A “Rogue’s Yarn” is a colored yarn of jute laid in a strand of rope to identify what materials are used in the rope’s manufacture.
Naval-grade manila (made from the abaca plant which is grown extensively in the Philipines and was shipped world-wide out of the Port of Manila) and is marked with one red yarn in each of two strands. Commercially made manila over 2 inches in circumference is marked as follows: Grade I, ‘Special’, one black rogue’s yarn in three strands; Grade II, ‘Standard’, one black rogue’s yarn in two strands; Grade III, ‘Merchant’, one black rogue’s yarn in one strand.
Commercial sisal (made from the leaves of the Agave sisalana plant) has a red rogue’s yarn while naval sisal has yellow in each of two strands.
Commercial hemp (we all know what plant that comes from) has no rogue’s yarn while naval hemp has red in all three strands.
Coir rope (made from coconut husks) has one strand marked with a yellow thread.
Originally the yarns were used only in naval rope and the color indicated the ropeyard that made it and it was introduced to stop theft by making it easily recognizable, naval rope being considered superior to all others. Because of that there was a lot of temptation to smuggle the line out of the rope yards and sell it to merchant vessels.
Today different colors are also used in yacht running rigging to identify different sheets, halyards, etc.
One More Good Adventure 
An interesting bit of lore I didn’t know – but I’m left wondering how that coir rope holds up. I’d think it would fray a good bit. But maybe it’s a stout, husk-y line 😉
The advantage of coir rope doesn’t lie in it’s strength but in the fact that it floats. In the days before chemists turned petroleum products into something other than a liquid with polypropylene it was the only rope that did. In emergencies at sea when heavy towing hawsers of manila, which will sink, could be to transferred to a ship in distress using coir rope that would be floated down wind/current to the disabled vessel and then the crew on the disabled ship would pull the hawser to themselves.
Ah! Perfectly reasonable.
Isn’t it funny the things you never stop to question – like, what did they do before that yellow and blue plastic line that makes such a mess after about six months in the sun ? 😉