Index
absorbing state, 26, 363
adaptive dynamics, 91
age at first infection, 235
age interval, 232
age pyramid, 228
age structure, 227
age-structured data, 314
agent-based models, 345
aggregation of hosts, 274
aggregation of parasites, 257
Akaike’s information criterion, 149
Allee effect, 247
Anderson-May approximation, 257
ansatz, 10
aperiodic matrix, 165
assortative network, 290
asymptotic speed of propagation, 241
autonomous system, 154
backward branching process, 17, 296
basic reproduction number, 4, 161
basic reproduction ratio, 4, 161
Bayes’ theorem, 340
Bayesian information criterion, 149
Bayesian statistics, 339, 341
between-host dynamics, 93
binomial distribution, 45
binomial likelihood, 318
birth pulse, 82
birthday problem, 54
bovine herpes virus, 120
Bovine viral diarrhea virus, 171
branching process, 5, 51
BSE, 231
case fatality, 20
cellular automaton, 287
central limit theorem, 66
characteristic equation, 10, 77
closed population, 3
cluster, 287
clustering coefficient, 290
coexistence, 99
cohort, 228
colonization, 325
compartmental models, 17
confidence interval for MLE, 130
connected component, 292
connectedness, 291
consistent estimator, 135
contact, 4, 265
consistency condition, 272
dependence, 41
duration, 266
intensity, 266
uniform, 41
contact coefficient, 229
contact matrix, 275
contact process, 41
contact rate, 4
contactee, 265
continuous random variable, 45
continuous-time branching process, 51
continuous-time Markov chain, 26
convergence stable, 99
core group, 41, 224, 277
core loop, 277
counting process, 50, 138
credibility interval, 340
critical branching process, 51
critical community size, 115
critical control effort, 199
critical vaccination coverage, 69, 114
critical vaccination effort, 199
cumulative force of infection, 62
δ-method, 135
d-age, 154
d-degree, 155
d-state, 154
damped oscillations, 77
degree correlation, 291
498
degree distribution, 287
demographic steady state, 181
demographic stochasticity, 5
demographic turnover, 3, 75
density function, 45
determinant, 77
diagonal transmission, 204
diffusion equation, 240
Dirac’s delta, 177
directed network, 289
disassortative network, 290
discrete-time Markov chain, 26
disease state, 154
dominant eigenvalue, 164
dominant eigenvector, 164
dominant Lyapunov exponent, 193
dormant infection, 120
Dulac test, 396
duration of an outbreak, 69
edge, 286
eigenvalue, 77
eigenvalue problem, 10
elasticity, 182
elimination, 85
EM-algorithm, 150
endemic, 74
endemic state, 233
endemic steady state, 76
epidemic, 3
approximating initial phase, 54
approximating main part, 58
approximating the final phase, 66
duration, 69
epidemiological data, 149
eradication, 85
Euler-Lotka equation, 228
evolutionarily stable strategy, 99
evolutionary dynamics, 91
expected infectivity, 33
exponential distribution, 17, 45, 49
exponential growth rate, 10, 212, 320
exponential random graphs, 293
exposed individual, 13
extinction probability, 52
extinction time, 74, 108
fade-out, 73
final size, 15
and partial vaccination, 68
INDEX
data, 311
in finite population, 24
in herds, 21
multi-type, 313
small populations, 312
final size for households, 285
final size in structured populations,
219
final size stochastic, 47
final-size distribution, 25, 281
final-size equation, 15
finite Markov chain, 180
finite population, 24
finite-dimensional range, 178
Floquet multiplier, 86, 193
Floquet theory, 193
fluctuating environment, 192
force of infection, 14, 17, 233
force of infection estimating, 318
force of mortality, 227
forward branching process, 297
fully connected network, 290
functional response, 267
fundamental matrix solution, 197
fungal pathogen, 239
Gaussian distribution, 45
‘general’ stochastic epidemic, 48
‘general’ stochastic model, 48
generalized linear model, 319
generation, 4
generation growth, 4
generation interval, 320
geometric distribution, 45, 375
giant component, 292
GLM, 319
global asymptotic stability, 81
gonorrhea, 277
graphs, 286
Greenwood experiments, 82
h-state, 154
distribution, 158
dynamics, 179
space, 156
hazard rate of death, 23
helminths, 251
herd immunity, 69
herds, 21
herpes, 36, 120
INDEX
HIV, 183
Holling argument, 267
Holling squared, 270
homogeneous mixing, 118
homogeneous space, 240
homogeneous system, 88
horizontal transmission, 204
hospital infections, 101, 127, 325
household epidemic model, 279
household transmission, 278
hybrid model, 82, 122, 252
i-state, 153
i.i.d., 46
ICU, 101, 127, 325
identifiability, 150
immigration-death process, 254
immune system, 92
imperfect vaccine, 87
imputation, 150
incidence, 10, 14
individual state, 153
individual-based simulation, 345
infected, 13
infected subsystem, 167
infection age, 4, 154
infection degree, 155, 253
infection pressure, 62
infection-free state, 76
infection-free steady state, 218
infectious agent, 3
infectious individual, 13
infectious period, 4
infective (individual), 13
infectivity, 33
infectivity function, 19, 23, 33, 369
inference, 127
complex models, 338
simple models, 337
initial growth rate, 4
inner product, 182, 241
intensity rate, 50
intensive care unit, 325
intensive care unit (ICU), 101
interacting particle system, 286
intrinsic growth rate, 10, 212, 320
invader, 94
invasion criterion, 386
invasion potential, 91
irreducible matrix, 165
499
isocline, 76
isolated subpopulation, 408
isotropic space, 240
Jacobi matrix, 381
Jensen’s inequality, 373
Kermack-McKendrick, 14
Kermack-McKendrick ODE model, 17,
34, 58
kernel, 173
Kostizin model, 255
Kronecker’s delta, 177
Laplace transform, 80
latency period, 4, 13
latent individual, 13
Latin hypercube sampling, 310
law of large numbers, 59, 61
law of mass action, 266, 302
left eigenvector, 181
left-continuous process, 139
life cycle, 251
life expectancy, 228
likelihood, 128
likelihood (of stochastic process), 139
likelihood-ratio test, 149
linearized stability, 76, 381
local asymptotic stability, 77
log-likelihood, 128
loop, 287
LOS, 127
macroparasite, 155, 251
macroparasites, 36
major outbreak, 25, 61, 62
malaria, 155
Malthusian parameter, 10, 54, 212
Markov chain, 36
Markov chain Monte Carlo, 150
Markov process, 49
Markov property, 49, 156
martingale, 138
zero-mean martingale, 138
mass-action kinetics, 266, 302
maximum likelihood estimate, 128, 141,
318
MCMC, 150
MCMC method, 341
mean age at infection, 78, 315
500
mean field, 304
measles, 73
measurable, 158
measure, 158
metapopulation, 92, 209
method of moments, 132, 148
Metropolis-Hastings algorithm, 343
Michaelis-Menten kinetics, 267
micro-simulations, 345
microcosm principle, 81
microparasite, 154
microparasites, 36
milker-killer dilemma, 92
minimal wave speed, 240
minor outbreak, 25, 61, 62
mixed Poisson distribution, 52
mixing, 71
ML-estimate, 128
ML-inference, 148
MLE, 128
model selection, 149
moment closure, 304
Monod equation, 267
monotonicity argument, 11
mosquito transmission, 5
multi-group separable mixing, 178, 179
multi-level mixing, 278
multi-type branching process, 207
multi-type final-size data, 313
mutation, 94
naive host, 253
naive population, 3
natural death rate, 35
negative binomial distribution, 257, 376
nested model, 93, 149
network, 286
network diameter, 292
network of acquaintances, 294
network terminology, 289
neutrality curve, 100
next-generation matrix, 163
next-generation operator, 173
NGM, 163
NGM with large domain, 167
NGM with small domain, 169
node, 286
non-negative matrix, 163
normal distribution, 45
normalized eigenvector, 164
INDEX
nosocomial infections, 101
notation, 13
nullcline, 76
one-dimensional range, 176
optional variation process, 139
order statistics, 63
oscillations, 77
overshoot phenomenon, 18
p-state, 157
pair approximation, 304
pair formation, 189, 268
parasite, 251
parasite load, 253
partial vaccination, 68, 208
Pasteurella muris, 82
percolation theory, 250
perfect vaccine, 29, 84
periodic dynamics, 193
Perron root, 244
Perron-Frobenius theory, 165
persistence, 73
pessimization principle, 95
phase transition, 115
phocine distemper virus, 20
Poisson distribution, 8, 45, 375
Poisson process, 8, 46
population density, 20, 29
population growth, 88
population size, 27
population state, 157
positive matrix, 163, 215
positive off-diagonal, 215
positive off-diagonal matrix, 105
posterior distribution, 340
power-law distribution, 292
prevalence, 14
primitive matrix, 165
prior distribution, 340
probability density, 128
probability generating function, 6, 52
probability measure, 158
probability of a major outbreak, 55,
205
probability of a minor outbreak, 7, 55
probability of extinction, 219
proportionate mixing, 176, 224
prototype stochastic model, 46, 280
protozoan parasites, 155
INDEX
pulse vaccination, 85
quasi-species, 93
quasi-stationary distribution, 106, 110,
111
quasi-stationary state, 74
quasi-steady state, 267
R0 , 4
for compartmental models, 36
and seasonality, 193
estimation, 309
for general h-state, 174
for life cycles, 260
for macroparasites, 251
for pair formation, 189
sensitivity analysis, 181
R∗ , 283
random graphs, 288
random jump process, 50
re-introduction, 73
reactivation, 120
real-time evolution, 212
real-time growth, 10, 212
recovered (individual), 13
recurrent outbreak, 73
reducible, 165
reducible matrix, 408
Reed-Frost model, 48
regulation, 87
regulation by macroparasites, 259
relaxation time, 77
renewal equation, 228
renewal point, 123, 170
repeated outbreaks, 73
reproduction number for households,
283
reproductive value, 181
resident, 94
right eigenvector, 181
Ross solution, 272
s(∞), 14
scale-free distribution, 301
scale-free network, 292
schistosomiasis, 252
seasonal dynamics, 193
SEIR model, 17
selection gradient, 98
Sellke construction, 62, 280
501
semigroup property, 153
sensitivity, 182
separable mixing, 176, 221
serial interval, 320
serological data, 314
sexual activity, 176
sexually transmitted disease, 183
short-disease approximation, 230, 314,
447
simulation studies, 344
SIR model, 17
SIRS model, 82
SIS model, 17, 82
small world model, 278
small-world property, 289
smallpox, 315
sojourn time, 37
spatial model, 239
spatio-temporal pattern, 288
spectral bound, 215
spectral radius, 164, 174, 215
spectrum, 215
speed of propagation, 240
stable age distribution, 227
stable distribution, 164, 174, 181
standard error, 135
state, 153
state at birth, 155
state at infection, 155
state space, 156
state-at-infection, 161
state-of-infectiousness, 170
statistical inference, 127
STD, 176, 183, 205, 223
STD on network, 299
stochastic epidemic model, 46
stochastic model with demography, 108
structured population, 153
subcritical, 205
subcritical branching process, 51
super-individuals, 278
super-spreader, 292
supercritical, 205
supercritical branching process, 51
superinfection, 92, 96
survival function, 227
susceptibility, 40
susceptible (individual), 13
symmetric contacts, 272
502 INDEX

targeted control, 200 wild type, 84

theory of happenings, 265 wind-borne propagules, 243
time derivative, 14 within-group contacts, 177
time to extinction, 112 within-host dynamics, 93
distribution, 110 worm-like parasites, 251
dormant infection, 120
sub-communities, 118 zero-mean process, 138
vaccinated populations, 114
time-scale argument, 267
trace, 77
trait, 153
transition, 25
transition matrix, 37, 167
transmission, 3
household structure, 279
opportunities, 271
rate, 14
rate constant, 17
transmission experiment, 319
transmission matrix, 167
transmission, indirect, 204
traveling-wave solution, 241
two-level mixing, 278
two-type branching process, 301
type, 154
Type I mortality, 312
Type II mortality, 312
type-reproduction number, 201
typical individual, 203
typical infected individual, 203

undirected network, 289

uniform mixing, 71

vaccination, 208, 234

vaccination coverage, 209
vaccination strategy, 234
vaccine efficacy, 209
variance-to-mean ratio, 259
variation-of-constants formula, 382
vector transmission, 200
vertex, 286
vertical transmission, 82, 204
virgin population, 3
virgin state, 76
virulence, 92
von Neumann neighborhood, 287

WAIFW matrix, 315

Wald’s identity, 281