Welcome to the community!
When you run a command in R console, the next prompt appears to start with >, provided your command was complete. If it's not, R prompts you to complete your command, and to indicate it, the next line starts with +.
For example, you say you tried to run the following code:
SIMPLE.MERGE <-merge(SUPERS, SAMPLE,by = intersect(ID_CHAR(SUPERS),ID_CHAR(SAMPLE))
Note that, here you have missed one closing parentheses ), corresponding to the one opening ( immediately after merge. If you run this very code with an extra ) at the end, or try to write ) in the line starting with +, your code will run, and you'll get your familiar > prompt.
Hope this helps.