I know flags were used, but how would they communicate changes in course or heading?
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Using the relative positions of two flags you spell messages like Morse code. The technique is called semaphore. It’s used in any capacity where you can see someone with whom you are attempting to communicate.
We don’t know how it was done in ancient times; it’s only assumed that flags were used and all the details have been lost. Modern navies developed flag communications that were able to send complex messages (like course changes) only in the late 18th century.
There were a few ways. First, as you mention, they used signal flags. They could use those flag to communicate courses and headings. In the present day, the [International Code of Signals](https://msi.nga.mil/api/publications/download?key=16694273/SFH00000/Pub102bk.pdf&type=view) describes how you can communicate heading, speed, position, weather, intent, distress, etc. all by a combination of [signal flags.](https://en.wikipedia.org/wiki/International_maritime_signal_flags). A very basic single flag message would raising the flag of the letter E, which means “I am altering course to starboard.”
Another methods is [semaphore.](https://en.wikipedia.org/wiki/Flag_semaphore) Using two flags, a signalman will place the flags at various angles to the their body. Each arrangement of flags will signal a letter. They can then either spell out whole words, or signal codes such as those mentioned in the ICS.
Morse is another method. Even without radio telegraphy sending the morse signals, you can still do visually and audibly. Visually, you can flash Morse with an [Aldis Lamp](https://en.wikipedia.org/wiki/Signal_lamp). Also, you can sound Morse on the ship’s whistle. In fact, the modern Collision Regulations still prescribe that you flash and sound whistle signals in collision avoidance to communicate your intention to the other vessel. For example, rule 34 a. says that you should sound one blast on the ship’s whistle to indicated that you are altering course to starboard, and 34 b. says that you should give single quick flash. A single quick is the letter E, and as I mentioned above, the letter E is code for “I am altering to starboard.”
The captains could’ve been issued orders at the start of the voyage. The captains could all agree to follow the first ship. Signals like lanterns at night and flags during the day. Possibly even sending longboats with messengers between ships with orders. Ships in the past were much slower and smaller so they could’ve pulled along side and shouted across.
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