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Look at this website .Picture of deck ,tar between the planking/wood(au natural)
It is a fund to save that ship plus also Gordon of Khartoums Steamer Bordein.(When they begin physically that project maybe i help them a little).
Quote from L.G. Carr Laughton, Old Figure-Heads and Sterns, [London 1925] Reprint Mineola 2001, p.275:
"Red,..., was from very early the regulation colour for inboard works, but during the French Revolutionary war it began to give way to yellow; and indeed other colours seem to have been used occasionally, for in the Thalia frigate in 1797 they painted the quarter-deck and forecastle blue. It appears that in 1801, red being still the regulation colour both for the sides inboard and for gun-carriages, the crews of ships were in the habit of repainting the gun-carriages yellow when they received them from the officers of the Ordnance; and this implies that the inboard works were also yellow, of which there is other evidence. In August 1807, the Navy Board instructed the dockyard officers to paint THE DECKS (BY WHICH IS MEANT THE SIDES AND THE DECK FITTINGS, NOT THE FLAT OF THE DECKS) [my emphasis] yellow when requested to do so by the captains. Light yellow was usually chosen. It is likely that both at the Nile and at Trafalgar most ships were yellow inboard, though probably a steadily decreasing number still kept red."
Well, it seems important to me that in the Royal Navy the term "deck" referred to the inboard sides and fittings only, NOT to the flat or planks of the deck. There seems to be no regulations as to the colour of the planks which, in my opinion, were left in their natural wood colour. And I'm quite sure that in the Spanish navy too, the reference to "decks" must also be understood to be a reference to the inboard sides, railings, etc., not the planks. Anyway, for practical reasons alone, it would have been absolutely useless and nonsensical to paint the flat of the deck as the colour would have disappeared within a day under the feet of the working crews, wheels of gun-carriages, etc.
I think the other posters are right in that the actual deck as we would understand it was left natural. Any paint job would not have lasted long in the sea air and storms, not to mention all that scrubbing by the crew.
On a visit to the Victory many years ago I was told the cockpit where the surgeon worked had a red deck to disguise the blood, which makes sense, but I think other planking was as nature intended.