Package 'hrp2malaRia'

DRC Seaosnal data to match regions from Parr et al. 2016 JID

Description

DRC Seaosnal data to match regions from Parr et al. 2016 JID

Usage

data(DRC)

Format

An object of class data.frame with 8 rows and 26 columns.

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Equilibrium conditions for model. Also stored internally for model use when package is not loaded

Description

Equilibrium conditions for model. Also stored internally for model use when package is not loaded

Usage

data(eq.0)

Format

An object of class list of length 4.

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Individual Based Malaria Simulator

Description

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

Usage

hrp2_Simulation(
  ID = NULL,
  saved.rds = 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

ID	ID of model run saved object when using didehpc tools. Default = NULL
saved.rds	File path for saved model run as rds. Default = NULL. Takes priority over ID/root
root	Name of context root when using didehpc tools to submit and save model runs. Default = NULL.
direct.input	R object for old model run to be restarted. Default = NULL. Takes priority over saved.rds and ID/root
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
ss	Seasonal fourier terms for rainfall. 7 needed (intercept and first 3 cos and sin terms). Default = NULL
fitness	Relative fitness of hrp2 deletions. Default = 1, i.e. no fitness cost. ## Diagnostics and nmf
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
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 ## Other params to do with reloading model runs
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 vectorsf S. ... - Series storage of various of the above

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hrp2malaria: Individual multiplicity of infection malaria model

Description

hrp2malaria: Individual multiplicity of infection malaria model

Author(s)

OJ Watson [email protected]

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Seasonality Shiny

Description

run_seasonality_shiny runs a shiny app that displays the outcomes of the seasonality investigation. The shiny shows how the bias in the observed prevalence of pfhrp2 deletions changes for each level 1 admin region changes throughout the transmission season

Usage

run_seasonality_shiny()

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