.. _glossary: Glossary ======== .. currentmodule:: epydemic .. glossary:: addition-deletion process A :term:`process` that adds and removes nodes from a network. The usual model :cite:`AdditionDeletionNetworks` adds nodes at a constant rate and with constant degree, removes nodes randomly at a constant rate, and connects new nodes to existing nodes according to some probabilistic attachment kernel. clustering The tendency to find small sets of nodes with multiple paths between them. The most common kind of clustering looks for triangles of edges connecting triples of nodes. This can be made precise by defining a *clustering coefficient* that counts the number of triangles present out of all the possible triangles that could be formed in the network. An example of a network :term:`microstructure`. community Another word for :term:`modularity`. compartments The possible dynamical states in a :term:`compartmented model of disease`. compartmented model of disease A disease model that represents the progression of a disease as a set of discrete compartments with transitions possible between them. Transitions typically occur with some base probability, which might be fixed or might vary across the course of the simulation. See Hethcote :cite:`Hethcote-CompartmentedModels` for a survey, component A set of nodes connected by edges. A node with a single component is called *fully connected*. contact tree The way in which individuals were infected during thhe infection. Each node is an infected individual, with edges representing the individuals that individual infected. While it's common talk of a contact *tree*, this will only be the case if there is an identifiable "patient zero" from whom all infections arise. In the more general case of multiple people initially infected, the contact tree will actually be a contact *forest* of multiple independent trees, each one rooted at an initially-infected individual. continuous time A simulation mode in which events occur at unique times represented by real numbers. No two events ever happen simultaneously, but they can be separated by an arbitrarily small interval. Continuous-time simulations can be made statistically exact and run faster for situations in which there are long periods where no events occur. degree distribution The way in which the numbers of neighbours each node has varies. The most basic measure of network topology. More precisely, the degree distribution is the probability :math:`p_k` that a node chosen at random from the network will have degree :math:`k`, for all values of :math:`k`. Networks can have the same degree distribution but different kinds of :term:`microstructure` and :term:`mesostructure`, so degree distribution isn't always enough on its own to characterise a network completely. discrete time A simulation mode in which time progresses in single integer timesteps. During each timestep a collection of events can occur. Discrete-time simulations can be easier to code and understand. dynamical state The state of a node or edge at some point in the simulation. These typically reflect the :term:`compartments` of the simulation, but may be more complex and comprise a vector of information. epidemic threshold The critical point of transmissibility at which an outbreak becomes an epidemic and infects a substantial fraction of the network. The existence and value of an epidemic threshold depend on the topology of the network as well as the disease parameters. event A simulation event that changes the state of the underlying network or simulation. Events can occur in :term:`continuous time` or :term:`discrete time`. event function A function called when an :term:`event` fires to perform the action required. Event functions take three arguments: the current simulation time and the element at which the event occurs (which will be selected by the chosen :term:`process dynamics`). Elements are typically either nodes or edges, depending in the :term:`locus` at which the event occurs. generating functions A mathematical tool for working with entire probability distributions, often used in network science research because of its flexibility. They're often used when describing the :term:`degree distribution` of a network. See Newman *et alia* :cite:`ArbitraryDegreeDistributions` for a network science introduction and Wilf :cite:`generatingfunctionology` for a more detailed treatment. giant connected component In :term:`percolation` (and other) processes, the giant connected component (sometimes called the GCC, or simply "the giant component") is a :term:`component` that occupies a substantial fraction of the network: basically the GCC forms when the size of the :term:`largest connected component` is "very large". The formal definition of when "large" becomes "giant" is quite complicated and not very practical; a common working definition is that the LCC is "giant" when it includes more that a hundredth of the network's nodes :cite:`PercolationSmearedPhaseTransition`. Gillespie simulation A simulation technique developed initially for *ab initio* chemistry simulations :cite:`Gillespie76,Gillespie77`. largest connected component The largest :term:`component` in the network. Often called the LCC, and sometimes called the :term:`giant connected component` when it becomes very large. In some cases we may also be interested in the sizes of other components: for example the second-largest connected component (SLCC) can give useful information. locus A "place" at which dynamics can occur, that is to say, where nodes can change compartments and any other tasks can happen. Each :term:`event` is associated with a particular locus: the locus contains the set of nodes or edges to which the event may be applied, while the event defines what happens. All loci are derived from the :class:`Locus` class. mesostructure A recognisable pattern in the nodes and edges that occupies a substantial fraction of the network. Usually independent of larger-scale properties like :term:`degree distribution`. A common mesostructure is :term:`modularity`. microstructure A recognisable pattern or :term:`motif` of nodes and edges that only affects a small number of nodes. The most common kind of microstructure is :term:`clustering`. modularity Also known as ":term:`community` structure", modular networks consist of sub-networks that are substantially more connected within themselves than they are to each other. motif A pattern of a small number of nodes and edges occurring frequently in a network. A triangle is a common motif, as are cycles and cliques. The building blocks of :term:`microstructure`. network generator A process that samples a class or ensemble of random networks to create an instance. A typical example is the class of networks with Poisson degree distribution (the ER networks), defined by the order and mean degree of the network. May generate ensembles with specific :term:`microstructure` or :term:`mesostructure`. percolation A process that randomly "occupies" nodes or edges in a network with a given probability. percolation threshold The occupation probability in a percolation process above which a :term:`giant connected component` forms. The size of the GCC rises rapidly once the threshold is passed, making the threshold generally "crisp". posted event An :term:`event` posted for a definite future time. The :term:`process dynamics` will execute the posted events at the appropriate time process A system that associates a state vector with each node (and possibly edge) in a network, and describes how they evolve over time. process dynamics The simulation approach used, which selects how and when each :term:`event` fires. Process dynamics execute events in time order from two possible sources: a random distribution that chooses an event based on their relative probability or rate; and any :term:`posted event` that has been scheduled. SEIR A :term:`compartmented model of disease` where nodes are Exposed to the disease and become infectious for a period before moving to being Infected. This can be used to model pre-symptomatic infectivity. SIS A :term:`compartmented model of disease` where nodes go from being Susceptible to the disease, to Infected and able to infect others, and then recover back to Susceptible. SIR A :term:`compartmented model of disease` where nodes go from being Susceptible to the disease, to Infected and able to infect others, and are then Removed and take no further part in the dynamics. stochastic event An :term:`event` whose occurrence is determined by a probability distribution. In a :term:`compartmented model of disease`, for example, the passage of an infection over an edge is a stochastic event, the rate and location of which are determined according to the distribution of infections. stochastic process A :term:`process` whose exact progression is determined by random variables drawn from particular probability distributions. stochastic dynamics Also known as Gillespie dynamics, this :term:`process dynamics` operates in :term:`continuous time` with one event occurring at each time point. synchronisation A :term:`process` that places an oscillator on each node in a network and allow them to interact. In many cases the intention is to have the oscillators converge to a common phase; this can be difficult to achieve, and gives rise to a huge set of interesting possible dynamics. synchronous dynamics A :term:`process dynamics` using :term:`discrete time`, where a simulation passes through a sequence of discrete timesteps which may include several (or no) events happening.