Simulating and Analysing Transmission Chain Statistics Using Branching Process Models
Check inputs to simulate_chains() and simulate_summary()
Check that the statistic and stat_threshold arguments are valid
Adjust next generation vector to match susceptible population size
Test if x is an epichains_summary object
Test if x is an epichains object
Log-likelihood of the size of chains with Negative-Binomial offspring ...
Samples chain lengths with given observation probabilities
Sample all possible offspring for the next generation
Determine and update the chain statistic being tracked
Validate an <epichains_summary> object
Validate an <epichains> object
epichains: Simulating and Analysing Transmission Chain Statistics Usin...
head and tail method for <epichains> class
Estimate the log-likelihood/likelihood for observed branching processe...
Print an <epichains_summary> object
Print an <epichains> object
Generate random numbers from the Borel distribution
Generate random numbers from a Gamma-Borel mixture distribution
Simulate a vector of transmission chains statistics (sizes/lengths)
Simulate transmission chains
Summary method for <epichains_summary> class
Aggregate cases in <epichains> objects by "generation" or "time", if...
Density of the Borel distribution
Adjust new offspring if it exceeds the susceptible population size
Check if the generation_time argument is specified as a function
Check if constructed random number generator for offspring exists and ...
Check inputs that control time events
Calculates the complementary log-probability
Create an <epichains_summary> object
Create an <epichains> object
Log-likelihood of the size of chains with gamma-Borel offspring distri...
Log-likelihood of the length of chains with geometric offspring distri...
Return a function for calculating chain statistics
Sample the number of susceptible offspring from all possible offspring
Construct a <epichains_summary> object
Construct an <epichains> object
Log-likelihood of the summary (size/length) of chains with generic off...
Log-likelihood of the length of chains with Poisson offspring distribu...
Log-likelihood of the size of chains with Poisson offspring distributi...
Samples size (the number of trials) of a binomial distribution
Summary method for <epichains> class
Provides methods to simulate and analyse the size and length of branching processes with an arbitrary offspring distribution. These can be used, for example, to analyse the distribution of chain sizes or length of infectious disease outbreaks, as discussed in Farrington et al. (2003) <doi:10.1093/biostatistics/4.2.279>.
Useful links