PRIMER v7: User Manual / Tutorial

For any up-to-date news about PRIMER, including details of upcoming PRIMER workshops, see our web...

PC with Intel compatible processor. Any modern Windows operating system (XP or later). Sufficien...

You need to be logged on as an administrator. You can keep version 6 or earlier versions installe...

Detailed information and examples of virtually all the analyses offered by PRIMER v7 are found in...

In examples in this manual you may see the main menu item PERMANOVA+. This is an add-on product t...

Application Areas PRIMER 7 (Plymouth Routines In Multivariate Ecological Research) consists prima...

Wizards and major new analysis options Dialog boxes generally are more ‘wizard’-based, unifying a...

Emphases & text symbols Text in bold indicates the menu items that need to be selected, > denotes...

Opening the examples After launching the PRIMER desktop by clicking on its icon, the first step i...

Reading data in from Excel As an example of reading in data from Excel, first open and examine th...

Basic MVA wizard To cater for users completely unfamiliar with the basic outputs from a multivari...

Pre-treatment of the data (sometimes in more than one way) is usually desirable. For assemblage d...

On active sheet Fal nematode abundance, run Wizards>Matrix display, not taking all the defaults i...

For environmental-type data, such as the Fal environment sheet, it is often appropriate to transf...

Resemblance calculation The next stage in both the Fal nematode and environment runs of the Basic...

The wizard then runs, for both biotic and abiotic data, Analyse>ANOSIM>(Model: One-way - A) & (Fa...

The Basic MVA wizards then run a cluster analysis, again on the respective resemblance matrices. ...

The Basic MVA wizard next produces non-metric MDS (nMDS) plots in 2-d and 3-d, together with thei...

The final step in the Basic MVA wizard is to break down the dissimilarities (or distances) betwee...

A further bubble plot you might like to try on the Fal nMDS is to superimpose abiotic variables f...

A trial version of PRIMER 7 is freely available, which is downloadable from the PRIMER-e web site...

The Help main menu has the entries shown, starting with View Help, the HTML Help system: This li...

The Help>About PRIMER menu item will tell you: which maintenance version number you are currently...

You will need to run Help>Install Licence at the point at which you have purchased an installatio...

Help>Get Examples V7 will take you to the data sets used throughout this manual [and Help>Get Exa...

The installation and subsequent run of Help>Get Examples V7 will have placed a number of sub-dire...

Whether the extensions *.pri, *.xls(x) etc display, or not, is a function of your Windows set-up;...

PRIMER 7 is fully forward-compatible from v6, and can input PRIMER 6, 5 and 4 data (*.pri and *.p...

Start the program by (double)-clicking on the desktop or task bar PRIMER 7 icon , giving the win...

Most users will already have their data stored in rectangular form in some other software, e.g. a...

At this point only the default row (variables V1, V2, …) and column labels (samples S1, S2, …) ha...

addition to attaching labels, the Edit menu allows a range of other edit functions on the data en...

Occasionally, cell values are accidentally deleted or rows/columns added in unintended places but...

Movement of rows or columns uses both highlighting and the cursor position. Rows (or columns) to ...

The Edit>Cut and Edit>Copy operations send part of a worksheet (or its factors/indicators) to the...

The data sheet can now be saved (as can any item created in the workspace) from the File menu. F...

Another new feature to PRIMER 7 is the option Undo Workspace which back-tracks for the work¬space...

Typically, a single workspace would encompass one or more inter-connected data sets which are ana...

It may sometimes be convenient to set the initial (default) directory to which PRIMER 7 opens eve...

File>Open>(File name: Ekofisk macrofauna counts.pri)>Open will read in the existing Ekofisk speci...

The abundance file Ekofisk macrofauna counts.pri is displayed within the PRIMER desktop. It shows...

Edit>Properties produces the Sample Data Properties dialog box, seen earlier, where information a...

Usually, rectangular data matrices of variables by samples, or samples by variables, will initial...

For the 39 sites around the Ekofisk oil-field, environmental data is available on concentrations ...

File>Open gives the same Open dialog box as previously but, importantly, the drop down menu on th...

The final option is whether a blank cell in the Excel sheet should be interpreted as a Missing va...

This study concerns meiofaunal abundances from a two-way layout of samples on a sand-flat in Eagl...

The directory C:\Examples v7\Tasmania meiofauna contains the PRIMER 7 files of separate nematode ...

PRIMER 7 will allow the same file to be opened into the workspace more than once, since the respo...

The Tasmania meiofauna directory also contains three different text format versions of the copepo...

Associated with each record are often one or more factors which define the conditions under which...

Read in the first of the above text files: File>Open>(Files of type: Text Files (*.txt, *.csv)) &...

There are no fixed size limits for arrays within PRIMER 7, simply an overall limit determined by ...

For data collection reasons, it may still be the case that data from essentially the same array a...

Output format options, with File>Save Data As, are generally the reverse of input choices. The de...

Take File>Open>(Filename: Tasmania copepods v4.pm1)>Type•Species-sample to input this (archival) ...

If you have been carrying out the manipulations in Section 1, by now you will have several sheets...

With Tasmania nematodes as the active window, select Edit>Factors from the main menu (or use the ...

In the Factors dialog box (obtained from Edit>Factors on Tasmania nematodes) take Add>(Add factor...

An alternative (and clumsier!) way of creating this factor would be type in the top half, then hi...

Finally, to make factors in the Tasmania nematodes sheet consistent with the text format copepod ...

As a further example of Fill>Value to quickly set up a factor of group levels you might like to r...

With the Tasmania nematodes sheet active, open the Factors dialog with Edit>Factors. Combining fa...

A further button on the Edit>Factors dialog box is Key, which you could examine with the factors ...

New factors can be created at several stages during an analysis, not just when the active window ...

Alternatively, the same endpoint could have been achieved by Adding three new blank factors to th...

As noted in Section 1, factors can be created as part of the Excel or text files which are the us...

Indicator is the term PRIMER uses for a factor defined on the variables not on the samples. It is...

Selection by indicator levels is demonstrated by Select>Variables>(•Indicator levels)>(Indicator ...

However, the full range of hierarchical indicators represented by a Linnaean classification (whi...

There are many cases in which analyses of different subsets of the samples or species are require...

Dietary data on the gut contents of 7 marine fish species found in nearshore waters of the lower ...

File>Open>Filename: WA fish diets %vol, and examine the factors sheet with Edit>Factors. The samp...

Thus, with the WA fish diets %vol datasheet as the active window, highlight all columns except th...

When all except columns A9, B3 and B4 are highlighted, take Select>Highlighted. Alternatively, ri...

Though most Save operations are on whole workspaces, occasionally a data matrix needs to be saved...

The highlighting route to selection can be bypassed altogether using the other options on the Sel...

It is important to note the effect of this second selection on WA fish diets %vol; it produces a ...

It may sometimes be easier to use the sample numbers, here Select>Samples>•Sample numbers> 1,2,5,...

Any of the options for selecting samples are also available for selecting variables, e.g. selecti...

There are, however, three other selection methods under Select>Variables that are specific to sel...

Looking ahead to Section 5, when the active window is a (triangular) resemblance matrix, selectio...

How the data are treated, prior to computation of a resemblance matrix (e.g. similarities), can h...

Several of the routines in PRIMER 7 also incorporate a check box for sending summary statistics u...

Pre-treatment>Standardise can also be used to standardise the matrix on the variables axis, e.g. ...

Transformation is usually applied to all the entries in an assemblage matrix of counts, biomass, ...

A major new feature in PRIMER 7 is the large number of additional plotting routines, one of the c...

Transformations may be appropriate for environmental variables too, though usually for a differen...

Temporarily deselect the Distance (as in Section 3), and run Plots>Draftsman Plot on the other 9 ...

Both the Draftsman and Histogram Plots show that several of the Ekofisk abiotic variables are hig...

It is typical of a suite of physico-chemical variables (or biomarkers, water-quality indices etc)...

When variables are on different measurement scales, there is little viable alternative to normali...

Sediment copepod assemblages (and other fauna) from five creeks of the Fal estuary, SW England, w...

There are other cases in which variables (species) might need prior weighting, e.g. when a specie...

Another example might be in attempting to reconcile two different types of data in the same matri...

Pre-treatment>Variability Weighting is a new option in PRIMER 7, which bears similarities to the ...

The directory C:\Examples v7\N Sea biomarkers holds a data sheet N Sea flounder biomarkers(.pri) ...

The remaining option on the Pre-treatment menu is Cumulate samples, which successively adds up th...

Sediment particle size data from 6 size ranges at 3 sites (A, B, C), at 2 depths (2m and 5m), and...

The smoothing effect can best be seen by Plots>Surface Plot of both Data1 and Data2 sheets – a fu...

Fundamental to the operation of PRIMER and (explicitly or implicitly) any fully multivariate anal...

A detailed discussion of the competing properties of different resemblance matrices is outside th...

The most commonly-used similarity coefficient for biological community analysis, because it obeys...

A simple modification to the Bray-Curtis coefficient adjusts its behaviour as samples become vani...

Data on coral communities at a site in Tikus Island, Thousand Islands, Indonesia, over the years ...

Euclidean distance, an appropriate measure for environmental (and other) data types, is defined a...

The remaining of the three choices in the initial list, Measure•Index of Association, is essentia...

PRIMER 7 allows the user choice of 44 other resemblances, firstly divided into two (mutually excl...

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

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

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

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

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

It is instructive to draw the other links between quantitative coefficients and the presence/abse...

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Though PRIMER 7 does not attempt to replicate all the facilities available in graphics presentati...

Assemblage data on 140 species of free-living marine nematodes at 19 sites (labelled 1-19) in the...

The dendrogram is displayed in a plot window, and a separate Results window gives a detailed list...

Returning to the main point of the previous example, the production of the dendrogram, note that ...

When the active window is a plot, levels of a factor can be displayed in place of sample labels a...

Label font sizes, typeface, colours etc can be changed with the (Labels:Data font) button, and si...

Still in the Graph Options dialog box, take the Titles tab and edit the main and sub-title conten...

Finally, on the General tab (also reached directly from Graph>General), thicken up all lines with...

Unlike Graph>Samples Labels & Symbols or Graph>General, which take you to the Graph Options dialo...

The order of samples on the (by default) x axis of a dendrogram is to a large extent arbitrary, s...

As discussed at the start of this section, if you have set SIMPROF running, with the (✓SIMPROF te...

PRIMER 7 now automatically displays the levels of a numeric factor in increasing order in a plot ...

Zooming is invoked by Graph>Zoom In or Zoom Out from the main menu, or by clicking on the Zoom in...

The similarity profile test (SIMPROF), Clarke KR, Somerfield PJ, Gorley RN 2008, J Exp Mar Biol E...

Densities from 24 species of zooplankton at 57 sites in the Bristol Channel and Severn Estuary, c...

In addition to the dendrogram plot itself, Analyse>CLUSTER (like all analysis routines) produces ...

SIMPROF can be run directly using Analyse>SIMPROF, rather than as part of another analysis such a...

The first dialog box from running Analyse>SIMPROF, however, is of a new option to PRIMER 7, a cho...

From the Bristol Channel zooplankton transformed data matrix Data1, select (say) the samples of t...

As in all permutation tests in PRIMER v7 (e.g. in ANOSIM, RELATE, BEST etc), a further output fro...

There are four possible Cluster mode choices within the Analyse>Cluster>CLUSTER dialog box, disti...

Now re-run Analyse>Cluster>CLUSTER>(Cluster mode•Single linkage), creating the SIMPROF factor Sin...

Note that the plots above required a certain amount of juxtaposition of different font sizes for ...

Two new clustering methods are introduced towards the end of Chapter 3 in CiMC, the first still a...

Using the Bristol Channel zooplankton workspace which should still be open, and with active sheet...

Note how each node is now lettered so that information about the R value for that split can be di...

PRIMER 7 also provides a choice of representations of the tree structure, using either the A% or ...

Another new introduction in PRIMER 7 is a form of non-hierarchical (flat) clustering, the analogu...

It will have been obvious from performing the worked examples of the previous sections that the s...

The Explorer tree not only makes it easy to navigate the sequence of steps taken in an analysis b...

From the Explorer tree for the above illustration, you can see that workspace has been saved as B...

Understanding the Explorer tree, however, is the key to managing your work pattern in PRIMER. In ...

In the display of the Explorer tree at the beginning of this section, the SIMPROF1 window was...

Met briefly in Section 1 and again above, renaming or deleting windows in the Explorer tree is an...

The name of a window can also be changed as part of the process of saving it, as a file external ...

Closing the second PRIMER desktop and returning to the original Bristol Channel ws workspace, not...

Certain graphs, such as MDS ordinations (Section 8) or Cluster dendrograms, can be validly rotate...

It is not permitted to edit directly the information in a results window. This tells you what ope...

Direct printing from PRIMER is also possible for analysis endpoints such as results windows, all ...

The concept of a Multi-plot is a new feature in PRIMER 7. This construction has already been met ...

In addition to automatic generation by certain routines, multi-plots can be created and populated...

PRIMER 7 has a new Plots main menu, available when the active window is a data matrix. This bring...

To conclude this section, it is worth remarking that care taken in structuring workspaces will of...

Chapter 5 of the CiMC methods manual describes the operation and rationale of multi-dimensional s...

A further new feature of nMDS in PRIMER 7 is the ability to minimise a combination of two stress ...

In addition to the ability in a previous PRIMER version to Graph>Special>Overlays>(✓Overlay clust...

The ability to display, on any ordination plot, external structure such as factors (e.g. for site...

From the directory C:\Examples v7\Exe nematodes, File>Open the workspace Exe ws, last seen in Sec...

As with all results windows, the MDS1 window first lists the resemblance sheet on which analysis ...

That the stress is low here is also evident from the Shepard diagrams for the 2-d and 3-d solutio...

One can also ask how well the (Euclidean) distances among points in the nMDS plot correlate with ...

For the MDS run above, two of the defaults taken for options in the MDS dialog were (Minimum stre...

nMDS ordinations (unlike mMDS) have no meaningful axis scales for the configuration, since they u...

A new feature in PRIMER 7 is the ability to automatically reflect in the axes and rotate an MDS c...

It is scarcely necessary here, with only 19 samples, to zoom in on part of the plot in order to s...

We have seen before that, whilst the Graph>Sample Labels & Symbols and General menus are universa...

There are a number of new diagnostic tools available in PRIMER 7 for assessing how well a low-d o...

It is worth saying, as we start to explore the wide range of tools which can be applied to an MDS...

The minimum spanning tree (MST, see CiMC for the Gower and Ross, 1969 reference) is used in the s...

The 2-d ordination plot shows a clear separation of the nematode assemblages at these 19 sites in...

The second way in which a cluster analysis can be displayed on a 2-d MDS plot, to aid assessment ...

Rather than creating a small number of (arbitrary) slices through a dendrogram, superimposed on a...

As we have seen for the nMDS run on the Exe nematode data, in the first graphic of this Section, ...

The 3-d Exe nematode nMDS plot should be in the current workspace as Graph5 under Multiplot1 (if ...

Whilst it is relatively easy to visualise a 3-d plot by rotation of the axes – and PRIMER 7 is no...

Re-open the workspace WA fish ws from C:\Examples v7\WA fish diets, which will provide an example...

Run nMDS at a wider range of dimensionalities than the default and ask for a scree plot: Analyse>...

The 3-d MDS plot box can be made to rotate horizontally, automatically (from whatever vertical pe...

Some data sets have a natural sequence to their samples, usually a time series (though this can b...

A trajectory joining points on an ordination is simply added using Graph>Special>Overlays and tak...

The time pattern above is evident from simple addition of the trajectory but there are occasions ...

In fact, if the animation is repeated with trajectories running across months, separately drawn f...

A clearer, static, example of the benefits of split trajectories on ordination plots is provided ...

The final two sections of the Graph>Special dialog concern overlaying vectors and ‘bubbles’ of nu...

The above MDS draws on all 174 species (with more abundant species given greater weight) but only...

A new feature in PRIMER 7 is that these bubbles will be plotted in different colours – or in mono...

The key to the left of the plot, which gives the root-transformed scale for Abra prismatica count...

A further new option on this Key dialog is to replace single-coloured circles with a (rectangular...

Abra prismatica appears to be a species which can tolerate the contaminant or disturbance effects...

One tempting alternative, commonly found in the literature, is to plot (species) variables as vec...

An important use for a bubble plot is in displaying the behaviour of a further measured variable,...

Given the inadequacies of vector plots for displaying species contributions to ordinations, but t...

The BC zooplankton density data sheet in C:\Examples v7\BC zooplankton was used in the last half ...

Another new feature in PRIMER 7 is the ability to construct bubble plots in 3-d ordinations, wher...

For these data, a segmented bubble plot on a 2-d ordination provides a succinct summary of the re...

It is worth repeating the point made at the start of these examples on bubble plots: if the routi...

A significant new feature in PRIMER 7 is the construction of metric MDS ordinations (mMDS), toget...

Show this by running the matching nMDS to the above mMDS, this time setting (Minimum stress: 0.00...

Another feature introduced in PRIMER 7 is more of a teaching tool than an analysis method per se,...

Close the World cities worksheet (it will not be needed again) and re-open workspace Morlaix ws, ...

The mMDS Shepard diagram above strongly suggests a middle course between simple metric and non-me...

Though usually greatly inferior to nMDS for typical ordinations from community similarities (e.g....

The PRIMER 7 nMDS dialog box includes a new option to (✓Fix Collapse). This addresses the problem...

A variation of the above, and a final new PRIMER 7 feature to discuss in this section, is the opt...

The series of ANOSIM (analysis of similarity) tests, accessed through Analyse>ANOSIM, operate on ...

Return to the W Australian fish diet data, introduced at the start of Section 4 and last seen und...

The table ending the results window gives the pairwise comparisons. For each pair of groups (fish...

Checking the (✓Pairwise tests to worksheet) box has also sent the above R values to a worksheet i...

ANOSIM applies equally well to data on environmental, biomarker or morphometric variables, which ...

However, for the Ekofisk oil-field study of the last section there is a postulated cause for bent...

An example of a 2-way crossed layout was introduced in Section 1, for meiofaunal communities in s...

For an example of a 2-way crossed ANOSIM test in a very different context, save and close the abo...

In the unordered 1-way design, replication is essential for any sort of test (otherwise how can y...

The test for an ordered factor (A) in the 2-way crossed design parallels the construction seen ea...

The 2-way crossed ANOSIM for an unordered factor, and with each combination of the two factors on...

Subtidal rocky reefs, at c10m depth, at the Calafuria station in the Ligurian Sea, N Italy, were ...

A dietary study of W Australian fish concerns composition by the volume of taxa (21 broad dietary...

The 3-way fully nested design has factor C at the lowest level, nested in B at the mid level, whi...

The two other possible 3-way designs can be written C(A$\times$B) and B$\times$C(A). The first is...

The three Wizards menu items carry out sequences of routines, all of which can be run separately ...

The benthic faunal study in the Fal estuary, Cornwall UK, was seen in Section 4. Sediment samples...

In the Fal estuary study, where there are environmental data matching each of the 27 sites, it is...

Finally, try running Analyse>Basic multivariate analysis on this environmental data matrix, Fal e...

Another significant addition to the descriptive tools now available in PRIMER 7 is that of Plots>...

A data set not met elsewhere in this manual but which is used a great deal in CiMC, e.g. to start...

Of the 110 species, many occur only in one or two replicates, often as singleton individuals, so ...

The next dialog box on Matrix display is (Transformation:       ), with default of Square roo...

The first branch takes the square root of the full matrix Frierfjord macrofauna counts, giving Da...

The Graph options taken automatically by Matrix Display to produce the final shade plot output ar...

Slightly more detail on how the seriate options are constructed, on both samples and species axes...

A good example of how ordering of species in a shade plot can aid interpretation is seen for macr...

A Western Australian study of the dietary assemblages of a single fish species (King Wrasse) were...

With OK to get back to the first dialog screen under Special, we now look at the options availabl...

A further option on the initial Special menu for a shade plot (✓3D>Opacity (0-100): 75) turns the...

A final choice on the Special dialog for shade plots can be useful when planning to compare plots...

The time-averaged Exe nematode community data were used extensively in Section 8 to illustrate nM...

The core task faced by the Special>Reorder operation is to reduce what is inevitably a high-d sim...

The final option that Reorder offers, attempting to find a useful ordering on a 1-d axis of a non...

For the final example of the options in shade plot, save and close Exe ws and return to the Brist...

The third item on the Wizards menu is Coherence plots. This is a combination of SIMPROF runs with...

A Type 2 SIMPROF test is not part of a Wizards>Coherent plots run, and there is a good case for c...

Type 3 SIMPROF can be run as a single test on the species set defined by the active matrix (which...

For this (reduced) Loch Linnhe data matrix, e.g. with the selection of 50 species made in Data1, ...

In order to display a shade plot carrying precisely the same information as the coherent species ...

A final possibility for this Loch Linnhe data is to display both horizontal and vertical division...

Save the workspace as Linnhe ws, close it and re-open the data on a suite of biomarkers (‘health’...

Shade plots are an excellently succinct way of displaying the abundance (or other quantity) of al...

Re-open the Bristol Channel ws workspace from C:\Examples v7\BC zooplankton, for which the shade ...

Earlier in the results window, tables are given of the contributions of each species to the Bray-...

A natural extension to the 1-way SIMPER is to the 2-way crossed design, so re-open the Tasmania w...

Save and close Tasmania ws and, as a last example, open the recently closed N Sea ws workspace. O...

Both the Edit (see Section 1) and Tools main menus carry out ‘housekeeping’ manipulations on a da...

Tools>Average and Sum operate in the same way on data sheets. For example, when (Samples• Average...

So far we have only seen variable information sheets, containing taxonomic (or other) hierarchies...

Use the open aggregation file, Groundfish taxonomy, to show the smaller set of Tools items (Tree,...

The other Tools menu item for aggregation sheets is distinctive to this case, namely Tools>Tree; ...

Tools>Duplicate operates in the same way whether the active window is a data array, resemblance m...

The nematode and copepod datasheets from 16 samples at a Tasmanian sand-flat (C:\Examples v7\ Tas...

Occasionally, use of strict label names does not give the this desired outcome, and the default b...

The best policy to avoid confusion is to use precise, unique species and sample labels (typically...

Perhaps the greatest benefit of the strict label matching in PRIMER is the ability to Tools>Merge...

The subject of missing data has arisen several times already (Sections 1, 3, 5) and the point mad...

Tools>Missing is designed to operate only on matrices for which: a) assumptions of multivariate n...

Transformation options for the Clyde environmental matrix, Clyde environment, are discussed in mo...

The following section (on PCA) will discuss further the choice of particular transformations to a...

Ranking is also a menu option when the active sheet is a resemblance (Tools>Rank distance), but i...

The Clyde environment sheet has samples as rows and variables as columns. This is the opposite of...

Unlike previous versions, in PRIMER 7 the Transform(individual) routine has been moved to a more ...

For an example of an Expression combining two (or more) variables, use the Clyde environmental sh...

Similarly, expressions can combine samples, or even factors (or indicators) on those samples (or ...

A useful variation of this, but one which needs more care, is to compute average body mass of eac...

Transforming resemblances remains in the Tools menu in PRIMER 7, since it is not an option for pr...

Tools operations on resemblances which are discussed elsewhere are: a) Dissim and Unravel in Sect...

PRIMER uses the term environmental variables as a shorthand for a wide variety of data types (inc...

Normalisation (subtracting the mean and dividing by the standard deviation, for each variable), a...

PCA is an ordination method in which samples, regarded as points in the high-dimensional variable...

Though the vector overlay has a tendency to clutter the plot, the changing contaminant load along...

The final table in the results window is headed Principal Component Scores – these can instead be...

Many of the options for manipulating PCA configurations are exactly the same as for MDS plots, co...

From the Graph>Special menu, remove the vector overlay by unchecking the (✓Overlay vectors) box o...

Of the other options on the Graph>Special menu, overlaying groups from a CLUSTER run (which to be...

As with MDS, use of Graph>Special>Main>Axes, with (Plot type•2D or •3D), allows any pairs or trip...

Another subtle distinction from MDS is that only a single PCA graph window is produced initially,...

An example where a 3-d plot is marginally more necessary is given by the biomarker data last see...

The main rationale for the Analyse>BEST procedure in PRIMER is to find the best match between the...

BEST amalgamated the earlier (PRIMER 5) BIOENV and BVSTEP procedures (hence BEST = Bio-Env + Step...

In what is one of the very few examples of ‘moving the furniture around’ between PRIMER 7 and ear...

After the initial choice of Method, the next area on the BEST dialog inputs the explanatory (fitt...

After the (✓Group variables(indicator)) check box, the next option is a Select variables/groups b...

On the right of this main dialog box for BEST is another option new to PRIMER 7, also covered in ...

On the mid-right of the main dialog for BEST, the box headed (Correlation method:) now offers thr...

The final area of the main BEST dialog, headed Permutations, which carries out the global BEST te...

The Next > button now takes you to a Results dialog box, which controls two features of the BEST ...

A study of diatom assemblages (abundances of 193 species) at 17 sites in the lagoons of Messol-on...

The question of statistical significance testing on the results of the Bio-Env (or BVStep) proced...

Another technique for linking sample patterns based on assemblage data to a suite of environmenta...

The Analyse>Cluster>LINKTREE routine has a number of features that are designed to mesh to the PR...

Continuing the lagoon diatom study, having first selected (highlighting then Select>Highlighted) ...

Low values of B% correspond to samples which are rather close together on the MDS plot and the qu...

Note that LINKTREE is able to tolerate some missing data in the abiotic matrix – the piecemeal fo...

The BEST routine in the previous section introduced the concept of measuring how closely related ...

Model matrices corresponding to more complicated structures than simple seriation or cyclicity ne...

A permutation test can be applied to the matching coefficient $\rho$ between any two resemblance ...

The Phuket coral-reef assemblages at equi-spaced positions down an onshore-offshore gradient (tr...

Given the breakdown of the serial gradient structure for 1987, is it now the case that the patter...

A new feature in PRIMER 7 parallels that discussed for the BEST analysis of the previous section,...

Return to the macrofaunal data set from the Ekofisk oilfield, with workspace Ekofisk ws last save...

The conclusion is, of course, consistent with the different, but closely-related, ordered ANOSIM ...

A RELATE test could equally well have been carried out between the Ekofisk community pattern and...

As an example of Tools>Expand Samples on a data matrix (or Tools>Expand on a resemblance matrix, ...

The Exe environment matrix does not seem (from Plots>Draftsman Plot or Histogram Plot) to contain...

The other two Model Matrix options are (Type•Cyclicity (factor as cycles)) and (Type•Euclidean 2D...

A 2-way RELATE version of the above test where there are no replicates, and the cyclic factor und...

Veale L et al 2014 J Fish Biol 85: 1320-1354 describe trawl sampling for nearshore estuarine fish...

As seen above, the $\rho$ statistic, which rank correlates the elements of two similarity matrice...

Chapter 10 of CiMC gives several examples of aggregating species matrices to higher taxa – using ...

The illustration below has calculated all combinations of species (sp), genus (gn) and family (fm...

The technique of 2nd stage plots has also been used (Clarke KR, Somerfield PJ, Chapman MG 2006, J...

Clarke KR, Somerfield PJ, Chapman MG 2006, J Exp Mar Biol Ecol 330: 55-80 discuss this analysis (...

A very different way of using 2nd stage matrices is best accessed through the alternative entry o...

Open the workspace Phuket ws, of coral cover for the Ko Phuket transect A, in C:\Examples v7\ Phu...

In the context of a 2-factor design, PRIMER makes a 2nd stage matrix very simple to produce but i...

The workspace Tees ws was saved in Section 9; if not available open the data Tees macrobenthic ab...

The Calafuria macroalgal recolonisation experiment monitored the same physical rock patches over ...

Another situation employing rank correlation ($\rho$) between two resemblance matrices is the BES...

There is one fundamental problem with applying BEST (Bio-Env) in many of the above scenarios: the...

The main application area for the BVStep routine introduced by Clarke KR & Warwick RM 1998, Oecol...

Re-open the Morlaix ws workspace in C:\Examples v7\Morlaix macrofauna from earlier in this sectio...

On B-C on 4rt, Analyse>BEST>(Method•BVSTEP) & (Worksheet: 4rt data), taking the defaults for all ...

Starting the iterative search process from a blank species list is certainly not guaranteed to ge...

One of the few multivariate routines not so far met is Analyse>MVDISP, applied to a resemblance m...

The illustration used here is a simple 1-way design of 3 mesocosm treatments: Control (C), Low (L...

PRIMER computes an extensive set of univariate diversity measures, covering most of the standard ...

One of the distinctive features of PRIMER is its inclusion of a suite of biodiversity measures ba...

The range of indices available is illustrated with the macrobenthic data Clyde macrofauna counts ...

For the diversity (variables) by samples matrix, Data1, Plots>Draftsman Plot>(✓Correlations to wo...

Soft-sediment macrofaunal assemblages (along with meiofauna and biomarker suites) were studied at...

In order to obtain a diversity measure which steps outside the species abundance distribution, an...

For the first set of measures (on the Taxdisc tab), the Taxonomy button gives a choice of whether...

Such tree structures (e.g. taxonomies) are one of a distinct worksheet type, Variable Information...

The other box in this Taxonomy (data) dialog can be used to alter the weights given to the variou...

The aggregation matrix for the NW European beam-trawl survey data on groundfish assemblages (93 s...

The sheet Data1 of this suite of diversity indices for each of the 277 samples, split into 9 sea ...

Wide-ranging biogeographic studies, and particularly historic data, are often restricted to simpl...

Further theoretical details and discussion can be found in Chapter 17 of CiMC, which also present...

A new option in PRIMER 7 recognises that computation time can become an issue for particular rela...

For an example, take the first of the 277 groundfish samples, the 0.25$^\circ$ rectangle S1. High...

It is impractical to produce detailed histograms, such as those above, for each of the 277 sample...

Another option on the TAXDTEST dialogs is that the simulation of random draws from the master lis...

The final option is to consider $\Delta^{\scriptscriptstyle +}$ and $\Lambda^{\scriptscriptstyle ...

PRIMER plots a range of what might be termed diversity curves, under the Plots>Geometric Class Pl...

These are essentially multiple frequency polygons, plotted on a single graph, for each sample in ...

Dominance plot is the convenient generic name for a family of curves also known as ranked species...

Macrobenthos in soft sediments of a site in Loch Linnhe, Scotland were monitored by Pearson TH 19...

ABC curves plot abundance and biomass k-dominance lines on the same plot, and are interpreted in ...

An attempt to run the routine with the matrices reversed, or to run it on a data type Environment...

Testing for differences in ABC curves for group structures of sites, times or treatments etc, whe...

The Tikus Island, Indonesia, data on % area cover of coral communities on 10 transects in the yea...

The final set of data in this section is of a benthic study by Gage JD & Coghill GG 1977, in Coul...

PRIMER therefore includes a number of S extrapolators – attempts to predict the true total number...

For this final section, we consider only cases in which the samples form a 1-way layout, i.e. the...

Ordination means plots are therefore a vital tool for interpretation but, in relation to their un...

The construction of approximate regions is approached through bootstrap averages. We only have on...

These averages can then be used to generate a bootstrap region for each of the g groups – at its ...

The Analyse>Bootstrap Averages routine allows both metric and non-metric options for the MDS ordi...

Though hopefully the above gives the motivation and an idea of the way the region estimates are c...

These b bootstrap averages for each of the g groups are then displayed in a low-d mMDS space and ...

The diet study for 7 species of W Australian fish, with a variable number of dietary samples from...

None of the above is necessary in order to create the means plot with regions based on bootstrap ...

The above study was not an example given in Chapter 18 of CiMC and was therefore discussed in det...

A final example of bootstrap regions which do strongly overlap, and for which the hypothesis test...