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I have two vector layers, one contains actual values (in this case % cover of native species), the other contains target vales of the same attribute. the polygons are not always of the same geometry.

I want to produce a resulting layer of polygons where the actual values are below the target values.

i.e. some sort of polygon spatial overlap where 'layer1', 'actual cover' < 'layer2', 'target cover'.

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Calculate the intersection (i.e. overlap) between the two layers (Vector > Geoprogressing Tools > Intersect...). Use the drop down menus to select the two layers, and specify a location to save the output shapefile.

The resulting layer will have attributes from both input layers (e.g. "actual cover" and "target cover"). You can then filter this layer (right click the layer in the layers panel, then Filter...) where "actual" > "target".

Equally, you could use the field calculator in the attribute table to create a new field, with a difference between "actual" and "target". You could then use this field to symbolise the output layer, showing areas above their target in a different colour to areas below.

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