PRIMER version 7

Minimise your assumptions. Maximise your insights.​

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Tel: +64 (9) 869-2230

E-mail: [email protected]

Thousands of researchers globally trust PRIMER for ingenuity and clarity in multivariate analysis.

Analyse ecological data, or any other data, that would benefit from a safe non-parametric approach​.

PRIMER v7 provides a wide range of univariate, graphical and multivariate routines for analysing arrays of species-by-samples data from community ecology.​

Data are typically of abundance, biomass, % area (or line) cover, presence/absence etc. and arise in biological monitoring of environmental impacts and more​ fundamental ecological studies. Also catered for are matrices of physical values and chemical concentrations, which are analysed in their own right or in​ parallel with biological assemblage data, e.g., to examine co-variation of biotic changes with physico-chemical conditions.​

Though the analysis requirements for biological assemblage data are a principle focus, the package is equally applicable (and increasingly being applied)​ to other data structures which are multivariate or can be treated as such.​

The unifying feature is that all datasets can be reduced to an appropriate triangular matrix representing the resemblance of every pair of samples in terms of​ their assemblages, suites of biomarkers, particle size distributions, shape of growth curves, etc. Clustering and ordination techniques are then able to​ display the relationships among samples, and permutation tests are used to test hypotheses.​

Robust

The methods make few, if any, assumptions about the form of the data. Non-metric ordination and permutation tests are fundamental to the approach, which is easy to implement and straightforward to interpret and explain.

Widely applicable

Confidence in interpretation and transparency of the methods explain why PRIMER has been adopted in marine, terrestrial and freshwater ecology, forestry, soil science, genetics, aquaculture, taxonomy, microbiology, medicine, economics, and more.

Highly acclaimed

A global ‘standard’ in community ecology and biodiversity research, led by the academic prowess of highly-cited and globally recognized researchers for over 20 years.

Easy manipulation of data and results

The PRIMER Workspace (*.pwk)

 

  • Work on multiple data-sets, graphics and output files simultaneously within a single interactive & intuitive graphical Windows environment.​
  • Keep track of all your work easily using the tree-like navigation pane.​
  • Input/output data from Excel, .csv, .txt or 3-column format.​
  • View and change the colours, fonts, look & feel of your plots and graphics on-screen.​
  • Copy/print/export results to .jpg, .emf, .tif, .gif, .png, .bmp or .rtf files.
  • Power and flexibility in specifying analyses.
  • Identify important subsets of samples or variables.​
  • Define group structures for tests and displays.​
  • Handle relatively large data sets (subject only to available Windows memory).​
  • Merge or split data on specified criteria.​
  • Unleash the time-saving power of in-built Wizards for matrix displays and core analyses.

Multivariate analysis is more than a stack of univariate parts.

Achieve a holistic view of your high-dimensional data by exploring and revealing its salient structures.

Ordination​

Ordination techniques for visualising data, including principal components analysis (PCA), plus non-metric, metric or threshold-metric multi-dimensional scaling (nMDS, mMDS, tmMDS).​

Visualise high-dimensional data in 2d or 3d. Customise text, colours and symbols. Add essential information with overlays, such as clusters, trajectories, bubbles, images, vectors, or minimum spanning trees.​

Use bootstrapping to show confidence regions on MDS plots. Spin, expand, rotate, animate, save and share your insightful images.

Clustering​

Perform hierarchical clustering into sample (or variable/species) groups, with single, complete, group-average or flexible-beta linkage options.​

Create cophenetic distance matrices and plot dendrograms. Customise, rotate, collapse, zoom in, or print them out over multiple pages to capture all of the finer details.​

Similarity profiles (SIMPROF) and associated permutation tests identify the coherence of groups of samples or species.​

Divisive clustering methods can be unconstrained (UNCTREE), or constrained by environmental (or other) variables (LINKTREE), while krCLUSTER does a non-parametric version of k-means clustering.​

Shade plots and Heat maps​

Display actual values in 2d or 3d with grey-scale or colour spectra of choice.​

Salient patterns are uncovered with ease.​

Samples and variables can be sorted according to various criteria, including gradients, clustering constraints, or groupings.​

Labels and symbols are easily modified and customised.

Non-parametric tests​

Permutation-based hypothesis testing using analysis of similarities (ANOSIM), which tests for differences between groups of multivariate samples from different times, locations, experimental treatments, etc. PRIMER’s algorithms now support most three-way designs for these fully non-parametric tests.​

Identify species primarily providing discrimination between two groups of samples (SIMPER).​

Test for seriation and other Mantel-type tests for sequential data in time or space.​

Relate matrices to one another or identify subsets of variables which together produce a ‘BEST’ Mantel-type match to a given resemblance matrix. ​

Permutation tests include variable-selection steps to ensure rigorous statistical inference.​

Biodiversity analyses​

Use taxonomic, functional and/or phylogenetic information to inform biodiversity assessments. Test against master lists using sub-sampling algorithms.​

Calculate a multitude of classic and novel diversity indices or summary statistics of individual variables, with aggregation tools for analysing data at higher taxonomic levels.​

Access a wide choice of flexible plotting functions for individual variables: line, histogram, scatter, bar, box, means, surface or Draftsman plots.​

Ecology-specific tools are at your fingertips, such as dominance plots, geometric class plots, or abundance biomass curves (ABC).​

Extensive manuals and examples​

PRIMER version 7 includes context-specific Help buttons, as well as extensive downloadable manuals in searchable pdf format:​

“Change in Marine Communities (3rd ed.)”, explaining all of the statistical methods underlying the software in non-mathematical terms; and​

“PRIMER v7: User Manual / Tutorial”, explaining precisely how to implement the methods and all software utilities.​

A large number of full genuine data sets are included with the package so that the user can replicate analyses given in the manual and authored scientific publications.​


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