Clustering and Classification methods for Biologists


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Discriminant Analysis

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There are two example analyses.

The data can be downloaded in two formats from the links below

DA Text Excel
Muscular Dystrophy muscdys.dat muscdys.xls
Multigroup Discriminantion corearea.dat corearea.xls

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Duchenne Muscular Dystrophy

We can envisage two questions.

  1. What differences, if any, are there in the potential predictors between carriers and non-carriers of Duchenne Muscular Dystrophy?
  2. Given a set of measurements isit possible to predict if someone is a carrier of Duchenne Muscular Dystrophy?

There are four potential predictors (original source of data and the units are unknown).

1. creatine kinase
2. hemopexin
3. lactate dehydrogenase
4. pyruvate kinase

3-D scatter plots, viewed in different projections, suggest that some projections look promising for separating the two groups.

Static 3D plot

Static 3D plot - different aspect

The example analyses were undertaken using SPSS. The output includes most of the optional analysis extras. The default output is much more abbreviated.

Two analyses are shown. The first uses all four variables and the second uses a stepwise procedure.

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Multigroup discrimination of eagle habitat

The question addressed by this analysis is 'Is it possible to discriminate between the core areas of golden eagle home ranges from three regions of Scotland?' The data consist of eight habitat variables. The values are the amounts of each habitat variables, measured as the number of 4 ha blocks within a region defined as a 'core area'.

NameDescription
POSTPost canopy forest : mature planted conifer forest
PREPre-canopy closure conifer forest (young trees)
BOGBog (flat water logged)
CALLCalluna (Heather) heathland
WETWet heath, mainly purple moor grass
STEEPSteeply sloping land
LT200Land below 200m
L4_600Land between 200 & 400m

Three analyses are available.

  1. Full model: all habitat variables used
  2. Stepwise analysis
  3. Pre-pruning of predictors

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