Package ‘EpiDynamics’

February 13, 2020

Type Package
Title Dynamic Models in Epidemiology
Depends R (>= 3.6)
Imports deSolve, reshape2, ggplot2, grid
Description Mathematical models of infectious diseases in humans and animals.
Both, deterministic and stochastic models can be simulated and plotted.
License GPL (>= 2)
LazyLoad yes

URL https://github.com/oswaldosantos/EpiDynamics
Version 0.3.1
Date 2020-02-12
RoxygenNote 7.0.2
NeedsCompilation no
Author Oswaldo Santos Baquero [aut, cre],
Fernando Silveira Marques [aut]
Maintainer Oswaldo Santos Baquero <[email protected]>
Repository CRAN
Date/Publication 2020-02-13 09:40:05 UTC

R topics documented:
EpiDynamics-package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
MultiStrainPartialImmunity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
PlotMods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
SEIR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
SEIR4AgeClasses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
SEIRnStages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
SIR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
sir2AgeClasses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
SIR2Stages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

1
2 EpiDynamics-package

SIR2TypesImports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
SIRAdditiveNoise . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
SIRBirthDeath . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
SIRCarrierState . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
SIRDemogStoch . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
SIRInducedMortality . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
SIRInducedMortality2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
SIRPartialImmunity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
SIRScaledAdditiveNoise . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
SIRSinusoidalBirth . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
SIRSinusoidalForcing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
SIRTauLeap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
SIRTermTimeForcing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
SIRVector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
SIS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
SIS2RiskGroups . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
SISDemogStoch . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
SISinusoidalTransmBrith . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
SISnRiskGroups . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
SISPairwiseApprox . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

Index 41

EpiDynamics-package The EpiDynamics Package

Description
Mathematical models of infectious diseases in humans and animals. Both, deterministic and stochas-
tic models can be simulated and plotted.

Details

Package: EpiDynamics
Type: Package
Version: 0.3.1
Date: 2020-02-11
Depends: R (>= 3.6)
Imports: deSolve, reshape2, ggplot2, grid
License: GPL (>= 2)
LazyLoad: yes
URL: http://oswaldosantos.github.io/EpiDynamics
Authors: Oswaldo Santos Baquero <[email protected]>
Fernando Silveira Marques <[email protected]>
Maintainer: Oswaldo Santos Baquero <[email protected]>
MultiStrainPartialImmunity 3

MultiStrainPartialImmunity
Partial immunity model that cycles (P 4.2).

Description
Solves multi-strain where the strains are arranged in a circle and each strain offers partial immunity
(in terms of reduced transmission) to its neighbours.

Usage
MultiStrainPartialImmunity(pars = NULL, init = NULL, time = NULL, ...)

Arguments
pars vector with 2 vectors and 2 values in the following order: beta, gamma, mu
and a. The first element of each vector corresponds to the first strain, the second
element to the second strain and so on. mu is the per capita death rate and alpha
is the modified transmission rate due to partial immunity.
init vector with 3 vectors in the following order: S, P and L. The first element
of each vector corresponds to the first strain, the second element to the second
strain and so on. Si + Pi + Li = 1 but sum(Si) could be greater than 1.
time time sequence for which output is wanted; the first value of times must be the
initial time.
... further arguments passed to ode function.

Details
This is the R version of program 4.2 from page 123 of "Modeling Infectious Disease in humans and
animals" by Keeling & Rohani.

Value
list. The first element, *$model, is the model function. The second, third and fourth elements
are the vectors (*$pars, *$init, *$time, containing the pars, init and time arguments of the
function. The fifth element *$results is a data.frame with up to as many rows as elements in
time. First column contains the time. Second, third and fourth columns contain the proportion of
susceptibles, infectious and recovered.

References
Keeling, Matt J., and Pejman Rohani. Modeling infectious diseases in humans and animals. Prince-
ton University Press, 2008.
4 PlotMods

See Also
ode.

Examples
# Parameters and initial conditions.
parameters <- c(beta = rep(40, 4), gamma = rep(9.98, 4),
mu = 0.02, a = 0.4 )

initials <- c(S = c(0.08, 0.1, 0.1, 0.11),

P = c(0.4, 0.3, 0.3, 0.29),
L = c(0.15, 0.02, 0.1, 0.01))

# Solve and plot.

mlti.strain.pi <- MultiStrainPartialImmunity(pars = parameters,
init = initials,
time = 0:200)
PlotMods(mlti.strain.pi, variables = c('L1', 'L2', 'L3', 'L4'), grid = FALSE)

PlotMods Plot results of capm model functions

Description
Plot results of EpiDynamics’ functions.

Usage
PlotMods(
model.out = NULL,
variables = NULL,
x.label = NULL,
y.label = NULL,
legend.title = "variable",
line.size = 1,
text.size = 14,
grid = TRUE,
bifur = FALSE
)

Arguments
model.out output of aEpiDynamics’ function.
variables column index for the variables in model.out to be plotted.
x.label string with the name of x axis.
y.label string with the name of y axis.
SEIR 5

legend.title string with the legend title.

line.size scalar to define the thick of the lines (points for bifurcations) to be plotted.
text.size scalar to define the size of axis texts and titles.
grid logical to indicate if each variable must be plotted in a separated panel.
bifur logical to indicate if model.out represent a bifurcation.

Examples
# Parameters and initial conditions.
parameters <- list(beta0 = 17 / 13, beta1 = 0.1, gamma = 1 / 13,
omega = 2 * pi / 365, mu = 1 / (50 * 365))

initials <- c(S = 1 / 17, I = 1e-4,

R = 1 - 1 / 17 - 1e-4)

# Solve the system.

sir.sinusoidal.forcing <- SIRSinusoidalForcing(pars = parameters,
init = initials,
time = 0:(60 * 365))
PlotMods(sir.sinusoidal.forcing)

# Solve bifurcation dynamics for 20 years.

# If max(time) < 3650, bifurcation dynamics are solved for 3650 time-steps.
parameters2 <- list(beta0 = 17 / 13, beta1 = seq(0.001, 0.251, by = 0.001),
gamma = 1 / 13, omega = 2 * pi / 365, mu = 1 / (50 * 365))
# Uncomment the following lines:
# bifur <- SIRSinusoidalForcing(pars = parameters2,
# init = initials,
# time = 0:(20 * 365))
# PlotMods(bifur, bifur = TRUE)

SEIR SEIR model (2.6).

Description
Solves a SEIR model with equal births and deaths.

Usage
SEIR(pars = NULL, init = NULL, time = NULL, ...)

Arguments
pars vector with 4 values: the per capita death rate (and the population level birth
rate), the transmission rate, the movement form exposed to infectious and the
recovery rate. The names of these values must be "mu", "beta", "sigma" and
"gamma", respectively.
6 SEIR

init vector with 3 values: the initial proportion of proportion of susceptibles, ex-
posed, infectious and recovered. The names of these values must be "S", "E",
"I" and "R", respectively.
time time sequence for which output is wanted; the first value of times must be the
initial time.
... further arguments passed to ode function.
All parameters must be positive and S + E + I + R <= 1.

Details

This is the R version of program 2.6 from page 41 of "Modeling Infectious Disease in humans and
animals" by Keeling & Rohani.

Value

list. The first element, *$model, is the model function. The second, third and fourth elements
are the vectors (*$pars, *$init, *$time, containing the pars, init and time arguments of the
function. The fifth element *$results is a data.frame with up to as many rows as elements in
time. First column contains the time. Second to fifth column contain the proportion of susceptibles,
exposed, infectious and recovered.

References

Keeling, Matt J., and Pejman Rohani. Modeling infectious diseases in humans and animals. Prince-
ton University Press, 2008.

See Also

ode.

Examples

# Parameters and initial conditions.

parameters <- c(mu = 1 / (70 * 365), beta = 520 / 365,
sigma = 1 / 14, gamma = 1 / 7)
initials <- c(S = 0.1, E = 1e-04, I = 1e-04, R = 1 - 0.1 - 1e-4 - 1e-4)

# Solve and plot.

seir <- SEIR(pars = parameters, init = initials, time = 0:(60 * 365))
PlotMods(seir)
SEIR4AgeClasses 7

SEIR4AgeClasses SEIR model with 4 age classes and yearly aging (P 3.4).

Description
Solves a SEIR model with four different age-groups and yearly "movements" between the groups
mimicking the school year

Usage
SEIR4AgeClasses(pars = NULL, init = NULL, time = NULL, ...)

Arguments
pars list with: a matrix with the transmission rates, the rate at which individuals
move from the exposed to the infectious classes, the recovery rate, a vector with
death rates in each age group, and a vector with birth rates into the childhood
class. The names of these elements must be "beta", "sigma", "gamma", "mu",
and "nu", respectively, see example.
init vector with 16 values: initial proportions of the population that are susceptible,
exposed, infectious and recovered in a particular age group. The vector must be
named, see example. Requirements: S + E + I <= n for each age group and all
values must be positive.
time time sequence for which output is wanted; the first value of times must be the
initial time.
... further arguments passed to ode function.

Details
This is the R version of program 3.4 from page 87 of "Modeling Infectious Disease in humans and
animals" by Keeling & Rohani.
All rates are specified in days. Moreover, a vector n with the proportion of each age group. All
parameters must be positive.

Value
list of class SolveSIR4ACYA. The first element, *$model, is the model function. The second, third
and fourth elements are vectors (*$pars, *$init, *$time, respectively) containing the pars, init
and time arguments of the function. The fifth element *$results is a data.frame with up to as
many rows as elements in time. First column contains the time. The following columns contain the
proportion of susceptibles, exposed, infectious and recovered.

References
Keeling, Matt J., and Pejman Rohani. Modeling infectious diseases in humans and animals. Prince-
ton University Press, 2008.
8 SEIRnStages

See Also
ode.

Examples
# Parameters and initial conditions.
parameters <- list(beta = matrix(c(2.089, 2.089, 2.086, 2.037,
2.089, 9.336, 2.086, 2.037,
2.086, 2.086, 2.086, 2.037,
2.037, 2.037, 2.037, 2.037),
nrow = 4, ncol = 4),
sigma = 0.125, gamma = 0.2,
mu = c(0, 0, 0, 1) / (55 * 365),
nu = c(1 / (55 * 365), 0, 0, 0),
n = c(6, 4, 10, 55) / 75)

initials <- c(S = c(0.05, 0.01, 0.01, 0.008),

E = c(0.0001, 0.0001, 0.0001, 0.0001),
I = c(0.0001, 0.0001, 0.0001, 0.0001),
R = c(0.0298, 0.04313333, 0.12313333, 0.72513333))

# Solve and plot.

# Uncomment the following lines (running it takes more than a few seconds):
# seir4.age.classes <- SEIR4AgeClasses(pars = parameters,
# init = initials,
# time = 0:36500)
# PlotMods(seir4.age.classes,
# variables = c('I1', 'I2', 'I3', 'I4'), grid = F)

SEIRnStages SEIR model with n stages (P 3.5).

Description
Solves a SEIR model with multiple stages to create gamma-distributed exposed and infectious pe-
riods.

Usage
SEIRnStages(pars = NULL, init = NULL, time = NULL, ...)

Arguments
pars vector with 5 values: the transmission rate, the removal or recovery rate, the
death rate (we assume that nu=mu), the number of stages in the infected period
and the number of stages in the exposed period. The names of these elements
must be "beta", "gamma", "mu", "n" and "m", respectively, see example. All
rates are specified in days and all rates and parameters must be positive, more-
over, m < n.
SEIRnStages 9

init vector with n + 1 values: initial proportions of the population that are suscep-
tible and infected. The vector must be named, see example. Requirements: S +
all Infected <= 1.
time time sequence for which output is wanted; the first value of times must be the
initial time.
... further arguments passed to ode function.

Details

This is the R version of program 3.5 from page 94 of "Modeling Infectious Disease in humans and
animals" by Keeling & Rohani.

Value

list. The first element, *$model, is the model function. The second, third and fourth elements are
vectors (*$pars, *$init, *$time, respectively) containing the pars, init and time arguments of
the function. The fifth element *$results is a data.frame with up to as many rows as elements in
time. First column contains the time. The following columns contain the proportion of susceptibles
and infected.

References

Keeling, Matt J., and Pejman Rohani. Modeling infectious diseases in humans and animals. Prince-
ton University Press, 2008.

See Also

ode.

Examples
# Parameters and initial conditions.
n <- 13
parameters <- list(beta = 17 / 5, gamma = 1 / 13, mu = 1 / (55 * 365),
n = n, m = 8)

initials <- c(S = 0.05, I = 0.00001 * rep(1, n) / n)

# Solve and plot.

# Uncomment the following lines (running it takes more than a few seconds):
# seir.n.stages <- SEIRnStages(pars = parameters,
# init = initials,
# time = seq(1, 30 * 365, 1))
# PlotMods(seir.n.stages, variables = 2)
# PlotMods(seir.n.stages, variables = 3:13, grid = F)
10 SIR

SIR Simple SIR model (P 2.1).

Description

Solves a simple SIR model without births or deaths.

Usage

SIR(pars = NULL, init = NULL, time = NULL, ...)

Arguments

pars vector with 2 values: the transmission and recovery rates. The names of these
values must be "beta", and "gamma", respectively.
init vector with 3 values: the initial proportion of susceptibles, infectious and re-
covered. The names of these values must be "S", "I" and "R", respectively.
time time sequence for which output is wanted; the first value of times must be the
initial time.
... further arguments passed to ode function.

Details

This is the R version of program 2.1 from page 19 of "Modeling Infectious Disease in humans and
animals" by Keeling & Rohani.
All parameters must be positive and S + I + R <= 1.

Value

list. The first element, *$model, is the model function. The second, third and fourth elements
are the vectors *$pars, *$init and *$time, containing the pars, init and time arguments of the
function. The fifth element *$results is a data.frame with up to as many rows as elements in
time. First column contains the time. Second, third and fourth columns contain the proportion of
susceptibles, infectious and recovered.

References

Keeling, Matt J., and Pejman Rohani. Modeling infectious diseases in humans and animals. Prince-
ton University Press, 2008.

See Also

ode.
sir2AgeClasses 11

Examples
# Parameters and initial conditions.
parameters <- c(beta = 1.4247, gamma = 0.14286)
initials <- c(S = 1 - 1e-06, I = 1e-06, R = 1 - (1 - 1e-06 - 1e-06))

# Solve and plot.

sir <- SIR(pars = parameters, init = initials, time = 0:70)
PlotMods(sir)

sir2AgeClasses SIR model with 2 age classes (P 3.3).

Description
Solves a SIR model two different age-groups.

Usage
sir2AgeClasses(pars = NULL, init = NULL, time = NULL, ...)

Arguments
pars vector with 8 values: 4 transmission rates, 1 recovery rate, rate at which chil-
dren mature, death rate in the childhood group and death rate in the adult group.
The names of these values must be "betaCC","betaCA","betaAC", "betaAA",
"gamma", "lC","muC" and "muA", respectively. The letters after the word
"beta" denote transmission to any group from any group, e.g., "betaCA" rep-
resent transmission to children group from adult group. All parameters must be
positive. Parameters "nC" na "nu" (proportion of the population that are in the
childhood group and birth rate into the childhood class, respectively) are not de-
fined explicitly, but calculated as: nC = muA/(lC+muA) and nu = (lC+nuA)nC.
All rates are specified in years and all parameters must be positive
init vector with 4 values: the initial proportion of the population that are both sus-
ceptible and in the childhood group, the initial proportion of the population that
are both infectious and in the childhood group, the initial proportion of the pop-
ulation that are both susceptible and in the adult group, and the initial proportion
of the population that are both infectious and in the adult group. The names of
these values must be "SC", "IC", "SA" and "IA", respectively. Requirements:
SC + IC <= nC, and SA + IA <= nA = 1 - nC.
time time sequence for which output is wanted; the first value of times must be the
initial time.
... further arguments passed to ode function.

Details
This is the R version of program 3.3 from page 79 of "Modeling Infectious Disease in humans and
animals" by Keeling & Rohani.
12 SIR2Stages

Value
list. The first element, *$model, is the model function. The second, third and fourth elements
are the vectors (*$pars, *$init, *$time, containing the pars, init and time arguments of the
function. The fifth element *$results is a data.frame with up to as many rows as elements in
time. First column contains the time. The following columns contain the proportion of susceptibles,
infectious and recovered.

References
Keeling, Matt J., and Pejman Rohani. Modeling infectious diseases in humans and animals. Prince-
ton University Press, 2008.

See Also
ode.

Examples
# Parameters and initial conditions.
parameters <- c(betaCC = 100, betaCA = 10, betaAC = 10, betaAA = 20,
gamma = 10, lC = 0.0666667, muC = 0.0, muA = 0.016667)
initials <- c(SC = 0.1, IC = 0.0001, SA = 0.1, IA = 0.0001)

# Solve and plot.

sir2AgeClasses <- sir2AgeClasses(pars = parameters,
init = initials, time = seq(0, 100, 0.01))
PlotMods(sir2AgeClasses, variables = c('IA', 'IC'), grid = FALSE)

SIR2Stages SIR model with 2 age classes (P 3.3).

Description
Solves a SIR model two different age-groups.

Usage
SIR2Stages(pars = NULL, init = NULL, time = NULL, ...)

Arguments
pars vector with 8 values: 4 transmission rates, 1 recovery rate, rate at which chil-
dren mature, death rate in the childhood group and death rate in the adult group.
The names of these values must be "betaCC","betaCA","betaAC", "betaAA",
"gamma", "lC","muC" and "muA", respectively. The letters after the word
"beta" denote transmission to any group from any group, e.g., "betaCA" rep-
resent transmission to children group from adult group. All parameters must be
SIR2Stages 13

positive. Parameters "nC" na "nu" (proportion of the population that are in the
childhood group and birth rate into the childhood class, respectively) are not de-
fined explicitly but calculated as: nC = muA/(lC+muA) and nu = (lC+nuA)nC.
All rates are specified in years and all parameters must be positive
init vector with 4 values: the initial proportion of the population that are both sus-
ceptible and in the childhood group, the initial proportion of the population that
are both infectious and in the childhood group, the initial proportion of the pop-
ulation that are both susceptible and in the adult group, and the initial proportion
of the population that are both infectious and in the adult group. The names of
these values must be "SC", "IC", "SA" and "IA", respectively. Requirements:
SC + IC <= nC, and SA + IA <= nA = 1 - nC.
time time sequence for which output is wanted; the first value of times must be the
initial time.
... further arguments passed to ode function.

Details
This is the R version of program 3.3 from page 79 of "Modeling Infectious Disease in humans and
animals" by Keeling & Rohani.

Value
list. The first element, *$model, is the model function. The second, third and fourth elements
are the vectors (*$pars, *$init, *$time, containing the pars, init and time arguments of the
function. The fifth element *$results is a data.frame with up to as many rows as elements in
time. First column contains the time. The following columns contain the proportion of susceptibles,
infectious and recovered.

References
Keeling, Matt J., and Pejman Rohani. Modeling infectious diseases in humans and animals. Prince-
ton University Press, 2008.

See Also
ode.

Examples
# Parameters and initial conditions.
parameters <- c(betaCC = 100, betaCA = 10, betaAC = 10, betaAA = 20,
gamma = 10, lC = 0.0666667, muC = 0.0, muA = 0.016667)
initials <- c(SC = 0.1, IC = 0.0001, SA = 0.1, IA = 0.0001)

# Solve the system.

sir2stages <- SIR2Stages(pars = parameters,
init = initials, time = seq(0, 100, 0.01))
14 SIR2TypesImports

SIR2TypesImports SIR model with two types of imports (P 6.6).

Description
Solves a model with two types of stochastic imports and demographic stochasticit

Usage
SIR2TypesImports(pars = NULL, init = NULL, time = NULL, ...)

Arguments
pars vector with 5 parameters: transmission rate, recovery rate and per capita death
rate. The names of these values must be "beta", "gamma", "mu", "epsilon" and
"delta" respectively. All parameters must be positive. The birth rate is assumed
to be constant and equal to mu * N, therefore preventing extinction of the host
population.
init vector with 3 values: the initial population size that are susceptible, infectious
and the total population size. The names of these values must be "X", "Y" and
"N", respectively. All initial conditions must be positive and all refer to integer
numbers.
time time sequence for which output is wanted; the first value of times must be the
initial time.
... further arguments passed to ode function.

Details
This is the R version of program 6.6 from page 210 of "Modeling Infectious Disease in humans and
animals" by Keeling & Rohani.

Value
list. The first, second and third elements are the vectors (*$pars, *$init, *$time, containing the
pars, init and time arguments of the function. The fourth element *$results is a data.frame
with up to as many rows as elements in time. First column contains the time. The following columns
contain the number of susceptibles, infectious, recovered and boolean for epsilon and delta imports.

References
Keeling, Matt J., and Pejman Rohani. Modeling infectious diseases in humans and animals. Prince-
ton University Press, 2008.

See Also
ode.
SIRAdditiveNoise 15

Examples
# Parameters and initial conditions.
parameters <- c(beta = 1, gamma = 0.1, mu = 5e-4,
epsilon = 2e-5, delta = 0.01)
initials <- c(X = 5, Y = 2, N = 50)

# Solve and plot.

sir.2types.imports <- SIR2TypesImports(parameters, initials, 2 * 365)
PlotMods(sir.2types.imports)

SIRAdditiveNoise SIR model with constant additive noise (P 6.1).

Description
Solves a SIR model with constant additive noise added to the transmission rate.

Usage
SIRAdditiveNoise(pars = NULL, init = NULL, time = NULL, step = 1, ...)

Arguments
pars vector with 5 values: the transmission rate, the recovery rate, the birth (deadth)
rate, the amount of noise experienced in the transmission rate and the popula-
tion size assumed to be constant. The names of these values must be "beta",
"gamma", "mu", "noise", and "N" respectively.
init vector with 2 values: the initial number of susceptibles and infectious. The
names of these values must be "X", and "Y", respectively. "X" and "Y" must be
positive and are numbers not proportions.
time time sequence for which output is wanted; the first value of times must be the
initial time.
step step size to set the integration step and to scale the noise term.
... further arguments passed to ode function.

Details
This is the R version of program 6.1 from page 194 of "Modeling Infectious Disease in humans and
animals" by Keeling & Rohani.

Value
list. The first element, *$model, is the model function. The second, third and fourth elements
are the vectors *$pars, *$init and *$time, containing the pars, init and time arguments of the
function. The fifth element *$results is a data.frame with up to as many rows as elements in
time. First column contains the time. Second and third columns contain the number of susceptibles
and recovered.
16 SIRBirthDeath

References

Keeling, Matt J., and Pejman Rohani. Modeling infectious diseases in humans and animals. Prince-
ton University Press, 2008.

See Also

ode.

Examples
# Parameters and initial conditions.
parameters <- c(beta = 1, gamma = 1 / 10, mu = 1 / (50 * 365),
noise = 10, N = 1e6)
initials <- c(X = 1e5, Y = 500)

# Solve and plot.

sir.additive.noise <- SIRAdditiveNoise(pars = parameters, init = initials,
time = 0:(2 * 365), step = 1)
PlotMods(sir.additive.noise)

SIRBirthDeath SIR model with births and deaths (P 2.2).

Description

Solves a simple SIR model with equal births and deaths.

Usage

SIRBirthDeath(pars = NULL, init = NULL, time = NULL, ...)

Arguments

pars vector with 3 values: the per capita death rate (equal to the population level
birth rate), the transmission rate, and the recovery rate. The names of these
values must be "mu", "beta", and "gamma", respectively.
init vector with 3 values: the initial proportion of proportion of susceptibles, in-
fectious and recovered. The names of these values must be "S", "I" and "R",
respectively.
time time sequence for which output is wanted; the first value of times must be the
initial time.
... further arguments passed to ode function.
SIRCarrierState 17

Details
This is the R version of program 2.2 from page 27 of "Modeling Infectious Disease in humans and
animals" by Keeling & Rohani.
All parameters must be positive and S + I + R <= 1.

Value
list. The first element, *$model, is the model function. The second, third and fourth elements
are the vectors *$pars, *$init, *$time, containing the pars, init and time arguments of the
function. The fifth element *$results is a data.frame with up to as many rows as elements in
time. First column contains the time. Second, third and fourth columns contain the proportion of
susceptibles, infectious and recovered.

References
Keeling, Matt J., and Pejman Rohani. Modeling infectious diseases in humans and animals. Prince-
ton University Press, 2008.

See Also
ode.

Examples
# Parameters and initial conditions.
parameters <- c(mu = 1 / (70 * 365),
beta = 520 / 365, gamma = 1 / 7)
initials <- c(S = 0.1, I = 1e-4, R = 1 - 0.1 - 1e-4)

# Solve and plot.

sir.birth.death <- SIRBirthDeath(pars = parameters, init = initials,
time = 0:(60 * 365))
PlotMods(sir.birth.death)

SIRCarrierState SIR model with carrier state (2.7).

Description
Solves a SIR model with carrier state.

Usage
SIRCarrierState(pars = NULL, init = NULL, time = NULL, ...)
18 SIRCarrierState

Arguments
pars vector with 6 values: the per capita death, transmission, infectious-recovery
and carrier-recovery rates, the proportion of reduction in transmission from car-
riers compared with infectious and the proportion of infectious that become car-
riers. The names of these values must be "mu", beta", "gamma", "Gamma",
"epsilon" and "rho", respectively.
init vector with 4 values: the initial proportion of proportion of susceptibles, infec-
tious, carriers and recovered. The names of these values must be "S", "I", "C"
and "R", respectively.
time time sequence for which output is wanted; the first value of times must be the
initial time.
... further arguments passed to ode function.

Details
This is the R version of program 2.7 from page 44 of "Modeling Infectious Disease in humans and
animals" by Keeling & Rohani.
All parameters must be positive and S + I + C + R <= 1.

Value
list. The first element, *$model, is the model function. The second, third and fourth elements
are the vectors (*$pars, *$init, *$time, containing the pars, init and time arguments of the
function. The fifth element *$results is a data.frame with up to as many rows as elements in
time. First column contains the time. Second to fifth column contain the proportion of susceptibles,
infectious, cariers and recovered.

References
Keeling, Matt J., and Pejman Rohani. Modeling infectious diseases in humans and animals. Prince-
ton University Press, 2008.

See Also
ode.

Examples
# Parameters and initial conditions.
parameters <- c(mu = 1 / (50 * 365), beta = 0.2,
gamma = 0.1, Gamma = 0.001,
epsilon = 0.1, rho = 0.4)
initials <- c(S = 0.1, I = 1e-4, C = 1e-3, R = 1 - 0.1 - 1e-4 - 1e-3)

# Solve the system.

sir.carrier.state <- SIRCarrierState(pars = parameters,
init = initials, time = 0:60)
PlotMods(sir.carrier.state)
SIRDemogStoch 19

SIRDemogStoch SIR model with demographic stochasticity (P 6.4).

Description
Solves a SIR model with demographic stochasticity

Usage
SIRDemogStoch(pars = NULL, init = NULL, time = NULL, ...)

Arguments
pars vector with 3 parameters: transmission rate, recovery rate and per capita death
rate. The names of these values must be "beta", "gamma" and "mu", respec-
tively. All parameters must be positive and all rates are specified in days. The
birth rate is assumed to be constant and equal to mu * N, therefore preventing
extinction of the host population.
init vector with 3 values: the initial population size that are susceptible, infectious
and the total population size. The names of these values must be "X", "Y" and
"N", respectively. All initial conditions must be positive.
time time sequence for which output is wanted; the first value of times must be the
initial time.
... further arguments passed to ode function.

Details
This is the R version of program 6.4 from page 203 of "Modeling Infectious Disease in humans and
animals" by Keeling & Rohani.

Value
list. The first, second and third elements are the vectors (*$pars, *$init, *$time, containing the
pars, init and time arguments of the function. The fourth element *$results is a data.frame
with up to as many rows as elements in time. First column contains the time. The following columns
contain the proportion of susceptibles, infectious and recovered.

References
Keeling, Matt J., and Pejman Rohani. Modeling infectious diseases in humans and animals. Prince-
ton University Press, 2008.

See Also
ode.
20 SIRInducedMortality

Examples
# Parameters and initial conditions.
parameters <- c(beta = 1, gamma = 1 / 10, mu = 5e-4)
initials <- c(X = 500, Y = 25, N = 5e3)

# Solve and plot.

sir.demog.stoch <- SIRDemogStoch(pars = parameters,
init = initials, time = 2 * 365)
PlotMods(sir.demog.stoch)

SIRInducedMortality SIR model with disease induced mortality: Density-dependent trans-

mission (P 2.3).

Description
Solves a SIR model with a probability of mortality, and unequal births and deaths.

Usage
SIRInducedMortality(pars = NULL, init = NULL, time = NULL, ...)

Arguments
pars vector with 5 values: the probability that an infected individual dies from the
disease before recovering, the per capita death rate from natural causes, the pop-
ulation level birth rate, the transmission rate, and the recovery rate. The name
of these values must be: "rho", "mu", "nu", "beta", and "gamma", respectively.
All parameters must be positive.
init vector with 3 values: the initial number of susceptibles, infectious and recov-
ered. The names of these values must be "X", "Y" and "Z", respectively.
time time sequence for which output is wanted; the first value of times must be the
initial time.
... further arguments passed to ode function.

Details
This is the R version of program 2.3 from page 35 of "Modeling Infectious Disease in humans and
animals" by Keeling & Rohani.

Value
list. The first element, *$model, is the model function. The second, third and fourth elements
are the vectors *$pars, *$init and *$time, containing the pars, init and time arguments of
the function. The fifth element *$results is a data.frame with up to as many rows as elements
in time. First column contains the time. Second, third and fourth columns contain the number of
susceptibles, infectious and recovered.
SIRInducedMortality2 21

References
Keeling, Matt J., and Pejman Rohani. Modeling infectious diseases in humans and animals. Prince-
ton University Press, 2008.

See Also
ode.

Examples
# Parameters and initial conditions.
parameters <- c(rho = 0.5, mu = 1 / (70 * 365), nu = 1 / (70 * 365),
beta = 520 / 365.0, gamma = 1 / 7)
initials <- c(X = 0.2, Y = 1e-4, Z = 1 - 0.2 - 1e-4)

# Solve and plot.

# Uncomment the following lines (running it takes more than a few seconds):
# sir.induced.mortality <- SIRInducedMortality(pars = parameters,
# init = initials,
# time = 0:1e5)
# PlotMods(sir.induced.mortality)

SIRInducedMortality2 SIR model with disease induced mortality: frequency-dependent trans-

mission (P 2.4).

Description
Solves a SIR model with a probability of mortality, and unequal births and deaths

Usage
SIRInducedMortality2(pars = NULL, init = NULL, time = NULL, ...)

Arguments
pars vector with 5 values: the probability than an infected individual dies from the
disease before recovering, the per capita death rate from natural causes, the pop-
ulation level birth rate, the transmission rate, and the recovery rate. The names
of these values must be "rho", "mu", "nu", "beta", and "gamma", respectively.
All parameters must be positive.
init vector with 3 values: the initial number of susceptibles, infectious and recov-
ered. The names of these values must be "X", "Y" and "Z", respectively.
time time sequence for which output is wanted; the first value of times must be the
initial time.
... further arguments passed to ode function.
22 SIRPartialImmunity

Details

This is the R version of program 2.4 from page 36 of "Modeling Infectious Disease in humans and
animals" by Keeling & Rohani.

Value

list. The first element, *$model, is the model function. The second, third and fourth elements
are the vectors (*$pars, *$init, *$time, containing the pars, init and time arguments of the
function. The fifth element *$results is a data.frame with up to as many rows as elements in
time. First column contains the time. Second, third and fourth columns contain the number of
susceptibles, infectious and recovered.

References

Keeling, Matt J., and Pejman Rohani. Modeling infectious diseases in humans and animals. Prince-
ton University Press, 2008.

See Also

ode.

Examples
# Parameters and initial conditions.
parameters<- c(rho = 0.5,mu = 1 / (70 * 365.0),nu= 1 / (70 * 365.0),
beta = 520 / 365.0, gamma = 1 / 7)
initials <- c(X = 0.2, Y = 1e-4, Z = 1 - 0.2 - 1e-4)

# Solve and plot.

sir.induced.mortality2 <- SIRInducedMortality2(pars = parameters,
init = initials,
time = 0:1e4)
PlotMods(sir.induced.mortality2)

SIRPartialImmunity SIR model with partial immunity (P 4.1).

Description

Solves a model with partial immunitiy.

Usage

SIRPartialImmunity(pars = NULL, init = NULL, time = NULL, ...)

SIRPartialImmunity 23

Arguments
pars vector with 9 values: the death, birth, transmission and recovery rates, the
modified susceptiblity to strain i for those individuals recovered from the other
strain and the modified transmission rate of strain i from those individuals that
have recovered from the other strain. The name of these values must be "mu",
"v", "beta1", "beta2", "gamma1", "gamma2", "alpha1", "aplha2", "a1", "a2".
The numbers 1 and 2 at the end of parameters names stand for strain 1 and strain
2.
init vector with 8 values: In this formulation NAB refers to the proportion of the
population who are A with respect to strain 1 and B with respect to strain
2. Thus, initial values must be named: "NSS", "NIS", "NRS", "NRI", "NSI",
"NSR", "NIR" and "NRR". The sum of initial values must be <= 1.
time time sequence for which output is wanted; the first value of times must be the
initial time.
... further arguments passed to ode function.

Details
This is the R version of program 4.1 from page 118 of "Modeling Infectious Disease in humans and
animals" by Keeling & Rohani.

Value
list. The first element, *$model, is the model function. The second, third and fourth elements
are the vectors (*$pars, *$init, *$time, containing the pars, init and time arguments of the
function. The fifth element *$results is a data.frame with up to as many rows as elements in
time. First column contains the time. Second, third and fourth columns contain the proportion of
susceptibles, infectious and recovered.

References
Keeling, Matt J., and Pejman Rohani. Modeling infectious diseases in humans and animals. Prince-
ton University Press, 2008.

See Also
ode.

Examples
# Parameters and initial conditions.
parameters <- c(mu = 1 / (70 * 365), beta1 = 260 / 365,
beta2 = 520 / 365, gamma1 = 1 / 7,
gamma2 = 1 / 7, alpha1 = 0.5,
alpha2 = 0.4, a1 = 0.4, a2 = 0.5)

initials <- c(NSS = 0.1, NIS = 1e-4, NRS = 0.02, NRI = 0,

NSI = 1e-4, NSR = 0.5, NIR = 0, NRR = 0.3798)
24 SIRScaledAdditiveNoise

# Solve and plot.

sir.partial.immunity <- SIRPartialImmunity(pars = parameters,
init = initials,
time = 0:(100 * 365))
PlotMods(sir.partial.immunity, variables = c('NIS', 'NIR'), grid = FALSE)

SIRScaledAdditiveNoise
SIR model with Scaled additive noise (P 6.2).

Description
Solves a SIR model with scaled additive noise.

Usage
SIRScaledAdditiveNoise(pars = NULL, init = NULL, time = NULL, ...)

Arguments
pars vector with 5 parameters: transmission rate, recovery rate, per capita death
rate, the total population size and the number of steps that will change noise
term. The names of these values must be "beta", "gamma", "mu", "N" and
"step", respectively. All parameters must be positive and all rates are specified
in days. The birth rate is assumed to be constant and equal to mu * N, therefore
preventing extinction of the host population. Noise terms are generated as a
function of the time step and its magnitude is a function of the rate of each
process.
init vector with 2 values: the initial population size that are susceptible and infec-
tious. The names of these values must be "X" and "Y", respectively. All initial
conditions must be positive.
time time sequence for which output is wanted; the first value of times must be the
initial time.
... further arguments passed to ode function.

Details
This is the R version of program 6.2 from page 197 of "Modeling Infectious Disease in humans and
animals" by Keeling & Rohani.

Value
list. The first element, *$model, is the model function. The second, third and fourth elements
are the vectors (*$pars, *$init, *$time, containing the pars, init and time arguments of the
function. The fifth element *$results is a data.frame with up to as many rows as elements in
time. First column contains the time. The following columns contain the proportion of susceptibles,
infectious and recovered.
SIRSinusoidalBirth 25

References
Keeling, Matt J., and Pejman Rohani. Modeling infectious diseases in humans and animals. Prince-
ton University Press, 2008.

See Also
ode.

Examples
# Parameters and initial conditions.
parameters <- c(beta = 1, gamma = 1 / 10, mu = 1 / (50 * 365),
N = 1e6, step = 1)
initials <- c(X = 1e5, Y = 500)

# Solve and plot.

sir.scaled.additive.noise <-
SIRScaledAdditiveNoise(pars = parameters,
init = initials, time = 5 * 365)
PlotMods(sir.scaled.additive.noise)

SIRSinusoidalBirth SIR model with sinusoidal births (P 5.3).

Description
Solves a SIR model with sinusoidal forcing of the birth rate.

Usage
SIRSinusoidalBirth(pars = NULL, init = NULL, time = NULL, ...)

Arguments
pars list with: the transmission rate, the mean birth rate, a scalar (or a vector to
create bifurcations) with the amplitude of sinuoidal forcing for the birth rate,
the frequency of the oscillations, the per capita death rate and the recovery rate.
The names of these values must be "beta", "alpha0", "alpha1", "w", "mu" and
"gamma", respectively. All rates must be specified in days and alpha1 <= 1.
init vector with 3 values: the initial proportion of susceptibles and infectious. The
names of these values must be "S" and "I", respectively. All parameters must be
positive and S + I <= 1.
time time sequence for which output is wanted; the first value of times must be the
initial time.
... further arguments passed to ode function.
26 SIRSinusoidalBirth

Details
This is the R version of program 5.3 from page 184 of "Modeling Infectious Disease in humans and
animals" by Keeling & Rohani. To create bifurcations, alpha1 must be a vector. For bifurcations,
if max(time) < 3650), time is defined as c(0:3650). Here, different to the original Python code, we
wrote equations for the R population as R = 1 - S - I.

Value
list. The first element, *$model, is the model function. The second element is a list with the
the *$pars argument. The third and fourth elements are the vectors (*$init, *$time, containing
the init and time arguments of the function. The fifth element *$results is a data.frame with
up to as many rows as elements in time. First column contains the time. Second, third and fourth
columns contain the proportion of susceptibles, infectious and recovered.

References
Keeling, Matt J., and Pejman Rohani. Modeling infectious diseases in humans and animals. Prince-
ton University Press, 2008.

See Also
ode.

Examples

# Parameters and initial conditions (bifurcation plot of infectious)

parameters <- list(beta = 17 / 13, alpha0 = 1 / (50 * 365),
alpha1 = 0.25, w = 2 * pi / 365 ,
mu = 1 / (50 * 365), gamma = 1 / 13)

parameters2 <- list(beta = 17 / 13, alpha0 = 1 / (50 * 365),

alpha1 = seq(0, 0.99, 0.01), w = 2 * pi / 365 ,
mu = 1 / (50 * 365), gamma = 1 / 13)

initials <- c(S = 1 / 17, I = 1e-4, R = 1 - (1 / 17 + 1e-4))

# Solve and plot.

sir.sinusoidal.birth <- SIRSinusoidalBirth(pars = parameters,
init = initials,
time = 0:(20 * 365))
PlotMods(sir.sinusoidal.birth)

# Bifurcations
# Uncomment the following lines (running it takes more than a few seconds):
# bifurcation <- SIRSinusoidalBirth(pars = parameters2,
# init = initials,
# time = 0:(20 * 365))
# PlotMods(bifur, bifur = TRUE)
SIRSinusoidalForcing 27

SIRSinusoidalForcing SIR model with sinusoidal forcing (P 5.1).

Description
Solves a SIR model with sinusoidal forcing of the transmission rate.

Usage
SIRSinusoidalForcing(pars = NULL, init = NULL, time = NULL, ...)

Arguments
pars list with 4 values: the death rate, the mean transmission rate, a scalar (or
a vector to create bifurcations) with the amplitude of sinusoidal forcing, the
frequency of oscillations and the recovery rate. The names for these values must
be: "mu", "beta0", "beta1", "omega" and "gamma", respectively.
init vector with 3 values: initial proportion of proportion of susceptibles, infectious
and recovered. The names of these values must be "S", "I" and "R", respectively.
All parameters must be positive and S + I <= 1.
time time sequence for which output is wanted; the first value of times must be the
initial time.
... further arguments passed to ode function.

Details
This is the R version of program 5.1 from page 160 of "Modeling Infectious Disease in humans and
animals" by Keeling & Rohani.
When beta1 is a vector in pars, it must be a sequence between 0 and 1.

Value
list. The first element, *$model, is the model function. The second, third and fourth elements
are the vectors (*$pars, *$init, *$time, containing the pars, init and time arguments of the
function. The fifth element *$results is a data.frame with up to as many rows as elements in
time. First column contains the time. Second, third and fourth columns contain the proportion of
susceptibles, infectious and recovered.

References
Keeling, Matt J., and Pejman Rohani. Modeling infectious diseases in humans and animals. Prince-
ton University Press, 2008.

See Also
ode.
28 SIRTauLeap

Examples
# Parameters and initial conditions.
parameters <- list(beta0 = 17 / 13, beta1 = 0.1, gamma = 1 / 13,
omega = 2 * pi / 365, mu = 1 / (50 * 365))

initials <- c(S = 1 / 17, I = 1e-4,

R = 1 - 1 / 17 - 1e-4)

# Solve and plot.

sir.sinusoidal.forcing <- SIRSinusoidalForcing(pars = parameters,
init = initials,
time = 0:(60 * 365))
PlotMods(sir.sinusoidal.forcing)

# Solve bifurcation dynamics for 20 years.

# If max(time) < 3650, bifurcation dynamics are solved for 3650 time-steps.
parameters2 <- list(beta0 = 17 / 13, beta1 = seq(0.001, 0.251, by = 0.001),
gamma = 1 / 13, omega = 2 * pi / 365, mu = 1 / (50 * 365))
# Uncomment the following lines (running it takes more than a few seconds):
# bifur <- SIRSinusoidalForcing(pars = parameters2,
# init = initials,
# time = 0:(20 * 365))
# PlotMods(bifur, bifur = TRUE)

SIRTauLeap SIR model with tau leap method (P 6.5).

Description
SIR model with demographic stochasticity approximated using the tau-leap method and assuming
Poisson distributions.

Usage
SIRTauLeap(pars, init, end.time)

Arguments
pars vector with 5 values: the transmission, recovery and death rates, the population
size assumed to be constant and the time step. The names of these values must
be "beta", "gamma", "mu", "N" and "tau" respectively.
init vector with 3 values: the initial number of susceptibles, infectious and recov-
ered, respectively. The names of these values must be "X", "Y" and "Z" respec-
tively.
end.time end time to be simulated.
SIRTermTimeForcing 29

Details
This is the R version of program 6.5 from page 204 of "Modeling Infectious Disease in humans and
animals" by Keeling & Rohani.

Value
list. The first three elements are the vectors *$pars, *$init and *$time, containing the pars,
init and end.time arguments of the function. The fourth element *$results is a data.frame
with up to as many rows as time steps determined by the parameters tau and end.time. The
first column contains the time steps. The second, third and fourth columns contain the number of
susceptibles, infectious and recovered.

References
Keeling, Matt J., and Pejman Rohani. Modeling infectious diseases in humans and animals. Prince-
ton University Press, 2008.

Examples
# Parameters and initial conditions.
parameters <- c(beta = 1, gamma = 1 / 10, mu = 5e-4, N = 50, tau = 1)
initials <- c(X = 5, Y = 1, Z = 44)
end.time <- 2 * 365

# Solve and plot.

sir.demog.stoch <- SIRTauLeap(pars = parameters, init = initials,
end.time = end.time)
PlotMods(sir.demog.stoch)

SIRTermTimeForcing SIR model with corrected term-time forcing (P 5.2).

Description
Solves a SIR model with corrected term-time forcing of the transmission rate.

Usage
SIRTermTimeForcing(
pars = NULL,
init = NULL,
term.times = terms,
cicles = 10,
low.term.first = TRUE,
...
)
30 SIRTermTimeForcing

Arguments

pars list with 4 values: the mean transmission rate, a scalar (or a vector to create
bifurcations) with the amplitude of sinusoidal forcing, the removal recovery rate,
and the per capita death rate. The names for these values must be: "beta0",
"beta1", "gamma", and "mu", respectively. All parameters must be positive and
beta1 <= 1.
init vector with 3 values: the initial proportion of proportion of susceptibles, in-
fectious and recovered. The names of these values must be "S", "I" and "R",
respectively. S + I + R <= 1.
term.times vector indicating the term times (see details and example).
cicles value indicating how many times term.times must be simulated (see details
and example).
low.term.first logical. If TRUE (default), the first term-time is considered -1, the second 1, the
tirth -1 and so on. When FALSE, the first term-time is 1, the second -1, and so on
(see example).
... further arguments passed to ode function.

Details

This is the R version of program 5.2 from page 171 of "Modeling Infectious Disease in humans and
animals" by Keeling & Rohani.
This model is based on the behaviour os measles and other child-hood diseases. Transmission rate
is low during term == -1 (e.g. holydas term) and high during term == 1 (e.g. school term). We can
define the year as the temporal unit of cicles and each cicle is composed by a term-time sequence
(see example).

Value

list. The first element, *$model, is the model function. The second, third and fourth elements are
vectors (*$pars, *$init, *$time, respectively) containing the pars, init and time arguments of
the function. The fifth element *$results is a data.frame with up to as many rows as elements
in time. First column contains the time. Second, third and fourth columns contain the proportion of
susceptibles, infectious and recovered.

References

Keeling, Matt J., and Pejman Rohani. Modeling infectious diseases in humans and animals. Prince-
ton University Press, 2008.

See Also

ode.
SIRVector 31

Examples
## Parameters and initial conditions.
initials <- c(S = 1/17, I = 1e-4, R = 1 - 1/17 - 1e-4)
parameters <- list(beta0 = 17 / 13, beta1 = 0.25,
gamma = 1 / 13, mu = 1 / (50 * 365))

## Term-times and cycles

# In a year-unit cicle, holidays happen for example
# between days 1 and 6, 101 and 115, 201 and 251,
# 301 and 307 and 308 and 365.
# Setting low.term.first == TRUE (default) we define the
# previous term-times as low terms.
# Simulate 10 years.
terms <- c(1, 6, 100, 115, 200, 251, 300, 307, 356, 365)
cicles <- 10

# Solve and plot.

sir.term.time.forcing <- SIRTermTimeForcing(pars = parameters,
init = initials,
term.times = terms,
cicles = 10)
PlotMods(sir.term.time.forcing)

# Solve bifurcation dynamics for 20 years.

# If the number of time-units per cicle (e.g. days) times
# the number of cicles (e.g. number of days) is less
# than 3650, bifurcation dynamics are solved for 3650
# time-steps
parameters2 <- list(beta0 = 17 / 13,
beta1 = seq(0, 0.3, by = 0.001),
gamma = 1 / 13, mu = 1 / (50 * 365))
# Uncomment the following lines (running it takes more than a few seconds):
# bifur <- SIRTermTimeForcing(pars = parameters2, init = initials,
# term.times = terms, cicles = 10)
# PlotMods(bifur, bifur = TRUE)

SIRVector SIR model for mosquito vectors (P 4.4).

Description

Solves a simple SIR model for mosquito vectors.

Usage

SIRVector(pars = NULL, init = NULL, time = NULL, ...)

32 SIRVector

Arguments
pars vector with 8 values: the human mortality rate (muH), the mosquito mortality
rate (muM), the human birth rate (vH), the mosquito birth rate (vM), the trans-
mission probability from humans to mosquitos following a bite (betaHM), the
transmission probability from mosquitos to humans, following a bite (betaMH),
the human recovery rate (gamma) and the rate at which humans are bitten (r).
Abbreviations in parenthesis indicate the names which must be given to the val-
ues.
init vector with 4 values: the initial numbers of susceptible humans, susceptible
mosquitos, infectious humans and infectious mosquitos. The names of this val-
ues must be "XH", "XM", "YH" and "YM", respectively.
time time sequence for which output is wanted; the first value of times must be the
initial time.
... further arguments passed to ode function.

Details
This is the R version of program 4.2 from page 123 of "Modeling Infectious Disease in humans and
animals" by Keeling & Rohani.

Value
list. The first element, *$model, is the model function. The second, third and fourth elements are
vectors (*$pars, *$init, *$time, respectively) containing the pars, init and time arguments of
the function. The fifth element *$results is a data.frame with up to as many rows as elements
in time. First column contains the time. Second, third and fourth columns contain the proportion of
susceptibles, infectious and recovered.

References
Keeling, Matt J., and Pejman Rohani. Modeling infectious diseases in humans and animals. Prince-
ton University Press, 2008.

See Also
ode.

Examples
# Parameters and initial conditions.
parameters <- c(muH = 5.5e-5, muM = 0.143,
vH = 5.5e-2, vM = 1.443e3,
betaHM = 0.5, betaMH = 0.8,
gamma = 0.033, r = 0.5 / 1e3)

initials <- c(XH = 1e3, XM = 1e4, YH = 1, YM = 1)

# Solve and plot.

sir.vector <- SIRVector(pars = parameters,
SIS 33

init = initials,
time = 0:1000)
PlotMods(sir.vector)

SIS Simple SIS model (P 2.5).

Description
Solves a simple SIS model without births or deaths.

Usage
SIS(pars = NULL, init = NULL, time = NULL, ...)

Arguments
pars vector with 2 values: the transmission and recovery rates. The names of these
values must be "beta", and "gamma", respectively.
init vector with 2 values: the initial proportion of proportion of susceptibles and
infectious. The names of these values must be "S" and "I", respectively.
time time sequence for which output is wanted; the first value of times must be the
initial time.
... further arguments passed to ode function.

Details
This is the R version of program 2.5 from page 39 of "Modeling Infectious Disease in humans and
animals" by Keeling & Rohani.
All parameters must be positive and S + I <= 1.

Value
list. The first element, *$model, is the model function. The second, third and fourth elements are
the vectors (*$pars, *$init, *$time, containing the pars, init and time arguments of the func-
tion. The fifth element *$results is a data.frame with up to as many rows as elements in time.
First column contains the time. Second and third columns contain the proportion of susceptibles
and infectious.

References
Keeling, Matt J., and Pejman Rohani. Modeling infectious diseases in humans and animals. Prince-
ton University Press, 2008.

See Also
ode.
34 SIS2RiskGroups

Examples
# Parameters and initial conditions.
parameters <- c(beta = 1.4247, gamma = 0.14286)
initials <- c(S = 1 - 1e-06, I = 1e-06)

# Solve and plot.

sis <- SIS(pars = parameters, init = initials, time = 0:70)
PlotMods(sis)

SIS2RiskGroups SIS model with 2 risk groups (P 3.1).

Description

Solves a SIS model with high-risk (H) and low-risk (L).

Usage

SIS2RiskGroups(pars = NULL, init = NULL, time = NULL, ...)

Arguments

pars vector with 6 values: 4 transmission rates, 1 recovery rate and the proportion of
the population that are in the high-risk group. The names of these values must be
"betaHH","betaHL","betaLL", "betaLH", "gamma" and "nH", respectively. The
letters after the word "beta" denote transmission to any group from any group,
e.g., "betaHL" represent transmission to high-risk group from low-risk group.
All parameters must be positive.
init vector with 2 values: the initial proportion of infectious in the high-risk group
and the intial proportion of infectious in the low-risk group. The names of these
values must be "IH" and "IL", respectively.
time time sequence for which output is wanted; the first value of times must be the
initial time.
... further arguments passed to ode function.

Details

This is the R version of program 3.1 from page 58 of "Modeling Infectious Disease in humans and
animals" by Keeling & Rohani.
All parameters must be positive and nH <= 1, IH(0) <= nH, IL(0) <= 1-nH.
SISDemogStoch 35

Value
list. The first element, *$model, is the model function. The second, third and fourth elements
are the vectors (*$pars, *$init, *$time, containing the pars, init and time arguments of the
function. The fifth element *$results is a data.frame with up to as many rows as elements in
time. First column contains the time. The following columns contain the proportion of susceptibles
and infectious.

References
Keeling, Matt J., and Pejman Rohani. Modeling infectious diseases in humans and animals. Prince-
ton University Press, 2008.

See Also
ode.

Examples
# Parameters and initial conditions.
parameters <- c(betaHH = 10.0, betaHL = 0.1, betaLH = 0.1,
betaLL = 1.0, gamma = 1, nH = 0.2)
initials <- c(IH = 0.00001, IL = 0.001)

# Solve and plot.

sis2risk.groups<- SIS2RiskGroups(pars = parameters,
init = initials, time = 0:15)
PlotMods(sis2risk.groups, variables = c('IL', 'IH'), grid = FALSE)

SISDemogStoch SIS model with demographic stochasticity (P 6.3).

Description
SIS model with event-driven or demographic stochasticity.

Usage
SISDemogStoch(pars, init, end.time)

Arguments
pars vector with 3 values: the transmission and recovery rates and the popula-
tion size assumed to be constant. The names of these values must be "beta",
"gamma", and "N" respectively.
init initial number of infectious.
end.time end time to be simulated.
36 SISinusoidalTransmBrith

Details

This is the R version of program 6.3 from page 202 of "Modeling Infectious Disease in humans and
animals" by Keeling & Rohani.

Value

list. The first three elements are the vectors *$pars, *$init and *$time, containing the pars,
init and end.time arguments of the function. The fourth element *$results is a data.frame
with up to as many rows as time steps created during the stochastic simulations. The second column
contains the number of infectious.

References

Keeling, Matt J., and Pejman Rohani. Modeling infectious diseases in humans and animals. Prince-
ton University Press, 2008.

Examples

# Parameters and initial conditions.

parameters <- c(beta = 0.03, gamma = 1 / 100, N = 100)
initials <- 70

# Solve and plot.

sis.demog.stoch <- SISDemogStoch(pars = parameters,
init = initials, end.time = 10 * 365)
PlotMods(sis.demog.stoch)

SISinusoidalTransmBrith
Rabbit Hemorrhagic Disease model with sinusoidal transmission rate
and per capita birth rate (P 5.4).

Description

Solves the Rabbit Hemorrhagic Disease, in which both transmission rate and birth rates can be
seasonally forced.

Usage

SISinusoidalTransmBrith(pars = NULL, init = NULL, time = NULL, ...)

SISinusoidalTransmBrith 37

Arguments
pars list with: the mean transmission rate, the amplitude of sinuoidal forcing (trans-
mission), the mean birth rate, the amplitude of sinuoidal forcing for the birth
rate, the frequency of the oscillations, the recovery rate, the per capita death
rate, the mortality rate due to infection, and the carrying capacity. The names of
these values must be "beta0", "beta1", "alpha0", "alpha1", "w", "gamma", "mu",
"m" and "K", respectively. All parameters must be positive, alpha1, beta1 <= 1.
init vector with 3 values: the initial numbers of susceptible hosts (rabbits), infec-
tious hosts (rabbits) and total population size. The names of these values must
be "X", "Y" and "N", respectively. All initial values must be positive and X(0)
+ Y(0) <= N(0).
time time sequence for which output is wanted; the first value of times must be the
initial time.
... further arguments passed to ode function.

Details
This is the R version of program 5.4 from page 186 of "Modeling Infectious Disease in humans and
animals" by Keeling & Rohani.

Value
list. The first element, *$model, is the model function. The second element is a list with the
*$pars argument. The third and fourth elements are the vectors *$init and *$time, containing
the init and time arguments of the function. The fifth element *$results is a data.frame with
up to as many rows as elements in time. First column contains the time. Second, third and fourth
columns contain the number of susceptibles, infectious and recovered.

References
Keeling, Matt J., and Pejman Rohani. Modeling infectious diseases in humans and animals. Prince-
ton University Press, 2008.

See Also
ode.

Examples
# Parameters and initial conditions.
parameters <- list(beta0 = 0.936, beta1 = 0.1, alpha0 = 0.02, alpha1 = 0.1,
w = 2 * pi / 365, gamma = 0.025, mu = 0.01, m = 0.475,
K = 10000)
initials <- c(X = 0.5, Y = 0.01, N = 0.6)

# Solve and plot.

sis.rhdm <- SISinusoidalTransmBrith(pars = parameters,
init = initials,
time = 0:(60 * 365))
38 SISnRiskGroups

PlotMods(sis.rhdm)

SISnRiskGroups SIS model with multiple risk groups (P 3.2).

Description
Solves a SIS model with n different risk-groups.

Usage
SISnRiskGroups(pars = NULL, init = NULL, time = NULL, ...)

Arguments
pars list with: the number of risk groups, a (m x m) matrix with the transmission
rates, a vector with the recovery rates (one for each risk group) and a vector
with the proportions of the population that are in each risk group. The names of
these elements must be "m", "beta", "gamma" and "n", respectively (see exam-
ple). All rates are specified in years.
init vector with m * 2 values: the initial proportions of susceptibles and infectious
in each risk group. The names of these values must be "S1",..., "Sm" and "I1",...,
"Im", respectively (see example). All initial states must be positive and Si + Ii =
ni, i= 1, ..., m.
time time sequence for which output is wanted; the first value of times must be the
initial time.
... further arguments passed to ode function.

Details
This is the R version of program 3.2 from page 64 of "Modeling Infectious Disease in humans and
animals" by Keeling & Rohani.
All parameters must be positive, and ni <= 1, sum(ni) = 1, i = 1, ..., m.

Value
list. The first element, *$model, is the model function. The second, third and fourth elements
are the vectors (*$pars, *$init, *$time, containing the pars, init and time arguments of the
function. The fifth element *$results is a data.frame with up to as many rows as elements in
time. First column contains the time. The following columns contain the proportion of susceptibles
and infectious of each risk group.

References
Keeling, Matt J., and Pejman Rohani. Modeling infectious diseases in humans and animals. Prince-
ton University Press, 2008.
SISPairwiseApprox 39

See Also
ode.

Examples
# Parameters and initial conditions.
tmp <-matrix(c(0, 3, 10, 60, 100))
beta <- 0.0016 * tmp %*% t(tmp)
parameters <- list(m = 5, beta = beta,
gamma = c(0.2, 0.2, 0.2, 0.2, 0.2),
n = c(0.06, 0.31, 0.52, 0.08, 0.03))
initials <- c(I = c(0, 0, 0, 0, 1e-5))

# Solve and plot.

sis.n.riks.groups <- SISnRiskGroups(pars = parameters,
init = initials,
time = 0:30)
PlotMods(sis.n.riks.groups, grid = FALSE)

SISPairwiseApprox Pairwise SIS approximation model (P 7.8).

Description
Solves a pairwise approximation to the SIS model on a random network of N individuals, each with
n contacts.

Usage
SISPairwiseApprox(pars = NULL, init = NULL, time = NULL, ...)

Arguments
pars vector with 4 values: the transmission rate across a contact, the recovery rate
for infectious individuals, the number of connections per individual in the pop-
ulation and the number of individuals in the population. The names of these
values must be "tau", "gamma", "n" and "N" respectively.
init vector with 3 values: the initial number of of susceptibles, infectious and
susceptible-infectious pairs. The names of these values must be "X", "Y" and
"XY", respectively.
time time sequence for which output is wanted; the first value of times must be the
initial time.
... further arguments passed to ode function.
40 SISPairwiseApprox

Details
This is the R version of program 7.8 from page 285 of "Modeling Infectious Disease in humans and
animals" by Keeling & Rohani.
All parameters must be positive.

Value
list. The first element, *$model, is the model function. The second, third and fourth elements
are the vectors *$pars, *$init and *$time, containing the pars, init and time arguments of
the function. The fifth element *$results is a data.frame with up to as many rows as elements
in time. First column contains the time. Second, third and fourth columns contain the number of
susceptibles, infectious and susceptible-infectious pairs.

References
Keeling, Matt J., and Pejman Rohani. Modeling infectious diseases in humans and animals. Prince-
ton University Press, 2008.

See Also
ode.

Examples
# Parameters and initial conditions.
n <- 4; N <- 1e4; Y <- 1; X <- N - Y
parameters <- c(tau = 0.1, gamma = 0.05, n = n, N = N)
initials <- c(X = X, Y = Y, XY = n * Y * X / N)

# Solve and plot.

sis.pairwise.approx <- SISPairwiseApprox(pars = parameters,
init = initials, time = 0:100)
PlotMods(sis.pairwise.approx)
Index

∗Topic package SISinusoidalTransmBrith, 36

EpiDynamics-package, 2 SISnRiskGroups, 38
SISPairwiseApprox, 39
data.frame, 3, 6, 7, 9, 10, 12–15, 17–20,
22–24, 26, 27, 29, 30, 32, 33, 35–38, vector, 3, 5–16, 18–21, 23–25, 27, 28, 30,
40 32–35, 37–39

EpiDynamics-package, 2

list, 3, 6, 7, 9, 10, 12–15, 17–20, 22–27, 29,

30, 32, 33, 35–38, 40

MultiStrainPartialImmunity, 3

ode, 3, 4, 6–27, 30, 32–35, 37–40

PlotMods, 4

SEIR, 5
SEIR4AgeClasses, 7
SEIRnStages, 8
SIR, 10
sir2AgeClasses, 11
SIR2Stages, 12
SIR2TypesImports, 14
SIRAdditiveNoise, 15
SIRBirthDeath, 16
SIRCarrierState, 17
SIRDemogStoch, 19
SIRInducedMortality, 20
SIRInducedMortality2, 21
SIRPartialImmunity, 22
SIRScaledAdditiveNoise, 24
SIRSinusoidalBirth, 25
SIRSinusoidalForcing, 27
SIRTauLeap, 28
SIRTermTimeForcing, 29
SIRVector, 31
SIS, 33
SIS2RiskGroups, 34
SISDemogStoch, 35

41