Glossary • ramp.xds

This glossary defines the core terminology used in ramp.xds. Terms are grouped by theme. For functions related to a given concept, see help.search("term", fields = "concept").

Model Structure

xds object: The central data structure in ramp.xds, an R list of class xds_obj. It holds the model components, parameters, initial values, outputs, and metadata needed to define and solve a dynamical system for malaria transmission. Built by xds_setup() and its wrappers.
Dynamical Component: Each component defines a set of state variables and dynamics to model a set of linked biological processes. There are three core components in an xds model and one optional component: + the human / host component (XH), + the adult mosquito component (MY), + the aquatic / immature mosquito component (L), and + an optional component to compute other dynamic variables (V).
Module: A specific implementation of a component. For example, macdonald, GeRM, and SI are modules for the MY component; SIS and hMoI are modules for the XH component. Each module is implemented as a set of S3 methods dispatching on the module class name.
Patch: The basic spatial unit for mosquito ecology and transmission. A model has nPatches patches. Adult mosquitoes live in patches, which are connected by dispersal. Blood feeding, egg laying, and transmission are computed at the patch level.
Stratum: The basic unit of human / host population structure. A model has nStrata strata within each host species. Strata represent sub-populations that may differ in location, risk, age, or other attributes. Transmission exposure is computed for each stratum.
Habitat: The basic unit for immature mosquito ecology. A model has nHabitats habitats, which are distributed across patches according to a habitat membership matrix. Immature mosquito populations develop in aquatic habitats: eggs are laid by adults that hatch into the first larval instar; there are four distinct instars before pupation; and aduls emerge from the pupae.

Adult Mosquito Bionomics

In the MY component, adult mosquito bionomic parameters include parameters that describe mosquito life-history traits that govern transmission potential, and the parasite’s extrinsic incubation period (EIP). In ramp.xds, we use a standard naming convention for core bionomic parameters, listed below

$f$ — blood feeding rate: The per-capita rate at which a mosquito takes blood meals per day. Together with $q$, it determines the human blood feeding rate, the number of human blood meals, per mosquito, per day.
$q$ — human blood feeding fraction: The fraction of blood meals taken on humans (as opposed to other vertebrate hosts).
$\nu$ — egg laying rate: The per-capita daily rate at which mosquitoes lay eggs. Since the eggs are laid in a batch, another parameter sets the total number of eggs laid
$g$ — mosquito mortality rate: The per-capita daily mortality rate of adult mosquitoes while in a patch. The daily survival probability is $e^{-g}$.
$\sigma$ — emigration rate: The per-capita daily rate at which mosquitoes leave a patch. Together with the dispersal kernel, $\sigma$ determines the spatial redistribution of mosquitoes.
$\mu$ — emigration loss: The fraction of emigrating mosquitoes that are lost: it includes mortality conditioned on emigration, and loss of emigrating mosquitoes from the system.
$\tau$ — extrinsic incubation period (EIP): The time lag between the bite that infects a mosquito and the moment when it becomes infective.
$K$ — mosquito dispersal matrix: A matrix that describes how mosquitoes move around with a standard form: the diagonal terms are , and the columns sum to .
$\Omega$ — mosquito mortality matrix: A matrix that combines mortality and emigration to describe mosquito mortality and dispersal.
$\Upsilon$ — mosquito survival through the EIP: A matrix describing survival and dispersal through a fixed EIP. It is used in delay differential to compute the proportion of mosquitoes that survive to become infectious.

Transmission

EIR — Entomological Inoculation Rate: The number of infectious bites received per person per unit time. The daily EIR (dEIR) is the per-day rate; the annual EIR (aEIR) integrates over a year. The EIR is the primary measure of transmission intensity from mosquitoes to humans. Use help.search("EIR", fields = "concept") to find related functions.
$\beta$ — blood feeding / mixing matrix: A matrix of dimension nStrata × nPatches that describes the distribution of bites from mosquitoes in each patch onto human strata. It reflects both the spatial distribution of humans and their relative attractiveness to mosquitoes.
$\kappa$ — net infectiousness: The probability that a mosquito taking a blood meal on a human population becomes infected, averaged over all strata. Computed as a weighted sum of per-stratum infectiousness $c_i$ weighted by human population size.
$b$ — mosquito-to-human transmission efficiency: The probability that an infectious bite results in a human infection. Also called the sporozoite transmission efficiency.
$c$ — human-to-mosquito transmission efficiency: The probability that a mosquito becomes infected when taking a blood meal on an infectious human. Also called the gametocyte transmission efficiency.
$Z$ — infective mosquito density: The density of infectious (sporozoite-positive) adult mosquitoes per patch. Combined with $fq$ and $\beta$, $Z$ determines the EIR experienced by each human stratum.
$fqZ$ — infective biting density: The product of the human biting rate ($fq$) and the infective mosquito density ($Z$), giving the rate of infectious bites per unit area per day in each patch.
FoI — Force of Infection: The per-capita rate at which susceptible humans become infected per unit time. The FoI depends on the EIR and the exposure model (Poisson, negative binomial, etc.).
local fraction: The fraction of bites in a patch that are on resident (non-travelling) humans, as opposed to visitors. Used to partition the EIR between local exposure and travel-related exposure.

Epidemiology

PR — Parasite Rate (Prevalence): The proportion of the human population that is infected at a given time. Also called PfPR when referring specifically to Plasmodium falciparum. Can be measured by microscopy (true_pr), PCR, or rapid diagnostic test.
aEIR — annual EIR: The EIR integrated or summed over a full year (365 days). A common summary statistic for transmission intensity.
AR — Attack Rate: The cumulative probability of infection over a given time period. Related to the FoI via the exposure model.

Model Dynamics

xde — differential equation model: A model solved as a system of differential equations, either ordinary (ode) or delay (dde). Set via xds_obj$xde. Solved using routines from deSolve.
ode — ordinary differential equation: The default form of an xde model, where the right-hand side depends only on the current state.
dde — delay differential equation: An xde model in which the right-hand side depends on the state at earlier times, specifically at the lagged time $t - \tau$ where $\tau$ is the extrinsic incubation period (EIP). Used by modules such as GeRM.
dts — discrete time system: A model solved by iterating a map (difference equations) rather than integrating differential equations. Set via xds_obj$xde = "dts". Used by the RMdts and basicM_dts modules.

Forcing & Exogenous Variables

forcing: Exogenous (externally imposed) variation in model inputs, such as seasonal mosquito emergence driven by rainfall. Models can be forced via emergence (Lambda), the EIR (eir), or other mechanisms.
trace function: A function of time $t$ used to specify an exogenous input to the model. Built using make_function() and parameterised with makepar_* helpers. Trace functions can represent constant, seasonal, trend-driven, or spline-interpolated signals.
seasonality: Periodic, typically annual, variation in transmission-relevant quantities such as mosquito emergence, rainfall, or EIR. Represented in ramp.xds via the F_season family of functions.
trend: A long-term directional change in a forcing variable, independent of seasonality. Represented via the F_trend family of functions.

Spatial Structure

dispersal kernel: A matrix (or function used to build one) that describes the probability that a mosquito emigrating from one patch settles in each other patch. See setup_K_matrix().
residency matrix: A matrix describing which patch each human stratum is resident in. Used to weight exposure and compute patch-level averages.
travel: Exposure to infectious bites outside a person’s home patch. Modelled via the travel EIR and the visitor dynamics interface.