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I am attempting to calculate mean NDVI at different time points with 100m and 500m radii of certain co-ordinates. Thus far I have used 'Raster Calculator' to calculate the NDVIs and have used 'Vector -> Geoprocessing Tools -> Fixed distance buffer' to calculate the buffers. My screen looks like:

QGIS screenshot

How do I calculate the mean NDVI for each layer in each buffer?

I am hoping to end up with a 9 column csv table I can then import into R with the column headings:

id; lat; long; ndvi_100m_summer1990; ndvi_500m_summer1990; ndvi_100m_spring1990; ndvi_500m_spring1990; ndvi_100m_summer1991; ndvi_500m_summer1991

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You can use the QGIS Zonal Statistics Plugin to summarize raster data within vector features. The plugin writes the statistics to the vector layer. To export the shapefile attributes to csv format, do the following in QGIS:

right click layer > Save As... > Comma Separated Value [CSV]

From the plugin documentation:

With the icon_zonal_statistics Zonal statistics plugin, you can analyze the results of a thematic classification. It allows you to calculate several values of the pixels of a raster layer with the help of a polygonal vector layer (see figure_zonal_statistics). You can calculate the sum, the mean value and the total count of the pixels that are within a polygon. The plugin generates output columns in the vector layer with a user-defined prefix.

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For anyone still looking for an answer:

1- You can use Zonal Statistics plugin in qgis. It is old and no longer supported in the recent qgis versions, so download it manually and install it as zip file. It will give an error though, but if you search in processing toolbox, you will find it installed and working.

2- Zone Statistics as table in ArcGIS. -

Google both methods and you will find support

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