How do the conditions of anchorage reflect the conditions inside the ship?

The anchorage smells of rot, and Dr. Livesey notes there's a fever present. The crew is much the same, though their "rot" is the thought of treasure and mutiny. A double dose of sickness.

There was not a breath of air moving, nor a sound but that of the
surf booming half a mile away along the beaches and against the rocks
outside. A peculiar stagnant smell hung over the anchorage--a smell of
sodden leaves and rotting tree trunks. I observed the doctor sniffing
and sniffing, like someone tasting a bad egg.

"I don't know about treasure," he said, "but I'll stake my wig there's
fever here."

If the conduct of the men had been alarming in the boat, it became truly
threatening when they had come aboard. They lay about the deck growling
together in talk. The slightest order was received with a black look and
grudgingly and carelessly obeyed. Even the honest hands must have caught
the infection, for there was not one man aboard to mend another. Mutiny,
it was plain, hung over us like a thunder-cloud.