hrp2_Simulation: Individual Based Malaria Simulator

Description Usage Arguments Details Value

Description

hrp2_Simulation simulates an individual based malaria system considering multiplicity of infection and infection status of individuals.

Usage

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hrp2_Simulation(ID = NULL, root = NULL, direct.input = NULL,
  years = 0.5, time.step = 1, states = c(1, 2, 3, 4, 5, 6),
  storage = 50, storage_capture = 30, just_storage_results = FALSE,
  N = 1000, max.age = 60, strains.0 = 10, desired.freq = NULL,
  d.death = 21, EIR = 20/365, a.0 = 8 * 365, rho = 0.85,
  zeta.sd = 1.67, omega = 0.8405912, theta = 1, ft = 0.4, rdt.det = 1,
  rdt.nonadherence = 0, microscopy.use = 0, include.nmf = FALSE,
  fever.age.breaks = c(-0.1, 1, 2, 3, 4, 5, 7, 9, 11, 13, 15, 20, 25, 30,
  101), annual.nmf.per.age.bracket = c(2.235, 1.841, 1.503, 1.175, 0.928,
  0.67, 0.486, 0.512, 0.475, 0.429, 0.652, 0.747, 0.804, 0.789),
  nmf.multiplier = 1, ss = NULL, fitness = 1, mu.0 = 0.132,
  beta = c(0.05879106, 0.07108894), a.k = 0.30677, delay.mos = 10,
  delay.gam = 12, d.E = 12, d.I = 200, d.T = 5, d.D = 5, d.U = 110,
  d.P = 25, d.A = d.I - d.D, d.1 = 0.160527, d.ID = 10 * 365,
  I.D0 = 1.577533, k.D = 0.476614, u.D = 9.44512, a.D = 8001.99,
  f.D0 = 0.007055, g.D = 4.8183, b.0 = 0.590076, b.1 = 0.5, d.B = 10 *
  365, I.B0 = 43.8787, k.B = 2.15506, u.B = 7.19919, phi.0 = 0.791666,
  phi.1 = 0.000737, d.CA = 10950, I.C0 = 18.02366, k.C = 2.36949,
  u.C = 6.06349, P.M = 0.774368, d.CM = 67.6952, g.1 = 1.82425,
  c.S = 0, c.D = 0.0676909, c.T = 0.322 * c.D, c.U = 0.0062, c.A = 0,
  c.P = 0)

Arguments

years

Length of Simulation (years). Default = 0.5

time.step

Simulation time interval considered in days. Has to be 1.

states

Vector of the compartmental states. Default = c(1, 2, 3, 4, 5, 6), which are c("S","D","A","U","T","P")

storage

Number of last time steps to store. If storage = 0 (default), then all results are stored

storage_capture

Number of previous time steps used to calculate mean measures for series. Default = 30

just_storage_results

Boolean for keeping just the storage results. ## Demographic paramaters

N

Population Size. Default = 1000

max.age

Maximum age (years). Default = 100

strains.0

Ratio of wild type strains to hrp2 at initialisation. Must be an integer. Default = 10

desired.freq

Desired hrp2 deletion frequency to be enforced when a previous simulation is reloaded

d.death

Average life expectancy (years). Deafult = 21 ## Epidemiological Parameters

EIR

Maximum EIR / day. Default = 20/365,

a.0

Age-dependent biting parameter (days). Default = 8*365

rho

Age-dependent biting parameter (days). Default = 0.85

zeta.sd

sd of lognormal distribution used to generate indiviudal specific biting. Default = 1.67

omega

BM age scaling parameter. Default = 0.75 ## Entomological parameters

theta

Seasonal effects. Default = 1

ft

Probability of receiving assesment. Default = 0.4

rdt.det

Probability of detecting malaria given mono infection of hrp2' strains. Default = 1

rdt.nonadherence

Probability of non adherence to test result. Default = 0, i.e. perfect adherence

microscopy.use

Probability of microscopy use. Default = 0, i.e. no microscopy

include.nmf

Boolean detailing whether to include nmf section. Default = FALSE

fever.age.breaks

Age breaks for fevers

annual.nmf.per.age.bracket

Annual number of non malarial fevers for each age bracket in fever.age.breaks. Default is mean across 5 representative surveys from Burundi 2012, Liberia 2009/2011 and Nigeria 2010/2015

nmf.multiplier

Multiplication for annual.nmf.per.age.bracket to introduce sensitivity. Default = 1 ## delays and durations

mu.0

Baseline mosquito mortality. Default = 0.132

beta

Birthrate in form of y = beta[1]*EIR + beta[2]. Default = c(0.0572289,0.0696121)

a.k

Daily biting rate. Default = 0.30667 ## Diagnostics and nmf

delay.mos

Mosquito extrinsic incubation period (days). Default = 10

delay.gam

Delay from emergence of blood-stage parasites to onward infectivity (days). Default = 12.5

d.E

Latent period delay in pre-erythrocytic stage (days). Default = 12

d.I

Patent infection duration with no immunity (including disease) (days). Default = 200

d.T

Clinical disease duration with treatment (days). Default = 5

d.D

Clinical disease duration without treatment (days). Default = 5

d.U

Sub-patent infection duration (days). Default = 100

d.P

Prophylaxis with SP following treatment duration (days). Default = 25

d.A

Asymptomatic infection duration (days). Default = d.I - d.D ## Pre-erythrocytic immunity parameters

d.1

= 0.161 Probability with maximum immunity

d.ID

= 10*365 Inverse of decay rate

I.D0

Scale parameter. Default = 1.58

k.D

Shape parameter. Default = 0.477

u.D

Duration in which immunity is not boosted (days). Default = 9.45

a.D

Scale parameter relating age to immunity (days). Default = 21.923*365

f.D0

Parameter relating age to immunity. Default = 0.0071

g.D

Shape parameter relating age to immunity. Default = 4.81 ## Blood stage immunity parameters

b.0

Probability with no immunity. Default = 0.590

b.1

Maximum relative reduction. Default = 0.5

d.B

Inverse of decay rate (days). Default = 10*365

I.B0

Scale parameter. Default = 43.9

k.B

Shape parameter. Default = 2.16

u.B

Duration in which immunity is not boosted (days). Default = 7.2 ## Acquired and maternal immunity parameters

phi.0

Probability with no immunity. Default = 0.7916

phi.1

Maximum relative reduction. Default = 0.00074

d.CA

Inverse of decay rate (days). Default = 30*365

I.C0

Scale parameter. Default = 18.0

k.C

Shape parameter. Default = 2.37

u.C

Duration in which immunity is not boosted (days). Default = 6.06

P.M

New-born immunity relative to mother’s. Default = 0.774

d.CM

Inverse of decay rate of maternal immunity (days). Default = 67.7 ## contributions to infectious reservoir by state and age

g.1

Relates infectiousness probability of detection. Default = 1.82

c.S

Contribution from S. Default = 0

c.D

Contribution from D. Default = 0.068

c.T

Contribution from T. Default = 0.32 * c.D

c.U

Contribution from U. Default = 0.0062

c.A

Contribution from A. Default = c.U + (c.D - c.U)*q^g.1, where q is the probability of detection of parasites as calculated using pre-erythrcytic immunity and age

c.P

Contribution from P. Default = 0

Details

The simulator considers individuals to progress through the Griffin 2016 model.

The model also introduces a further acknowledgement of the hrp2 strains present in hosts, and the effects of this on detection.

The model first allocates a fixed length for all storage and proceeds in a ring like fashion allowing for delays to be incorporated.

## Simulation parameters

Value

Result a list of 59 elements including the following Time - Vector of time steps considered Status - Matrix of individuals' infection status by Time Last_Infection_Time - Vector of individual's last infection Last_Bite_Time - Vector of individual's last bite Age - Vector of individual's ages N.Sens - Matrix of individuals' MOI of RDT sensitive strains by Time N.Dels - Matrix of individuals' MOI of RDT resistant strains by Time I.B - Vector of individual's blood stage immunity I.CA - Vector of individual's acquired immunity I.CM - Vector of individual's maternal immunity I.D - Vector of individual's pre-erythrocytic immunity Counter - Simulation step counter d.EIR - daily EIR in individuals > 18 years I.Reservoir - Vector of each strains weighted contribution to the last step's I.Reservoir Sv - Susceptible mosquito population Ev - Exposed mosquito population Iv - Infected mosquito population Prev - Daily prevalence N.Sens/N.Dels - sum of sensitive to diagnostic and deletion strains Incidence - Clinical cases / population / per day Mono - monoinfected individual proportions FOIv - Force of infection to vectors S. ... - Series storage of various of the above


eLifeProduction/hrp2malaRia_2019 documentation built on May 9, 2019, 12:04 a.m.