Summarizes the epidemiological features of a nosoi simulation

This function provides summary information about the simulation (number of infected hosts, R0, etc.) as a list.

nosoiSummary(object)

# S3 method for nosoiSim
summary(object, ...)

Arguments

object	Output of a nosoi simulation (object of class nosoiSim).
...	further arguments passed to or from other methods.

Value

All computed data is provided in a list:

R0

Provides a sublist with number of inactive hosts at the end of the simulation N.inactive, mean R0 R0.mean, and R0 distribution R0.dist. For more details, see getR0.

dynamics

data.table with the count of currently infected (i.e. active) hosts at each time step of the simulation (by state if the simulation was in a discrete structured host population). For more details, see getDynamic.

cumulative

data.table with the cumulative count of infected hosts at each time step of the simulation. For more details, see getCumulative.

See also

You can directly compute each elements of the list without using the summarise function. See getR0, getDynamic and getCumulative.

Examples

# \donttest{
t_incub_fct <- function(x){rnorm(x,mean = 5,sd=1)}
p_max_fct <- function(x){rbeta(x,shape1 = 5,shape2=2)}
p_Exit_fct  <- function(t){return(0.08)}

proba <- function(t,p_max,t_incub){
 if(t <= t_incub){p=0}
 if(t >= t_incub){p=p_max}
 return(p)
}

time_contact <- function(t){round(rnorm(1, 3, 1), 0)}

test.nosoi <- nosoiSim(type="single", popStructure="none",
                      length=40,
                      max.infected=100,
                      init.individuals=1,
                      nContact=time_contact,
                      param.nContact=NA,
                      pTrans = proba,
                      param.pTrans = list(p_max=p_max_fct,
                                          t_incub=t_incub_fct),
                      pExit=p_Exit_fct,
                      param.pExit=NA)
#> Starting the simulation
#> Initializing ...
#>  running ...
#> done. 
#> The simulation has run for 4 units of time and a total of 1 hosts have been infected.


nosoiSummary(test.nosoi)
#> $R0
#> $R0$N.inactive
#> [1] 1
#> 
#> $R0$R0.mean
#> [1] 0
#> 
#> $R0$R0.dist
#> [1] 0
#> 
#> 
#> $dynamics
#>    t Count type
#> 1: 0     0    H
#> 2: 1     1    H
#> 3: 2     1    H
#> 4: 3     1    H
#> 5: 4     0    H
#> 6: 5     0    H
#> 
#> $cumulative
#>    t Count type
#> 1: 0     0    H
#> 2: 1     1    H
#> 3: 2     1    H
#> 4: 3     1    H
#> 5: 4     1    H
#> 6: 5     1    H
#> 
# }