nosoiSim {nosoi} | R Documentation |
Top-level function to use nosoi
.
Description
This function determines which general settings the user wants to use for his simulation. All other arguments are passed down to the chosen simulator itself, such as singleNone
, singleDiscrete
, singleContinuous
, dualNone
, dualDiscrete
or dualContinuous
.
Usage
nosoiSim(type = "single", popStructure = "none", ...)
Arguments
type |
specifies which type of pathogen we are interested in, either "single" or "dual"-host (e.g. arboviruses). |
popStructure |
specifies if the population in which the transmission is to occur is structured ("none", "discrete" or "continuous"). |
... |
arguments to be passed on to the chosen simulator itself, such as |
Value
An object of class nosoiSim
, containing all results of the simulation. Class nosoiSim
object have the following slots:
- total.time
Number of time steps the simulation ran (integer).
- type
String giving the simulation type ("single" or "dual" host).
- host.info.A: object of class
nosoiSimOne
-
- N.infected
Number of infected hosts (integer).
- table.hosts
Table containing the results of the simulation (see
getTableHosts
for more details on the table).- table.state
Table containing the results of the simulation, focusing on the movement history of each host (see
getTableState
for more details on the table).- prefix.host
String containing the prefix used to name hosts (character string).
- popStructure
String giving the population structure (one of "none", "discrete" or "continuous").
- host.info.B: object of class
nosoiSimOne
-
Same structure as
host.info.A
, but for host B (if it exists).
See Also
- Individual simulation functions:
-
singleNone
,singleDiscrete
,singleContinuous
,dualNone
,dualDiscrete
anddualContinuous
. - Functions to extract the results:
- Summary statistics functions:
Examples
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)
test.nosoi