Timothy was a native to the islands and so he knew that hurricane season could be upon them while they were on the island. This particular hurricane came rather early though. Timothy was nervous because he said when a hurricane came this early it was usually bad. He could feel the hurricane in the air around them and knew that he had to prepare. Perhaps he could feel the pressure and humidity change around them.
To prepare for the storm and the event that he did not live through the storm Timothy made fishing poles and hooks for Phillip. He lashed these and other supplies high on palm tree. Timothy stripped the raft of anything that looked like it could be useful and added it to their supplies. The two ate a lot of fish and coconut and drank a lot of water because Timothy thought the fish would stay away for a week. Timothy also lashed himself and Phillip to a palm as soon as the storm hit and used his own body to shield Phillip.
The way Timothy knew that the storm was coming was that there was like a gun shot out in the sea.
Timothy knew when the Sea "shot" or when they heard the gunshot Timothy knew there was a storm coming.