We learned how to use different tools in R and QGIS for working with vector data and modifying or creating new data by doing different operations such as merging, clipping, intersecting, creating buffers, and more. We also learned how to use different spatial queries in QGIS and R. In doing so, we have seen how important it is for two different layers to have the same projection system. We haven't touched upon many other tasks, such as using the rgeos package for calculating distance between geometries using gDistance() or using gUnaryUnion() for taking the union of two shapefiles. With the tools you are equipped with now, you can easily understand other functionalities not covered here and should now be able to perform most of these data manipulation tasks. In doing so, you might already have developed some preferences between QGIS and R for performing each operation...
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