is intended and how to apply them to packages. The problematic licence ‘Artistic-1.0’ has been removed.
    • 

  • The breaks argument in hist.default() can now be a function that returns the breakpoints to be used (previously it could only return the suggested number of breakpoints).
    • 



LONG VECTORS


This section applies only to 64-bit platforms.


    

  • There is support for vectors longer than 2^31 – 1 elements. This applies to raw, logical, integer, double, complex and character vectors, as well as lists. (Elements of character vectors remain limited to 2^31 – 1 bytes.)
    • 

  • Most operations which can sensibly be done with long vectors work: others may return the error ‘long vectors not supported yet’. Most of these are because they explicitly work with integer indices (e.g. anyDuplicated() and match()) or because other limits (e.g. of character strings or matrix dimensions) would be exceeded or the operations would be extremely slow.
    • 

  • length() returns a double for long vectors, and lengths can be set to 2^31 or more by the replacement function with a double value.
    • 

  • Most aspects of indexing are available. Generally double-valued indices can be used to access elements beyond 2^31 – 1.
    • 

  • There is some support for matrices and arrays with each dimension less than 2^31 but total number of elements more than that. Only some aspects of matrix algebra work for such matrices, often taking a very long time. In other cases the underlying Fortran code has an unstated restriction (as was found for complex svd()).
    • 

  • dist() can produce dissimilarity objects for more than 65536 rows (but for example hclust() cannot process such objects).
    • 

  • serialize() to a raw vector is unlimited in size (except by resources).
    • 

  • The C-level function R_alloc can now allocate 2^35 or more bytes.
    • 

  • agrep() and grep() will return double vectors of indices for long vector inputs.
    • 

  • Many calls to .C() have been replaced by .Call() to allow long vectors to be supported (now or in the future). Regrettably several packages had copied the non-API .C() calls and so failed.
    • 

  • .C() and .Fortran() do not accept long vector inputs. This is a precaution as it is very unlikely that existing code will have been written to handle long vectors (and the R wrappers often assume that length(x) is an integer).
    • 

  • Most of the methods for sort() work for long vectors.
    • 



    

  • rank(), sort.list() and order() support long vectors (slowly except for radix sorting).
    • 

  • sample() can do uniform sampling from a long vector.
    • 



PERFORMANCE IMPROVEMENTS


    

  • More use has been made of R objects representing registered entry points, which is more efficient as the address is provided by the loader once only when the package is loaded.

    This has been done for packages base, methods, splines and tcltk: it was already in place for the other standard packages.
    

    Since these entry points are always accessed by the R entry points they do not need to be in the load table which can be substantially smaller and hence searched faster. This does mean that .C / .Fortran / .Call calls copied from earlier versions of R may no longer work – but they were never part of the API.
    • 

  • Many .Call() calls in package base have been migrated to .Internal() calls.
    • 

  • solve() makes fewer copies, especially when b is a vector rather than a matrix.
    • 

  • eigen() makes fewer copies if the input has dimnames.
    • 

  • Most of the linear algebra functions make fewer copies when the input(s) are not double (e.g. integer or logical).
    • 

  • A foreign function call (.C() etc) in a package without a PACKAGE argument will only look in the first DLL specified in the ‘NAMESPACE’ file of the package rather than searching all loaded DLLs. A few packages needed PACKAGE arguments added.
    • 

  • The @<- operator is now implemented as a primitive, which should reduce some copying of objects when used. Note that the operator object must now be in package base: do not try to import it explicitly from package methods.
    • 



SIGNIFICANT USER-VISIBLE CHANGES


    

  • Packages need to be (re-)installed under this version (3.0.0) of R.
    • 

  • There is a subtle change in behaviour for numeric index values 2^31 and larger. These never used to be legitimate and so were treated as NA, sometimes with a warning. They are now legal for long vectors so there is no longer a warning, and x[2^31] <- y will now extend the vector on a 64-bit platform and give an error on a 32-bit one.
    • 

  • It is now possible for 64-bit builds to allocate amounts of memory limited only by the OS. It may be wise to use OS facilities (e.g. ulimit in a bash shell, limit in csh), to set limits on overall memory consumption of an R process, particularly in a multi-user environment. A number of packages need a limit of at least 4GB of virtual memory to load.

    64-bit Windows builds of R are by default limited in memory usage to the amount of RAM installed: this limit can be changed by command-line option –max-mem-size or setting environment variable R_MAX_MEM_SIZE.
    • 



 

		







	
Interview Dr. Ian Fellows Fellstat.com #rstats Deducer

	

		April 3, 2013 1:59 pm / 1 Comment	

	
Here is an interview with Dr Ian Fellows, creator of acclaimed packages in R like Deducer and the Founder and President of Fellstat.com


fellstat


Ajay- Describe your involvement with the Deducer Project, and the various plugins associated with it. What has been the usage and response for Deducer from R Community.




Ian- Deducer is a graphical user interface for data analysis built on R. It sprung out of a disconnect between the toolchain used by myself and the toolchain of the psychologists that I worked with at the University of California, San DIego. They were primarily SPSS user, whereas I liked to use R, especially for anything that was not a standard analysis.




I felt that there was a big gap in the audience that R serves. Not all consumers or producers of statistics can be expected to have the computational background (command-line programming) that R requires. I think it is important to recognize and work with the areas of expertise that statistical users have. I’m not an expert in psychology, and they didn’t expect me to be one. They are not experts in computation, and I don’t think that we should expect them to be in order to be a part of the R toolchain community.ian




This was the impetus behind Deducer, so it is fundamentally designed to be a familiar experience for users coming from an SPSS background and provides a full implementation of the standard methods in statistics, and data manipulation from descriptives to generalized linear models. Additionally, it has an advanced GUI for creating visualizations which has been well received, and won the John Chambers award for statistical software in 2011.




Uptake of the system is difficult to measure as CRAN does not track package downloads, but from what I can tell there has been a steadily increasing user base. The online manual has been accessed by over 75,000 unique users, with over 400,000 page views. There is a small, active group of developers creating add-on packages supporting various sub-diciplines of statistics. There are 8 packages on CRAN extending/using Deducer, and quite a few more on r-forge.




Ajay- Do you see any potential for Deducer as an enterprise software product (like R Studio et al)




Ian- Like R Studio, Deducer is used in enterprise environments but is not specifically geared towards that environment. I do see potential in that realm, but don’t have any particular plan to make an enterprise version of Deducer.




Ajay- Describe your work in Texas Hold’em Poker. Do you see any potential for R for diversifying into the casino analytics – which has hitherto been served exclusively by non open source analytics vendors.




Ian- As a Statistician, I’m very much interested in problems of inference under uncertainty, especially when the problem space is huge. Creating an Artificial Intelligence that can play (heads-up limit) Texas Hold’em Poker at a high level is a perfect example of this. There is uncertainty created by the random drawing of cards, the problem space is 10^{18}, and our opponent can adapt to any strategy that we employ.




While high level chess A.I.s have existed for decades, the first viable program to tackle full scale poker was introduced in 2003 by the incomparable Computer Poker Research group at the University of Alberta. Thus poker represents a significant challenge which can be used as a test bed to break new ground in applied game theory. In 2007 and 2008 I submitted entries to the AAA’s annual computer poker competition, which pits A.I.s from universities across the world against each other. My program, which was based on an approximate game theoretic equilibrium calculated using a co-evolutionary process called fictitious play, came in second behind the Alberta team.








Ajay- Describe your work in social media analytics for R. What potential do you see for Social Network Analysis given the current usage of it in business analytics and business intelligence tools for enterprise.






Ian- My dissertation focused on new model classes for social network analysis (http://arxiv.org/pdf/1208.0121v1.pdf and http://arxiv.org/pdf/1303.1219.pdf). R has a great collection of tools for social network analysis in the statnet suite of packages, which represents the forefront of the literature on the statistical modeling of social networks. I think that if the analytics data is small enough for the models to be fit, these tools can represent a qualitative leap in the understanding and prediction of user behavior.




Most uses of social networks in enterprise analytics that I have seen are limited to descriptive statistics (what is a user’s centrality; what is the degree distribution), and the use of these descriptive statistics as fixed predictors in a model. I believe that this approach is an important first step, but ignores the stochastic nature of the network, and the dynamics of tie formation and dissolution. Realistic modeling of the network can lead to more principled, and more accurate predictions of the quantities that enterprise users care about.




The rub is that the Markov Chain Monte Carlo Maximum Likelihood algorithms used to fit modern generative social network models (such as exponential-family random graph models) do not scale well at all. These models are typically limited to fitting networks with fewer than 50,000 vertices, which is clearly insufficient for most analytics customers who have networks more on the order of 50,000,000.




This problem is not insoluble though. Part of my ongoing research involves scalable algorithms for fitting social network models.






Ajay- You decided to go from your Phd into consulting (www.fellstat.com) . What were some of the options you considered in this career choice.






Ian- I’ve been working in the role of a statistical consultant for the last 7 years, starting as an in-house consultant at UCSD after obtaining my MS. Fellows Statistics has been operating for the last 3 years, though not fulltime until January of this year. As I had already been consulting, it was a natural progression to transition to consulting fulltime once I graduated with my Phd.




This has allowed me to both work on interesting corporate projects, and continue research related to my dissertation via sub-awards from various universities.




Ajay- What does Fellstat.com offer in its consulting practice.




Ian- Fellows Statistics offers personalized analytics services to both corporate and academic clients. We are a boutique company, that can scale from a single statistician to a small team of analysts chosen specifically with the client’s needs in mind. I believe that by being small, we can provide better, close-to-the-ground responsive service to our clients.




As a practice, we live at the intersection of mathematical sophistication, and computational skill, with a hint of UI design thrown into the mix. Corporate clients can expect a diverse range of analytic skills from the development of novel algorithms to the design and presentation of data for a general audience. We’ve worked with Revolution Analytics developing algorithms for their ScaleR product, the Center for Disease Control developing graphical user interfaces set to be deployed for world-wide HIV surveillance, and Prospectus analyzing clinical trial data for retinal surgery. With access to the cutting edge research taking place in the academic community, and the skills to implement them in corporate environments, Fellows Statistics is able to offer clients world-class analytics services.




Ajay- How does big data affect the practice of statistics in business decisions.




Ian- There is a big gap in terms of how the basic practice of statistics is taught in most universities, and the types of analyses that are useful when data sizes become large. Back when I was at UCSD, I remember a researcher there jokingly saying that everything is correlated rho=.2. He was joking, but there is a lot of truth to that statement. As data sizes get larger everything becomes significant if a hypothesis test is done, because the test has the power to detect even trivial relationships.




Ajay- How is the R community including developers coping with the Big Data era? What do you think R can do more for Big Data?




Ian- On the open source side, there has been a lot of movement to improve R’s handling of big data. The bigmemory project and the ff package both serve to extend R’s reach beyond in-memory data structures.  Revolution Analytics also has the ScaleR package, which costs money, but is lightning fast and has an ever growing list of analytic techniques implemented. There are also several packages integrating R with hadoop.






Ajay- Describe your research into data visualization including word cloud and other packages. What do you think of Shiny, D3.Js and online data visualization?






Ian- I recently had the opportunity to delve into d3.js for a client project, and absolutely love it. Combined with Shiny, d3 and R one can very quickly create a web visualization of an R modeling technique. One limitation of d3 is that it doesn’t work well with internet explorer 6-8. Once these browsers finally leave the ecosystem, I expect an explosion of sites using d3.




Ajay- Do you think wordcloud is an overused data visualization type and how can it be refined?




Ian- I would say yes, but not for the reasons you would think. A lot of people criticize word clouds because they convey the same information as a bar chart, but with less specificity. With a bar chart you can actually see the frequency, whereas you only get a relative idea with word clouds based on the size of the word.




I think this is both an absolutely correct statement, and misses the point completely. Visualizations are about communicating with the reader. If your readers are statisticians, then they will happily consume the bar chart, following the bar heights to their point on the y-axis to find the frequencies. A statistician will spend time with a graph, will mull it over, and consider what deeper truths are found there. Statisticians are weird though. Most people care as much about how pretty the graph looks as its content. To communicate to these people (i.e. everyone else) it is appropriate and right to sacrifice statistical specificity to design considerations. After all, if the user stops reading you haven’t conveyed anything.




But back to the question… I would say that they are over used because they represent a very superficial analysis of a text or corpus. The word counts do convey an aspect of a text, but not a very nuanced one. The next step in looking at a corpus of texts would be to ask how are they different and how are they the same. The wordcloud package has the comparison and commonality word clouds, which attempt to extend the basic word cloud to answer these questions (see: http://blog.fellstat.com/?p=101).




About-




Dr. Ian Fellows is a professional statistician based out of the University of California, Los Angeles. His research interests range over many sub-disciplines of statistics. His work in statistical visualization won the prestigious John Chambers Award in 2011, and in 2007-2008 his Texas Hold’em AI programs were ranked second in the world.


Applied data analysis has been a passion for him, and he is accustomed to providing accurate, timely analysis for a wide range of projects, and assisting in the interpretation and communication of statistical results. He can be contacted at info@fellstat.com



		







	
New Delhi UseRs March 2013 MeetUp #rstats

	

		March 20, 2013 2:57 am / Leave a Comment	

	
The fifth New Delhi UseRs Meet Up happened at Mimir Tech’s premises in Green Park, New Delhi. I presented on using GUIs for easier transitioning to R from other software but limited it to Deducer (for data visualization -specifically templates and facets in GGPLOT) and Rattle (for Data Mining). We also discussed a couple of things including how to apply R in other business domains, and open source alternatives to Meetup.com .




		







	
Interview Jeroen Ooms OpenCPU #rstats

	

		March 18, 2013 2:29 am / 1 Comment	

	
Below an interview with Jeroen Ooms, a pioneer in R and web development. Jeroen contributes to R by developing packages and web applications for multiple projects.


jeroen


Ajay- What are you working on these days?

Jeroen- My research revolves around challenges and opportunities of using R in embedded applications and scalable systems. After developing numerous web applications, I started the OpenCPU project about 1.5 year ago, as a first attempt at a complete framework for proper integration of R in web services. As I work on this, I run into challenges that shape my research, and sometimes become projects in their own. For example, the RAppArmor package provides the security framework for OpenCPU, but can be used for other purposes as well. RAppArmor interfaces to some methods in the Linux kernel, related to setting security and resource limits. The github page contains the source code, installation instructions, video demo’s, and a draft of a paper for the journal of statistical software. Another example of a problem that appeared in OpenCPU is that applications that used to work were breaking unexpectedly later on due to changes in dependency packages on CRAN. This is actually a general problem that affects almost all R users, as it compromises reliability of CRAN packages and reproducibility of results. In a paper (forthcoming in The R Journal), this problem is discussed in more detail and directions for improvement are suggested. A preprint of the paper is available on arXiv: http://arxiv.org/abs/1303.2140.


I am also working on software not directly related to R. For example, in project Mobilize we teach high school students in Los Angeles the basics of collecting and analyzing data. They use mobile devices to upload surveys with questions, photos, gps, etc using the ohmage software. Within Mobilize and Ohmage, I am in charge of developing web applications that help students to visualize the data they collaboratively collected. One public demo with actual data collected by students about snacking behavior is available at: http://jeroenooms.github.com/snack. The application allows students to explore their data, by filtering, zooming, browsing, comparing etc. It helps students and teachers to access and learn from their data, without complicated tools or programming. This approach would easily generalize to other fields, like medical data or BI. The great thing about this application is that it is fully client side; the backend is simply a CSV file. So it is very easy to deploy and maintain.


Ajay-What’s your take on difference between OpenCPU and RevoDeployR ?

Jeroen- RevoDeployR and OpenCPU both provide a system for development of R web applications, but in a fairly different context. OpenCPU is open source and written completely in R, whereas RevoDeployR is proprietary and written in Java. I think Revolution focusses more on a complete solution in a corporate environment. It integrates with the Revolution Enterprise suite and their other big data products, and has built-in functionality for authentication, managing privileges, server administration, support for MS Windows, etc. OpenCPU on the other hand is much smaller and should be seen as just a computational backend, analogous to a database backend. It exposes a clean HTTP api to call R functions to be embedded in larger systems, but is not a complete end-product in itself.


OpenCPU is designed to make it easy for a statistician to expose statistical functionality that will used by web developers that do not need to understand or learn R. One interesting example is how we use OpenCPU inside OpenMHealth, a project that designs an architecture for mobile applications in the health domain. Part of the architecture are so called “Data Processing Units”, aka DPU’s. These are simple, modular I/O units that do various sorts of data processing, similar to unix tools, but then over HTTPS. For example, the mobility dpu is used to calculate distances between gps coordinates via a simple http call, which OpenCPU maps to the corresponding R function implementing the harversine formula.


Ajay- What are your views on Shiny by RStudio?

Jeroen- RStudio seems very promising. Like Revolution, they deliver a more full featured product than any of my projects. However, RStudio is completely open source, which is great because it allows anyone to leverage the software and make it part of their projects. I think this is one of the reasons why the product has gotten a lot of traction in the community, which has in turn provided RStudio with great feedback to further improve the product. It illustrates how open source can be a win-win situation. I am currently developing a package to run OpenCPU inside RStudio, which will make developing and running OpenCPU apps much easier.


Ajay- Are you still developing excellent RApache web apps (which IMHO could be used for visualization like business intelligence tools?) 

Jeroen-   The OpenCPU framework was a result of those webapps (including ggplot2 for graphical exploratory analysis, lme4 for online random effects modeling, stockplot for stock predictions and irttool.com, an R web application for online IRT analysis). I started developing some of those apps a couple of years ago, and realized that I was repeating a large share of the infrastructure for each application. Based on those experiences I extracted a general purpose framework. Once the framework is done, I’ll go back to developing applications :) 


Ajay- You have helped  build web apps, openCPU, RAppArmor, Ohmage , Snack , mobility apps .What’s your thesis topic on? 

Jeroen- My thesis revolves around all of the technical and social challenges of moving statistical computing beyond the academic and private labs, into more public, accessible and social places. Currently statistics is still done to mostly manually by specialists using software to load data, perform some analysis, and produce results that end up in a report or presentation. There are great opportunities to leverage the open source analysis and visualization methods that R has to offer as part of open source stacks, services, systems and applications. However, several problems need to be addressed before this can actually be put in production. I hope my doctoral research will contribute to taking a step in that direction.


Ajay- R is RAM constrained but the cloud offers lots of RAM. Do you see R increasing in usage on the cloud? why or why not? 

Jeroen-   Statistical computing can greatly benefit from the resources that the cloud has to offer. Software like OpenCPU, RStudio, Shiny and RevoDeployR all provide some approach of moving computation to centralized servers. This is only the beginning. Statisticians, researchers and analysts will continue to increasingly share and publish data, code and results on social cloud-based computing platforms. This will address some of the hardware challenges, but also contribute towards reproducible research and further socialize data analysis, i.e. improve learning, collaboration and integration.


That said, the cloud is not going to solve all problems. You mention the need for more memory, but that is only one direction to scale in. Some of the issues we need to address are more fundamental and require new algorithms, different paradigms, or a cultural change. There are many exciting efforts going on that are at least as relevant as big hardware. Gelman’s mc-stan implements a new MC method that makes Bayesian inference easier and faster while supporting more complex models. This is going to make advanced Bayesian methods more accessible to applied researchers, i.e. scale in terms of complexity and applicability. Also Javascript is rapidly becoming more interesting. Performance of Google’s javascript engine V8 outruns any other scripting language at this point, and the huge Javascript community provides countless excellent software libraries. For example D3 is a graphics library that is about to surpass R in terms of functionality, reliability and user base. The snack viz that I developed for Mobilize is based largely on D3. Finally, Julia is another young language for technical computing with lots of activity and very smart people behind it. These developments are just as important for the future of statistical computing as big data solutions.


About-

You can read more on Jeroen and his work at  http://jeroenooms.github.com/ and reach out to him here http://www.linkedin.com/in/datajeroen

		






	

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