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 |