Capt. and Mrs. Allen have at least one son, Jowles:
January 1, 1663/64: "By and by comes Captain Allen and his son Jowles and his wife, who continues pretty still. They would have had me set my hand to a certificate for his loyalty, and I know not what his ability for any employment. But I did not think it fit, but did give them a pleasing denial, and after sitting with me an hour they went away."
From this entry it seems likely the Allens are from a Puritan background, and Pepys probably did not sign for political reasons.
Chart showing the number of references in each month of the diary’s entries.