# Check on aggregation files

Use the open aggregation file, <ins>Groundfish taxonomy</ins>, to show the smaller set of **Tools** items (**Tree**, **Check**, **Duplicate**) available when the active window is of *variable information*. **Tools>Duplicate** has been seen previously for worksheets and plots (in Sections [3](https://learninghub.primer-e.com/books/primer-v7-user-manual-tutorial/chapter/3-highlighting-and-selection-select) and [8](https://learninghub.primer-e.com/books/primer-v7-user-manual-tutorial/chapter/8-multi-dimensional-scaling-non-metric-nmds-metric-mmds-combined-mds)). Here it has the same effect, taking a copy of the <ins>Groundfish taxonomy</ins> window, called <ins>Vinf1</ins>, to the head of a fresh branch in the Explorer tree. Insert the following errors in <ins>Vinf1</ins> to demonstrate the **Tools>Check** option: 

   a) overwrite <ins>Raja clavata</ins> (row 4) in the Species column with <ins>Raja radiata</ins> (by taking **Edit>Labels>Variables** and double clicking in the <ins>Raja clavata</ins> label and typing in the incorrect name); 
   
   b) whilst in the Labels dialog change <ins>Squalus acanthias</ins> (row 10) to <ins>Squaliformes</ins> (note that upper or lower case does not  make a difference when matching names), and **OK** to exit back to the <ins>Vinf1</ins> sheet, then delete <ins>Squalus</ins> and <ins>Squalidae</ins> from the genus and family name for that taxon;
   
c) change <ins>Rajidae</ins> to <ins>Torpedinidae</ins> as the family name for <ins>Raja naevus</ins> (row 2). 

(Note that the row/column numbers of an entry can be found by clicking on it – the status bar at the bottom right displays the current cursor position). Then **Tools>Check** finds three types or error:

1) *Duplicate Species* in row 4 (the repeat of <ins>Raja radiata</ins>) – labels (samples or variables) should always be unique in a PRIMER worksheet, otherwise matching conflicts can easily result; 

2) *Missing Values* (blanks) in row 10. This represents a common situation where only coarser-scale identifications can be made for some taxa. Nonetheless, aggregation sheets need to be complete, in order to avoid incorrect matching. E.g. another species from a completely different order but with a blank family (and genus) entry would be pooled with the *Squaliformes* abundance when the matrix is aggregated to genus or family level, because both entries have the same (blank) family name. Similar problems would occur with taxonomic distinctness calculations (Section [15](https://learninghub.primer-e.com/books/primer-v7-user-manual-tutorial/chapter/15-biodiversity-measures-and-tests-diverse-taxdtest)). So blank entries should be filled with the names from the immediate right or left, depending on the context (often it make sense to fill from right to left). Here put <ins>Squaliformes</ins> in the two blanks – the routine does not object to the same name being used in different taxonomic levels. 

3) *Inconsistent taxa* in rows 2, 8 and 9. In fact there is only one mistake, the family identification of *Raja naevus*, picked up in the correct row (2) because *Raja* has been established by row 1 to be a genus name in the Rajidae family, thus cannot also be a genus name in the family *Torpedinidae*. Quite often, however, an error is not discovered until a conflict occurs much later in the sheet, on a row which may be correct. This is seen in the *inconsistent* identification of the two *Torpedo* genera though neither are wrong. PRIMER 7 has greatly improved its diagnostics here, by listing not just the row and column on which the conflict occurred (in the first 5 columns of the output: row, species name, column, entry in that column, entry in the following column) but also what the conflict with an earlier row was (in the final three columns of the output: the earlier row, its species name, the entry in the earlier row causing the current conflict). So, *Torpedo marmorata* (row 8) in family *Torpedinidae* cannot be in order *Torpediniformes* because in a previous row (it identifies row 2) the family *Torpedinidae* were given as in order *Rajiformes*. With this level of diagnostics, errors in aggregation files (they commonly occur!) should be more easily fixed.

[![ScreenshotPage206a.png](https://learninghub.primer-e.com/uploads/images/gallery/2024-08/scaled-1680-/screenshotpage206a.png)](https://learninghub.primer-e.com/uploads/images/gallery/2024-08/screenshotpage206a.png)