R/comp_fcn.R
comp_fcn.RdThis function serves as a placeholder in order to generate documentation on how to specify the comp_fcn string. It also checks that the aggregation term is correctly specified.
comp_fcn(fcn, aggregation, compartments = NULL)function of each the model compartments, e.g. log(I_ADJ) would apply the log function to each of the adjacent compartments prior to aggregation.
either sum or prod for whether the sum or product of the model compartments is desired.
list of compartments to be substituted for the reserved word, e.g. all adjacent compartments would be substituted for I_ADJ. This argument is generated internally and should not be provided by the user.
Nothing. Text string is parsed internally by sub_comp_rate and
sub_comp_emit.
comp_fcn facilitates quick specification of rates that depend on
multiple compartments. It is provided as part of a rate string, and is parsed
and evaluated internally in order to generate a usable function of model
compartments. In particular, it allows a user to consisely specify a function
that is to be applied to each desired model compartment, and whether the
resulting quantities should be added or multiplied together.
# The following rate specification would be used to model the force
# of infection as the sum of beta times the number of infecteds in an
# individual's own compartment, and gamma times the sum of the log number of
# infecteds in adjacent compartments.