Introduction to Statistical Packages
Eugene Tseytlin
Deparment of BioMedical Informatics
University of Pittsburgh
Expectations



NOT to become an expert in any statistical
software package
NOT to become an expert statistician
Present an Overview of what solutions are
available with emphasis on free open source
software
About Me
Who

Senior Software Developer
Where

Department of BioMedical Informatics, University of Pittsburgh
Areas of Expertise

Intelligent Tutoring Systems (ITS)

Natural Language Processing (NLP)

Digital Imaging: digital microscopy and fMRI

Machine Learning
Technologies

Java, Matlab, R, RapidMiner, SAS, C/C++, OWL, PHP, Perl
Introduction




Overview of what is available for statistical
analysis
Overview of what is popular today and what are
the trends for tomorrow
Overview of some individual software packages
Overview of the dataset that we will be using in
next lecture
Available Statistical Packages
Proprietary
Free Software

Excel

LibreOffice Calc

SPSS

PSPP

MINITAB

EpiInfo

SAS

R
What is Used? (Academia)
Figure 7a. Use of data analysis software in academic publications as measured by hits on Google Scholar.
What is Used? (Survey)
What is Used? (Job Market)
Microsoft Excel
Microsoft Excel
COST




PRO
Individual License for
Microsoft Office Professional
$350

Microsoft Office University
Student License: $99

Volume Discounts available
for large organizations and
universities
Free Starter Version
available on some new PCs

Nearly ubiquitous and is
often pre-installed on new
computers
User friendly
Very good for basic
descriptive statistics, charts
and plots
CON


Costs money
Not sufficient for anything
beyound the most basic
statistical analysis
Minitab
Minitab
COST

$1,395.00 per single user
license
PRO


CON




Costs Money
Not suitable for very
complicated statistical
computation and analysis
Not often used in academic
research
Easy to learn and use
Often taught in schools in
introductory statistics courses
Widely used in engineering
for process improvement
SPSS
SPSS
COST

From $1000 to $12000 per
license depending on license
type.
PRO

Easy to learn and use

More powerful then Minitab

CON


Very expensive
Not adequate for modeling
and cutting edge statistical
analysis


One of the most widely
used statistical packages in
academia and industry
Has a command line
interface in addition to menu
driven user intefrace
One of the most powerful
statistical package that is also
easy to use.
SAS
SAS
COST

Complicated pricing model

$8,500 first year license fee
CON

PRO


Very very expensive


Not user friendly

Steap learning curve

Relatively poor graphics
capabilities
Widely accepted as the
leader in statistical analysis
and modeling
Widely used in the industry
and academia
Very flexible and very
powerful.
LibreOffice Calc
LibreOffice Calc
LibreOffice is a free and open source office suite,
developed by The Document Foundation. It is
descended from OpenOffice.org, from which it
was forked in 2010




OpenOffice vs LibreOffice
Star → Sun → Oracle → Apache, Document
Foundation
OpenOffice
http://www.openoffice.org/download
LibreOffice
http://www.libreoffice.org/download/
LibreOffice Calc
PRO


Very similar to Microsoft
Excel in functionality and
look and feel (earlier
versions)
User friendly
COST

CON



Very good for basic
descriptive statistics, charts
and plots
Inter-operable with Microsoft
Office
Free
Not sufficient for anything
beyound the most basic
statistical analysis
EpiInfo
EpiInfo
Epi Info is public domain statistical software for epidemiology
developed by Centers for Disease Control and Prevention
(CDC)
Epi Info has been in existence for over 20 years and is currently
available for Microsoft Windows. The program allows for
electronic survey creation, data entry, and analysis. Within the
analysis module, analytic routines include t-tests, ANOVA,
nonparametric statistics, cross tabulations and stratification with
estimates of odds ratios, risk ratios, and risk differences, logistic
regression (conditional and unconditional), survival analysis
(Kaplan Meier and Cox proportional hazard), and analysis of
complex survey data. The software is in the public domain, free,
and can be downloaded from http://www.cdc.gov/epiinfo. Limited
support is available
EpiInfo
PRO


Consists of multiple modules to
accomplish various tasks beyond just
statistical analysis.
ability to rapidly develop a
questionnaire
COST

CON





customize the data entry process
quickly enter data into that
questionnaire
analyze the data
Free
Not a dedicated
statistical package
Not as powerful as
commercial alternative
for performing
advanced analysis
and modeling
PSPP
PSPP
COST

Free
PRO



Aims as a free SPSS
alternative with an interface
that closely resembles SPSS
User friendly
Good enough for basic
statistical analysis
CON



Lacks many advanced
statistical tests and features
that are present in SPSS
Last version released in 2010
Not very well known nor
widely used
R
R
R provides a wide variety of statistical and graphical techniques, including linear and
nonlinear modeling, classical statistical tests, time-series analysis, classification,
clustering, and others. R is easily extensible through functions and extensions, and
the R community is noted for its active contributions in terms of packages. There are
some important differences, but much code written for S runs unaltered. Many of R's
standard functions are written in R itself, which makes it easy for users to follow the
algorithmic choices made.
R is highly extensible through the use of user-submitted packages for specific functions
or specific areas of study. Due to its S heritage, R has stronger object-oriented
programming facilities than most statistical computing languages. Extending R is also
eased by its permissive lexical scoping rules.[10]
According to Rexer's Annual Data Miner Survey in 2010, R has become the data mining
tool used by more data miners (43%) than any other.[11]
Another strength of R is static graphics, which can produce publication-quality graphs,
including mathematical symbols. Dynamic and interactive graphics are available
through additional packages.[12]
R
PRO





Widely used and accepted in
industry and academia
Very powerful and flexible
Very large user base
Lots of books and manuals
Several User Interface Shells
available
COST

Free / Open Source
CON

Not user friendly

Requires steep learning curve
Dataset
The Dataset and Story Library
http://lib.stat.cmu.edu/DASL/
DASL (pronounced "dazzle") is an online library of datafiles and
stories that illustrate the use of basic statistics methods. We
hope to provide data from a wide variety of topics so that
statistics teachers can find real-world examples that will be
interesting to their students. Use DASL's powerful search engine
to locate the story or datafile of interest.
Brain Size and Intelligence
Are the size and weight of your brain indicators of your mental capacity? In
this study by Willerman et al. (1991) the researchers use Magnetic
Resonance Imaging (MRI) to determine the brain size of the subjects. The
researchers take into account gender and body size to draw conclusions
about the connection between brain size and intelligence.
http://lib.stat.cmu.edu/DASL/Stories/BrainSizeandIntelligence.html
Methods

Correlation

Regression

Scatterplot
Brain Size and Intelligence
Description: Willerman et al. (1991) collected a sample of 40 right-handed Anglo
introductory psychology students at a large southwestern university. Subjects took
four subtests (Vocabulary, Similarities, Block Design, and Picture Completion) of the
Wechsler (1981) Adult Intelligence Scale-Revised. The researchers used Magnetic
Resonance Imaging (MRI) to determine the brain size of the subjects. Information
about gender and body size (height and weight) are also included. The researchers
withheld the weights of two subjects and the height of one subject for reasons of
confidentiality.
Number of cases: 40
Variable Names:
Gender: Male or Female
FSIQ: Full Scale IQ scores based on the four Wechsler (1981) subtests
VIQ: Verbal IQ scores based on the four Wechsler (1981) subtests
PIQ: Performance IQ scores based on the four Wechsler (1981) subtests
Weight: body weight in pounds
Height: height in inches
MRI_Count: total pixel Count from the 18 MRI scans
Conclusion



Statistical analysis is an integral part of any
study and publication
While commercial statistical software may cost
an arm and a leg, free alternatives do exists.
While some free alternatives don't measure up,
others are growing and expending rapidly and
may overtake commercial software in features
and popularity
References
https://sites.google.com/site/r4statistics/popularity
http://en.freestatistics.info/
http://lib.stat.cmu.edu/
http://www.comfsm.fm/~dleeling/statistics/notes000.html