LBExperiment-class: Class "LBExperiment"

In RLadyBug: Analysis of Infectious Diseases using Stochastic Epidemic Models

Description

S4 class containing the data and the layout of the infectious disease data

Slots

data:

Data Frame with six columns: x, y, E, I, R, D

layout:

Object of class "LBLayout"

T:

A "numeric" specifying how long the epidemic was observed.

Methods

data2events

signature(object = "LBExperiment"): convert the data.frame of events for each individual to a time order data.frame of events for the entire Experiment. The information about each individual is lost. This function is used internally.

show

signature(object = "LBExperiment"): shows all slots of the LBExperiment object.

setLayout<-

signature(object = "LBExperiment"): sets the Layout.

plot

signature(signature(x="LBExperiment", y="missing"), function(x, y, type=NULL, options=NULL, ...)) The type argument should be a formula specifying the desired type of plot. By providing an additional options list individual parameters for the plots are provided. Valid formulae are

state ~ time | position

The number of susceptible, infectious and recovered as a function of time for each unit. Warning: in case there are many units this plot might be rather useless.

state ~ time

shows the total number of susceptible, infectious and recovered (i.e. summed over all units) as a function of time. Individual options are

stacked

boolean whether stacked boxplots or just time-series are shown.

state ~ 1|position

illustrates the three multivariate time series (susceptible, exposed, infected) as a "film" with noOfPics pictures. Individual options are

chart

Either "pie" or "bar", where the latter is default.

justInf

if FALSE pie charts with the number of S(t),E(t),I(t) are shown, otherwise only the number of infectious is shown, where the radius shows the proportion.

noOfPics

How many pictures in the animation. If not saved set the "History" attribute of the X11.

PDF

If TRUE the results are saved in PDF Files with the base name name.

name

Base name of the generated PDF Files. The actual files are then names name-addstr-number.pdf

addstr

This is added to the base name.

individual ~ time

shows all events for each individual

individual ~ time | position

show individual histories of each individual aligned to the same time axis

Additional parameters to the underlying plot rountine, e.g. xlab, legend=FALSE, color, are passed using ....

Examples

sim.layout <- new( "LBLayout", S0=matrix( c( 13, rep( 14, 7 ) ), ncol=4 ),
                  E0=matrix( c(  1, rep(  0, 7 ) ), ncol=4 ) )
sim.opts <- new( "LBOptions", seed=2006,
                            LBmodel=c( "gamma", "gamma", "gamma", FALSE ),
                            ignoreData=c( FALSE, FALSE, FALSE ),
                            initBeta =list( init=0.125,
                                        gamma=0.001, delta=0.001 ),
                            initBetaN=list( init=0.018,
                                        gamma=0.001, delta=0.001 ),
                            initIncu=list( asis=FALSE, const=FALSE,
                                    g=6.697, g.gamma=0.001, g.delta=0.001,
                                    d=0.84, d.gamma=0.001,d.delta=0.001 ),
                            initInf=list( 1.772, 0.001, 0.001, 0.123, 0.001, 0.001 ),
                            initDia=list( 149.126, 0.001, 0.001,
                                    8.737, 0.001, 0.001 ) )
exp <- simulate( sim.opts, layout=sim.layout )
plot(exp,type = state ~ time)
plot(exp,type = state ~ time, options=list(stacked=FALSE))

RLadyBug documentation built on May 2, 2019, 5:50 p.m.