Mastering Scientific Computing with R: Employ professional quantitative methods to answer scientific questions with a powerful open source data analysis environment

Paul Gerrard

$54.99

3.6 (7 Ratings)

Paperback Jan 2015 432 pages 1st Edition

Paul Gerrard

$54.99

3.6 (7 Ratings)

Paperback Jan 2015 432 pages 1st Edition

What do you get with Print?

Instant access to your digital eBook copy whilst your Print order is Shipped

Paperback book shipped to your preferred address

Download this book in EPUB and PDF formats

Access this title in our online reader with advanced features

DRM FREE - Read whenever, wherever and however you want

View table of contents

Preview Book

Mastering Scientific Computing with R

Chapter 2. Statistical Methods with R

This chapter will present an overview of how to summarize your data and get useful statistical information for downstream analysis. We will also show you how to plot and get statistical information from probability distributions and how to test the fit of your sample distribution to well-defined probability distributions. We will also go over some of the functions used to perform hypothesis testing including the Student's t-test, Wilcoxon rank-sum test, z-test, chi-squared test, Fisher's exact test, and F-test.

Before we begin, we will load the gene expression profiling data from the E-GEOD-19577 study entitled "MLL partner genes confer distinct biological and clinical signatures of pediatric AML, an AIEOP study" from the ArrayExpress website to use as a sample dataset for some of our examples. For simplicity, we will not go into the details of how the data was generated, except to mention that the study evaluates the expression...

Probability distributions

R makes it very easy to plot and get statistical information on many probability distributions. For those who are not familiar with probability distributions, they are defined as a table or an equation that links each outcome of a statistical experiment with its probability of occurrence. A summary of many common probability distributions available in R is available in the following table:

Probability distribution	R name
Beta	beta
Binomial	binom
Cauchy	cauchy
Chi square	chisq
Exponential	exp
F	f
Gamma	gamma
Geometric	geom
Hypergeometric	hyper
Logistic	logis
Lognormal	lnorm
Negative Binomial	nbinom
Normal	norm
Poisson	pois
Student t	t
Uniform	unif
Tukey	tukey
Weibull	weib
Wilcoxon	wilcox

You can also get this summary in R by entering help("distributions"). For additional probability distributions, and the packages needed to load them, you can consult the CRAN distributions page at http://cran.r-project.org/web/views...

Description

If you want to learn how to quantitatively answer scientific questions for practical purposes using the powerful R language and the open source R tool ecosystem, this book is ideal for you. It is ideally suited for scientists who understand scientific concepts, know a little R, and want to be able to start applying R to be able to answer empirical scientific questions. Some R exposure is helpful, but not compulsory.

Who is this book for?

What you will learn

Master data management in R
Perform hypothesis tests using both parametric and nonparametric methods
Understand how to perform statistical modeling using linear methods
Model nonlinear relationships in data with kernel density methods
Use matrix operations to improve coding productivity
Utilize the observed data to model unobserved variables
Deal with missing data using multiple imputations
Simplify highdimensional data using principal components, singular value decomposition, and factor analysis

Estimated delivery fee Deliver to United States

Economy delivery 10 - 13 business days

Free ~~$6.95~~

Premium delivery 6 - 9 business days

$21.95

(Includes tracking information)

What do you get with Print?

Instant access to your digital eBook copy whilst your Print order is Shipped

Paperback book shipped to your preferred address

Download this book in EPUB and PDF formats

Access this title in our online reader with advanced features

DRM FREE - Read whenever, wherever and however you want

Frequently bought together

$54.99

$54.99

$54.99

Total $ 164.97

FAQs

What is the delivery time and cost of print book?

Shipping Details

USA:

Economy: Delivery to most addresses in the US within 10-15 business days

Premium: Trackable Delivery to most addresses in the US within 3-8 business days

UK:

Economy: Delivery to most addresses in the U.K. within 7-9 business days.
Shipments are not trackable

Premium: Trackable delivery to most addresses in the U.K. within 3-4 business days!
Add one extra business day for deliveries to Northern Ireland and Scottish Highlands and islands

EU:

Premium: Trackable delivery to most EU destinations within 4-9 business days.

Australia:

Economy: Can deliver to P. O. Boxes and private residences.
Trackable service with delivery to addresses in Australia only.
Delivery time ranges from 7-9 business days for VIC and 8-10 business days for Interstate metro
Delivery time is up to 15 business days for remote areas of WA, NT & QLD.

Premium: Delivery to addresses in Australia only
Trackable delivery to most P. O. Boxes and private residences in Australia within 4-5 days based on the distance to a destination following dispatch.

India:

Premium: Delivery to most Indian addresses within 5-6 business days

Rest of the World:

Premium: Countries in the American continent: Trackable delivery to most countries within 4-7 business days

Asia:

Premium: Delivery to most Asian addresses within 5-9 business days

Disclaimer:
All orders received before 5 PM U.K time would start printing from the next business day. So the estimated delivery times start from the next day as well. Orders received after 5 PM U.K time (in our internal systems) on a business day or anytime on the weekend will begin printing the second to next business day. For example, an order placed at 11 AM today will begin printing tomorrow, whereas an order placed at 9 PM tonight will begin printing the day after tomorrow.

Unfortunately, due to several restrictions, we are unable to ship to the following countries:

Afghanistan
American Samoa
Belarus
Brunei Darussalam
Central African Republic
The Democratic Republic of Congo
Eritrea
Guinea-bissau
Iran
Lebanon
Libiya Arab Jamahriya
Somalia
Sudan
Russian Federation
Syrian Arab Republic
Ukraine
Venezuela

What is custom duty/charge?

Customs duty are charges levied on goods when they cross international borders. It is a tax that is imposed on imported goods. These duties are charged by special authorities and bodies created by local governments and are meant to protect local industries, economies, and businesses.

Do I have to pay customs charges for the print book order?

The orders shipped to the countries that are listed under EU27 will not bear custom charges. They are paid by Packt as part of the order.

List of EU27 countries: www.gov.uk/eu-eea:

A custom duty or localized taxes may be applicable on the shipment and would be charged by the recipient country outside of the EU27 which should be paid by the customer and these duties are not included in the shipping charges been charged on the order.

How do I know my custom duty charges?

The amount of duty payable varies greatly depending on the imported goods, the country of origin and several other factors like the total invoice amount or dimensions like weight, and other such criteria applicable in your country.

For example:

If you live in Mexico, and the declared value of your ordered items is over $ 50, for you to receive a package, you will have to pay additional import tax of 19% which will be $ 9.50 to the courier service.
Whereas if you live in Turkey, and the declared value of your ordered items is over € 22, for you to receive a package, you will have to pay additional import tax of 18% which will be € 3.96 to the courier service.

How can I cancel my order?

Cancellation Policy for Published Printed Books:

You can cancel any order within 1 hour of placing the order. Simply contact [email protected] with your order details or payment transaction id. If your order has already started the shipment process, we will do our best to stop it. However, if it is already on the way to you then when you receive it, you can contact us at [email protected] using the returns and refund process.

Please understand that Packt Publishing cannot provide refunds or cancel any order except for the cases described in our Return Policy (i.e. Packt Publishing agrees to replace your printed book because it arrives damaged or material defect in book), Packt Publishing will not accept returns.

What is your returns and refunds policy?

Return Policy:

We want you to be happy with your purchase from Packtpub.com. We will not hassle you with returning print books to us. If the print book you receive from us is incorrect, damaged, doesn't work or is unacceptably late, please contact Customer Relations Team on [email protected] with the order number and issue details as explained below:

If you ordered (eBook, Video or Print Book) incorrectly or accidentally, please contact Customer Relations Team on [email protected] within one hour of placing the order and we will replace/refund you the item cost.
Sadly, if your eBook or Video file is faulty or a fault occurs during the eBook or Video being made available to you, i.e. during download then you should contact Customer Relations Team within 14 days of purchase on [email protected] who will be able to resolve this issue for you.
You will have a choice of replacement or refund of the problem items.(damaged, defective or incorrect)
Once Customer Care Team confirms that you will be refunded, you should receive the refund within 10 to 12 working days.
If you are only requesting a refund of one book from a multiple order, then we will refund you the appropriate single item.
Where the items were shipped under a free shipping offer, there will be no shipping costs to refund.

On the off chance your printed book arrives damaged, with book material defect, contact our Customer Relation Team on [email protected] within 14 days of receipt of the book with appropriate evidence of damage and we will work with you to secure a replacement copy, if necessary. Please note that each printed book you order from us is individually made by Packt's professional book-printing partner which is on a print-on-demand basis.

What tax is charged?

Currently, no tax is charged on the purchase of any print book (subject to change based on the laws and regulations). A localized VAT fee is charged only to our European and UK customers on eBooks, Video and subscriptions that they buy. GST is charged to Indian customers for eBooks and video purchases.

What payment methods can I use?

You can pay with the following card types:

Visa Debit
Visa Credit
MasterCard
PayPal

What is the delivery time and cost of print books?

Shipping Details

USA:

Economy: Delivery to most addresses in the US within 10-15 business days

Premium: Trackable Delivery to most addresses in the US within 3-8 business days

UK:

Economy: Delivery to most addresses in the U.K. within 7-9 business days.
Shipments are not trackable

Premium: Trackable delivery to most addresses in the U.K. within 3-4 business days!
Add one extra business day for deliveries to Northern Ireland and Scottish Highlands and islands

EU:

Premium: Trackable delivery to most EU destinations within 4-9 business days.

Australia:

India:

Premium: Delivery to most Indian addresses within 5-6 business days

Rest of the World:

Premium: Countries in the American continent: Trackable delivery to most countries within 4-7 business days

Asia:

Premium: Delivery to most Asian addresses within 5-9 business days

Unfortunately, due to several restrictions, we are unable to ship to the following countries:

Afghanistan
American Samoa
Belarus
Brunei Darussalam
Central African Republic
The Democratic Republic of Congo
Eritrea
Guinea-bissau
Iran
Lebanon
Libiya Arab Jamahriya
Somalia
Sudan
Russian Federation
Syrian Arab Republic
Ukraine
Venezuela

Filter reviews by

All

Amazon verified reviews

Arnold Salvacion Mar 01, 2015

High recommended!My review of the book can be found in http://r-nold.blogspot.com/2015/03/book-review-mastering-scientific.html

Amazon Verified review

Visier68 Feb 28, 2015

“Mastering Scientific Computing with R” is a comprehensive book that combines an entry-level approach to data analysis with content targeted to experienced users, who are aiming to streamline their workflow.The author starts with an overview of R, explaining data types and other fundamental concepts, which should be sufficient for novice readers to understand how R differs in its coding style from traditional programming languages. On the other hand, the book is intentionally not written as a cookbook for data analysis. Hence, readers will benefit from previous experience with tools like RStudio and IPython, supporting experiments with functions and code snippets from the book for interactive learning.The first part is covering basic stuff like distributions, hypothesis testing, linear plus nonlinear models and PCA. For advanced users, things get more interesting with Structural Equation Modeling (SEM) in chapter 7, where the author provides a brief but good illustration of practical applications with OpenMx. The book includes a well-written chapter on simulation, explaining the powerful features of Monte Carlo method. It is followed by a chapter on optimization, which is equally useful in solving analytical problems.A strength of this book is that it provides in-depth information regarding some more advanced analytical procedures without being limited to specific domains like bioinformatics or econometrics, making it a recommended addition to the analyst’s bookshelf.What I am missing is a part covering practical deployment of the methodology described, especially in terms of reproducible research and scientific publishing. Reproducibility is essential, and R excels here by encouraging users to focus on scripting and automation rather than point-and-click. This is mentioned several times, but deserves more attention given its importance in science.Tools like Markdown and Pandoc support the creation of fully dynamic documents with minimal effort, which has vastly improved streamlining of workflows in scientific publishing. It would be useful to include some examples and references to further reading.While “Mastering Scientific Computing with R” is quite readable for novice users, I would recommend the book to people who are already familiar with basic tools and building blocks of data analysis, aiming to improve their knowledge about algorithms and standard procedures that typically make up a scientific workflow. But the book is also useful for non-scientific applications and the information provided may be easily transferred for exploitation in any specific domain.

Kongi Feb 27, 2015

The book is helpful to people who are just learning how to use R for modelling and simulation. It could be considered as an introduction to Scientific Computing using R not Mastering. I recommend topics such as high performance, parallel computation to be added in further editions of the book.Still glad i bought the book because i picked few points from it.

TCM Feb 28, 2015

The “mastering series” provides advanced tutorials and this was exactly what I was looking for. This book goes beyond most other books on R and gives insights into topics such as generalized linear models (GLM), principal component analysis (PCA) and Monte Carlo simulations. The introduction of this book is too advanced for R beginners but provides a good repetition of R’s capabilities and strength. For the rest of this book the reader needs a good grasp of R, statistics and mathematics. As such it distinguishes itself from most other book on R I have seen so far and meets my level of expectation. In any case, this book cannot be recommended as an entry level introduction neither to R nor statistics but is very useful for scientist interested in exploring possibilities for sound data analysis.

Al Feb 18, 2015

This book looks more like an overview of a variety of topics than a Mastering book. I wouldn't recommeded for an in depth coverage of the topics it exposes. Although it could be used as a quick guide to implement a variety of scientific methods in R. I purchase it as part of Packt Publishing $5 Christmas bonanza. For that price, you can't go wrong.One thing missing that I would've liked to see covered is reproducible research. I would think any new scientific programming book in R will cover this topic or at least gives examples of reproducible research.

Mastering Scientific Computing with R: Employ professional quantitative methods to answer scientific questions with a powerful open source data analysis environment

What do you get with Print?

Mastering Scientific Computing with R

Chapter 2. Statistical Methods with R

Descriptive statistics

Probability distributions

Fitting distributions

Hypothesis testing

Summary

Page 1 of 6

Description

Who is this book for?

What you will learn

Product Details

What do you get with Print?

Product Details

Frequently bought together

Table of Contents

Recommendations for you

Customer reviews

Filter reviews by

People who bought this also bought

About the author

FAQs

Mastering Scientific Computing with R: Employ professional quantitative methods to answer scientific questions with a powerful open source data analysis environment

What do you get with Print?

Contact Details

Shipping Address

Billing Address

Description

Who is this book for?

What you will learn

Product Details

What do you get with Print?

Contact Details

Shipping Address

Billing Address

Product Details

Packt Subscriptions

Frequently bought together

Table of Contents

Recommendations for you

Customer reviews

Filter reviews by

People who bought this also bought

About the author

FAQs