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NumFocus- The Python Statistical Community

I really liked the mature design, and foundation of this charitable organization. While it is similar to FOAS in many ways (http://www.foastat.org/projects.html) I like the projects . Excellent projects and some of which I think should be featured in Journal of Statistical Software- (since there is a seperate R Journal) unless it wants to be overtly R focused.

 

In the same manner I think some non Python projects should try and reach out to NumFocus (if it is not wanting to be so  PyFocus-ed)

Here it is NumFocus

NumFOCUS supports and promotes world-class, innovative, open source scientific software. Most individual projects, even the wildly successful ones, find the overhead of a non-profit to be too large for their community to bear. NumFOCUS provides a critical service as an umbrella organization which removes the burden from the projects themselves to raise money.

Money donated through NumFOCUS goes to sponsor things like:

  • Coding sprints (food and travel)
  • Technical fellowships (sponsored students and mentors to work on code)
  • Equipment grants (to developers and projects)
  • Conference attendance for students (to PyData, SciPy, and other conferences)
  • Fees for continuous integration and other software engineering tools
  • Documentation development
  • Web-page hosting and bandwidth fees for projects

Core Projects

NumPy

static/images/NumPY.pngNumPy is the fundamental package needed for scientific computing with Python. Besides its obvious scientific uses, NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases. Repositories for NumPy binaries: http://www.lfd.uci.edu/~gohlke/pythonlibs/#numpy, a variety of versions – http://sourceforge.net/projects/numpy/files/NumPy/, version 1.6.1 – http://sourceforge.net/projects/numpy/files/NumPy/1.6.1/.

SciPy

static/images/scipy.pngSciPy is open-source software for mathematics, science, and engineering. It is also the name of a very popular conference on scientific programming with Python. The SciPy library depends on NumPy, which provides convenient and fast N-dimensional array manipulation. The SciPy library is built to work with NumPy arrays, and provides many user-friendly and efficient numerical routines such as routines for numerical integration and optimization.

Matplotlib

static/images/matplotlib.png2D plotting library for Python that produces high quality figures that can be used in various hardcopy and interactive environments. matplolib is compatiable with python scripts and the python and ipython shells.

IPython

static/images/ipython.pngHigh quality open source python shell that includes tools for high level and interactive parallel computing.

SymPy

static/images/SymPy2.jpgSymPy is a Python library for symbolic mathematics. It aims to become a full-featured computer algebra system (CAS) while keeping the code as simple as possible in order to be comprehensible and easily extensible. SymPy is written entirely in Python and does not require any external libraries.

Other Projects

Cython

static/images/cython.pngCython is a language based on Pyrex that makes writing C extensions for Python as easy as writing them in Python itself. Cython supports calling C functions and declaring C types on variables and class attributes, allowing the compiler to generate very efficient C code from Cython code.

pandas

static/images/pandas.pngpandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures and data analysis tools for the Python programming language.

PyTables

static/images/logo-pytables-small.pngPyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the NumPy package. It features an Pythonic interface combined with C / Cython extensions for the performance-critical parts of the code. This makes it a fast, yet extremely easy to use tool for very large amounts of data. http://pytables.github.com/

scikit-image

static/images/scikitsimage.pngFree high-quality and peer-reviewed volunteer produced collection of algorithms for image processing.

scikit-learn

static/images/scikitslearn.pngModule designed for scientific pythons that provides accesible solutions to machine learning problems.

Scikits-Statsmodels

static/images/scikits.pngStatsmodels is a Python package that provides a complement to scipy for statistical computations including descriptive statistics and estimation of statistical models.

Spyder

static/images/spyder.pngInteractive development environment for Python that features advanced editing, interactive testing, debugging and introspection capabilities, as well as a numerical computing environment made possible through the support of Ipython, NumPy, SciPy, and matplotlib.

Theano

static/images/theano_logo_allblue_200x46.pngTheano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.

Associated Projects

NumFOCUS is currently looking for representatives to enable us to promote the following projects. For information contact us at: info@NumFOCUS.org.

Sage

static/images/sage.pngOpen source mathematics sofware system that combines existing open-source packages into a Python-based interface.

NetworkX

NetworkX is a Python language software package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.

Python(X,Y)

static/images/pythonxy.pngFree scientific and engineering development software used for numerical computations, and analysis and visualization of data using the Python programmimg language.

 

Iris for Big Data #rstats #bigdata

Quote of the Day-

it is impossible to be a data scientist without knowing iris 

#Anonymous #Quotes

 

Revolution Analytics has been nice enough to provide both datasets and code for analyzing Big Data in R.

http://www.revolutionanalytics.com/subscriptions/datasets/

http://packages.revolutionanalytics.com/datasets/

Site was updated so here are the new links

 

while the Datasets collection is still elementary, as a R Instructor I find this list extremely useful. However I wish they look at some other repositories and make .xdf and “tidy” csv versions. A little bit of RODBC usage should help, and so will some descriptions. Maybe they should partner with Quandl, DataMarket, or Infochimps on this initiative than do it alone.

 

Overall there can be a R package (like a Big Data version of the famous datasets package in R)

But a nice and very useful effort

Revolution R Datasets

More code-

http://blog.revolutionanalytics.com/2013/08/big-data-sets-for-r.html

Also a recent project made by a student of mine on Revolution Datasets and using their blog posts.

Note how much more better the above project is than use the mini and super clean datasets within R (like Boston)

 

Hat TIP- R’s very own Mr Smith
Unrelated-
For more on IRIS

 

Using ifelse in R for creating new variables #rstats #data #manipulation

The ifelse function is simple and powerful and can help in data manipulation within R. Here I create a categoric variable from specific values in a numeric variable

> data(iris)

> iris$Type=ifelse(iris$Sepal.Length<5.8,”Small Flower”,”Big Flower”)
> table(iris$Type)
Big Flower Small Flower
77           73

The parameters  of ifelse is quite simple

Usage

ifelse(test, yes, no)
Arguments

test
an object which can be coerced to logical mode.

yes
return values for true elements of test.

no
return values for false elements of tes

 

So many R Packages Everywhere, which one do I use? #rstats

Some thoughts on R Packages

  • CRAN is no longer the sole repository for many useful R packages. This includes R Forge, Google Code and increasingly Github
  • CRAN lacks the flexibility and social aspect of Github.
  • CRAN Views is the only thing that lists subject wide listing of R packages. The categorization is however done more on methods than on use cases or business domains.
  • Multiple R packages for the same thing. Which one do I use? Only Stack Overflow helps with that. No rating , no recommendation system
  • The packages suggested by R package feature needs better and automatic association analysis . Right now it is manual and dependent on package author and maintainer.
  • Quis custodiet ipsos custodes? Who guards the guardians of R packages. In an era of cyber security, we need better transparency on security measures within R packages especially given the international nature of the project.  I am very sure I ( or anyone) can create R code to communicate discretely especially on Windows

  • I would rather not install anything on my local machine, and read the package directly from the CRAN . CRAN was designed in an era of low bandwidth- this needs to be upgraded.
  • Note I am refraining respectfully from the atrocious nature of aesthetics in the home website. Many statisticians feel no use of making R user friendly. My professors at U tenn (from which I dropped out in 2 sems) were horrified when I took courses in graphic design as I wanted to know more on the A and B, which make the A/B testing of statistical design. Now that I am getting older, I get horrified by the lack of HTML, CSS and JQuery by some of the brightest programmers in this project.
  • Please comment below.

 

Using R for Cricket Analysis #rstats #IPL

#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

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

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.

 

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