The position at the end of Pepys' career is well summarised in the table overleaf drawn up by him—one of the many instances of his fondness for methodical statements.

The last entry is of especial interest. When the stricter regulation enforced had prevented many officers from wearing flags who would, in similar circumstances, undoubtedly have had that privilege in the first half of the century, much importance was attached to the right to exhibit a naked flagstaff. One striking instance of this occurs in 1687, when Sir Roger Strickland was appointed Vice-Admiral of the fleet under the Duke of Grafton, ordered to transport the Queen of Portugal (the king's sister) to Lisbon. Strickland, not unnaturally, wanted to wear a flag as Vice-Admiral. Not many years earlier he would have done this as a matter of course; now he had to obtain the king's permission, which was granted. But he had omitted Pepys from his reckoning. The king's sign manual warrant was accompanied by a long letter from Pepys dissuading him from exercising the right:

a thing so extraordinary, so irregular, and so unjustified by any practice past, and unlikely to be ever imitated in time to come, as this which you have thus contended for, of having two of the Top Flags of England exposed to sea, in view of the two greatest Rivalls of England for Sea Dominion and Glory (I mean the Dutch and French) with no better provision for supporting the Honour thereof, then Six Ships, and two of them such as carry not above 190 men and 54 guns between them, and this too obtained through meer force of Importunity,

and hinting that the king will take it well if he does not hoist the flag, though he may bear the flagstaff. Like a wise man, he took Mr Secretary's hint, and resigned the honour. The king thereupon authorised Strickland to bear the naked staff only, and informed that officer that he was pleased to find that Pepys' advice had been taken, for it had been offered with his privity.

A DESIGNATION OF THE SEVERAL FLAGS AND COLOURS
USED IN THE ROYAL NAVY OF ENGLAND FOR DISTINGUISHING
DEGREES OF COMMAND THEREIN (Table Part 1)
The several Degrees of Command in use in the Navy of EnglandThe various Flags and Colours used in the Navy of England denoting command
StandardAnchor of the Ld AdmiralUnion or Jack FlagRed FlagWhite Flag
Ld High Adml of EnglandAt the Maintop the King being aboard or not at all in the FleetAt the Maintop the King being in the Fleet aboard another ship———
Vice Adml of England——At the Foretop wh a distinction pendant under it——
Rear Adml of England——At the Mizentop wh a Distinction Pendant under it——
Admiral of a Fleet of 3 Squadrons with nine flags——At the Maintop——
Admiral of the White Squadron————At the Maintop
Admiral of the Blue Squadron—————
{
Vice {
Admiral {
of {
the {		Red———At the Foretop—
White
or		————At the Foretop
Blue—————
{
Rear {
Admiral {
of {
the {		Red———At the Mizentop—
White
or		————At the Mizentop
Blue—————
Admiral of the Fleet wh 3 flags only——At the Maintop——
Vice Adml of the same——At the Foretop——
Rear Adml of the same——At the Mizentop——
Adml or Commander in Chief of a squadron with one flag——At the Maintop——
Private Captain—————

A DESIGNATION OF THE SEVERAL FLAGS AND COLOURS
USED IN THE ROYAL NAVY OF ENGLAND FOR DISTINGUISHING
DEGREES OF COMMAND THEREIN (Table Part 2)
[NOTE: Column 1 has been duplicated for clarity]
The several Degrees of Command in use in the Navy of EnglandThe various Flags and Colours used in the Navy of England denoting command
Blue FlagJackEnsigne OrdinaryPendant OrdinaryPendant of DistinctionFlag Staff Naked
Ld High Adml of England—At the BowspritAt the Poop with an anchor in it——At the Fore and Mizen tops
Vice Adml of England—DoAt the poop—At the Foretop under the Union FlagAt the Main and Mizen tops
Rear Adml of England—DoDo—At the Mizentop under the Union FlagAt the Main and Fore tops
Admiral of a Fleet of 3 Squadrons with nine flags—DoDo——At the Fore and Mizen tops
Admiral of the White Squadron—DoDo White——At the Fore and Mizen tops
Admiral of the Blue SquadronAt the MaintopDoDo Blue——At the Fore and Mizen tops
{
Vice {
Admiral {
of {
the {		Red—DoDo Red——}
} At the
} Main and
} Mizen tops
}
White
or		—DoDo White——
BlueAt the ForetopDoDo Blue——
{
Rear {
Admiral {
of {
the {		Red—DoDo Red——}
} At the
} Main and
} Fore tops
}
White
or		—DoDo White——
BlueAt the MizentopDoDo Blue——
Admiral of the Fleet wh 3 flags only—DoDo Ordinary——At the Fore and Mizen tops
Vice Adml of the same—DoDo——At the Main and Mizen tops
Rear Adml of the same—DoDo——At the Main and Fore tops
Adml or Commander in Chief of a squadron with one flag—DoDo——At the Mizen and Fore tops
Private Captain—DoDo White or Blue, when of either of those squadronsAt the Maintop when alone or in Compy with a Senior Captn, and in the Colour to be answerable to the SquadronAt the Maintop when eldest captain in company with Private shipsAt the Maintop or Mizentop according to the highest flag he may at any time before have had the Honour of wearing

Although Pepys' influence ceased at the Revolution, and his proposed "establishment" of flags was never ratified, the work of regulation and restriction went on through the reigns of William and Mary and Anne, culminating in the abolition of the Lord Admiral's standard and the confining of the Union flag at the masthead to the "Admiral of the Fleet." Nevertheless, several curious anomalies remained until the opening years of the eighteenth century. Officers appointed to the chief command of squadrons sent to the Mediterranean or West Indies were, whatever their rank, usually authorised to wear the Union flag at the main so soon as they had left the Channel. Thus in 1690 Captain Lawrence Wright was authorised to wear the Union flag at the main when sent to the West Indies in command of a small squadron.