epidemic {InfNet} | R Documentation |
This function is the one to be called in R by the user to execute the simulation.
epidemic(n, p, obs.time, ini.inf, distrib, param, distrib2 = "full", param2 = 0, BETA, GAMMA, ETA, SUSC, filename, sonia = FALSE, random = FALSE, filename.son)
n |
Number of local networks |
p |
Number of individuals in each local network (vector or scalar if all entries are equal) |
obs.time |
The time period to observe |
ini.inf |
Initial infectives in each local network (vector or scalar if all entries are equal) |
distrib |
Name of the distribution for the nodes' degree in each local network (vector of characters or only one string if all entries are equal) |
param |
parameter distribution for each local network. It must be a list in wich each element is a number of vector. The elements can be: "fixed","poisson","zerotpoisson","geometric","zerotgeometric","poly.logarithmic","logarithmic","power.law","full","none" |
distrib2 |
Name of the distribution for the connection among local networks. The option "fixed" has a vector of parameters that correspond to the nodes' degree. The"poly.logarithmic" distribution has a vector of legth two as parameter (alpha, kappa) |
param2 |
Parameter distribution for distrib2 (scalar or vector). The entries can be: "fixed","poisson","zerotpoisson","geometric","zerotgeometric","poly.logarithmic","logarithmic","power.law","full","none" |
BETA |
Infection rate among connected nodes |
GAMMA |
Removal rate of infective nodes |
ETA |
Immigration rate of infectives (ETA=0 if not immigration) |
SUSC |
Immigration rate of susceptibles (SUS=0 if not immigration) |
filename |
File where to save the simulation result (R format) |
sonia |
Sonia=T to generate the SoNIA file |
random |
random=T if the radious length are not equal within each local network |
filename.son |
Filename of the SoNIA file |
n |
Number of local networks |
nodes.hist |
Matrix with the status of the nodes during the observed period |
edges.hist |
Matrix of connection and their status during the observed period |
p |
Number of nodes in each local network |
p.hist |
Number of non removed nodes in each local network during the observed period |
suscp.hist |
Number or susceptible individual in each local network |
infp.hist |
Number of infective individual in each local network |
remp.hist |
Number of removed individula from each local network |
network.edges |
Non occupied nodes at the end time |
time.hist |
events time |
indexes |
local network and final status of all nodes |
FirsT Version
Lilia Ramirez Ramirez and Mary Thompson
a<-epidemic(10,50,5,c(1,2,rep(1,8)),distrib="poisson",param=as.list(2,rep(1,7),rep(2.3,2)),distrib2="full",BETA=0.8,GAMMA=0.5,filename="temp",sonia=TRUE,filename.son="temp.son") ##---- Should be DIRECTLY executable !! ---- ##-- ==> Define data, use random, ##-- or do help(data=index) for the standard data sets. ## The function is currently defined as function(n,p,obs.time,ini.inf,distrib,param,distrib2="full",param2=0,BETA,GAMMA,ETA,SUSC,filename, sonia=FALSE, random=FALSE,filename.son){ result<-epidemic.sim(n,p,obs.time, ini.inf,distrib,param,distrib2,param2,BETA,GAMMA,ETA,SUSC) save(result, file=filename) if(sonia==TRUE){ print("inicia formato") for.sonia<-format.output(result,random) print("done") write.table(for.sonia, file=filename.son , row.names=F,quote=F, sep="\t") } return(result) }