pis.fit {postinfectious} | R Documentation |
Estimating the incubation period distribution of a post-infectious syndrome
Description
This function estimates the incubation period distribution of a post-infectious syndrome with maximum likelihood estimation. The incubation period distribution of the antecedent infection and the post-infectious syndrome are allowed to be lognormal ("LN
"), Weibull ("WB
") or gamma ("GM
") distributed. The data set is allowed to have cases with the actecedent diseases whose incuation periods come from different distributions (see Examples).
Usage
pis.fit(data,postinfect=c("LN","WB","GM"),theta)
Arguments
data |
A data.frame containing at least 4 columns. The first two columns represent (1) the time between the symptom onset of the antecedent infection and post-infectious syndrome and (2) the incubation period distribution of the antecedent infection (only " |
postinfect |
The incubation period distribution of the post-infectious disease. It can only be " |
theta |
A vector of two numbers as the initial value for optimisation. |
Details
For each observed case, let S_{0}
and S
be the incubation period of the antecedent infection and post-infectious syndrome, respectively. As the antecedent infection is the antigenic factor of the post-infectious syndrome, they both share the same time of infection exposure. The difference between S_{0}
and S
, denoted by X
, is the time between the two symptom onsets. Also let \theta_{0}
and \theta
be the set of the parameters of the distribution of S_{0}
and S
then the likelihood of such observed case is given by,
\int_{-\infty}^{\infty}f_0(S_0,\theta_0)f(S_0+X,\theta)dS_0
where f_0
and f
are the probability density function of S_{0}
and S
, respectively. \theta
is then estimated by maximising the sum of likelihood of all observed cases.
Value
Parameter |
Estimates of the parameters of the incubation period distribution of the post-infectious syndrome. |
SE |
Standard errors of |
AIC |
Akaike Information Criterion. |
Convergence |
The convergence message of |
Median |
The median incubation period distribution of the post-infectious syndrome. |
Theta.initial |
Initial values used in |
Distribution |
The Distribution assumed in the estimation, i.e. " |
Author(s)
Char Leung
Examples
#generate artificial data
S<-c(56,37,32,7,8,3,5)
S0<-c(2,1,3,1,1,1,3)
X<-S-S0
f0<-c(rep("LN",4),rep("WB",3))
phi<-matrix(c(rep(c(0,1),4),rep(c(1,2),3)),byrow=TRUE,ncol=2)
data<-data.frame(X,f0,phi)
pis.fit(data,"LN",theta=c(2.5,1))