Hi,
Can you explain why the files can't be in the directory? The reason this is needed, is because if you publish something, that project folder gets uploaded to the server and there it can only read uploaded files (e.g. in the project (sub)folder).
The only way around this (if you really can't have some data locally) is to have it accessible over the internet and load it with its URL. Another scenario is dedicated storage like SQL servers or cloud storage where you need authentication and login (often they have R packages) in order to access the data.
Example to get data over internet
test = read.csv("https://raw.githubusercontent.com/datapackage-examples/sample-csv/master/sample.csv", sep = ",", header = T)
Please elaborate if this is not helping 
PJ