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For example, if the Raster has integer values ranging from -1 to 3 and the value that I am only interested in is 3, I then want to assign values -1 to 2 to 0 and then have the 3 value set to the value of 1. (Similar idea to IDRISI Raster REASSIGN tool.)

I am ultimately trying to find the frequency of a certain cell value in a time series of Rasters of the same extent. To find the frequency of 'cloud' pixels in a certain area over the course of 15 years.

For example, using Raster Calculator to add up the above output Rasters into a single Raster to find the frequency of that cell value since it would have a value of 1 in each Raster.

Additionally, if there is some kind of tool in QGIS that would do a time series frequency comparison on a per pixel basis like the above described that would be good, but so far I have not found such a tool in QGIS.

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    You're asking too many questions here :) The forum is set up so that you can ask single things (e.g., reassign or sum or time series) so there's a useful answer for other people as time goes on. – Paulo Raposo Jun 8 '16 at 15:05
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There's the QGIS Raster Calculator: https://docs.qgis.org/2.2/en/docs/user_manual/working_with_raster/raster_calculator.html

Also, you can use r.reclass from GRASS within QGIS: https://grass.osgeo.org/grass64/manuals/r.reclass.html

Or, Reclassify Grid Values, from SAGA, available, again, from within QGIS: http://www.saga-gis.org/saga_module_doc/2.1.4/grid_tools_15.html

A note: GRASS and SAGA are available by default in QGIS on Windows if one used the typical full installer. Else, on something like Linux, SAGA is a separate install, but then QGIS can be set up to use SAGA from within itself.

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