Difference between revisions of "Supported beta-diversity Measures"

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(New page: Qualitative measures (require a rooted split system): * Bray-Curtis (aka: normalized weighted UniFrac, Sorensen, Steinhaus, Odum, percentage difference, pairwise Whittaker) * Canberra * Ch...)
 
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Qualitative measures (require a rooted split system):
+
Qualitative measures requiring a rooted split system:
* Bray-Curtis (aka: normalized weighted UniFrac, Sorensen, Steinhaus, Odum, percentage difference, pairwise Whittaker)
+
* Bray-Curtis (aka: Sorensen, PhyloSor, Dice's index, pairwise Whittaker)
 +
* Canberra
 +
* Coefficient of similarity
 +
* Euclidean
 +
* Gower
 +
* Kulczynski (aka: Kulczynski-Cody, Sokal-Sneath)
 +
* Lennon compositional difference
 +
* Manhattan (aka: Hamming distance)
 +
* Soergel (aka: unweighted UniFrac, Jaccard, Ruzicka)
 +
* Tamas coefficient (TC) (aka: simple matching coefficient)
 +
* Weighted correlation
 +
 
 +
Quantitative measures requiring a rooted split system (use -w flag):
 +
* Bray-Curtis (aka: normalized weighted UniFrac, percentage difference)
 
* Canberra
 
* Canberra
* Chi-squared
 
 
* Coefficient of similarity
 
* Coefficient of similarity
 
* Complete tree
 
* Complete tree
* Fst
+
* Euclidean
 
* Gower
 
* Gower
* Hellinger
+
* Kulczynski
* Kulczynski (aka: Kulczynski-Cody, Sokal-Sneath)
 
 
* Lennon compositional difference
 
* Lennon compositional difference
* Mean nearest neighbour distance (aka: comdistnn)
+
* Manhattan (aka: weighted UniFrac)
* Mean phylogenetic distance (aka: comdist)
 
 
* Morisita-Horn
 
* Morisita-Horn
* Pearson product-moment correlation coefficient
+
* Soergel (aka: Ruzicka, Marczewski-Steinhaus, percentage remoteness)
* Rao's Hp
+
* Tamas coefficient
* Soergel (aka: Jaccard, unweighted UniFrac, Ruzicka, Marczewski-Steinhaus, percentage remoteness)
+
* Weighted correlation
* Species profile
 
* Tamas coefficient (TC) (aka: simple matching coefficient)
 
* Whittaker index of association
 
 
* Yue-Clayton (aka: similarity ratio)
 
* Yue-Clayton (aka: similarity ratio)
  
Quantitative measures (require a rooted split system):
+
Root-invariant quantitative measures (use -w flag):
 
+
* Complete tree
Quantitative measures (can be computed over rooted or unrooted split systems):
 
* Manhattan
 
 
* Euclidean
 
* Euclidean
 +
* Gower
 +
* Manhattan (aka: weighted UniFrac)

Revision as of 21:32, 10 April 2012

Qualitative measures requiring a rooted split system:

  • Bray-Curtis (aka: Sorensen, PhyloSor, Dice's index, pairwise Whittaker)
  • Canberra
  • Coefficient of similarity
  • Euclidean
  • Gower
  • Kulczynski (aka: Kulczynski-Cody, Sokal-Sneath)
  • Lennon compositional difference
  • Manhattan (aka: Hamming distance)
  • Soergel (aka: unweighted UniFrac, Jaccard, Ruzicka)
  • Tamas coefficient (TC) (aka: simple matching coefficient)
  • Weighted correlation

Quantitative measures requiring a rooted split system (use -w flag):

  • Bray-Curtis (aka: normalized weighted UniFrac, percentage difference)
  • Canberra
  • Coefficient of similarity
  • Complete tree
  • Euclidean
  • Gower
  • Kulczynski
  • Lennon compositional difference
  • Manhattan (aka: weighted UniFrac)
  • Morisita-Horn
  • Soergel (aka: Ruzicka, Marczewski-Steinhaus, percentage remoteness)
  • Tamas coefficient
  • Weighted correlation
  • Yue-Clayton (aka: similarity ratio)

Root-invariant quantitative measures (use -w flag):

  • Complete tree
  • Euclidean
  • Gower
  • Manhattan (aka: weighted UniFrac)