input.params.creator: Create a default parameter configuration list.

In wdelva/RSimpactHelp: Pre- and Post-simulation helper functions for RSimpact Cyan

Description

Create a default parameter configuration list as a starting point for a parameter optimisation algorithm. At this stage, only the most relevant parameters are modifiable.

Usage

input.params.creator(mortality.normal.weibull.shape = 5,
  mortality.normal.weibull.scale = 65,
  mortality.normal.weibull.genderdiff = 0, periodiclogging.interval = 1,
  syncrefyear.interval = 1, formation.hazard.type = "agegapry",
  person.art.accept.threshold.dist.type = "fixed",
  person.art.accept.threshold.dist.fixed.value = 0.5,
  person.eagerness.man.type = "independent",
  person.eagerness.woman.type = "independent",
  person.eagerness.man.dist.type = "gamma",
  person.eagerness.woman.dist.type = "gamma",
  person.eagerness.man.dist.gamma.a = 0.231989836885,
  person.eagerness.man.dist.gamma.b = 45,
  person.eagerness.woman.dist.gamma.a = 0.231989836885,
  person.eagerness.woman.dist.gamma.b = 45,
  person.agegap.man.dist.type = "normal",
  person.agegap.woman.dist.type = "normal",
  person.agegap.man.dist.normal.mu = 0,
  person.agegap.woman.dist.normal.mu = 0,
  person.agegap.man.dist.normal.sigma = 1,
  person.agegap.woman.dist.normal.sigma = 1,
  formation.hazard.agegapry.numrel_man = -0.5,
  formation.hazard.agegapry.numrel_woman = -0.5,
  formation.hazard.agegapry.gap_factor_man_exp = -0.35,
  formation.hazard.agegapry.gap_factor_woman_exp = -0.35,
  formation.hazard.agegapry.gap_factor_man_age = 0.05,
  formation.hazard.agegapry.gap_factor_woman_age = 0.05,
  formation.hazard.agegapry.meanage = -0.1,
  formation.hazard.agegapry.numrel_diff = -0.1,
  formation.hazard.agegapry.gap_factor_man_const = 0,
  formation.hazard.agegapry.gap_factor_woman_const = 0,
  formation.hazard.agegapry.gap_agescale_man = 0.23,
  formation.hazard.agegapry.gap_agescale_woman = 0.1,
  formation.hazard.agegapry.eagerness_sum = 0.1,
  person.vsp.tofinalaids.x = 12, person.vsp.toaids.x = 7,
  formation.hazard.agegapry.eagerness_diff = -0.048,
  dissolution.alpha_0 = -0.52, dissolution.alpha_4 = -0.05,
  debut.debutage = 15, population.simtime = 40, population.nummen = 500,
  population.numwomen = 500, population.eyecap.fraction = 0.2,
  hivseed.type = "amount", hivseed.amount = 20, hivseed.age.min = 20,
  hivseed.age.max = 30, hivseed.time = 10,
  hivtransmission.param.a = -1.0352239,
  hivtransmission.param.b = -89.339994, hivtransmission.param.c = 0.4948478,
  hivtransmission.param.f1 = log(5),
  hivtransmission.param.f2 = log(log(2.5)/log(5))/5,
  mortality.aids.survtime.C = 62, mortality.aids.survtime.k = -0.2,
  conception.alpha_base = -2.35, diagnosis.baseline = -100,
  monitoring.cd4.threshold = 0.1, monitoring.fraction.log_viralload = 0.3,
  population.msm = "no", person.eagerness.man.msm.dist.type = "fixed",
  person.eagerness.man.msm.dist.fixed.value = 0,
  formationmsm.hazard.type = "simple",
  formationmsm.hazard.simple.alpha_0 = 2,
  formationmsm.hazard.simple.alpha_12 = -0.4,
  formationmsm.hazard.simple.alpha_5 = -0.2,
  formationmsm.hazard.simple.alpha_6 = 0,
  formationmsm.hazard.simple.alpha_7 = 0,
  birth.pregnancyduration.dist.type = "fixed",
  birth.pregnancyduration.dist.fixed.value = 268/365,
  birth.boygirlratio = 1/2.01, simulation.type = "simpact-cyan",
  monitoring.cd4.threshold.prestudy = 350,
  monitoring.cd4.threshold.instudy.controlstage = 350,
  dropout.interval.dist.type = "exponential")

Arguments

mortality.normal.weibull.shape	Specifies the shape of a Weibull distribution to make sure everyone has a limited lifespan (5)
mortality.normal.weibull.scale	Specifies the scale parameter to base the Weibull distribution on (65)
mortality.normal.weibull.genderdiff	Specifies if the gender needs to be taken into account for the scale parameter of the Weibull distribution (0)
periodiclogging.interval	Allow the periodic log of the events and write teh output to a csv file (1)
syncrefyear.interval	Specifies the time interval with which a reference simulation time should be saved (1)
formation.hazard.type	Type of hazard function for relationship formation. Choose between "simple", "agegap" and "agegapry".
person.art.accept.threshold.dist.type	This specfies the ART acceptance distribution for each person
person.art.accept.threshold.dist.fixed.value	The value for the fixed distribution
person.eagerness.man.type	Type of man distribution for "eagerness" (~ sexual activity) in the population ("independent")
person.eagerness.woman.type	Type of man distribution for "eagerness" (~ sexual activity) in the population ("independent")
person.eagerness.man.dist.type	Type of man distribution for "eagerness" (~ sexual activity) in the population ("gamma")
person.eagerness.woman.dist.type	Type of women distribution for "eagerness" (~ sexual activity) in the population ("gamma")
person.eagerness.man.dist.gamma.a	Shape parameter (kappa parameter on wiki page) of Gamma distribution of "eagerness" (0.125)
person.eagerness.man.dist.gamma.b	Scale parameter (theta parameter on wiki page) of Gamma distribution of "eagerness" (8)
person.eagerness.woman.dist.gamma.a	Shape parameter (kappa parameter on wiki page) of Gamma distribution of "eagerness" (0.125)
person.eagerness.woman.dist.gamma.b	Scale parameter (theta parameter on wiki page) of Gamma distribution of "eagerness" (8)
person.agegap.man.dist.type	Distribution of preferred age differences for men ("normal")
person.agegap.woman.dist.type	Distribution of preferred age differences for women ("normal")
person.agegap.man.dist.normal.mu	Mean of preferred age differences distribution for men (-4)
person.agegap.woman.dist.normal.mu	Mean of preferred age differences distribution for women (-4)
person.agegap.man.dist.normal.sigma	Standard deviation of preferred age differences distribution for men (3)
person.agegap.woman.dist.normal.sigma	Standard deviation of preferred age differences distribution for women (3)
formation.hazard.agegapry.numrel_man	Effect of number of ongoing relationships on the relationship formation rate for men (-0.2)
formation.hazard.agegapry.numrel_woman	Effect of number of ongoing relationships on the relationship formation rate for women (-0.2)
formation.hazard.agegapry.gap_factor_man_exp	Effect of deviation from preferred age difference on the relationship formation rate for men (-0.2)
formation.hazard.agegapry.gap_factor_woman_exp	Effect of deviation from preferred age difference on the relationship formation rate for women (-0.2)
formation.hazard.agegapry.gap_factor_man_age	Funnel effect in men (0.05)
formation.hazard.agegapry.gap_factor_woman_age	Funnel effect in women (0.05)
formation.hazard.agegapry.meanage	Effect of increasing mean age of the candidate couple on the relationship formation rate (-0.1)
formation.hazard.agegapry.numrel_diff	Effect of absolute difference in number of ongoing relationships on the relationship formation rate (-0.1)
formation.hazard.agegapry.gap_factor_man_const	Baseline parameter for men (0).
formation.hazard.agegapry.gap_factor_woman_const	Baseline parameter for women (0).
formation.hazard.agegapry.gap_agescale_man	Effect of male age on preferred age difference (~ 1 - slope in regression model FemaleAge ~ MaleAge) (0.3)
formation.hazard.agegapry.gap_agescale_woman	Effect of male age on preferred age difference (~ 1 - slope in regression model FemaleAge ~ MaleAge) (0.3)
formation.hazard.agegapry.eagerness_sum	Effect of the sum of eagerness values in both partners on the relationship formation rate (1)
person.vsp.tofinalaids.x	Effect of "final" AIDS stage versus chronic HIV infection on infectiousness (12)
person.vsp.toaids.x	Effect of "initial" AIDS stage versus chronic HIV infection on infectiousness (7)
formation.hazard.agegapry.eagerness_diff	Effect of absolute difference in eagerness on the relationship formation rate (-1)
dissolution.alpha_0	Baseline parameter for relationship dissolution rate. (0.1)
dissolution.alpha_4	Effect of increasing mean age of the couple on relationship dissolution rate (-0.05)
debut.debutage	The age a person must have to become sexually active.(14)
population.simtime	Indication of how many year should the simulation run for.(40) e.g 40 years
population.nummen	Indication of how many men should be in the initial seeded population (500) e.g 500 men
population.numwomen	Indication of how many women should be in the initial seeded population (500) e.g 500 women
population.eyecap.fraction	Allow for the indication of how many people can a person possible engage in a relation with. (0.2)
hivseed.type	Allows for a selection of method on seeding HIV. (amount) e.g if amount number of people else if fraction then a fraction will be set to HIV+
hivseed.amount	These number of people will be seeded to be HIV+ (20)
hivseed.age.min	This allows for the minimal age to be set seeded as HIV+ (20)
hivseed.age.max	Maximum age at which HIV seeding will be infected (30)
hivseed.time	The time within the simulation when the HIV seeding is to take place (10) e.g after 10 years in the simulation
hivtransmission.param.a	Baseline parameter for HIV transmission rate in serodiscordant couples (-1.0352239)
hivtransmission.param.b	Parameter "b" for the linear component of the effect of viral load on the HIV transmission rate in serodiscordant couples (-89.339994)
hivtransmission.param.c	Parameter "c" for the exponential component of the effect of viral load on the HIV transmission rate in serodiscordant couples (0.4948478)
hivtransmission.param.f1	Effect of youngest age on HIV susceptibility (log(5) ~1.6 such that the hazard is x 5 in 15 year olds)
hivtransmission.param.f2	Effect of female age on HIV susceptibility (log(log(2.5) / log(5)) / 5 ~-0.11 such that the hazard is x 2.5 in 20 year olds, compared to the reference (>>25 year olds)
mortality.aids.survtime.C	HIV-based time of death parameter
mortality.aids.survtime.k	HIV-based time of death parameter
conception.alpha_base	Baseline parameter for conception rate. (-3)
diagnosis.baseline	Baseline parameter for the diagnosis event (-100)
monitoring.cd4.threshold	The value of cd4 that triggers eligibility for treatment if below this value
monitoring.fraction.log_viralload	the setpoint viral load will be dropped by this fraction
population.msm	"yes" or "no". Default is "no".
birth.pregnancyduration.dist.type	duration of pregnancy
birth.pregnancyduration.dist.fixed.value	the option is fixed and set to 9 months
birth.boygirlratio	the probability of a newly born to be boy
simulation.type	To distinguish parameters that vary from the type of simulation being perfomed (simpact-cyan) e.g you can use maxart as well
monitoring.cd4.threshold.prestudy	cd4 values prestudy
monitoring.cd4.threshold.instudy.controlstage	cd4 values during the control phase
dropout.interval.dist.type	Distribution of time till ART programme non-retention # @param monitoring.cd4.threshold.instudy.transitionstage cd4 threshold when site is transitioning # @param monitoring.cd4.threshold.instudy.interventionstage cd threshold not needed during the intervention stage

Value

a list of model parameters that can be used as input for simpact.run()

Examples

cfg.list <- input.params.creator(conception.alpha_base = -3,
formation.hazard.type = "agegapry",
formation.hazard.agegapry.numrel_man = -1,
formation.hazard.agegapry.numrel_woman = -1)

wdelva/RSimpactHelp documentation built on Dec. 26, 2019, 3:42 a.m.