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16.2 Example: Fal biota (one-way case)

Let's look at an example of a means plot for a one-way case using biotic data ($p$ = 131 taxa) from the Fal estuary. The data consist of counts of organisms living in benthic sediments obtained from $n$ = 5-7 sites in each of 5 creeks running into the Fal estuary, Cornwall, UK ( Somerfield et al. (1994a) , Somerfield et al. (1994b) ). These 5 creeks had differing levels of heavy metals in their sediments, due to historical tin and copper mining in their respective valleys. Interest lies in identifying whether the 5 creeks also differed in their diversity of benthic infauna. The full set of biotic data (macrofauna and also the meiofauna - comprised of nematodes and copepods) are contained in the file 'Fal_all_biotic_taxa.pri', found in the 'Fal_benthic_fauna' folder in 'Examples_P8'.

  1. Start by calculating some univariate diversity measures for each sample. Open the 'Fal_all_biotic_taxa.pri' file in PRIMER 8, then click Analyse > DIVERSE..., take all the defaults and click 'OK'.

02._Diverse_Fal_estuary.png

This will produce a sheet, called 'Data1' with values for various diversity indices for each of the sampling units.

03._Diversity_data_Fal.png

  1. Calculate a means plot that shows the means $\pm$ 1 standard error for the 5 creeks for each of these diversity measures. From the 'Data1' sheet, click Plots > Means Plot....

04._Diverse_Fal_Means_plot_menu.png

Leave all of the defaults and click 'OK'.

05._Diverse_Fal_Means_plot_dialog_b.png

The result will be a 'Multi plot' item, that includes 6 individual plots - one for each of the 6 diversity measure variables in the original 'Data1' sheet.

06._Diverse_Fal_Multi-plot.png

  1. View an individual plot by clicking on it. For example, you can click on the plot in the top left-hand corner of 'MultiPlot1' to see a means plot for the variable of species richness ('S', the number of different taxa). Alternatively, you can click on 'Graph1' in the Explorer tree.

07._Diverse_Fal_Species_richness.png

  1. To change the colours, symbols or line types, you can click Graph > Special..., which shows you a dialog with a plethora of options to modify all of these details of your means plot. For example, you can click the 'Key...' button next to the factor to change the colours/symbols, or choose to $\bullet$ Join means, including the option to choose a custom colour for the joining line, like this:

08._Diverse_Fal_S_join_means.png

This will yield the following modified plot:

09._Diverse_Fal_S_plot_with_line.png

  1. You can also choose to show the means as bars instead. Click Graph > Special..., then (Display Means as > $\bullet$ Bars) and (Error bars > Appearance > $\bullet$ Custom).

10a._Diverse_Fal_S_bars+custom_dialog.png

This yields the following plot:

10._Diverse_Fal_S_bars.png

Next, we shall consider some multi-factor plots.

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