QRE1113 breakout with IR LED control
With that breakout board, you can do fairly slowly on and off by connecting the vcc pin of the breakout to an arduino pin. However the problem is with the capacitor in the schematic where if the vcc pulse is quick enough, voltage could actually seep through the capacitor to the vcc at its off state and possibly trigger the output. So basically you would want to remove that capacitor so you can use it for PWM. You could cut the connection to the capacitor:



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