DengueSimR01            Simulated dataset of dengue transmission with
                        basic reproductive number of 1
DengueSimR02            Simulated dataset of dengue cases with basic
                        reproductive number of 2
DengueSimRepresentative
                        Simulated dataset of dengue cases with
                        representative underlying population
est.transdist           Estimate transmission distance
est.transdist.bootstrap.ci
                        Bootstrap mean transmission distance values
est.transdist.temporal
                        Change in mean transmission distance over time
est.transdist.temporal.bootstrap.ci
                        Bootstrapped confidence intervals for the
                        change in mean transmission distance over time
est.transdist.theta.weights
                        Estimate transmission distance theta values by
                        replication
est.wt.matrix           Calculate the Infector-Infectee Wallinga-Teunis
                        matrix
est.wt.matrix.weights   Estimate matrix of basic Wallinga-Teunis
                        weights
get.cross.K             Cross type K function using homotypic and
                        heterotypic case types
get.cross.PCF           Cross type Pair Correlation Function using
                        homotypic and heterotypic case types
get.pi                  Generalized version of 'get.pi'
get.pi.bootstrap        Bootstrap 'get.pi' values.
get.pi.ci               Calculate bootstrapped confidence intervals for
                        'get.pi' values.
get.pi.permute          get the null distribution of the 'get.pi'
                        function
get.pi.typed            Optimized version of 'get.pi' for typed data.
get.pi.typed.bootstrap
                        runs bootstrapping on 'get.pi.typed'
get.pi.typed.permute    get the null distribution of the get.pi.typed
                        function
get.tau                 generalized version of 'get.tau'
get.tau.bootstrap       Bootstrap 'get.tau' values.
get.tau.ci              Bootstrap confidence interval for the 'get.tau'
                        values
get.tau.permute         get the null distribution of the 'get.tau'
                        function
get.tau.typed           Optimized version of 'get.tau' for typed data
get.tau.typed.bootstrap
                        runs bootstrapping for 'get.tau.typed'
get.tau.typed.permute   get the null distribution for the
                        'get.tau.typed' function
get.theta               Generalized version of 'get.theta'
get.theta.bootstrap     Bootstrap 'get.theta' values.
get.theta.ci            Calculate bootstrapped confidence intervals for
                        'get.theta' values.
get.theta.permute       get the null distribution of the 'get.theta'
                        function
get.theta.typed         Optimized version of 'get.theta' for typed
                        data.
get.theta.typed.bootstrap
                        runs bootstrapping on 'get.theta.typed'
get.theta.typed.permute
                        get the null distribution of the
                        get.theta.typed function
get.transdist.theta     Get weights of transmission distance theta
sim.epidemic            Simulation of an epidemic in space and time
sim.plot                Plot output of simulated epidemic
