# Functions and Data for "Epidemics: Models and Data in R (2nd Edition)"

## Documentation for package ‘epimdr2’ version 1.1-1

- DESCRIPTION file
- Package NEWS
- Package README

## 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.
chabaudi | Daily measures of malaria infected mice.
cholera | Dacca cholera death data.
coyne | Edition 1 Gradient-function for Coyne et al's rabies model
coyne2 | Edition 2 Gradient-function for Coyne et al's rabies model
cspring | Colorado Springs network
dalziel | Measles incidence across 40 US cities
ebola | Sierra-Leone Ebola 2015 data.
euthamia | Euthamia graminifolia rust 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
gonnet | De et al. 2004 gonorrhea contact matrix
gravity | A function to calculate the matrix of gravity coupling based on distance and population size
gypsymoth | Defoliated by gypsy moth each in northeast US 1975-2002.
icelandflu | Monthly incidence of influenza-like illness in Iceland between 1980 and 2009.
jacobian | A Jacobian matrix calculator
leslie | A function to calculate asymptotic growth, sensitivity and elasticity for age-structured populations
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 piecewise-constant catalytic model
m4494 | Measles in England and Wales 1944-1994.
magono | Massachusetts 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.
nbmod | The Nicholson-Bailey model
nbspat.app | Launch a shiny-app simulating the spatially-extended Nicholson-Bailey parasitoid model
nextgenR0 | Next generation matrix R0 calculator
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.
pdv | Cumulative death count of harbor seals from CDV.
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
polymod | POLYMOD contact-rate data by Age.
r0fun | Function to calculate R0 from a contact matrix
rabbit | Rabbit _Bordetella bronchiseptica_ data.
rabies | Raccoon rabies data.
retrospec | Function to predict efficacy of outbreak-response vaccination campaign
ringlattice | Function to generate a ring lattice
ross.app | Launch a shiny-app simulating a Ross-Macdonald model
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
silene | Antler smut on wild campion.
sim.cb | Function to simulate the chain-binomial model
sir.app | Launch a shiny-app simulating the SIR model
sirAgemod | Gradient-function for the age-structured SIR model with possibly heterogeneous mixing
sirChainmod | Gradient-function for the chain-SIR model
sirmod | Gradient-function for the SIR model
sirNetmod | Function to simulate an epidemic on a network
sirSpatmod | Gradient function for a spatially-extended SIR model
sirvmod | Gradient-function for the SIR model with outbreak-response vaccination
sirwmod | Gradient-function for the SIRWS model
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
tsirSim | Function to simulate the stochastic TSIR
tsirSim2 | Function to simulate the seasonally-forced TSIR
tsirSpat | Function to simulate the spatially-extended seasonally-forced TSIR
twostrain | Gradient-function for the two-strain SIR model
twostrain.app | Launch a shiny-app simulating a two-strain SIR model
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.
us | 2005 US Life table.
usflu | US 1975/76 ILI data.
variants | US SARS-CoV-2 variant data.
waller | Rabies month of first appearance across Connecticut.
wattsStrogatz | Function to generate a Watts-Strogatz network