5. Resemblance: similarities, dissimilarities and distances
Resemblance matrices
Fundamental to the operation of PRIMER and (explicitly or implicitly) any fully multivariate anal...
Standard resemblance choices
A detailed discussion of the competing properties of different resemblance matrices is outside th...
Bray-Curtis similarity
The most commonly-used similarity coefficient for biological community analysis, because it obeys...
Zero-adjusted Bray-Curtis
A simple modification to the Bray-Curtis coefficient adjusts its behaviour as samples become vani...
(Tikus Island coral cover)
Data on coral communities at a site in Tikus Island, Thousand Islands, Indonesia, over the years ...
Euclidean distances
Euclidean distance, an appropriate measure for environmental (and other) data types, is defined a...
Index of Association
The remaining of the three choices in the initial list, Measure•Index of Association, is essentia...
Accessing other resemblance measures
PRIMER 7 allows the user choice of 44 other resemblances, firstly divided into two (mutually excl...
Distance measures
The distance measures defined by L&L and calculated by PRIMER 7 (in addition to $D_1$) are: $ D_2...
‘Modified Gower’
Anderson MJ, Ellingsen KE, McArdle BH 2006, Ecol Lett 9: 683-693 used Czekanowski’s mean characte...
Similarity to dissimilarity
L&L also assign $D_{14}$ to Bray-Curtis dissimilarity, the complement of $S_{17}$, defined earlie...
Quantitative similarity measures
In addition to Bray-Curtis $S_{17}$, and its zero-adjusted modification, PRIMER 7 also calculates...
Presence/ Absence similarities
There are numerous similarity measures defined for simple species lists, i.e. when the data consi...
Quantitative measures on P/A data; Unravelling resemblances; Scatter plots
It is instructive to draw the other links between quantitative coefficients and the presence/abse...
Other coefficients
Returning to the quantitative resemblance coefficients in the •Others list, five further measures...
Between-curve distances
Another useful application of multivariate methods was touched on at the end of Section 4, namely...
(Plymouth particle-size analysis)
An example of a particle-size analysis (PSA) matrix has already been seen for Danish sediments at...
Taxonomic distinctness/ aggregation files
A later section (15) discusses univariate diversity indices that can be computed from each sample...
Taxonomic dissimilarity measures
This concept of taxonomic distinctness can be carried over from a diversity index to a dissimilar...
(Groundfish of European shelf waters)
Assemblage data from 93 groundfish species, those that could be reliably sampled and identified i...
Relatedness supplied as resemblances
Note the alternative means of supplying the variable information, to these dissimilarity measures...
Analysing between variables
The introduction above of the concept of ‘distances’ among species raises the issue of how best t...
Correlation between variables
One context in which resemblances between variables is often of primary interest is in dealing wi...
Correlation as similarity
Use of a correlation matrix between all pairs of variables as input to a multivariate ordination ...
Corrections for missing data
Returning to the main purpose of resemblance measures, to describe similarity among samples, an i...
Saving & opening triangular matrices
File>Save Resem As will save a resemblance matrix in internal binary PRIMER v7 (*.sid) format, th...