R: Estimate Global Clustering in Infectious Disease

# Estimate Global Clustering in Infectious Disease

## Documentation for package ‘IDSpatialStats’ version 0.4.0

- DESCRIPTION file
- Package README

## Help Pages

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