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SIMPROF on large matrices

PRIMER v7: User Manual / Tutorial 6. Clustering methods (CLUSTER, SIMPROF...

The dendrogram itself is rapidly calculated, at least for the agglomerative methods, since no sea...

Updated 6 months ago by Arden

SIMPROF tests

PRIMER v7: User Manual / Tutorial 6. Clustering methods (CLUSTER, SIMPROF...

All of the clustering methods are able to exploit ‘similarity profile’ (SIMPROF) permutation test...

Updated 6 months ago by Arden

Clustering methods & choice of linkage

PRIMER v7: User Manual / Tutorial 6. Clustering methods (CLUSTER, SIMPROF...

PRIMER 7 now carries out a wider range of clustering methods than previously: a) hierarchical agg...

Updated 6 months ago by Arden

Saving & opening triangular matrices

PRIMER v7: User Manual / Tutorial 5. Resemblance: similarities, dissimila...

File>Save Resem As will save a resemblance matrix in internal binary PRIMER v7 (*.sid) format, th...

Updated 6 months ago by Arden

Corrections for missing data

PRIMER v7: User Manual / Tutorial 5. Resemblance: similarities, dissimila...

Returning to the main purpose of resemblance measures, to describe similarity among samples, an i...

Updated 6 months ago by Arden

Correlation as similarity

PRIMER v7: User Manual / Tutorial 5. Resemblance: similarities, dissimila...

Use of a correlation matrix between all pairs of variables as input to a multivariate ordination ...

Updated 6 months ago by Arden

Correlation between variables

PRIMER v7: User Manual / Tutorial 5. Resemblance: similarities, dissimila...

One context in which resemblances between variables is often of primary interest is in dealing wi...

Updated 6 months ago by Arden

Analysing between variables

PRIMER v7: User Manual / Tutorial 5. Resemblance: similarities, dissimila...

The introduction above of the concept of ‘distances’ among species raises the issue of how best t...

Updated 6 months ago by Arden

Relatedness supplied as resemblances

PRIMER v7: User Manual / Tutorial 5. Resemblance: similarities, dissimila...

Note the alternative means of supplying the variable information, to these dissimilarity measures...

Updated 6 months ago by Arden

(Groundfish of European shelf waters)

PRIMER v7: User Manual / Tutorial 5. Resemblance: similarities, dissimila...

Assemblage data from 93 groundfish species, those that could be reliably sampled and identified i...

Updated 6 months ago by Arden

Taxonomic dissimilarity measures

PRIMER v7: User Manual / Tutorial 5. Resemblance: similarities, dissimila...

This concept of taxonomic distinctness can be carried over from a diversity index to a dissimilar...

Updated 6 months ago by Arden

Taxonomic distinctness/ aggregation files

PRIMER v7: User Manual / Tutorial 5. Resemblance: similarities, dissimila...

A later section (15) discusses univariate diversity indices that can be computed from each sample...

Updated 6 months ago by Arden

(Plymouth particle-size analysis)

PRIMER v7: User Manual / Tutorial 5. Resemblance: similarities, dissimila...

An example of a particle-size analysis (PSA) matrix has already been seen for Danish sediments at...

Updated 6 months ago by Arden

Between-curve distances

PRIMER v7: User Manual / Tutorial 5. Resemblance: similarities, dissimila...

Another useful application of multivariate methods was touched on at the end of Section 4, namely...

Updated 6 months ago by Arden

Other coefficients

PRIMER v7: User Manual / Tutorial 5. Resemblance: similarities, dissimila...

Returning to the quantitative resemblance coefficients in the •Others list, five further measures...

Updated 6 months ago by Arden

Presence/ Absence similarities

PRIMER v7: User Manual / Tutorial 5. Resemblance: similarities, dissimila...

There are numerous similarity measures defined for simple species lists, i.e. when the data consi...

Updated 6 months ago by Arden

Quantitative similarity measures

PRIMER v7: User Manual / Tutorial 5. Resemblance: similarities, dissimila...

In addition to Bray-Curtis $S_{17}$, and its zero-adjusted modification, PRIMER 7 also calculates...

Updated 6 months ago by Arden

Distance measures

PRIMER v7: User Manual / Tutorial 5. Resemblance: similarities, dissimila...

The distance measures defined by L&L and calculated by PRIMER 7 (in addition to $D_1$) are: $ D_2...

Updated 6 months ago by Arden

Similarity to dissimilarity

PRIMER v7: User Manual / Tutorial 5. Resemblance: similarities, dissimila...

L&L also assign $D_{14}$ to Bray-Curtis dissimilarity, the complement of $S_{17}$, defined earlie...

Updated 6 months ago by Arden

‘Modified Gower’

PRIMER v7: User Manual / Tutorial 5. Resemblance: similarities, dissimila...

Anderson MJ, Ellingsen KE, McArdle BH 2006, Ecol Lett 9: 683-693 used Czekanowski’s mean characte...

Updated 6 months ago by Arden