Functions and Data for "Epidemics: Models and Data in R"

BarabasiAlbert | Function to generate a Barabasi-Albert network |

black | Black's measles seroprevalence data. |

burnett | Burnett's Parasitoid-Host data. |

ccs | UK measles CCS data. |

chainSIR | Gradient-function for the chain-SIR model |

cholera | Dacca cholera death data. |

coyne | Gradient-function for Coyne et al's rabies model |

dalziel | Measles incidence across 40 US cities |

ebola | Sierra-Leone Ebola 2015 data. |

ferrari | Ferrari et al. 2005 outbreak data. |

filipendula | Filipendula rust data. |

fiv | FIV infection in cats. |

flowField | Flowfield |

flu | Boarding school influenza data. |

gillespie | Gillespie exact algorithm |

gm | Defoliated by gypsy moth each in northeast US 1975-2002. |

gonnet | De et al. 2004 gonorrhea contact matrix |

gra | Euthamia graminifolia rust data. |

Icelandflu | Monthly incidence of influenza-like illness in Iceland... |

integrandpc | Auxillary function used by llik.pc |

litter | Bordetella bronchiseptica in rabbit kittens. |

llik.cb | Negative log-likelihood function for the chain-binomial model |

llik.pc | Function to estimate parameters for the picewise-constant... |

magono | Massachusetts gonorrhea data. |

May.app | Launch a shiny-app simulating May's Parasitoid-host Model... |

meas | Bi-weekly measles incidence in London from 1944-65. |

mossong | POLYMOD contact-rate data by Age. |

NB | The Nicholson-Bailey model |

NetworkSIR | Function to simulate an epidemic on a network |

niamey | Weekly measles incidence from 2003-04 in Niamey, Niger. |

niamey_daily | Day of appearance of each measles case from 2003-04 outbreak... |

orv.app | Launch a shiny-app to study outbreak-response vaccination... |

pagiard | Weekly incidence of giardia in Pennsylvania between 2006 and... |

paili | Weekly deaths from Influenza-like illness in Pennsylvania... |

palymes | Weekly incidence of Lymes disease in Pennsylvania between... |

pameasle | Weekly incidence of measles in Pennsylvania between 1928 and... |

pertcop | Weekly whooping cough incidence from 1900-1937 in Copenhagen,... |

peru | Rubella in Peru data. |

plot.cm | Function to plot an object of class CM |

plot.netSIR | Function to plot a netSIR object |

r0fun | Function to calculate R0 from a contact matrix |

rabbit | Rabbit _Bordetella brochiseptica_ data. |

rabies | Raccoon rabies data. |

retrospec | Function to predict efficacy of outbreak-response vaccination... |

ringlattice | Function to generate a ring lattice |

SEIR.app | Launch a shiny-app simulating the seasonal SEIR model |

seirmod | Gradient-function for the SEIR model |

seirmod2 | Gradient-function for the forced SEIR model |

SEIRS.app | Launch a shiny-app simulating the SEIRS model |

SH9 | Daily measures of malaria infected mice. |

silene2 | Antler smut on wild campion. |

sim.cb | Function to simulate the chain-binomial model |

SimTsir | Function to simulate the stochastic TSIR |

SimTsir2 | Function to simulate the seasonally-forced TSIR |

siragemod | Gradient-function for the age-structured SIR model with... |

SIR.app | Launch a shiny-app simulating the SIR model |

sirmod | Gradient-function for the SIR model |

sirwmod | Gradient-function for the SIRWS model |

sivmod | Gradient-function for the SIR model with outbreak-response... |

summary.cm | Function to calculate the degree distribution for an object... |

summary.netSIR | Function to summarize a netSIR object |

tau | Gillespie tau-leap algorithm |

TSIR.app | Launch a shiny-app simulating TSIR model |

TSIRllyap | Function to calculate the local Lyapunov exponents for the... |

TSIRlyap | Function to do Lyapunov exponent calculations from a TSIR... |

tydiphtheria | Weekly incidence of diphtheria in Philadelphia between 1914... |

tymeasles | Weekly incidence of measles in Philadelphia between 1914 and... |

tyscarlet | Weekly incidence of scarlet fever in Philadelphia between... |

tywhooping | Weekly incidence of whooping cough in Philadelphia between... |

usflu | US 1975/76 ILI data. |

WattsStrogatz | Function to generate a Watts-Strogats network |

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