The User button is fitted to the case, with this button you can enable/disable the LCD backlight.
With the MENU (Calibrate mode) button you can step through the menu: you can enable/disable GPS, and calibrate the pH-sensor with pH-buffers 4,7 and 10.
The SET (Calibrate) button must be used to activate a specific menu option.
you need to rename the lorawan-keys_example.h file into lorawan-keys.h and change the content, see LMIC documentation.
pH meter
The pH meter must be calibrated on a regular basis, there is no temperature compensation build in, but maybe someone can add that to the software, would be nice.
Assembly-tips
Desolder the T-Beam lIPO-holder, we don't use it: the pH-sensor drains the 18650 battery too fast.