PRIMER-E

Home

PRIMER 7

For a list of changes to previous version see here...

The statistical methods underlying the software are explained in non-mathematical terms in an extensive 'methods manual', which also shows outcomes from many literature studies, e.g. of environmental effects of oil spills, drilling mud disposal, sewage pollution etc on soft-sediment benthic assemblages, disturbance or climatic effects on coral reef composition or fish communities, more fundamental biodiversity and community ecology patterns, mesocosm studies with multi-species outcomes etc. Many of these full data sets are included with the package so that the user can replicate the analyses given in the manual for himself/herself.

The full integration within a standard Windows environment allows: easy manipulation of data and results, e.g. in input/output from Excel spreadsheets or other sources; the ability to view and manipulate data and some derived files/plots on screen, in multiple windows; standard Windows printing and export to Windows .emf or .bmp files (graphics) and .rtf files (text); flexibility in specifying analyses, particularly for subsets of data and in defining group structures for tests and displays; ability to handle relatively large data sets (subject to available Windows memory and, primarily, time constraints - as with all non-parametric and permutation-based methods, computation time can be long).

Screen_small.png (56420 bytes)
Click to enlarge...

A further unique feature of PRIMER 7 is the ability to calculate biodiversity indices based on the taxonomic distinctness or relatedness of the species making up a quantitative sample or species list, indices whose statistical properties are robust to variations in sampling effort. These routines allow formal hypothesis tests for change in biodiversity structure at a location (as measured by average and variation in taxonomic 'breadth' of the species list), from that 'expected' from a larger, regional species pool. It provides a possible way of comparing biodiversity patterns over wide space and time scales, when sampling effort is not controlled.

SHADE PLOT

Display actual values. Samples and variables can be sorted using various criteria, and constraints such as clustering can be applied.

CLUSTER

Hierarchical clustering in to sample (or species) groups. Rotate, collapse, zoom plots, multi-page printout

cluster.png (4787 bytes)

In addition there is LINKTREE and UNCTREE to do divisive clustering.
NEW - krCluster does a non-parametric version of k-means clustering

MDS & PCA

Ordination by non-metric or metric multidimensional scaling (nMDS and mMDS) and principal components (PCA). Overlay clusters, trajectories, bubble plots.
NEW - Bootstrap averages puts confidence intervals on an MDS plot. Additional MDS overlays such as minimum spanning trees.

mds.png (10752 bytes)

ANOSIM

To summarise patterns in species composition and environmental variables; permutation-based hypothesis testing (ANOSIM), an analogue of univariate ANOVA which tests for differences between groups of (multivariate) samples from different times, locations, experimental treatments etc.
NEW - Now supports most 3 way designs.

SIMPER

Identifies the species primarily providing the discrimination between two observed sample clusters.

BEST

The linking of multivariate biotic patterns to suites of environmental variables. Includes permutation tests.

RELATE

Comparative (Mantel-type) tests on similarity matrices.

TAXDTEST

Taxonomic distinctness tests.

taxdtest.png (11897 bytes)

Other

Standard diversity indices; summary statistics; dominance plots also histogram, box, line, bar plots; species abundance distributions; aggregation of arrays to allow data analysis at higher taxonomic levels, etc.

For further information contact:

PRIMER-E (Quest Research Limited)
ecentre, Gate 5, Oaklands Rd
Massey University, Albany
Auckland 0632, New Zealand

Tel: +64 (9) 869-2230
E-mail:
primer@primer-e.com