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
sirNetmod               Function to simulate an epidemic on a network
sirSpatmod              Gradient function for a spatially-extended SIR
                        model
sirmod                  Gradient-function for the 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
