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I am working with a NDVI image and a an interpolated yield map in ArcGIS 10.3.1. They are both projected in the same coordinate system and the cell sizes are equal. I interpolated the yield harvester points using IDW interpolation method. The final product I want to achieve is the correlation (R-squared). I am new to GIS and have been stuck on this for a while trying to use various spatial analyst tools in ArcToolbox but have been unsuccessful. I have clipped the interpolated yield map to another polygon that I have created, however it does not overlay the NDVI completely.

Is it possible to extract the overlaying pixels values and import this into R software where I can perform further stats?

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It is likely statistical overkill to sample every single cell in your rasters. For the same statistical result, you could create a random point layer with the Create Random Points tool and choose the number of points with which you would like to represent your data and choose the extent of your rasters. Next, you can use the Extract Multi Values to Points tool to populate the points with the values from both of your rasters. You will now have values from both of your rasters assigned to your random points and can export this table to work with it in R if you desire.

Using random points instead of sampling the entire dataset will likely yield similar statistical results and may better deal with spatial dependence issues with your interpolated raster. However, if you do want to sample the entire raster datasets, you could use the Raster to Point tool to get a point layer that will sample from all the cells.

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