I think it is important that we understand what is your actual problem:
apparently you have a matrix (not a data.frame) with numbers (and NA) (so not factors) and you want to replace the number 0 by FALSE and the number 1 by TRUE and NA by ?? .
According the documentation the plyr::revalue function works only on characters or factors.
BTW the function plyr::mapvalues is mentioned that also handles numbers.
My suggestion: create a small input x (x being your data source) exactly as your data source.
So if there are characters you specify characters, numbers if numbers etc.
And show us how you do this (not showing only the print result).
And check the reference about reprex I mentioned: it is really useful.
Also tell us what you want to achieve apart from changing zeros and ones:
if you are starting with R then maybe want to learn to use tidyverse packages (e.g. dplyr has nice data.frame capabilities) or do just want to avoid it and use the basic R functions?