I think it really needs to be done on a case to case basis.
Vaccines that have a proven effectiveness of nearly wiping out a disease eg. measles, smallpox (when it was around), etc. should be mandatory.
A vaccine such as the flu, that while it is effective, may not be effective in the year, administration should be up to the person outside of key positions such as health care. Vaccines do have side effects, and when the effectiveness certainty is below a certain level, it should be personal choice as the effects of side effects may outweigh the total health gain.
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