4. Getting data in to PRIMER

• Opening example data
• Importing data from Excel
• Post-import data checks
• Save your data & workspace

Opening example data

Data from the Fal estuary

Example datasets in PRIMER can be obtained via the Help menu item. In trial mode, click Help > Get Examples Trial..., and you can download the following four files of example data (held in a folder called 'Examples Trial') to a location of your choice:

• Fal environment.pri (measured values for 12 environmental variables x 27 sites)
• Fal environment.xls (same as above, but in Excel format)
• Fal nematode abundance.pri (abundances of 62 nematode species x 27 sites)
• Fal nematode taxonomy.agg (taxonomic hierarchy for the 62 nematode species)

These data come from a study of benthic infaunal communities in soft sediments from 27 sites over five creeks of the Fal estuary, SW England ( Somerfield et al. (1994a) , Somerfield et al. (1994b) ). Sediments at these sites were contaminated to varying degrees by heavy metals, from historic mining activities. Both faunal counts (nematodes) and environmental measures were obtained from the same set of sites. (Note: the extension *.pri indicates a file containing a data matrix that has been saved in PRIMER 7's own internal (binary) format, unreadable by other software or earlier versions of PRIMER. Similarly, the *.agg extension indicates an aggregation-type file for PRIMER.)

Open the Fal data in PRIMER

To open the species-by-samples data matrix, launch PRIMER, then click File > Open from the main menu, navigate to the 'Examples trial' directory in the location you have specified, and select 'Fal nematode abundance.pri'. Click Open to display the species matrix.

Alternatively, because this is a PRIMER file type (*.pri), you can instead use Windows Explorer to navigate to your specified folder and just double-click on the file name. This will launch a PRIMER session, with the data matrix open in the PRIMER desktop.

Properties of the data

Click on Edit > Properties and you will see that PRIMER-format *.pri sheets carry other information about the data matrix as well, including:

• Title,
• Data type,
• Array size (number of columns and rows),
• Orientation (whether samples are found in columns or rows),
• a Description, and
• a History of what pre-treatments (such as a transformation) have been applied to them.

Factors associated with the data

Click on Edit > Factors, and you can see that a subsidiary sheet of three factors is also linked to this worksheet: 'Creek', a single-letter abbreviation for the creeks, the full 'Creek name' and a numeric 'Position' factor identifying the location of each sampling site down each creek.

Note that additional factors could be added here by clicking Add, and also combinations of levels of existing factors can be created by clicking on Combine.

Importing data from Excel

Step 1. Ensure your data are in a format suitable for import into PRIMER

Suppose we have a dataset in Excel that is already in a suitable format for import into PRIMER. The environmental data from the Fal estuary provides an example of this. These data are found in the file 'Fal environment.xls' and consist of values for each of 12 environmental variables measured from sediments collected from 27 sites across 5 tidal creeks in the Fal Estuary (available from within PRIMER by clicking Help > Get Examples Trial..., as seen in the last section).

Important things to note about this file:

• There is a title for the dataset ('Fal estuary environmental variables') in the very first (upper left-hand) cell (A1). This title is optional, but handy as a naming convention.
• The cell immediately under the title (cell A2) is empty.
• There are column labels ('R1', 'R2', ...) in row 2. These are unique labels for the sampling units (Sites in this case).
• There are row labels ('%silt/clay', '% organic carbon', ...) in column A. These are unique names associated with each variable.
• The entries for every cell in the matrix of data itself (beginning with cell B3) all contain numerical values only. There are no non-numeric characters. This means that you may not use 'NaN' or 'NAN' to denote missing values. If data are missing from a cell, then it should be left blank. In addition, symbols such as '<' or '>' (for 'less than' or 'greater than') are similarly not permitted or accepted as valid data values within the data matrix.
• In this example, the variables are rows and the sampling units (sites) are columns. It is perfectly ok to have this formatted the other way around, with variables as columns and sampling units as rows. You will specify the orientation of your data matrix explicitly when you import your Excel file into PRIMER.

This format must be adhered to precisely, with no extra blank rows or columns, or extra headers, otherwise PRIMER will not be able to open it successfully.

Other things to note:

• Factors: You can label the sampling units as belonging to a level of one (or more) factors by skipping a line at the bottom of the matrix and placing this 'factor information' there. In the above image you can see that there are three factors: 'Creek' (row 16), 'Creek name' (row 17) and 'Position' (row 18).
• Indicators: You can similarly label variables as belonging to particular groups in the same manner; this is done along the other margin of the data matrix (e.g., after skipping a column, for this example). This might be useful for doing analyses on subsets of variables belonging to different types, such as physical vs chemical variables. In a case where variables are species, one might want to consider subsets of variables corresponding to families, functional groups, etc.

Inclusion of one (or more) factors (to specify groups of samples) or indicators (to specify groups of variables) is optional. If you have more than one factor, then these are given one after the next (in adjacent rows); do not put blank rows between multiple factors. The initial single blank row (or column) is there simply to demarcate the difference between the data matrix itself and additional information about the data matrix upon import.

Step 2. Open PRIMER and import the data from Excel

Once your Excel file is ready, open up PRIMER and choose File > Open. Look at the bottom of the dialog box and you will see next to the words 'File name:' that the only files that PRIMER can see is: 'All PRIMER Files...'. Click on 'All PRIMER Files...' and change this to 'Excel Files...'. Once you have done this, you should be able to browse and see the Excel data file that you want.

1. Click on the name of your Excel file in the browser (here it is 'Fal environment.xls'), then click Open.

2. This will initiate PRIMER's Excel File data-import Wizard. Choose the name of the specific sheet within your Excel file that contains your data and the type of data you are importing. Here, we have (Excel worksheet: Sheet1) & (Data type $\bullet$Sample data), then click Next >.

3. Choose the correct orientation, type of data and the meaning of blank entries (if any). For this example, we have (Orientation $\bullet$Samples are columns) & (Data type $\bullet$Environmental) & (Blank = $\bullet$Missing value), then click Finish.

4. You will now see your data file has been imported and is nicely displayed in the PRIMER workspace. It appears in its own window, and its name also appears in the 'Explorer tree'-type window shown on the left-hand side of the PRIMER desktop.

Step 3. Post-import data checks

After import, make sure you have specified the orientation correctly by examining the labels on the columns and rows of the data frame. In the above example, you can see that the columns are 'Samples' (a periwinkle-coloured strip across the top) and rows are 'Variables' (an olive green-coloured strip along the left margin). If you happen to get this the wrong way around (e.g., if your variables are actually columns instead of rows), this can easily be changed (swapped around) by choosing Edit > Properties and toggling the radio button for 'Samples as' to either '$\bullet$Columns' or '$\bullet$Rows', whichever is appropriate.

To be sure that the import has been fully successful, including all data points, factors and indicators that may have been included in your original Excel file, you can see additional information attached to your data matrix by clicking on your imported dataset in PRIMER, and doing the following:

• Look at the data properties, size of the matrix, etc.: Click Edit > Properties. Note that you can add a useful 'Description' of your data into this dialog if you like. (For the Fal environmental dataset, we can see there are 12 variables and 27 sites, etc.).

• Look at the Factors (if any): Click Edit > Factors. (For the Fal environmental dataset, you will see the same three factors of 'Creek', 'Creek name' and 'Position' that we saw in the Excel file).

• Look at the Indicators (if any): Click Edit > Indicators. (For the Fal environmental dataset, there are no indicators).

Post-import data checks

Check the orientation

After import, make sure you have specified the orientation correctly by examining the labels on the columns and rows of the data frame. For example, after importing the Fal environmental data from Excel (see the previous page), you can see that the columns are 'Samples' (a periwinkle-coloured strip across the top) and rows are 'Variables' (an olive green-coloured strip along the left margin).

If you happen to get this the wrong way around (e.g., if your variables are actually columns instead of rows), this can easily be changed (swapped around) by choosing Edit > Properties and toggling the radio button for 'Samples as' to either '$\bullet$Columns' or '$\bullet$Rows', whichever is appropriate.

Check the properties, factors and indicators

To be sure that the import has been fully successful, including all data points, factors and indicators that may have been included in your original Excel file, you can see additional information attached to your data matrix by clicking on your imported dataset in PRIMER, and doing the following:

• Look at the data properties, size of the matrix, etc.: Click Edit > Properties.... Note that you can add a useful 'Description' of your data into this dialog if you like. (For the Fal environmental dataset, we can see there are 12 variables and 27 sites, etc.).

• Look at the Factors (if any): Click Edit > Factors.... (For the Fal environmental dataset, you will see the same three factors of 'Creek', 'Creek name' and 'Position' that we saw in the Excel file).

• Look at the Indicators (if any): Click Edit > Indicators.... (For the Fal environmental dataset, there were no indicators, but you could add some here, if you wish).

Run PRIMER's data-checking tool

As an additional option, you can run PRIMER's internal data-checking tool to find and identify certain other features that might be present in your data, including:

• Missing values,
• Negative values,
• Duplicate samples,
• Duplicate variables,
• All-zero samples,
• All-zero variables, and/or
• Estimated values

To run this routine, start by clicking on your datasheet, then click on Tools > Check...:

For the Fal environmental data, none of these features occurred (see below), and we are ready to proceed with subsequent analyses.

Save your data & workspace

Save your data in PRIMER (*.pri) format

To save a data sheet in PRIMER (*.pri) format, click on the data sheet inside the PRIMER workspace you want to save and click File > Save Data As....

Note the default file-type for saving a data file is 'PRIMER Data Files (*.pri)', as shown in the box labeled 'Save as type:' in the 'Save' dialog. You can change this (by clicking in the 'Save as type:' box) in order to save the data in some other format of choice, such as *.txt, *.csv *.xls, *.xlsx, or in a PRIMER format compatible with older versions of the PRIMER software.

Save your entire PRIMER workspace (*.pwk)

Generally, you will want to save your data plus all of the work you have done in PRIMER to analyse that dataset. To save the entire PRIMER workspace, click File > Save Workspace As...

Type the file name you wish (e.g., Fal environment.pwk), and click Save. This will save the entire PRIMER workspace (not just the datasheet), including all elements you may have created during the PRIMER session (e.g., data, graphics, analyses, etc.), all of which you are able to navigate and see listed (in hierarchical fashion) within the Explorer tree window on the left-hand side of the open PRIMER workspace.

A PRIMER workspace file is identifiable by using the file extension *.pwk in the file name. Double-clicking on a file with this extension will open up that entire PRIMER workspace within the PRIMER software.