Define the parameters that will be used when simulating data from the inbuilt SIMPLEGEN transmission model.
define_epi_model_parameters(
project,
a = 0.3,
p = 0.868,
mu = -log(p),
u = 12,
v = 10,
g = 12,
prob_infection = seq(0.8, 0.5, l = 50),
prob_acute = seq(1, 0.1, l = 50),
prob_AC = 1,
duration_acute = dpois(1:100, 10),
duration_chronic = dpois(1:500, 100),
detectability_microscopy_acute = 0.8,
detectability_microscopy_chronic = 0.8 * 100 * dgeom(0:500, 1/100),
detectability_PCR_acute = 1,
detectability_PCR_chronic = 1,
time_treatment_acute = dgeom(1:25, 1/5),
time_treatment_chronic = dgeom(1:100, 1/20),
treatment_seeking_mean = 0.5,
treatment_seeking_sd = 0.1,
duration_prophylactic = dgeom(1:25, 1/5),
infectivity_acute = 0.115,
infectivity_chronic = 0.078,
max_inoculations = 5,
H = 1000,
seed_infections = 100,
M = 1000,
mig_mat = diag(1),
life_table = life_table_Mali()
)a SIMPLEGEN project, as produced by the
simplegen_project() function.
human blood feeding rate. The proportion of mosquitoes that feed on humans each day.
mosquito probability of surviving one day.
mosquito instantaneous death rate. mu = -log(p) unless
specified otherwise.
intrinsic incubation period. The number of days from initial inoculation to blood-stage infection in a human host.
extrinsic incubation period. The number of days from initial inoculation to becoming infectious in a mosquito.
lag time between human blood-stage infection and production of gametocytes.
probability that a human becomes infected after being bitten by an infected mosquito. If a vector, then each subsequent value applies to each subsequent infectious bite.
probability that an infection passes to the acute stage rather than going directly to the chronic stage. If a vector, then each subsequent value applies to each subsequent infection.
probability that an infection in the acute stage passes to the chronic stage rather than recovering directly. If a vector, then each subsequent value applies to each subsequent infection.
specifies the probability distribution of duration (in days) of acute or chronic disease. Can be a vector or a list. If a list then the first element specifies the probability distribution for the first incident of disease, the second element for the second incident and so on (the final element is used for all remaining incidents). If a single vector then the same probability distribution is used for all incidents of disease. Values are automatically normalised to a proper probability mass distribution internally (i.e. a distribution that sums to 1).
specifies the probability of parasite detection via microscopy at each day since entering the acute or chronic stages. Can be a vector or a list. If a list then the first element specifies the probability distribution for the first incident of disease, the second element for the second incident and so on (the final element is used for all remaining incidents). If a single vector then the same probability distribution is used for all incidents of disease. This is not a probability distribution, meaning values each day can be between 0 and 1.
equivalent to `detectability_microscopy_acute` and `detectability_microscopy_chronic`, but for detection via polymerase chain reaction (PCR).
the probability
distribution of time (in days since entering the acute or chronic stages)
until requiring treatment. At this time, the host seeks treatment according
to their host-specific treatment seeking parameter (see
treatment_seeking_alpha and treatment_seeking_beta). Can be a
vector or a list. If a list then the first element specifies the
probability distribution for the first incident of disease, the second
element for the second incident and so on (the final element is used for
all remaining incidents). If a single vector then the same probability
distribution is used for all incidents of disease. Values are automatically
normalised to a proper probability mass distribution internally (i.e. a
distribution that sums to 1).
treatment seeking is
modelled in two stages; first, the time at which hosts require treatment is
drawn from the probability distribution in time_treatment_acute or
time_treatment_chronic, and second, whether they go ahead with
treatment seeking at this point depends on their personal host-specific
treatment seeking probability. These latter probabilities are drawn
independently for each host at birth from a Beta distribution with mean
`treatment_seeking_mean` and standard deviation `treatment_seeking_sd`.
Hence, these parameters describe the average propensity to seek treatment
in the population, and the degree of inequality in treatment seeking. Note
that `treatment_seeking_sd`` must be less than
`sqrt(treatment_seeking_mean*(1 - treatment_seeking_mean))``, otherwise the
Beta distribution is undefined.
vector defining the probability distribution of duration (in days) of prophylaxis following treatment.
the probability of onward infectivity to mosquitoes at each day since entering the acute or chronic states. Can be a vector or a list. If a list then the first element specifies the infectivity for the first incident of disease, the second element for the second incident and so on (the final element is used for all remaining incidents). If a single vector then the same infectivity is used for all episodes of disease.
maximum number of inoculations that an individual can carry simultaneously.
vector specifying human population size in each deme.
vector specifying the initial number of infected human hosts in each deme. Infected hosts are assumed to have just been bitten, meaning they have just entered the latent phase.
vector specifying mosquito population size (strictly the number of adult female mosquitoes) in each deme.
migration matrix specifying the daily probability of human migration. The source deme is given in rows, the destination deme in columns.
vector specifying the probability of death of a human host
in each one-year age group. Defaults to a life table taken from Mali - see
?life_table_Mali for details.