Introduction to R project

Marek Majdan

Training in essential biostatistics for Public Health Professionals in BiH, Marek Majdan, PhD; marekmajdan@gmail.com

R project

• Statistical computing environment and software

• Absolutely free• Updated by statisticians• Very powerfull • Basically unlimited capability

Training in essential biostatistics for Public Health Professionals in BiH, Marek Majdan, PhD; marekmajdan@gmail.com

R project - principle

Editor R Engine

Numerical output

Graphical Output

SCRIPT

Training in essential biostatistics for Public Health Professionals in BiH, Marek Majdan, PhD; marekmajdan@gmail.com

Script example

library (RODBC)library(foreign)library(Hmisc)library(Design)library(graphics)

barb <- sqlFetch(odbcConnectExcel("d:/barb_data_new.xls"),sqtable = "data", na.strings = "NA", as.is = T)

summary(barb)describe(barb)describe(barb$barb_group)

##normality tests

shapiro.test(barb$AGE_CORRECTED)

Training in essential biostatistics for Public Health Professionals in BiH, Marek Majdan, PhD; marekmajdan@gmail.com

Packages

• Base package• Contributed packages

- specific functions written for specific purposes- not included in the base package- can be installed any time

Training in essential biostatistics for Public Health Professionals in BiH, Marek Majdan, PhD; marekmajdan@gmail.com

R EDITOR

NUMERICAL OUTPUT

GRAPHICAL OUTPUT

Training in essential biostatistics for Public Health Professionals in BiH, Marek Majdan, PhD; marekmajdan@gmail.com

Installing R

Training in essential biostatistics for Public Health Professionals in BiH, Marek Majdan, PhD; marekmajdan@gmail.com

Installing R

Training in essential biostatistics for Public Health Professionals in BiH, Marek Majdan, PhD; marekmajdan@gmail.com

Installing Packages

1.

2.3.

Training in essential biostatistics for Public Health Professionals in BiH, Marek Majdan, PhD; marekmajdan@gmail.com

Writing scripts

• Every package contains ‘functions’ for performing various operations with data

• Every function has a specific form and arguments needed

• Every function has a specific output• An algorithm of functions to perform a specific

sequence of actions is a script

Training in essential biostatistics for Public Health Professionals in BiH, Marek Majdan, PhD; marekmajdan@gmail.com

Example I.

• Function: library• To load a specific package• Form: library (name of package)

library (Epicalc)library (Hmisc)

Training in essential biostatistics for Public Health Professionals in BiH, Marek Majdan, PhD; marekmajdan@gmail.com

Example II.

• Function: plot• To plot a graph• Simple form: plot(x)• Complex form with a number of additional

arguments:plot(x <- sort(rnorm(47)), type = "s", main = "plot(x, type = \"s\")") points(x, cex = .5, col = "dark red")

Training in essential biostatistics for Public Health Professionals in BiH, Marek Majdan, PhD; marekmajdan@gmail.com

Important notes

• Case sensitivity

Plot ≠ plot ≠ PLOT

• Avoid using punctuation and spaces in names of databases or variables (e.g. use ‘age_category’ instead ‘Age category’)

Training in essential biostatistics for Public Health Professionals in BiH, Marek Majdan, PhD; marekmajdan@gmail.com

Importing data to R from Excel

• Package: RODBC• Function: X=sqlFetch(odbcConnectExcel(“Y"),sqtable = “Z", na.strings = "NA", as.is = T)

X=name of database in R after importingY=path to excel file on diskZ=name of excel sheet

Training in essential biostatistics for Public Health Professionals in BiH, Marek Majdan, PhD; marekmajdan@gmail.com

R commander

• Graphical user interface (GUI)• Makes basic statistical computations simple

but puts certain restrictions on R• Installing R commander: install package

‘Rcmdr’ using the standard package installing procedure

• Function: library(Rcmdr) to start R commander

Training in essential biostatistics for Public Health Professionals in BiH, Marek Majdan, PhD; marekmajdan@gmail.com

R commander

Training in essential biostatistics for Public Health Professionals in BiH, Marek Majdan, PhD; marekmajdan@gmail.com