How to clip a spatial polygon to a large matrix (that is plotted as a large trellis,

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I would first like to issue a disclaimer that I am a novice at GIS, and I have only just begun learning R. So if I use the wrong terminology for something or my question is confusing, please help clear that up for me.

So for my work, we are planning on mapping tons and tons of weather data all across the globe. For practice, the guy providing our data provided us with some "example" data to play with. My boss would like for me to create my maps in R. These maps are intended to be return period maps (https://en.wikipedia.org/wiki/Return_period). The data is supposed to be in netcdf format.

I've managed to find several tutorials that have helped me to actually map the netcdf data. Here's the code:

#set working directorysetwd("D:\\stuff")#add librarieslibrary(maptools)library(ncdf4)library(RColorBrewer)library(lattice)library(rasterVis)#add madagascar shapefileproj
 
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