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

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

## Documentation for package ‘epimdr’ version 0.6-4

- DESCRIPTION file.

## Help Pages

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 | Flow field
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 gonorhea contact matrix
gra | Euthamia graminifolia rust data.
Icelandflu | Monthly incidence of inflenza-like illness in Iceland between 1980 and 2009.
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 catalytic model
magono | Massachustets gonorrhea data.
May.app | Launch a shiny-app simulating May's Parasitoid-host Model model
meas | Bi-weekly measles incidence in London from 1944-65.
mossong | POLYMOD contact-rate data by Age.
NB | The Nicholson-Bailey model
netSIR | Function to simulate an epidemic on a network
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 in Niamey, Niger.
orv.app | Launch a shiny-app to study outbreak-response vaccination campaigns
pagiard | Weekly incidence of giardia in Pennsylvania between 2006 and 2014.
paili | Weekly deaths from Influenza-like illness in Pennsylvania between 1972 and 1998.
palymes | Weekly incidence of Lymes disease in Pennsylvania between 2006 and 2014.
pameasle | Weekly incidence of measles in Pennsylvania between 1928 and 1969.
pertcop | Weekly whooping cough incidence from 1900-1937 in Copenhagen, Denmark.
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 campaign
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 stocastic TSIR
SimTsir2 | Function to simulate the seasonally-forced TSIR
SIR.app | Launch a shiny-app simulating the SIR model
siragemod | Gradient-function for the age-structured SIR model with possibly heterogeneous mixin
sirmod | Gradient-function for the SIR model
sirwmod | Gradient-function for the SIRWS model
sivmod | Gradient-function for the SIR model with outbreak-response vaccination
summary.cm | Function to calculate the degree distribution for an object of class CM
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 TSIR
TSIRlyap | Function to do Lyapunov exponent calculations from a TSIR simulation
tydiphtheria | Weekly incidence of diphtheria in Philadelphia between 1914 and 1947.
tymeasles | Weekly incidence of measles in Philadelphia between 1914 and 1947.
tyscarlet | Weekly incidence of scarlet fever in Philadelphia between 1914 and 1947.
tywhooping | Weekly incidence of whooping cough in Philadelphia between 1925 and 1947.
usflu | US 1975/76 ILI data.
WattsStrogatz | Function to generate a Watts-Strogats network