For simulation purposes, a quick approach would be to abstract the PHY layer as providing a 'Data rate' for transmissions, coupled with an SNR/BER model at the receiver to decide on packet error. 

Let us say we wish to modify the 802.15.4 PHY with OFDM PHY (say for implementing 802.15.4g) then the steps could be -

1. Understand and work through the section on How to write your own code in the user manual. Co-relate the code flow with the event trace
2. Understand the working of PHY_OUT event in the transmitter and modify the data rate calculation
3. Understand the working of PHY_IN event in the receiver and modify the SNR/BER calculations
4. 802.11_OFDMPhy.c file has the OFDM PHY codes

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