Scribd
Upload
44 views7 pages

Clad Cluster Analysisi Slides-Clusteranalysis

Uploaded by

Federico Garcia
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
44 views7 pages

Clad Cluster Analysisi Slides-Clusteranalysis

Uploaded by

Federico Garcia
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
You are on page 1/ 7

Multivariate Fundamentals: Distance

Cluster Analysis
Objective: Group data points into classes of similar points based on a
series of variables

Useful to find the true groups that are assumed to really exist, BUT if the
analysis generates unexpected groupings it could inform new relationships
you might want to investigate

Also useful for data reduction by finding which data points are similar and
allow for subsampling of the original dataset without losing information

Alfred Louis Kroeber (1876-1961)


The math behind cluster analysis A B C D …
A 0 1.8 0.6 3.0

Once we calculate a distance matrix between points we B 1.8 0 2.5 3.3


C 0.6 2.5 0 2.2
use that information to build a tree
D 3.0 3.3 2.2 0
…
Ordination – visualizes the information
in the distance calculations
The result of a cluster analysis is a
tree or dendrogram
0.6
1.8 4
2.5
3.0 2.2
3
3.3

distance
2

1
If distances are not equal between points we D
can draw a “hanging tree” to illustrate
A C
distances 0 B
Building trees & creating groups

1. Nearest Neighbour Method – create groups by starting with the smallest


distances and build branches
In effect we keep asking data matrix “Which plot is my nearest neighbour?” to add
branches

2. Centroid Method – creates a group based on smallest distance to group


centroid rather than group member
First creates a group based on small distance then uses the centroid of that group to
find which additional points belong in the same group

3. Wards Method – creates groups such that variance is minimized within


clusters
Looks for spherical clusters
The process starts with all points in individual clusters (bottom up) and the process
repeatedly merges a pair of clusters such that when merged there is a minimum
increase in total within-cluster variance This process continues until a single group
including all points (the top of the tree) is defined
Building trees & creating groups
One of the problems with Cluster Analysis is that different methods may
produce different results – generally no accepted best method

Good News: If your data really has clear groups all methods will find them and
give you similar results

Therefore it is best to try multiple algorithms and see what groups logically
make sense
If you have a dummy dataset with pre-determined groups you can use it to see
which algorithm best recreates what you expect
Cluster analysis in R Distance matrix of your data rows
based on your predictor variables
You need to calculate this before
running the cluster analysis

CA in R: We create distance
hclust(distMatrix,method) (stats package) matrices in Lab 5

What type of algorithm should be used to cluster points and define groups
" ward.D" = Ward’s minimum variance method
" ward.D2" = Ward’s minimum variance method – however dissimilarities are squared before clustering
"single" = Nearest neighbours method
"complete" = distance between two clusters is defined as the maximum distance between an observation in one
cluster and an observation in the other cluster
"average" = distance between two clusters is defined as the mean distance between an observation in one
cluster and an observation in the other cluster
"mcquitty " = when two clusters are be joined, the distance of the new cluster to any other cluster is calculated as
the average of the distances of the soon to be joined clusters to that other cluster
"median" = uses group median
"centroid" = uses group centroid
Cluster analysis in R

From the output plot we can


compare the groups cluster
analysis has generated
Each collection of branches
could be considered a group
It is up to you to decide how far
down the tree you want to
specify your groups
We want small distances and
groups that logically make
sense

You might also like