### Introduction

### Theory, R functions & Examples

en:mix:bci-perm-plot

Use species data from permanent tropical forest plot in Barro Colorado Island and analyse it in the following way:

- original data are counts of individuals per plot - transform them (use logarithmic transformation)
- calculate distance matrix using Bray-Curtis measure
- classify the plots by numerical classification (use matrix of Bray-Curtis distances and
*beta flexible*cluster algorithm) - draw resulting dendrogram and draw boxes around 5 clusters
- calculate NMDS on transformed data
- draw NMDS ordination diagram, where individual plots will be classified by different colours and symbols according to the result of classification (5 clusters)
- draw the scatterplot, where individual plots will be distributed according to their real geographical position in the field (the coordinates could be found in
`BCI.env`

file - variables`UTM.NS`

for latitude and`UTM.EW`

for longitude); color and symbol of the plots should again respect the classification into 5 clusters

The solution should look somehow like this:

Hints:
You need these libraries: `vegan`

, `BiodiversityR`

and `cluster`

!

`log (x+1)`

or`log1p (x)`

`vegdist`

`as.hclust`

,`plot`

,`rect.hclust`

`metaMDS`

`ordiplot`

,`points`

(arguments`col`

and`pch`

),`cutree`

`plot`

, coordinates: x = BCI.env$UTM.EW, y = BCI.env$UTM.NS

en/mix/bci-perm-plot.txt · Last modified: 2017/10/11 20:36 (external edit)