Introduction to Statistical Packages

Eugene TseytlinDeparment 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 Excel SPSS MINITAB SAS

Free Software LibreOffice Calc PSPP EpiInfo 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 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

PRO 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 Easy to learn and use

Often taught in schools in introductory statistics courses

Widely used in engineering for process improvement

CON Costs Money

Not suitable for very complicated statistical computation and analysis

Not often used in academic research

SPSS

SPSS

COST From $1000 to $12000 per

license depending on license type.

CON Very expensive

Not adequate for modeling and cutting edge statistical analysis

PRO Easy to learn and use

More powerful then Minitab

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 Very very expensive

Not user friendly

Steap learning curve

Relatively poor graphics capabilities

PRO 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 CalcLibreOffice 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

Very good for basic descriptive statistics, charts and plots

Inter-operable with Microsoft Office

COST Free

CON 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

customize the data entry process

quickly enter data into that questionnaire

analyze the data

COST Free

CON 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 Libraryhttp://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/popularityhttp://en.freestatistics.info/http://lib.stat.cmu.edu/http://www.comfsm.fm/~dleeling/statistics/notes000.html