4 Protocol 2 - Petrographic data

The following example applies protocol 2 to confirm workshops’ petrographic groups.

Protocol 2 consist in:

  1. Select ordinal petrographic data;
  2. Transform to ranks;
  3. Extended Gower distance, using:
  1. Relative ranking difference (RRD)
  2. Neighbor interchange (NI)
  1. Apply ordination procedure:
  1. Principal Coordinates Analysis (PCoA)
  2. Non-metric Dimensional Scaling (NMDS)
  1. Perform PERMANOVA & PERMDISP tests;

Last, search for outliers and re-do protocol excluding outliers.

NOTE: The initial procedures must be ran at least once before any protocol can be applied.

The key references on the Extended Gower distance are:

Pavoine, S., Vallet, J., Dufour, A.-B., Gachet, S., Daniel, H., 2009. On the challenge of treating various types of variables: application for improving the measurement of functional diversity. Oikos 118, 391-402. doi:10.1111/j.1600-0706.2008.16668.x

Podani, J., 1999. Extending Gower’s General Coefficient of Similarity to Ordinal Characters on JSTOR. Taxon 48, 331-340. doi:10.2307/1224438

Gower, J.C., 1971. A General Coefficient of Similarity and Some of Its Properties. Biometrics 27, 857-871. doi:10.2307/2528823