The file 'R/SLIAR-mgroup-ode.R' contains code for a simple SLIAR model with two structures. The defaults assume the structures are age (younger, middle, older) and vaccine status (vaccinated, unvaccinated). Erlang distributions of sojourn times are implimented by doubling the L,I,and A compartments. The default parameters assume L is latent, I is infectious, but isolated, and A is infectious and non-isoloting (mild, easily-dismssed symptoms). Thus, Ra, Ri, and Rh are recovered asymptomatic, isolating, and hospitalized, respectively.
Note the SLIAR structure is really S->L->{AIH}->R where A,I and H are parallel routes of progression and everyone begins their infectious period without symptoms (i.e., in A).
Run the model with default parameters as follows:
source('R/SLIAR-mgroup-ode.R')
res = ode_sim(param)
res_wide = ode_reshape_wide(res)
res_long = ode_reshape_long(res_wide)
res will contain a matrix version of the solution, with one column for time and columns for each state variable.
res_wide names the columns and reshapes the data into a form more amenable to plotting.
res_long contains a longer version for other plotting options
plot results with commands like
gplot(
subset(res_wide,status=='vaccinated'),
aes(x=time,y=Rh)
) +
geom_line(aes(col=age))
or
ggplot(
subset(res_wide,age=='younger'&status=='vaccinated'),
aes(x=time)
) +
geom_line(aes(y=L1))+geom_line(aes(y=A1))
or
ggplot(
subset(res_long,age=='younger'&status=='vaccinated'),
aes(x=time,y=value,col=stage)
) +
geom_line()