# Analysis of community ecology data in R

David Zelený

### Others

en:pcoa_nmds

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# Ordination analysis

## PCoA & NMDS (unconstrained ordination)

### Theory

#### Principal Correspondence Analysis (PCoA)

This method is also known as MDS (Metric Multidimensional Scaling). While PCA preserves Euclidean distances among samples and CA chi-square distances, PCoA provides Euclidean representation of a set of objects whose relationship is measured by any similarity or distance measure chosen by the user. As well as PCA and CA, PCoA returns a set of orthogonal axes whose importance is measured by eigenvalues. This means that calculating PCoA on Euclidean distances among samples yields the same results as PCA calculated on covariance matrix of the same dataset (if scaling 1 is used).

#### Non-metric Multidimensional Scaling (NMDS)

Non-metric alternative to PCoA analysis - it can use any distance measure among samples, and the main focus is on projecting the relative position of sample points into low dimensional ordination space (two or three axes). The method is distance based, not eigenvalue based - it means that it does not attempt to maximize the variance preserved by particular ordination axes and resulting projection could therefore be rotated in any direction.

The algorithm goes like this (simplified):

1. Specify the number of dimensions m you want to use (into which you want to scale down the distribution of samples in multidimensional space - that's why it's scaling).
2. Construct initial configuration of all samples in m dimensions as a starting point of iterative process. The result of the whole iteration procedure may depend on this step, so it's somehow crucial - the initial configuration could be generated by random, but better way is to help it a bit, e.g. by using PCoA ordination as a starting position.
3. An iterative procedure tries to reshuffle the objects in given number of dimension in such a way that the real distances among objects reflects best their compositional dissimilarity. Fit between these two parameters is expressed as so called stress value - the lower stress value the better.
4. Algorithm stops when new iteration cannot lower the stress value - the solution has been reached.
5. After the algorithm is finished, the final solution is rotated using PCA to ease its interpretation (that's why final ordination diagram has ordination axes, even if original algorithm doesn't produce any).
en/pcoa_nmds.1548498909.txt.gz · Last modified: 2019/01/26 18:35 by David Zelený