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

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Documentation for package ‘epimdr2’ version 1.0-9

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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.
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.
integrandpc Auxiliary function used by llik.pc
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