An introduction to R: get
familiar with R
Guangxu Liu
Bio7932
Outline
1.
2.
3.
4.
5.
6.
Download and installation of R
Get familiar with R
Input data and read data from file
Commonly used R code
Something need to be aware
Reference for R
Step by step proc.
1.Downloading R
official website: www.R-project.org
Where to
download R.
After we choose the correct server and computer system,
we will get something like below.
What we want is
here!
Choose again?!!
Here it
is!
Installation:
Proc:
Simply use the download installation file.
Available options:
Choose install direction
language (English, simple Chinese only) ?
Set up the methods for viewing help
information(html, txt, chm)
Select components, customize ….
2. Get familiar with R (Sorry about using chinese version)
File; Edit; Others; Package; Help
function
Basic introduction of R, such as
Version…
Working place, where we write
code, see the verbal or numerial
results
3. Input data and read data from file
Basic proc:
x<-function()
x=data name; <- assignment;
function()=the methods for reading data
Function():
c() for example, x<-c(1,2,3,4,5)
read.table()
scan()
Read data using Rcmdr package
Examples: Read data with Rcmdr package
Load package
from package
option
Rcmdr
Rcmdr windows (right windows below)
Rcmdr-Data-Inport data (Thanks god, Rcmdr is in English!)
File can be read
by Rcmdr
includes
txt,spss,mintab,
stata,excel….
For example:
open the excel file contains
the data, select the data
you want to input and copy
it by right click and copy or
ctl+c.
Then switch back to Rcmdr
windows and choose data
input from txt & clipboard
Data name
1.Variable name in
first line or not
2. NA
How the data
are separated
(Tabs here for
excel)
All setting
looks fine
now
Read the
data
The R code for what
we did
Output window? Do
not show graphic
results
General
information of
the data
An example show how t-test results displayed in output windows
T test R code
Results form the t-test
Lot’s
functions
here, such as
make graph,
load statistics
package
If we make graph (box plot for example)
R code for
box plot
Graph result shows in R graphics window (right windows)
View data and edit data after data input
View data
and edit
your data
View data window
shows the data
Edit data in the
data edit windows
4. Commonly used R code
ls()
show all the available data (objects)
in the work space or memory
rm()
delete data, remove objects
?
get online help about ***
lm()
fit a simple regression and look at it
resid() residuals from one model
fitted() fits from one model
plot() scatter plot
5. Something needs to be kept in mind
Capital letter matters: v≠V
Data (Objects) are vector or matrix
Some examples
Use ls()
show the
data in
workspace
VCL and vcl
are different
data objects
Commends: don’t use capital letter at all is a good idea
Use “?ls” to learn
more about ls()
fuction
Online help
(don’t need
internet
connection
in fact)
Use ?lm learn
more about lm()
There are lot’s
components in lm()
Details about all those
components
A simple example (without data input part)
Use f to view
the data f in
workspace
Step 1:
Read and built
a new data
with name f
Data from fertilization data of Liu (2006), and we know there
should have a simple linear relationship between ln and density.
Density=log(sperm/egg density) ln=log(fertilized egg/unfertilized egg).
So the model will be ln=a+b*density+error
Use fm<-lm(ln~density,data=f) to build up the linear model
fm<-lm(ln~density,data=f)
Assign fm as
the linear model
Model is based
There ln and
on ln and density,
density come from
use ln as dependent
and density as variable
Use fm to view fm
Shows
what’s
fm
Use summary(fm) to see more details
Details of
fm,
including df,
SE, t value
and P
Use plot(fitted(fm),resid(fm),xlab="fitted",ylab="residual",main="residual vs
fits") check residual vs fits. Graph shown on the right side window
Here xlab(),ylab(),main()
are R codes to give x,y
and the whole graph
labels.
6.Reference for R (http://www.r-project.org)
This makes me change my
presentation title to “An
introduction to R: get familiar
with R”
1.Free reference on R official website
2. Practical Regression and Anova using R, Julian J. Faraway, 2002
Thanks
Picture above from www.R-project.org