title: What is the difference between R vegan species-scores, and Primer Spearman rank correlation of species to axis?
body: <p>In constrained ordination analysis, like <code>CAP</code> or <code>dbRDA</code>, researchers often want to know how much of the dissimilarity is attributed to specific species. In <code>Primer PERMANOVA</code>, <code>Spearman rank</code> or <code>Pearson correlations</code> of species to the axis is an option to that provides an estimate of the species that characterise the variation between assemblages of species when using CAP or RDA. In R, <code>vegan</code> provides a different measurement, known as species scores, which can be calculated <strong>but not without careful consideration of the potential shortcomings</strong> <a href="https://github.com/vegandevs/vegan/issues/254#issuecomment-334071917" rel="nofollow noreferrer">https://github.com/vegandevs/vegan/issues/254#issuecomment-334071917</a>. 
  and <a href="https://stackoverflow.com/questions/46531969/vegan-dbrda-species-scores-are-empty-despite-community-matrix-provided">vegan dbrda species scores are empty despite community matrix provided</a>, when using capscale.</p>
  
  <p>I would like to better understand how the correlations and species scores are calculated in <code>Primer PERMANOVA</code>. Firstly, is there a real difference in what these methods aim to show? What are the benefits and shortcomings of the using <code>Spearman</code> or <code>Pearson correlations</code> over R- <code>vegan</code>'s species scores? Does the method of calculating the species-to-axis correlations in Primer suffer from similar problems as detailed in the above links for species scores in <code>capscale</code> or <code>dbrda</code> in R? In Primer, what are the variables used from the community matrix and axis to calculate the correlations between them? Are these raw or the transformed data? And finally, if the correlation method is a better estimate of the relative amount by which species cause differences between assemblages than species scores in R, should this be considered as an alternative to R vegan' species scores? </p>