Merge remote-tracking branch 'upstream/master' into update-upstream

# Conflicts:
#	.Rhistory
#	NAMESPACE
#	R/pathEmPlot.R
#	R/transformJMPnat.R
#	R/transformJMPsubnat.R
#	man/getLoadings.Rd
#	man/t_JMPnat.Rd

MAJOR CHANGE: updated getLoadings function to account for dual pits, urine diversion, and pit additives

Merged updates from upstream remote. Made changes, because the package cannot be build out of the box. Functions calls are not allowed in all scripts of /R folder. Need to be changed in upstream remote.