The pop.predict function stores resulting trajectories into a directory called output.dir/prediction. Here the argument sim.dir should correspond to output.dir (i.e. without the “prediction” part).
In addition to retrieving prediction results, the get.pop.prediction function also looks for a file called cache.rda and loads it into an environment called cache. If it does not exist, it creates an empty cache environment. See pop.map - Section Performance and Caching. The environment can be cleaned up using the pop.cleanup.cache function which also deletes the cache.rda file on disk. If write.to.cache is FALSE, other functions are not allowed to manipulate the cache.rda file.