Generates several microsimulated cohorts with desired specifications.
microsim(seed=1234, nsim, transition, abs_states, sympt_states, prob_sympt, size,
p_men, min_age, max_age, utilityCoefs, costCoefs.md, costCoefs.nmd,
costCoefs.i, disc=3, vacc=FALSE, vacc.age=NULL, ndoses=NULL, vacc.cov=NULL,
vacc.eff=NULL, vacc.type=NULL, vacc.prop=NULL, vaccprice.md=NULL,
vaccprice.nmd=NULL, vaccprice.i=NULL, screening=FALSE, screenType=0,
scrSchema=0, screenPeriod=NULL, cytoType=NULL, screenPrice.md=NULL,
screenPrice.nmd=NULL, screenPrice.i=NULL, colpoPrice.md=NULL,
colpoPrice.nmd=NULL, colpoPrice.i=NULL, hpvTestPrice.md=NULL,
hpvTestPrice.nmd=NULL, hpvTestPrice.i=NULL, cytoHpvPrice.md=NULL,
cytoHpvPrice.nmd=NULL, cytoHpvPrice.i=NULL, biopsPrice.md=NULL,
biopsPrice.nmd=NULL, biopsPrice.i=NULL, screenCoverage=NULL, screenSensi=NULL,
screenSensi2=NULL, screenSensi3=NULL, colpoSensi=NULL, biopSensi=NULL,
hpvTestSensi=NULL, treatProbs, nAnnualVisits=0, nAnnualVisitsLSIL=0,
nAnnualVisitsHSIL=0, cytoHPVPeriod=0, cytoHPVPostColpo=0,
cytoHPVPostBiop=NULL, cytoLSILperiod=0, cytoHSILperiod=0, switchAge=0,
C_period=NULL, hpvPeriod=0, nCores=1)Data frame containing the simulated cohorts and the individual history for each person in each simulated cohort.
seed to be used in the simulation. Default value is 1234.
number of cohorts to be simulated.
transition probabilities matrix.
vector with the absorbing states.
vector with the health states that might present symptoms.
vector with the probability of presenting symptoms for each health state that might present symptoms. Should have the same length of sympt_states.
number of individuals on each simulated cohort.
proportion of men in the simulated cohorts.
lowest age in the cohort.
largest age in the cohort.
vector with the utilities for each health state.
vector with the direct medical costs for each health state.
vector with the direct non medical costs for each health state.
vector with the indirect costs for each health state.
discount rate in percentage. Default value is 3.
boolean value specifying if the considered scenario includes vaccination. Default value is FALSE.
vector with ages at vaccination if the considered scenario includes vaccination. Default value is NULL.
number of doses of vaccine if the considered scenario includes vaccination. Default value is NULL.
vaccine coverage if the considered scenario includes vaccination. Default value is NULL.
vaccine effectivity if the considered scenario includes vaccination. Default value is NULL.
type of vaccine if the considered scenario includes vaccination, character with values biv for bivalent, quad for quadrivalent and nona for nonavalent vaccines. Default value is NULL.
proportion of vaccinated women on each age group if the considered scenario includes vaccination. Default value is NULL.
vaccine direct medical costs if the considered scenario includes vaccination. Default value is NULL.
vaccine direct non medical costs if the considered scenario includes vaccination. Default value is NULL.
vaccine indirect if the considered scenario includes vaccination. Default value is NULL.
boolean specifying if the considered scenario includes screening of any type. Default value is FALSE.
type of screening. 1 stands for organized screening, 2 stands for opportunistic screening. Default value is 0 (no screening).
screening schema. 1 stands for cytology alone with repeat cytology for triage, 2 stands for cytology with HPV triage, 3 stands for HPV with cytology triage and 4 stands for HPV genotyping with cytology triage. Default value is 0 (no screening).
screening period (in years). Default value is NULL (no screening).
type of cytology. 0 stands for conventional cytology, 1 stands for Liquid Based Cytology (LBC). Default value is NULL (no cytology).
medical direct cost of cytology. Default value is NULL.
non-medical direct cost of cytology. Default value is NULL.
indirect cost of cytology. Default value is NULL.
medical direct cost of colposcopy. Default value is NULL.
non-medical direct cost of colposcopy. Default value is NULL.
indirect cost of colposcopy. Default value is NULL.
medical direct cost of HPV test. Default value is NULL.
non-medical direct cost of HPV test. Default value is NULL.
indirect cost of HPV test. Default value is NULL.
medical direct cost of HPV reflex test, in case cytoType=1. Default value is NULL.
non-medical direct cost of HPV reflex test, in case cytoType=1. Default value is NULL.
indirect cost of HPV reflex test, in case cytoType=1. Default value is NULL.
medical direct cost of biopsy. Default value is NULL.
non-medical direct cost of biopsy. Default value is NULL.
indirect cost of biopsy. Default value is NULL.
cytology coverage for each age group. Default value is NULL.
cytology sensitivity for each age group. Default value is NULL.
cytology sensitivity after cytology for each age group. Default value is NULL.
cytology sensitivity after HPV test for each age group. Default value is NULL.
colposcopy sensitivity for each age group. Default value is NULL.
biopsy sensitivity for each age group. Default value is NULL.
HPV test sensitivity for each age group. Default value is NULL.
probability of recuperation after treatment for each FIGO I - FIGO IV states.
number of annual visits after colposcopy for screening schema 1. Default value is 0.
number of annual visits after LSIL for screening schema 2. Default value is 0.
number of annual visits after HSIL for screening schema 2. Default value is 0.
cytology and HPV test protocol period for screening schemas 3 and 4. Default value is 0.
cytology and HPV test protocol period after colposcopy protocol for screening schemas 3 and 4. Default value is 0.
cytology and HPV test protocol period after biopsy protocol for screening schemas 2. Default value is NULL.
period for cytology after LSIL detection for screening schame 2. Default value is 0.
period for cytology after HSIL detection for screening schame 2. Default value is 0.
age at which screening protocol changes for screening schemas 3 and 4. Default value is 0.
vector with screening periods (in years) before and after switch age for screening schemas 3 and 4. Default value is NULL.
period for HPV test in screening schema 2. Default value is 0.
number of cores of the computer. Default value is 1.
David Moriña (Universitat de Barcelona), Pedro Puig (Universitat Autònoma de Barcelona) and Mireia Diaz (Institut Català d'Oncologia)
Georgalis L, de Sanjosé S, Esnaola M, Bosch F X, Diaz M. Present and future of cervical cancer prevention in Spain: a cost-effectiveness analysis. European Journal of Cancer Prevention 2016;25(5):430-439.
Moriña D, de Sanjosé S, Diaz M. Impact of model calibration on cost-effectiveness analysis of cervical cancer prevention 2017;7.
mSimCC-package, bCohort, costs, le,
plotCIN1Incidence, plotCIN2Incidence, plotCIN3Incidence,
plotIncidence, plotMortality, plotPrevalence,
qalys, yls
data(probs)
nsim <- 3
p.men <- 0
size <- 20
min.age <- 10
max.age <- 84
#### Natural history
hn <- microsim(seed=1234, nsim, probs, abs_states=c(10, 11), sympt_states=c(5, 6, 7, 8),
prob_sympt=c(0.11, 0.23, 0.66, 0.9),
size, p.men, min.age, max.age,
utilityCoefs = c(1, 1, 0.987, 0.87, 0.87, 0.76, 0.67, 0.67, 0.67, 0.938, 0, 0),
costCoefs.md = c(0, 0, 254.1, 1495.9, 1495.9, 5546.8, 12426.4, 23123.4,
34016.6, 0, 0, 0),
costCoefs.nmd = c(0, 0, 81.4, 194.1, 194.1, 219.1, 219.1, 219.1, 219.1, 0, 0, 0),
costCoefs.i = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), disc=3,
treatProbs=c(0,0,1,1,1,0.9894,0.9422,0.8262,0.5507,0,0,0),
nCores=1) ### individual level
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