A B C.......Q R S! Coilín Minto Department of Biology, Dalhousie University.

Slides:



Advertisements
Similar presentations
Alejandro Buren & Paul Regular Introduction to BIOL 7220 September 2012.
Advertisements

Introduction to S-Plus by Francesco Ferretti Analysis of Biological Data Course Winter term 2007 Dalhousie University.
How to improve your Data Analysis Processes in your Web Application / ERP using RClass Juan Antonio Breña Moral
Writing functions in R Some handy advice for creating your own functions.
A Conceptual Introduction to Multilevel Models as Structural Equations
Statistical Methods Lynne Stokes Department of Statistical Science Lecture 7: Introduction to SAS Programming Language.
1 Using Octave to Introduce Programming to Technical Science Students Nuno C. Marques Francisco Azevedo CENTRIA, DI-
Actuarial Modeling in R CAS Predictive Modeling Seminar Las Vegas October, 2007 Glenn Meyers, FCAS, MAAA Jim Guszcza, FCAS, MAAA.
R Mohammed Wahaj. What is R R is a programming language which is geared towards using a statistical approach and graphics Statisticians and data miners.
Introduction to GTECH 201 Session 13. What is R? Statistics package A GNU project based on the S language Statistical environment Graphics package Programming.
Data Analytics and Dynamic Languages Lee E. Edlefsen, Ph.D. VP of Engineering 1.
SHOU Haochang ( 寿昊畅 ) Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health July 11th, 2011 Nanjing University, China *Thanks to.
Experiences in Integration of the 'R' System into Kepler Dan Higgins – National Center for Ecological Analysis and Synthesis (NCEAS), UC Santa Barbara.
An introduction to R Honors 207 Cognitive Science (These Slides were Shamelessly Stolen from Dr. Pablo Gomez, DePaul University)
Introduction to R A. Di Bucchianico. Introduction to R2 Types of statistical software command-line software –requires knowledge of syntax of commands.
R – a brief introduction Johannes Freudenberg Cincinnati Children’s Hospital Medical Center
How to Use the R Programming Language for Statistical Analyses Part I: An Introduction to R Jennifer Urbano Blackford, Ph.D. Department of Psychiatry Kennedy.
What is R Muhammad Omer. What is R  R is the programing language software for statistical computing and data analysis  The R language is extensively.
Statistics – O. R. 892 Object Oriented Data Analysis J. S. Marron Dept. of Statistics and Operations Research University of North Carolina.
What is R By: Wase Siddiqui. Introduction R is a programming language which is used for statistical computing and graphics. “R is a language and environment.
Basic R Programming for Life Science Undergraduate Students Introductory Workshop (Session 1) 1.
Epi Info™ 7 Introductory Training
1 An Introduction – UCF, Methods in Ecology, Fall 2008 An Introduction By Danny K. Hunt & Eric D. Stolen Getting Started with R (with speaker notes)
Data Visualization using R
SAS Workshop Lecture 1 Lecturer: Annie N. Simpson, MSc.
An introduction to R: get familiar with R Guangxu Liu Bio7932.
National Oceanographic Atmospheric Administration Stock Assessments Mentor: Michael H. Prager Ph.D. Written By: Anthony Anderson Kaiem Frink.
Data, graphics, and programming in R 28.1, 30.1, Daily:10:00-12:45 & 13:45-16:30 EXCEPT WED 4 th 9:00-11:45 & 12:45-15:30 Teacher: Anna Kuparinen.
Introduction to SAS BIO 226 – Spring Outline Windows and common rules Getting the data –The PRINT and CONTENT Procedures Manipulating the data.
Intro to R R is a free version of S-plus R is a free version of S-plus Can be used interactively but script or syntax files are commonly used to record.
Sébastien Lê Agrocampus Rennes A very short introduction to “R” The “Rcmdr” package and its environment.
Introduction to Applied Statistical Analysis A practical course for handling datasets.
Introduction to R Lecture 1: Getting Started Andrew Jaffe 8/30/10.
Actuarial Modeling in R CAS Spring Meeting June, 2007 Glenn Meyers, FCAS, MAAA Jim Guszcza, FCAS, MAAA.
Piotr Wolski Introduction to R. Topics What is R? Sample session How to install R? Minimum you have to know to work in R Data objects in R and how to.
Using Software in Teaching Statistics Damon Berridge, Centre for Applied Statistics, Dept of Mathematics & Statistics ESRC NCRM.
Installing R CRAN: –(R homepage: –Windows 95 and later  Base –rw2001.exe.
R Brown-Bag Seminar 2: Hands-on Antony Karanja Ndungu Research Methods Group-ICRAF.
R Introduction and Training Patrick Gurian, Drexel University CAMRA 1st QMRA Summer Institute August 7, 2006.
STAT 251 Lab 1. Outline Lab Accounts Introduction to R.
An Introduction to R Statistical Computing AMS 597 Stony Brook University Spring 2009 By Tianyi Zhang.
Introduction to R Carol Bult The Jackson Laboratory Functional Genomics (BMB550) Spring 2011.
Matlab Introduction  Getting Around Matlab  Matrix Operations  Drawing Graphs  Calculating Statistics  (How to read data)
A GUI framework for PySAL Team members: Dae-hyun You, Sanjay Paul, Jianhua Huang, Ki-hwan Seo, Evan Palmer GPH 598: Geocomputation, Fall 2011.
Subjects Review Introduction to Statistical Learning Midterm: Thursday, October 15th :00-16:00 ADV2.
訊號與系統 廖文淵 德霖技術學院資訊工程系 Introduction to MATLAB.
NET 222: COMMUNICATIONS AND NETWORKS FUNDAMENTALS ( NET 222: COMMUNICATIONS AND NETWORKS FUNDAMENTALS (PRACTICAL PART) Tutorial 2 : Matlab - Getting Started.
Jeff Howbert Introduction to Machine Learning Winter Machine Learning MATLAB Essentials.
Introduction to CADStat. CADStat and R R is a powerful and free statistical package [
Introductory Data Analysis F73DA2. Contact Times (Spring Term 2008) Monday 4: : Lecture in LT3 Tuesday 2: : Lecture in LT3 Wednesday
Introduction to R Aedín Culhane
Lecture 11 Introduction to R and Accessing USGS Data from Web Services Jeffery S. Horsburgh Hydroinformatics Fall 2013 This work was funded by National.
Pinellas County Schools
Introduction to Data Manipulation, Analysis, and Visualization with R Patrick Grof-Tisza.
R Brown-Bag Seminar 2.1 Topic: Introduction to R Presenter: Faith Musili ICRAF-Geoscience Lab.
Data Tools: R and RStudio
Introduction to R Fish 552: Lecture 1.
Introduction to R.
QQ Registration & Usage
2017年6月4日更新 1. イントロダクション 東北大学 大学院工学研究科 嶋田 慶太.
Software for scientific calculations
MatLab Programming By Kishan Kathiriya.
Introduction to R Programming with AzureML
R Programming.
STA 511 Statistical Computing
Introduction to R.
Today’s Beginner Workshop
Communication and Coding Theory Lab(CS491)
May 31-June 2, 2016, Missouri Botanical Garden
Graphic Libraries for The User Interface
Presentation transcript:

A B C Q R S! Coilín Minto Department of Biology, Dalhousie University

Please note Applied introductory class on use of the S language Procedures for a basic analysis of biological data My perspective

Class outline Introduction to the software Workshop Biological example Questions please!

Historical perspective S language and environment developed by John Chambers and colleagues at Bell Laboratories (formerly AT&T, now Lucent Technologies) S-Plus, a commercial version of S by Insightful Software since 1987, now at version 7 R is a GNU project that started in the mid-1990s Current production version released on June 20th is 2.2.1

What can S do for me? Statistical and graphical capabilities –linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering,... –Scatterplots, histograms, q-q plots, maps, … –A well-developed programming language (S) Highly expandable through hundreds of packages

Why use S? Incredibly flexible Accessible/intuitive language Well supported (especially R) Powerful language capabilities

Calculations in S > 19*5 [1] 95 > log(2) [1] >seq(0,5) [1] > plot(cos(seq(0,10,length=100))) > exp(2) [1]

In the beginning <- 1. Create object (vector, matrix, list) > marsupial.vec <- c(“kangaroo”, “possum”, “koala”) # character > marsupial.vec [1] "kangaroo" "possum" "koala" > fib.vec <- c(0, 1, 1, 2, 3, 5, 8, 13) # numeric > fib.vec [1] > unit.mat <- matrix(c(1,0,0,0,1,0,0,0,1),ncol=3) > unit.mat [,1] [,2] [,3] [1,]1 0 0 [2,]0 1 0 [3,]0 0 1

In the beginning 2. Basic manipulations > length(fib.vec) [1] 8 > max(fib.vec) [1] 13 > dim(unit.mat) [1] 3 3 > diag(unit.mat) [1] 1 1 1

Basic steps in an analysis 2. Plot your data > plot(), boxplot(), histogram() 3. Obtain suitable function a. Function available: call function b. Function not loaded in session: library(function) c. Function not downloaded: install.packages(package) then b. NB. Only in R (open source) Please refer to code on webpage 1. Import your data > read.table() Use drop down # easier File: Load library # S-plus Packages: Load package # R

Basic steps in an analysis 4. Analyse / fit models > model1 <- lm(variable.y~variable.x) > summary(model1) > pca1 <- princomp(x, scores=T, cor = ) > summary(pca1) > dfa1 <- discrim(y~x, data=, family=) # S-plus > dfa1 <- lda(y~x, data=) # R > summary(dfa1) > pca1 <- princomp(x, scores=T, cor = ) > summary(pca1)

Mandlebrot set code written by Martin Maechler

Help ? function # brings up a help page # manualshttp://cran.r-project.org/ This contains information on subscribing to S-news and sending messages to the list. A searchable archive of recent messages is available at: Modern Applied Statistics with S-PLUS Venables and Ripley : “The de facto "bible" of statistical analysis with S-PLUS”. This can be acceModern Applied Statistics with S-PLUS

Workshop steps Vectors –Numeric, character Sequences Matrices Plots –Scatter, box, histogram Marsupial example (don’t worry about finishing this) # file:marsupial.code.txt. Written in R