The digital temperature sensor (DS18B20) can be calibrated by adjusting the difference directly to the .ino code. Otherwise, if the compensation and the slope required a calibration, it can be done by changing the value on line #453, DallasTemperature.cpp in the \libraries\DallasTemperature folder.
For pH and DO probes, you can calibrate the probes with accompanying solutions. You have to use the sample code by Atlas Scientific and follow the instruction by this file. The pH probe came with 3 standard solutions: 4.0, 7.00, 10.0 to update the incline/slope of the calibration curve. Zero oxygen solution contains Sodium Sulfite (NaSO3) is the must-have solution to set the origin for the DO curve.
Please follow pages 26 and 50 for the pH probe for calibration and temperature compensation, and also pages 7-8 and 50 for DO probe. First, please re-upload the generic code provided by Atlas, open the Serial Monitor and key in a proper command.