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As you wife was granted an EEA family permit, in order to join you in the UK and then applied for a EEA residence card means that your wife will only be legible to apply for naturalisation after she has got PR for 5 years and then apply a year after that. The Home Office when assessing her naturalisation application will see that she came to the UK and remained under the EEA law rather than the Immigration rules.
I hope this clarifies this as it seems that you were also considering the same.
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As your wife joined you in the UK under EEA Regulations, the UK domestic Immigration Rules will not apply and therefore as the previous expert has correctly pointed out, your wife will only be eligible for PR after 5 years of continuous residence in the UK.