R/build_gdata.R
In MESuRS-Lab/mwss: Stochastic simulations of infectious disease spread in healthcare systems structured as a networked metapopulation
Defines functions
build_gdata
Documented in
build_gdata
#' Generate global parameters dataset
#'
#' @description It calculates 1) the prevalence from daily incidence in the community and average disease duration,
#' 2) the probability of transmission per day spent in contact based on R0 and average disease duration,
#' 3) the time ratios of the epidemiological state based on average states duration,
#' 4) the proportion of time outside of work, and
#' 5) the proportion of probabilities of developing mild and severe symptoms for patients.
#'
#' Then the functions formats all global parameters required for the transitions as a named list readable by SimInf package.
#'
#' @importFrom magrittr %>%
#'
#' @param disease string. only Covid and Influenza are available
#' @param n_ctcH_PSA a positive number, the daily number of contacts with professionals per patient in the screening area
#' @param t_ctcH_PSA a positive number, the average duration of contact between professional and patient per day in the screening area (in days, ex: if 15 min, t_ctcH_PSA = 15/60/24)
#' @param n_ctcP_PSA a positive number, the daily number of contacts with other patients per patient in the screening area
#' @param t_ctcP_PSA a positive number, the average duration of contact between patients per day in the screening area (in days)
#' @param n_ctcH_PW a positive number, the number of contact between professional and patient per day in the ward
#' @param t_ctcH_PW a positive number, the average duration of contact between patients per day in the ward (in days)
#' @param n_ctcP_PW a positive number, the number of contacts with other patients per patient per day, in the ward
#' @param t_ctcP_PW a positive number, the average duration of contact between patients per day in the ward (in days)
#' @param n_ctcH_H a positive number, the number of contacts with professionals per professional per day
#' @param t_ctcH_H a positive number, the average duration of contact between professionals in the ward (in days)
#' @param t_ctcV_PW a positive number, the average duration of contact between patients per day in the ward (in days)
#' @param I a positive number, the daily incidence
#' @param d a positive number, the average disease duration (in days)
#' @param R0 a positive number, the basic reproduction number
#' @param tw a positive number, the average number of working hours per week (in hours)
#' @param tSA a positive number, the average duration (in days) before full admission (in screening area for clinical exam, administrative procedure, etc)
#' @param tIC a positive number, the average duration (in days) of stay in intensive care
#' @param tSL a positive number, the average duration (in days) of sick leave
#' @param tESL a positive number, the average duration (in days) of extended sick leave
#' @param tE a positive number, the average duration (in days) of epidemiological state E (exposed - non contagious)
#' @param tEA a positive number, the average duration (in days) of epidemiological state EA (exposed - contagious pre-asymptomatic)
#' @param tES a positive number, the average duration (in days) of epidemiological state ES (exposed - contagious pre-symptomatic)
#' @param tIA a positive number, the average duration (in days) of epidemiological state IA (infectious asymptomatic)
#' @param tIM a positive number, the average duration (in days) of epidemiological state IM (infectious with mild symptoms)
#' @param tIS a positive number, the average duration (in days) of epidemiological state IS (infectious with severe symptoms)
#' @param tLI a positive number, the average duration (in days) of low immunity persistence before return to non immune status
#' @param tHI a positive number, the average duration (in days) of high immunity persistence before return to low immune status
#' @param epsPPSA a positive ratio, the average infection-reducing ratio for patient infection during patient-to-patient contacts in the screening area (0 = no protection, 1 = complete protection/no infection possible)
#' @param epsHPSA a positive ratio, the average infection-reducing ratio for patient infection during professional-to-patient contacts in the screening area (0 = no protection, 1 = complete protection/no infection possible)
#' @param epsHPW a positive ratio, the average infection-reducing ratio for patient infection during professional-to-patient contacts in the ward (0 = no protection, 1 = complete protection/no infection possible)
#' @param epsPPW a positive ratio, the average infection-reducing ratio for patient infection during patient-to-patient contacts in the ward (0 = no protection, 1 = complete protection/no infection possible)
#' @param epsVPW a positive ratio, the average infection-reducing ratio for patient infection during visitor-to-patient contacts (0 = no protection, 1 = complete protection/no infection possible)
#' @param epsPHSA a positive ratio, the average infection-reducing ratio for professional infection during patient-to-professional contacts in the screening area (0 = no protection, 1 = complete protection/no infection possible)
#' @param epsPHW a positive ratio, the average infection-reducing ratio for professional infection during patient-to-professional contacts in the ward (0 = no protection, 1 = complete protection/no infection possible)
#' @param epsHHW a positive ratio, the average infection-reducing ratio for professional infection during professional-to-professional contacts (0 = no protection, 1 = complete protection/no infection possible)
#' @param ttestSA a positive number, the average duration (in days) of test in the screening area (from decision to test to action - such as transfer - after obtaining the test result)
#' @param ttestPW a positive number, the average duration (in days) of test in the ward for patient screening (from decision to test to action - such as transfer - after obtaining the test result)
#' @param ttestHW a positive number, the average duration (in days) of test for professional screening (from decision to test to action - such as sick leave - after obtaining the test result)
#' @param ttestsymp a positive number, the average duration (in days) of test for symptomatic individuals (from decision to test to action - such as sick leave or transfer - after obtaining the test result)
#' @param tbtwtestP a positive number, the average duration (in days) between two patient screening testing-events in the ward
#' @param tbtwtestH a positive number, the average duration (in days) between two professional screening testing-events in the ward
#' @param tbeftestPsymp a positive number, the average duration (in days) of symptomatic patients detection (before test)
#' @param tbeftestHsymp a positive number, the average duration (in days) of symptomatic professional detection (before test)
#' @param psympNI a positive probability, the conditional probability to be symptomatic when non immune
#' @param psympLI a positive probability, the conditional probability to be symptomatic despite a low immunity
#' @param psympHI a positive probability, the conditional probability to be symptomatic despite a high immunity
#' @param psevNI a positive probability, the conditional probability to develop severe symptoms when symptomatic and non immune
#' @param psevLI a positive probability, the conditional probability to develop severe symptoms when symptomatic and despite a low immunity
#' @param psevHI a positive probability, the conditional probability to develop severe symptoms when symptomatic and despite a high immunity
#' @param pISO probability, level of contact restrictions (confinement/quarantine/isolation) in case of positive test
#' @param pSL a positive probability, the probability for professional with mild symptoms of taking sick leave
#' @param pESL a positive probability, the probability for professional with severe symptoms of taking extended sick leave
#' @param pSLT positive probability, the additional probability for professionals of taking sick leave after positive test
#' @param pIC a positive probability, the probability for patient with severe symptoms to be transfer in intensive care
#' @param pdieIC a positive probability, the probability to die in intensive care
#' @param pLI a positive probability, the probability to have low immunity at the admission (proportion of individuals with low immunity in the community)
#' @param pHI a positive probability, the probability to have high immunity at the admission (proportion of individuals with high immunity in the community)
#' @param hNI2LI a positive probability, the daily probability to gain low immunity when non immune
#' @param hLI2HI a positive probability, the daily probability to gain high immunity when having low immunity
#' @param rinfLI a positive ratio, the average infection-reducing ratio for individuals with low immunity compared to non immune (can be interpreted as low immunity efficiency)
#' @param rinfHI a positive ratio, the average infection-reducing ratio for individuals with high immunity compared to non immune (can be interpreted as high immunity efficiency)
#' @param rsymp a ratio, the average ratio increasing or reducing the probability to develop symptoms for patients compared to general population (professionals)
#' @param rsev a ratio, the average ratio increasing or reducing the probability to develop severe symptoms for symptomatic patients compared to general population (professionals)
#' @param rEA a ratio, the ratio of excretion for individuals in epidemiological stage EA (exposed - contagious pre-asymptomatic)
#' @param rES a ratio, the ratio of excretion for individuals in epidemiological stage ES (exposed - contagious pre-symptomatic)
#' @param rIA a ratio, the ratio of excretion for individuals in epidemiological stage IA (infectious asymptomatic)
#' @param rIM a ratio, the ratio of excretion for individuals in epidemiological stage IM (infectious with mild symptoms)
#' @param rIS a ratio, the ratio of excretion for individuals in epidemiological stage IS (infectious with severe symptoms)
#' @param ptestPSAsymp a positive probability, the probability to test symptomatic patients in the screening area
#' @param ptestPSANI a positive probability, the probability to test non immune patients in the screening area
#' @param ptestPSALI a positive probability, the probability to test patients with low immunity in the screening area
#' @param ptestPSAHI a positive probability, the probability to test patients with high immunity in the screening area
#' @param ptestPWsymp a positive probability, the probability to test symptomatic patients in the ward (Diagnostic testing)
#' @param ptestPWNI a positive proportion, the proportion of non immune patients tested during screening testing in the ward
#' @param ptestPWLI a positive proportion, the proportion of patients with low immunity tested during screening testing in the ward
#' @param ptestPWHI a positive proportion, the proportion of patients with high immunity tested during screening testing in the ward
#' @param ptestHsymp a positive probability, the probability to test symptomatic professionals (Diagnostic testing)
#' @param ptestHNI a positive proportion, the proportion of non immune professionals tested during screening testing
#' @param ptestHLI a positive proportion, the proportion of professionals with low immunity tested during screening testing
#' @param ptestHHI a positive proportion, the proportion of professionals with high immunity tested during screening testing
#' @param senSA a positive probability, the sensibility of tests use within the screening area
#' @param speSA a positive probability, the specificity of tests use within the screening area
#' @param senW a positive probability, the sensibility of tests use for patient screening in the ward
#' @param speW a positive probability, the specificity of tests use for patient screening in the ward
#' @param senH a positive probability, the sensibility of tests use for professional screening
#' @param speH a positive probability, the specificity of tests use for professional screening
#' @param sensymp a positive probability, the sensibility of tests use for symptomatic individuals
#' @param spesymp a positive probability, the specificity of tests use for symptomatic individuals
#'
#' @return Named list of parameters
#'
#' @examples build_gdata()
#'
#' @export
build_gdata <- function(
disease = "Covid",
##### Infection
n_ctcH_PSA = NULL,
t_ctcH_PSA = NULL,
n_ctcP_PSA = NULL,
t_ctcP_PSA = NULL,
n_ctcH_PW = NULL,
t_ctcH_PW = NULL,
n_ctcP_PW = NULL,
t_ctcP_PW = NULL,
n_ctcH_H = NULL,
t_ctcH_H = NULL,
t_ctcV_PW = NULL,
I = NULL,
d = NULL,
R0 = NULL,
tw = NULL,
# https://www.gouvernement.fr/info-coronavirus/carte-et-donnees
tSA = NULL,
# average duration before full admission (in screening area for clinical exam, administrative procedure, etc)
tIC = NULL,
# average duration of stay in intensive care
tSL = NULL,
# average duration of sick leave
tESL = NULL,
# average duration of extended sick leave
tE = NULL,
# duration epidemiological state E
tEA = NULL,
# duration epidemiological state EA
tES = NULL,
# duration epidemiological state ES
tIA = NULL,
# duration epidemiological state IA
tIM = NULL,
# duration epidemiological state IM
tIS = NULL,
# duration epidemiological state IS
tLI = NULL,
# duration of partial immunity before return to non immune status
tHI = NULL,
# duration of full immunity before return to partial immune status
# patient protection
epsPPSA = NULL,
epsHPSA = NULL,
epsHPW = NULL,
epsPPW = NULL,
epsVPW = NULL,
# healthcare workers protection
epsPHSA = NULL,
#from patient in SA
epsPHW = NULL,
#from patient in W
epsHHW = NULL,
#from HW in W
## Test in ward
ttestSA = NULL,
# test duration in screening area
ttestPW = NULL,
# test duration in ward for screening patients
ttestHW = NULL,
# test duration in ward for screening professionals
ttestsymp = NULL,
# test duration for symptomatic
tbtwtestP = NULL,
# duration between two tests for patient
tbtwtestH = NULL,
# duration between two tests for HCWS
tbeftestPsymp = NULL,
# duration before test of symp patient
tbeftestHsymp = NULL,
# duration before test of symp HCWS
psympNI = NULL,
# probability to be symptomatic when non immune
psympLI = NULL,
# probability to be symptomatic when partially immune
psympHI = NULL,
# probability to be symptomatic when fully immune
psevNI = NULL,
# probability to develop severe symptoms when non immune
psevLI = NULL,
# probability to develop severe symptoms when partially immune
psevHI = NULL,
# probability to develop severe symptoms when fully immune
pISO = NULL,
# contact restriction in case of positive test
pSL = NULL,
# probability to take sick leave
pESL = NULL,
# probability to take extended sick leave
pSLT = NULL,
# probability to take EL/ESL after positive test
pIC = NULL,
# probability to be transfer in intensive care
pdieIC = NULL,
# probability to die in intensive care
###################################
pLI = NULL,
# probability to be PI at the admission (proportion of PI in the population)
pHI = NULL,
# probability to be FI at the admission (proportion of FI in the population)
hNI2LI = NULL,
# daily probability to become partially immune
hLI2HI = NULL,
# daily probability to become fully immune
rinfLI = NULL,
# partial immunity efficiency
rinfHI = NULL,
# partial immunity efficiency
rsymp = NULL,
# Ratio adjusting probability of symptoms for patients compared to general population (professionals)
rsev = NULL,
# Ratio adjusting probability of severity if symptoms for patients compared to general population (professionals)
rEA = NULL,
# Ratio of excretion for individuals in epidemiological stage EA (exposed - contagious pre-asymptomatic)
rES = NULL,
# Ratio of excretion for individuals in epidemiological stage ES (exposed - contagious pre-symptomatic)
rIA = NULL,
# Ratio of excretion for individuals in epidemiological stage IA (infectious asymptomatic)
rIM = NULL,
# Ratio of excretion for individuals in epidemiological stage IM (infectious with mild symptoms)
rIS = NULL,
# Ratio of excretion for individuals in epidemiological stage IS (infectious with severe symptoms)
ptestPSAsymp = NULL,
# probability to test symptomatic patients in the screening area
ptestPSANI = NULL,
# probability to test NI patients in the screening area
ptestPSALI = NULL,
# probability to test PI patients in the screening area
ptestPSAHI = NULL,
# probability to test FI patients in the screening area
ptestPWsymp = NULL,
# probability to test symptomatic patients in the ward
ptestPWNI = NULL,
# probability to test NI patients in the ward
ptestPWLI = NULL,
# probability to test PI patients in the ward
ptestPWHI = NULL,
# probability to test FI patients in the ward
ptestHsymp = NULL,
# probability to test symptomatic HCWS in the ward
ptestHNI = NULL,
# proportion of non immune professionals (healthcare workers) tested during screening testing
ptestHLI = NULL,
# probability to test PI HCWS
ptestHHI = NULL,
# probability to test FI HCWS
senSA = NULL,
speSA = NULL,
senW = NULL,
speW = NULL,
senH = NULL,
speH = NULL,
sensymp = NULL,
spesymp = NULL) {
if(! disease %in% c("Covid", "Influenza"))
stop(
"Disease parameter must be Covid or Influenza."
)
if(disease == "Covid"){
##### Infection
if(is.null(n_ctcH_PSA)) n_ctcH_PSA = 2
if(is.null(t_ctcH_PSA)) t_ctcH_PSA = 10 / 60 / 24
if(is.null(n_ctcP_PSA)) n_ctcP_PSA = 0
if(is.null(t_ctcP_PSA)) t_ctcP_PSA = 5 / 60 / 24
if(is.null(n_ctcH_PW)) n_ctcH_PW = 4
if(is.null(t_ctcH_PW)) t_ctcH_PW = 15 / 60 / 24
if(is.null(n_ctcP_PW)) n_ctcP_PW = 4
if(is.null(t_ctcP_PW)) t_ctcP_PW = 30 / 60 / 24
if(is.null(n_ctcH_H)) n_ctcH_H = 5
if(is.null(t_ctcH_H)) t_ctcH_H = 3 / 60 / 24
if(is.null(t_ctcV_PW)) t_ctcV_PW = 20 / 60 / 24
if(is.null(I)) I = 185 / 100000
if(is.null(d)) d = 10
if(is.null(R0)) R0 = 13
if(is.null(tw)) tw = 35
# https://www.gouvernement.fr/info-coronavirus/carte-et-donnees
if(is.null(tSA)) tSA = 2 / 24
# average duration before full admission (in screening area for clinical exam administrative procedure etc)
if(is.null(tIC)) tIC = 15
# average duration of stay in intensive care
if(is.null(tSL)) tSL = 14
# average duration of sick leave
if(is.null(tESL)) tESL = 28
# average duration of extended sick leave
if(is.null(tE)) tE = 5
# duration epidemiological state E
if(is.null(tEA)) tEA = 2
# duration epidemiological state EA
if(is.null(tES)) tES = 2
# duration epidemiological state ES
if(is.null(tIA)) tIA = 7
# duration epidemiological state IA
if(is.null(tIM)) tIM = 8
# duration epidemiological state IM
if(is.null(tIS)) tIS = 9
# duration epidemiological state IS
if(is.null(tLI)) tLI = 60
# duration of partial immunity before return to non immune status
if(is.null(tHI)) tHI = 150
# duration of full immunity before return to partial immune status
# patient protection
if(is.null(epsPPSA)) epsPPSA = 0.1
if(is.null(epsHPSA)) epsHPSA = 0.1
if(is.null(epsHPW)) epsHPW = 0.1
if(is.null(epsPPW)) epsPPW = 0.1
if(is.null(epsVPW)) epsVPW = 0.1
# healthcare workers protection
if(is.null(epsPHSA)) epsPHSA = 0.1
#from patient in SA
if(is.null(epsPHW)) epsPHW = 0.1
#from patient in W
if(is.null(epsHHW)) epsHHW = 0.1
#from HW in W
## Test in ward
if(is.null(ttestSA)) ttestSA = 2 / 24
# test duration in screening area
if(is.null(ttestPW)) ttestPW = 2 / 24
# test duration in ward for screening patients
if(is.null(ttestHW)) ttestHW = 2 / 24
# test duration in ward for screening professionals
if(is.null(ttestsymp)) ttestsymp = 2 / 24
# test duration for symptomatic
if(is.null(tbtwtestP)) tbtwtestP = 14
# duration between two tests for patient
if(is.null(tbtwtestH)) tbtwtestH = 30
# duration between two tests for HCWS
if(is.null(tbeftestPsymp)) tbeftestPsymp = 2 / 24
# duration before test of symp patient
if(is.null(tbeftestHsymp)) tbeftestHsymp = 1
# duration before test of symp HCWS
if(is.null(psympNI)) psympNI = 0.5
# probability to be symptomatic when non immune
if(is.null(psympLI)) psympLI = 0.2
# probability to be symptomatic when partially immune
if(is.null(psympHI)) psympHI = 0.1
# probability to be symptomatic when fully immune
if(is.null(psevNI)) psevNI = 0.5
# probability to develop severe symptoms when non immune
if(is.null(psevLI)) psevLI = 0.3
# probability to develop severe symptoms when partially immune
if(is.null(psevHI)) psevHI = 0.1
# probability to develop severe symptoms when fully immune
if(is.null(pISO)) pISO = 1
# contact restriction in case of positive test
if(is.null(pSL)) pSL = 0.3
# probability to take sick leave
if(is.null(pESL)) pESL = 1
# probability to take extended sick leave
if(is.null(pSLT)) pSLT = 0.01
# probability to take EL/ESL after positive test
if(is.null(pIC)) pIC = 0.3
# probability to be transfer in intensive care
if(is.null(pdieIC)) pdieIC = 0.005
# probability to die in intensive care
###################################
if(is.null(pLI)) pLI = 0.20
# probability to be PI at the admission (proportion of PI in the population)
if(is.null(pHI)) pHI = 0.5
# probability to be FI at the admission (proportion of FI in the population)
if(is.null(hNI2LI)) hNI2LI = 1 / 30
# daily probability to become partially immune
if(is.null(hLI2HI)) hLI2HI = 1 / 60
# daily probability to become fully immune
if(is.null(rinfLI)) rinfLI = 0.7
# partial immunity efficiency
if(is.null(rinfHI)) rinfHI = 0.5
# partial immunity efficiency
if(is.null(rsymp)) rsymp = 1
# Ratio adjusting probability of symptoms for patients compared to general population (professionals)
if(is.null(rsev)) rsev = 1
# Ratio adjusting probability of severity if symptoms for patients compared to general population (professionals)
if(is.null(rEA)) rEA = 0.35
# Ratio of excretion for individuals in epidemiological stage EA (exposed - contagious pre-asymptomatic)
if(is.null(rES)) rES = 1
# Ratio of excretion for individuals in epidemiological stage ES (exposed - contagious pre-symptomatic)
if(is.null(rIA)) rIA = 0.35
# Ratio of excretion for individuals in epidemiological stage IA (infectious asymptomatic)
if(is.null(rIM)) rIM = 1
# Ratio of excretion for individuals in epidemiological stage IM (infectious with mild symptoms)
if(is.null(rIS)) rIS = 1
# Ratio of excretion for individuals in epidemiological stage IS (infectious with severe symptoms)
if(is.null(ptestPSAsymp)) ptestPSAsymp = 1
# probability to test symptomatic patients in the screening area
if(is.null(ptestPSANI)) ptestPSANI = .75
# probability to test NI patients in the screening area
if(is.null(ptestPSALI)) ptestPSALI = 0.50
# probability to test PI patients in the screening area
if(is.null(ptestPSAHI)) ptestPSAHI = 0.1
# probability to test FI patients in the screening area
if(is.null(ptestPWsymp)) ptestPWsymp = 0.95
# probability to test symptomatic patients in the ward
if(is.null(ptestPWNI)) ptestPWNI = 0.75
# probability to test NI patients in the ward
if(is.null(ptestPWLI)) ptestPWLI = 0.50
# probability to test PI patients in the ward
if(is.null(ptestPWHI)) ptestPWHI = 0.10
# probability to test FI patients in the ward
if(is.null(ptestHsymp)) ptestHsymp = 0.85
# probability to test symptomatic HCWS in the ward
if(is.null(ptestHNI)) ptestHNI = 0.75
# proportion of non immune professionals (healthcare workers) tested during screening testing
if(is.null(ptestHLI)) ptestHLI = 0.50
# probability to test PI HCWS
if(is.null(ptestHHI)) ptestHHI = 0.20
# probability to test FI HCWS
if(is.null(senSA)) senSA = 0.85
if(is.null(speSA)) speSA = 0.95
if(is.null(senW)) senW = 0.85
if(is.null(speW)) speW = 0.95
if(is.null(senH)) senH = 0.85
if(is.null(speH)) speH = 0.95
if(is.null(sensymp)) sensymp = 1
if(is.null(spesymp)) spesymp = 1
}
if(disease == "Influenza"){
##### Infection
if(is.null(n_ctcH_PSA)) n_ctcH_PSA = 2
if(is.null(t_ctcH_PSA)) t_ctcH_PSA = 10 / 60 / 24
if(is.null(n_ctcP_PSA)) n_ctcP_PSA = 0
if(is.null(t_ctcP_PSA)) t_ctcP_PSA = 5 / 60 / 24
if(is.null(n_ctcH_PW)) n_ctcH_PW = 4
if(is.null(t_ctcH_PW)) t_ctcH_PW = 15 / 60 / 24
if(is.null(n_ctcP_PW)) n_ctcP_PW = 4
if(is.null(t_ctcP_PW)) t_ctcP_PW = 30 / 60 / 24
if(is.null(n_ctcH_H)) n_ctcH_H = 5
if(is.null(t_ctcH_H)) t_ctcH_H = 3 / 60 / 24
if(is.null(t_ctcV_PW)) t_ctcV_PW = 20 / 60 / 24
if(is.null(I)) I = 185 / 100000
if(is.null(d)) d = 7
if(is.null(R0)) R0 = 1.3
if(is.null(tw)) tw = 35
# https://www.gouvernement.fr/info-coronavirus/carte-et-donnees
if(is.null(tSA)) tSA = 2 / 24
# average duration before full admission (in screening area for clinical exam administrative procedure etc)
if(is.null(tIC)) tIC = 15
# average duration of stay in intensive care
if(is.null(tSL)) tSL = 14
# average duration of sick leave
if(is.null(tESL)) tESL = 28
# average duration of extended sick leave
if(is.null(tE)) tE = 1
# duration epidemiological state E
if(is.null(tEA)) tEA = 0
# duration epidemiological state EA
if(is.null(tES)) tES = 1
# duration epidemiological state ES
if(is.null(tIA)) tIA = 0
# duration epidemiological state IA
if(is.null(tIM)) tIM = 8
# duration epidemiological state IM
if(is.null(tIS)) tIS = 5
# duration epidemiological state IS
if(is.null(tLI)) tLI = 8
# duration of partial immunity before return to non immune status
if(is.null(tHI)) tHI = 150
# duration of full immunity before return to partial immune status
# patient protection
if(is.null(epsPPSA)) epsPPSA = 0.1
if(is.null(epsHPSA)) epsHPSA = 0.1
if(is.null(epsHPW)) epsHPW = 0.1
if(is.null(epsPPW)) epsPPW = 0.1
if(is.null(epsVPW)) epsVPW = 0.1
# healthcare workers protection
if(is.null(epsPHSA)) epsPHSA = 0.1
#from patient in SA
if(is.null(epsPHW)) epsPHW = 0.1
#from patient in W
if(is.null(epsHHW)) epsHHW = 0.1
#from HW in W
## Test in ward
if(is.null(ttestSA)) ttestSA = 2 / 24
# test duration in screening area
if(is.null(ttestPW)) ttestPW = 2 / 24
# test duration in ward for screening patients
if(is.null(ttestHW)) ttestHW = 2 / 24
# test duration in ward for screening professionals
if(is.null(ttestsymp)) ttestsymp = 2 / 24
# test duration for symptomatic
if(is.null(tbtwtestP)) tbtwtestP = 14
# duration between two tests for patient
if(is.null(tbtwtestH)) tbtwtestH = 30
# duration between two tests for HCWS
if(is.null(tbeftestPsymp)) tbeftestPsymp = 2 / 24
# duration before test of symp patient
if(is.null(tbeftestHsymp)) tbeftestHsymp = 1
# duration before test of symp HCWS
if(is.null(psympNI)) psympNI = 1 # 0.9
# probability to be symptomatic when non immune
if(is.null(psympLI)) psympLI = 1 # 0.8
# probability to be symptomatic when partially immune
if(is.null(psympHI)) psympHI = 1 # 0.7
# probability to be symptomatic when fully immune
if(is.null(psevNI)) psevNI = 0.6
# probability to develop severe symptoms when non immune
if(is.null(psevLI)) psevLI = 0.5
# probability to develop severe symptoms when partially immune
if(is.null(psevHI)) psevHI = 0.4
# probability to develop severe symptoms when fully immune
if(is.null(pISO)) pISO = 1
# contact restriction in case of positive test
if(is.null(pSL)) pSL = 0.3
# probability to take sick leave
if(is.null(pESL)) pESL = 1
# probability to take extended sick leave
if(is.null(pSLT)) pSLT = 0.01
# probability to take EL/ESL after positive test
if(is.null(pIC)) pIC = 0.3
# probability to be transfer in intensive care
if(is.null(pdieIC)) pdieIC = 0.005
# probability to die in intensive care
###################################
if(is.null(pLI)) pLI = 0.20
# probability to be PI at the admission (proportion of PI in the population)
if(is.null(pHI)) pHI = 0.5
# probability to be FI at the admission (proportion of FI in the population)
if(is.null(hNI2LI)) hNI2LI = 1 / 30
# daily probability to become partially immune
if(is.null(hLI2HI)) hLI2HI = 1 / 60
# daily probability to become fully immune
if(is.null(rinfLI)) rinfLI = 0.7
# partial immunity efficiency
if(is.null(rinfHI)) rinfHI = 0.5
# partial immunity efficiency
if(is.null(rsymp)) rsymp = 1
# Ratio adjusting probability of symptoms for patients compared to general population (professionals)
if(is.null(rsev)) rsev = 1
# Ratio adjusting probability of severity if symptoms for patients compared to general population (professionals)
if(is.null(rEA)) rEA = 0.35
# Ratio of excretion for individuals in epidemiological stage EA (exposed - contagious pre-asymptomatic)
if(is.null(rES)) rES = 1
# Ratio of excretion for individuals in epidemiological stage ES (exposed - contagious pre-symptomatic)
if(is.null(rIA)) rIA = 0.35
# Ratio of excretion for individuals in epidemiological stage IA (infectious asymptomatic)
if(is.null(rIM)) rIM = 1
# Ratio of excretion for individuals in epidemiological stage IM (infectious with mild symptoms)
if(is.null(rIS)) rIS = 1
# Ratio of excretion for individuals in epidemiological stage IS (infectious with severe symptoms)
if(is.null(ptestPSAsymp)) ptestPSAsymp = 1
# probability to test symptomatic patients in the screening area
if(is.null(ptestPSANI)) ptestPSANI = .75
# probability to test NI patients in the screening area
if(is.null(ptestPSALI)) ptestPSALI = 0.50
# probability to test PI patients in the screening area
if(is.null(ptestPSAHI)) ptestPSAHI = 0.1
# probability to test FI patients in the screening area
if(is.null(ptestPWsymp)) ptestPWsymp = 0.95
# probability to test symptomatic patients in the ward
if(is.null(ptestPWNI)) ptestPWNI = 0.75
# probability to test NI patients in the ward
if(is.null(ptestPWLI)) ptestPWLI = 0.50
# probability to test PI patients in the ward
if(is.null(ptestPWHI)) ptestPWHI = 0.10
# probability to test FI patients in the ward
if(is.null(ptestHsymp)) ptestHsymp = 0.85
# probability to test symptomatic HCWS in the ward
if(is.null(ptestHNI)) ptestHNI = 0.75
# proportion of non immune professionals (healthcare workers) tested during screening testing
if(is.null(ptestHLI)) ptestHLI = 0.50
# probability to test PI HCWS
if(is.null(ptestHHI)) ptestHHI = 0.20
# probability to test FI HCWS
if(is.null(senSA)) senSA = 0.85
if(is.null(speSA)) speSA = 0.95
if(is.null(senW)) senW = 0.85
if(is.null(speW)) speW = 0.95
if(is.null(senH)) senH = 0.85
if(is.null(speH)) speH = 0.95
if(is.null(sensymp)) sensymp = 0.85
if(is.null(spesymp)) spesymp = 0.95
}
### Checks
## Duration must be positive number
## Probabilities must be between 0 and 1
# Proportion of tested in dividuals
sapply(c(
ptestPSAsymp,
ptestPSANI,
ptestPSALI,
ptestPSAHI,
ptestPWsymp,
ptestPWNI,
ptestPWLI,
ptestPWHI,
ptestHsymp,
ptestHNI,
ptestHLI,
ptestHHI
), function(x)
if (x < 0 | x > 1)
stop(
"Proportion of tested individuals must fall between 0 (nobody is tested) and 1 (all group is tested)."
))
# Epidemiological stages durations
if((psympNI + psympLI + psympHI) < 3){
sapply(c(tE, tEA, tES, tIA, tIM, tIS, tLI, tHI), function(x)
if (x <= 0)
stop(
"Epidemiological stages and immunity durations must be strictly positive numbers."
))
} else {
sapply(c(tEA, tIA), function(x)
if (x != 0)
stop(
"With probabilities to be symptomatic equal to zero, asymptomatic epidemiological stages durations must be zero."
))
sapply(c(tE, tES, tIM, tIS, tLI, tHI), function(x)
if (x <= 0)
stop(
"Epidemiological stages and immunity durations must be positive numbers."
))
}
if (d <= 0)
stop(
"Epidemiological stages and immunity durations must be positive numbers."
)
if (d > sum(tE, tEA, tES, tIA, tIM, tIS))
stop(
"Total disease duration (d) must be inferior or equal to the sum of durations of all epidemiological stages (tE, tEA, tES, tIA, tIM, tIS)."
)
sapply(c(rinfLI, rinfHI), function(x)
if (x <= 0)
stop(
"Infection-reducing ratios related to immunity levels (rinfLI, rinfHI) must fall between 0 (no infection) and 1 (same probability to be infected that non immune)."
))
if (pLI + pHI < 0 | pLI + pHI > 1)
stop(
"The sum of probabilities to carry immunity (pLI and pHI) must fall between 0 (only non immune individuals at the admission) and 1 (only immune individuals at the admission)."
)
# Screening testing of patients
if (ptestPWNI > 0 | ptestPWLI > 0 | ptestPWHI > 0) {
if (tbtwtestP <= 0)
stop(
"If one of the proportions of patients tested during screening testing is positive (ptestPWNI + ptestPWLI + ptestPWHI > 0), the average duration between two screening programs (tbtwtestP) must be positive"
)
if (ttestPW <= 0)
stop(
"If one of the proportions of patients tested during screening testing is positive (ptestPWNI + ptestPWLI + ptestPWHI > 0), the average duration from test to reaction to result (ttestPW) must be positive"
)
if (senW < 0 | senW > 1 | speW < 0 | speW > 1)
stop(
"If one of the proportions of patients tested during screening testing is positive (ptestPWNI + ptestPWLI + ptestPWHI > 0), the test sensibilities and specificities must fall between 0 and 1 (senW and speW)."
)
}
if (tbtwtestP <= 0)
tbtwtestP <- 1
if (ttestPW <= 0)
ttestPW <- 1
# Screening testing of professionals
if (ptestHNI > 0 | ptestHLI > 0 | ptestHHI > 0) {
if (tbtwtestH <= 0)
stop(
"If one of the proportions of professionals tested during screening testing is positive (ptestHNI + ptestHLI + ptestHHI > 0), the average duration between two screening programs (tbtwtestH) must be positive"
)
if (ttestHW <= 0)
stop(
"If one of the proportions of professionals tested during screening testing is positive (ptestHNI + ptestHLI + ptestHHI > 0), the average duration from test to reaction to result (ttestH) must be positive"
)
if (senH < 0 | senH > 1 | speH < 0 | speH > 1)
stop(
"If one of the proportions of professionals tested during screening testing is positive (ptestHNI + ptestHLI + ptestHHI > 0), the test sensibilities and specificities must fall between 0 and 1 (senH and speH)."
)
}
if (tbtwtestH <= 0)
tbtwtestH <- 1
if (ttestHW <= 0)
ttestHW <- 1
# Screening area at the admission
if (ptestPSANI > 0 | ptestPSALI > 0 | ptestPSAHI > 0) {
if (ttestSA <= 0)
stop(
"If one of the proportions of patients tested in the screening area is positive (ptestPSANI + ptestPSALI + ptestPSAHI > 0), the average duration from test to reaction to result (ttestSA) must be positive"
)
if (senSA < 0 | senSA > 1 | speSA < 0 | speSA > 1)
stop(
"If one of the proportions of patients tested in the screening area is positive (ptestPSANI + ptestPSALI + ptestPSAHI > 0), the test sensibilities and specificities must fall between 0 and 1 (senSA and speSA)."
)
}
if (ttestSA <= 0)
ttestSA <- 1
if (tSA <= 0)
stop("The duration of screening at the admission (tSA) must be positive (in days).")
# Diagnostic testing
if (ptestPSAsymp > 0 | ptestPWsymp > 0 | ptestHsymp > 0) {
condi <-
"If one of the proportions of individuals tested for diagnostic testing is positive (ptestPSAsymp + ptestPWsymp + ptestHsymp > 0),"
if (ttestsymp <= 0)
stop(
paste(
condi,
"the average duration from test to reaction to result (ttestsymp) must be positive."
)
)
if (tbeftestPsymp <= 0 | tbeftestHsymp <= 0)
stop(
paste(
condi,
"the average duration before suspicion (tbeftestPsymp and tbeftestHsymp) must be positive."
)
)
if (sensymp < 0 | sensymp > 1 | spesymp < 0 | spesymp > 1)
stop(
"If one of the proportions of individuals tested for diagnostic testing is positive (ptestPSAsymp + ptestPWsymp + ptestHsymp > 0), the test sensibilities and specificities must fall between 0 and 1 (sensymp and spesymp)."
)
}
if (ttestsymp <= 0)
ttestsymp <- 1
if (tbeftestPsymp <= 0)
tbeftestPsymp <- 1
if (tbeftestHsymp <= 0)
tbeftestHsymp <- 1
## Contact restriction
# if (!is.logical(pISO))
# stop(
# "pISO must be logical. TRUE: patients are isolated and contacts are restricted in case of a positive test, FALSE: contact are not restricted but test is counted."
# )
## Intensive care
if (pIC < 0 | pIC > 1 | pdieIC < 0 | pdieIC > 1)
stop(
"The probability of being transfered and die in intensive care must fall between 0 (never transfered) and 1 (always transfered)."
)
if (pIC > 0 & tIC <= 0)
stop("Duration of intensive care stay (tIC) must be positive.")
## Sick leave
if (pSL < 0 | pSL > 1 | pESL < 0 | pESL > 1 | pSLT < 0 | pSLT > 1)
stop(
"The probabilities of taking sick leave (pSL, pESL, pSLT) must fall between 0 (never) and 1 (always)."
)
if (pSL + pESL + pSLT > 0 & (tSL <= 0 | tESL <= 0))
stop("Duration of sick leave (tSL and tESL) must be positive.")
### Build gdata
# p = R0 / (dCtc * nCtc * dInf)
# where
# p is the probability of transmission per minute spent in contact,
# dCtc is the average contact duration (in minutes),
# nCtc is the average number of contacts per person per day, and
# dInf is the average duration of infectivity (in days): approximately 10 days for COVID-19 [10].
bet01 <- function(x) {
if (x < 0)
x <- 0
if (x > 1)
x <- 1
x
}
psympPNI <- psympNI * rsymp %>% bet01
psevPNI <- psevNI * rsev %>% bet01
psympPLI <- psympLI * rsymp %>% bet01
psevPLI <- psevLI * rsev %>% bet01
psympPHI <- psympHI * rsymp %>% bet01
psevPHI <- psevHI * rsev %>% bet01
gdata = c(
tSA = tSA,
# average duration before full admission (in screening area for clinical exam, administrative procedure, etc)
tIC = tIC,
# average duration of stay in intensive care
tSL = tSL,
# average duration of sick leave
tESL = tESL,
# average duration of extended sick leave
tE = tE,
# duration epidemiological state E
tEA = tEA,
# duration epidemiological state EA
tES = tES,
# duration epidemiological state ES
tIA = tIA,
# duration epidemiological state IA
tIM = tIM,
# duration epidemiological state IM
tIS = tIS,
# duration epidemiological state IS
tLI = tLI,
# duration of partial immunity before return to non immune status
tHI = tHI,
# duration of full immunity before return to partial immune status
td = d,
# disease duration
## Contacts
ctcHPSA = n_ctcH_PSA * t_ctcH_PSA,
ctcPPSA = n_ctcP_PSA * t_ctcP_PSA,
ctcHPW = n_ctcH_PW * t_ctcH_PW,
ctcPPW = n_ctcP_PW * t_ctcP_PW,
ctcHH = n_ctcH_H * t_ctcH_H,
# n_ctcV_PW => see ldata
ctcV = t_ctcV_PW,
# Epsilon
# patient protection
epsPPSA = epsPPSA,
epsHPSA = epsHPSA,
epsHPW = epsHPW,
epsPPW = epsPPW,
epsVPW = epsVPW,
# healthcare workers protection
epsPHSA = epsPHSA,
#from patient in SA
epsPHW = epsPHW,
#from patient in W
epsHHW = epsHHW,
#from HW in W
## Test in ward
ttestSA = ttestSA,
# test duration in screening area
ttestPW = ttestPW,
# test duration in ward for screening of patients
ttestHW = ttestHW,
# test duration in ward for screening of professionals
ttestsymp = ttestsymp,
# test duration for symptomatic
tbtwtestP = tbtwtestP,
# duration between two tests for patient
tbtwtestH = tbtwtestH,
# duration between two tests for HCWS
tbeftestPsymp = tbeftestPsymp,
# duration before test of symp patient
tbeftestHsymp = tbeftestHsymp,
# duration before test of symp HCWS
# daily incidence in the community
hinc = I,
# daily incidence in the community
prev = I * d,
# prevalence (probability to be infected at the admission)
pconta = R0 / (8 * (30 / 60 / 24) * d),
# https://doi.org/10.1093/cid/ciaa682
# proportion of time outside of work
ptow = 1 - tw / ((24 - 8) * 7),
# 24 hours per days minus 8 sleeping hours time 7 days
psympNI = psympNI,
# probability to be symptomatic when non immune
psympLI = psympLI,
# probability to be symptomatic when partially immune
psympHI = psympHI,
# probability to be symptomatic when fully immune
psevNI = psevNI,
# probability to develop severe symptoms when non immune
psevLI = psevLI,
# probability to develop severe symptoms when partially immune
psevHI = psevHI,
# probability to develop severe symptoms when fully immune
pISO = pISO,
pSL = pSL,
# probability to take sick leave
pESL = pESL,
# probability to take extended sick leave
pSLT = pSLT,
# probability to take EL/ESL after positive test
pIC = pIC,
# probability to be transfer in intensive care
pdieIC = pdieIC,
# probability to die in intensive care
###################################
pLI = pLI,
# probability to be PI at the admission (proportion of PI in the population)
pHI = pHI,
# probability to be FI at the admission (proportion of FI in the population)
hNI2LI = hNI2LI,
# daily probability to become partially immune
hLI2HI = hLI2HI,
# daily probability to become fully immune
rinfLI = rinfLI,
# partial immunity efficiency
rinfHI = rinfHI,
# partial immunity efficiency
rEA = rEA,
# Ratio of excretion for individuals in epidemiological stage EA (exposed - contagious pre-asymptomatic)
rES = rES,
# Ratio of excretion for individuals in epidemiological stage ES (exposed - contagious pre-symptomatic)
rIA = rIA,
# Ratio of excretion for individuals in epidemiological stage IA (infectious asymptomatic)
rIM = rIM,
# Ratio of excretion for individuals in epidemiological stage IM (infectious with mild symptoms)
rIS = rIS,
# Ratio of excretion for individuals in epidemiological stage IS (infectious with severe symptoms)
# probability of symptoms for patients compared to general population (professionals)
psympPNI = psympPNI,
psevPNI = psevPNI,
psympPLI = psympPLI,
psevPLI = psevPLI,
psympPHI = psympPHI,
psevPHI = psevPHI,
ptestPSAsymp = ptestPSAsymp,
# probability to test symptomatic patients in the screening area
ptestPSANI = ptestPSANI,
# probability to test NI patients in the screening area
ptestPSALI = ptestPSALI,
# probability to test PI patients in the screening area
ptestPSAHI = ptestPSAHI,
# probability to test FI patients in the screening area
ptestPWsymp = ptestPWsymp,
# probability to test symptomatic patients in the ward
ptestPWNI = ptestPWNI,
# probability to test NI patients in the ward
ptestPWLI = ptestPWLI,
# probability to test PI patients in the ward
ptestPWHI = ptestPWHI,
# probability to test FI patients in the ward
ptestHsymp = ptestHsymp,
# probability to test symptomatic HCWS in the ward
ptestHNI = ptestHNI,
# probability to test NI HCWS
ptestHLI = ptestHLI,
# probability to test PI HCWS
ptestHHI = ptestHHI,
# probability to test FI HCWS
senSA = senSA,
speSA = speSA,
senW = senW,
speW = speW,
senH = senH,
speH = speH,
sensymp = sensymp,
spesymp = spesymp
)
# Use psevNI >> worst case scenario
with(data.frame(gdata %>% t),
cumd <<-
(1 - psympNI) * (tE + tEA + tIA) + psympNI * ((1 - psevNI) * (tE + tES + tIM) + psevNI * (tE + tES + tIS)))
gdata <- c(gdata,
with(
data.frame(gdata %>% t),
c(
rtE = tE / cumd,
# time ratio of the epidemiological state E over the whole infectious period (probability to be E at the admission when non susceptible)
rtEA = (1 - psympNI) * (tEA / cumd),
# time ratio of the epidemiological state EA over the whole infectious period (probability to be EA at the admission when non susceptible)
rtES = psympNI * (tES / cumd),
# time ratio of the epidemiological state ES over the whole infectious period (probability to be ES at the admission when non susceptible)
rtIA = (1 - psympNI) * (tIA / cumd),
# time ratio of the epidemiological state IA over the whole infectious period (probability to be IA at the admission when non susceptible)
rtIM = psympNI * (1 - psevNI) * (tIM / cumd),
# time ratio of the epidemiological state IM over the whole infectious period (probability to be IM at the admission when non susceptible)
rtIS = psympNI * psevNI * (tIS / cumd) # time ratio of the epidemiological state IS over the whole infectious period (probability to be IS at the admission when non susceptible)
)
))
return(gdata)
}
MESuRS-Lab/mwss documentation built on Sept. 12, 2023, 12:08 a.m.
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Defines functions build_gdata
Documented in build_gdata
#' Generate global parameters dataset
#'
#' @description It calculates 1) the prevalence from daily incidence in the community and average disease duration,
#' 2) the probability of transmission per day spent in contact based on R0 and average disease duration,
#' 3) the time ratios of the epidemiological state based on average states duration,
#' 4) the proportion of time outside of work, and
#' 5) the proportion of probabilities of developing mild and severe symptoms for patients.
#'
#' Then the functions formats all global parameters required for the transitions as a named list readable by SimInf package.
#'
#' @importFrom magrittr %>%
#'
#' @param disease string. only Covid and Influenza are available
#' @param n_ctcH_PSA a positive number, the daily number of contacts with professionals per patient in the screening area
#' @param t_ctcH_PSA a positive number, the average duration of contact between professional and patient per day in the screening area (in days, ex: if 15 min, t_ctcH_PSA = 15/60/24)
#' @param n_ctcP_PSA a positive number, the daily number of contacts with other patients per patient in the screening area
#' @param t_ctcP_PSA a positive number, the average duration of contact between patients per day in the screening area (in days)
#' @param n_ctcH_PW a positive number, the number of contact between professional and patient per day in the ward
#' @param t_ctcH_PW a positive number, the average duration of contact between patients per day in the ward (in days)
#' @param n_ctcP_PW a positive number, the number of contacts with other patients per patient per day, in the ward
#' @param t_ctcP_PW a positive number, the average duration of contact between patients per day in the ward (in days)
#' @param n_ctcH_H a positive number, the number of contacts with professionals per professional per day
#' @param t_ctcH_H a positive number, the average duration of contact between professionals in the ward (in days)
#' @param t_ctcV_PW a positive number, the average duration of contact between patients per day in the ward (in days)
#' @param I a positive number, the daily incidence
#' @param d a positive number, the average disease duration (in days)
#' @param R0 a positive number, the basic reproduction number
#' @param tw a positive number, the average number of working hours per week (in hours)
#' @param tSA a positive number, the average duration (in days) before full admission (in screening area for clinical exam, administrative procedure, etc)
#' @param tIC a positive number, the average duration (in days) of stay in intensive care
#' @param tSL a positive number, the average duration (in days) of sick leave
#' @param tESL a positive number, the average duration (in days) of extended sick leave
#' @param tE a positive number, the average duration (in days) of epidemiological state E (exposed - non contagious)
#' @param tEA a positive number, the average duration (in days) of epidemiological state EA (exposed - contagious pre-asymptomatic)
#' @param tES a positive number, the average duration (in days) of epidemiological state ES (exposed - contagious pre-symptomatic)
#' @param tIA a positive number, the average duration (in days) of epidemiological state IA (infectious asymptomatic)
#' @param tIM a positive number, the average duration (in days) of epidemiological state IM (infectious with mild symptoms)
#' @param tIS a positive number, the average duration (in days) of epidemiological state IS (infectious with severe symptoms)
#' @param tLI a positive number, the average duration (in days) of low immunity persistence before return to non immune status
#' @param tHI a positive number, the average duration (in days) of high immunity persistence before return to low immune status
#' @param epsPPSA a positive ratio, the average infection-reducing ratio for patient infection during patient-to-patient contacts in the screening area (0 = no protection, 1 = complete protection/no infection possible)
#' @param epsHPSA a positive ratio, the average infection-reducing ratio for patient infection during professional-to-patient contacts in the screening area (0 = no protection, 1 = complete protection/no infection possible)
#' @param epsHPW a positive ratio, the average infection-reducing ratio for patient infection during professional-to-patient contacts in the ward (0 = no protection, 1 = complete protection/no infection possible)
#' @param epsPPW a positive ratio, the average infection-reducing ratio for patient infection during patient-to-patient contacts in the ward (0 = no protection, 1 = complete protection/no infection possible)
#' @param epsVPW a positive ratio, the average infection-reducing ratio for patient infection during visitor-to-patient contacts (0 = no protection, 1 = complete protection/no infection possible)
#' @param epsPHSA a positive ratio, the average infection-reducing ratio for professional infection during patient-to-professional contacts in the screening area (0 = no protection, 1 = complete protection/no infection possible)
#' @param epsPHW a positive ratio, the average infection-reducing ratio for professional infection during patient-to-professional contacts in the ward (0 = no protection, 1 = complete protection/no infection possible)
#' @param epsHHW a positive ratio, the average infection-reducing ratio for professional infection during professional-to-professional contacts (0 = no protection, 1 = complete protection/no infection possible)
#' @param ttestSA a positive number, the average duration (in days) of test in the screening area (from decision to test to action - such as transfer - after obtaining the test result)
#' @param ttestPW a positive number, the average duration (in days) of test in the ward for patient screening (from decision to test to action - such as transfer - after obtaining the test result)
#' @param ttestHW a positive number, the average duration (in days) of test for professional screening (from decision to test to action - such as sick leave - after obtaining the test result)
#' @param ttestsymp a positive number, the average duration (in days) of test for symptomatic individuals (from decision to test to action - such as sick leave or transfer - after obtaining the test result)
#' @param tbtwtestP a positive number, the average duration (in days) between two patient screening testing-events in the ward
#' @param tbtwtestH a positive number, the average duration (in days) between two professional screening testing-events in the ward
#' @param tbeftestPsymp a positive number, the average duration (in days) of symptomatic patients detection (before test)
#' @param tbeftestHsymp a positive number, the average duration (in days) of symptomatic professional detection (before test)
#' @param psympNI a positive probability, the conditional probability to be symptomatic when non immune
#' @param psympLI a positive probability, the conditional probability to be symptomatic despite a low immunity
#' @param psympHI a positive probability, the conditional probability to be symptomatic despite a high immunity
#' @param psevNI a positive probability, the conditional probability to develop severe symptoms when symptomatic and non immune
#' @param psevLI a positive probability, the conditional probability to develop severe symptoms when symptomatic and despite a low immunity
#' @param psevHI a positive probability, the conditional probability to develop severe symptoms when symptomatic and despite a high immunity
#' @param pISO probability, level of contact restrictions (confinement/quarantine/isolation) in case of positive test
#' @param pSL a positive probability, the probability for professional with mild symptoms of taking sick leave
#' @param pESL a positive probability, the probability for professional with severe symptoms of taking extended sick leave
#' @param pSLT positive probability, the additional probability for professionals of taking sick leave after positive test
#' @param pIC a positive probability, the probability for patient with severe symptoms to be transfer in intensive care
#' @param pdieIC a positive probability, the probability to die in intensive care
#' @param pLI a positive probability, the probability to have low immunity at the admission (proportion of individuals with low immunity in the community)
#' @param pHI a positive probability, the probability to have high immunity at the admission (proportion of individuals with high immunity in the community)
#' @param hNI2LI a positive probability, the daily probability to gain low immunity when non immune
#' @param hLI2HI a positive probability, the daily probability to gain high immunity when having low immunity
#' @param rinfLI a positive ratio, the average infection-reducing ratio for individuals with low immunity compared to non immune (can be interpreted as low immunity efficiency)
#' @param rinfHI a positive ratio, the average infection-reducing ratio for individuals with high immunity compared to non immune (can be interpreted as high immunity efficiency)
#' @param rsymp a ratio, the average ratio increasing or reducing the probability to develop symptoms for patients compared to general population (professionals)
#' @param rsev a ratio, the average ratio increasing or reducing the probability to develop severe symptoms for symptomatic patients compared to general population (professionals)
#' @param rEA a ratio, the ratio of excretion for individuals in epidemiological stage EA (exposed - contagious pre-asymptomatic)
#' @param rES a ratio, the ratio of excretion for individuals in epidemiological stage ES (exposed - contagious pre-symptomatic)
#' @param rIA a ratio, the ratio of excretion for individuals in epidemiological stage IA (infectious asymptomatic)
#' @param rIM a ratio, the ratio of excretion for individuals in epidemiological stage IM (infectious with mild symptoms)
#' @param rIS a ratio, the ratio of excretion for individuals in epidemiological stage IS (infectious with severe symptoms)
#' @param ptestPSAsymp a positive probability, the probability to test symptomatic patients in the screening area
#' @param ptestPSANI a positive probability, the probability to test non immune patients in the screening area
#' @param ptestPSALI a positive probability, the probability to test patients with low immunity in the screening area
#' @param ptestPSAHI a positive probability, the probability to test patients with high immunity in the screening area
#' @param ptestPWsymp a positive probability, the probability to test symptomatic patients in the ward (Diagnostic testing)
#' @param ptestPWNI a positive proportion, the proportion of non immune patients tested during screening testing in the ward
#' @param ptestPWLI a positive proportion, the proportion of patients with low immunity tested during screening testing in the ward
#' @param ptestPWHI a positive proportion, the proportion of patients with high immunity tested during screening testing in the ward
#' @param ptestHsymp a positive probability, the probability to test symptomatic professionals (Diagnostic testing)
#' @param ptestHNI a positive proportion, the proportion of non immune professionals tested during screening testing
#' @param ptestHLI a positive proportion, the proportion of professionals with low immunity tested during screening testing
#' @param ptestHHI a positive proportion, the proportion of professionals with high immunity tested during screening testing
#' @param senSA a positive probability, the sensibility of tests use within the screening area
#' @param speSA a positive probability, the specificity of tests use within the screening area
#' @param senW a positive probability, the sensibility of tests use for patient screening in the ward
#' @param speW a positive probability, the specificity of tests use for patient screening in the ward
#' @param senH a positive probability, the sensibility of tests use for professional screening
#' @param speH a positive probability, the specificity of tests use for professional screening
#' @param sensymp a positive probability, the sensibility of tests use for symptomatic individuals
#' @param spesymp a positive probability, the specificity of tests use for symptomatic individuals
#'
#' @return Named list of parameters
#'
#' @examples build_gdata()
#'
#' @export
build_gdata <- function(
disease = "Covid",
##### Infection
n_ctcH_PSA = NULL,
t_ctcH_PSA = NULL,
n_ctcP_PSA = NULL,
t_ctcP_PSA = NULL,
n_ctcH_PW = NULL,
t_ctcH_PW = NULL,
n_ctcP_PW = NULL,
t_ctcP_PW = NULL,
n_ctcH_H = NULL,
t_ctcH_H = NULL,
t_ctcV_PW = NULL,
I = NULL,
d = NULL,
R0 = NULL,
tw = NULL,
# https://www.gouvernement.fr/info-coronavirus/carte-et-donnees
tSA = NULL,
# average duration before full admission (in screening area for clinical exam, administrative procedure, etc)
tIC = NULL,
# average duration of stay in intensive care
tSL = NULL,
# average duration of sick leave
tESL = NULL,
# average duration of extended sick leave
tE = NULL,
# duration epidemiological state E
tEA = NULL,
# duration epidemiological state EA
tES = NULL,
# duration epidemiological state ES
tIA = NULL,
# duration epidemiological state IA
tIM = NULL,
# duration epidemiological state IM
tIS = NULL,
# duration epidemiological state IS
tLI = NULL,
# duration of partial immunity before return to non immune status
tHI = NULL,
# duration of full immunity before return to partial immune status
# patient protection
epsPPSA = NULL,
epsHPSA = NULL,
epsHPW = NULL,
epsPPW = NULL,
epsVPW = NULL,
# healthcare workers protection
epsPHSA = NULL,
#from patient in SA
epsPHW = NULL,
#from patient in W
epsHHW = NULL,
#from HW in W
## Test in ward
ttestSA = NULL,
# test duration in screening area
ttestPW = NULL,
# test duration in ward for screening patients
ttestHW = NULL,
# test duration in ward for screening professionals
ttestsymp = NULL,
# test duration for symptomatic
tbtwtestP = NULL,
# duration between two tests for patient
tbtwtestH = NULL,
# duration between two tests for HCWS
tbeftestPsymp = NULL,
# duration before test of symp patient
tbeftestHsymp = NULL,
# duration before test of symp HCWS
psympNI = NULL,
# probability to be symptomatic when non immune
psympLI = NULL,
# probability to be symptomatic when partially immune
psympHI = NULL,
# probability to be symptomatic when fully immune
psevNI = NULL,
# probability to develop severe symptoms when non immune
psevLI = NULL,
# probability to develop severe symptoms when partially immune
psevHI = NULL,
# probability to develop severe symptoms when fully immune
pISO = NULL,
# contact restriction in case of positive test
pSL = NULL,
# probability to take sick leave
pESL = NULL,
# probability to take extended sick leave
pSLT = NULL,
# probability to take EL/ESL after positive test
pIC = NULL,
# probability to be transfer in intensive care
pdieIC = NULL,
# probability to die in intensive care
###################################
pLI = NULL,
# probability to be PI at the admission (proportion of PI in the population)
pHI = NULL,
# probability to be FI at the admission (proportion of FI in the population)
hNI2LI = NULL,
# daily probability to become partially immune
hLI2HI = NULL,
# daily probability to become fully immune
rinfLI = NULL,
# partial immunity efficiency
rinfHI = NULL,
# partial immunity efficiency
rsymp = NULL,
# Ratio adjusting probability of symptoms for patients compared to general population (professionals)
rsev = NULL,
# Ratio adjusting probability of severity if symptoms for patients compared to general population (professionals)
rEA = NULL,
# Ratio of excretion for individuals in epidemiological stage EA (exposed - contagious pre-asymptomatic)
rES = NULL,
# Ratio of excretion for individuals in epidemiological stage ES (exposed - contagious pre-symptomatic)
rIA = NULL,
# Ratio of excretion for individuals in epidemiological stage IA (infectious asymptomatic)
rIM = NULL,
# Ratio of excretion for individuals in epidemiological stage IM (infectious with mild symptoms)
rIS = NULL,
# Ratio of excretion for individuals in epidemiological stage IS (infectious with severe symptoms)
ptestPSAsymp = NULL,
# probability to test symptomatic patients in the screening area
ptestPSANI = NULL,
# probability to test NI patients in the screening area
ptestPSALI = NULL,
# probability to test PI patients in the screening area
ptestPSAHI = NULL,
# probability to test FI patients in the screening area
ptestPWsymp = NULL,
# probability to test symptomatic patients in the ward
ptestPWNI = NULL,
# probability to test NI patients in the ward
ptestPWLI = NULL,
# probability to test PI patients in the ward
ptestPWHI = NULL,
# probability to test FI patients in the ward
ptestHsymp = NULL,
# probability to test symptomatic HCWS in the ward
ptestHNI = NULL,
# proportion of non immune professionals (healthcare workers) tested during screening testing
ptestHLI = NULL,
# probability to test PI HCWS
ptestHHI = NULL,
# probability to test FI HCWS
senSA = NULL,
speSA = NULL,
senW = NULL,
speW = NULL,
senH = NULL,
speH = NULL,
sensymp = NULL,
spesymp = NULL) {
if(! disease %in% c("Covid", "Influenza"))
stop(
"Disease parameter must be Covid or Influenza."
)
if(disease == "Covid"){
##### Infection
if(is.null(n_ctcH_PSA)) n_ctcH_PSA = 2
if(is.null(t_ctcH_PSA)) t_ctcH_PSA = 10 / 60 / 24
if(is.null(n_ctcP_PSA)) n_ctcP_PSA = 0
if(is.null(t_ctcP_PSA)) t_ctcP_PSA = 5 / 60 / 24
if(is.null(n_ctcH_PW)) n_ctcH_PW = 4
if(is.null(t_ctcH_PW)) t_ctcH_PW = 15 / 60 / 24
if(is.null(n_ctcP_PW)) n_ctcP_PW = 4
if(is.null(t_ctcP_PW)) t_ctcP_PW = 30 / 60 / 24
if(is.null(n_ctcH_H)) n_ctcH_H = 5
if(is.null(t_ctcH_H)) t_ctcH_H = 3 / 60 / 24
if(is.null(t_ctcV_PW)) t_ctcV_PW = 20 / 60 / 24
if(is.null(I)) I = 185 / 100000
if(is.null(d)) d = 10
if(is.null(R0)) R0 = 13
if(is.null(tw)) tw = 35
# https://www.gouvernement.fr/info-coronavirus/carte-et-donnees
if(is.null(tSA)) tSA = 2 / 24
# average duration before full admission (in screening area for clinical exam administrative procedure etc)
if(is.null(tIC)) tIC = 15
# average duration of stay in intensive care
if(is.null(tSL)) tSL = 14
# average duration of sick leave
if(is.null(tESL)) tESL = 28
# average duration of extended sick leave
if(is.null(tE)) tE = 5
# duration epidemiological state E
if(is.null(tEA)) tEA = 2
# duration epidemiological state EA
if(is.null(tES)) tES = 2
# duration epidemiological state ES
if(is.null(tIA)) tIA = 7
# duration epidemiological state IA
if(is.null(tIM)) tIM = 8
# duration epidemiological state IM
if(is.null(tIS)) tIS = 9
# duration epidemiological state IS
if(is.null(tLI)) tLI = 60
# duration of partial immunity before return to non immune status
if(is.null(tHI)) tHI = 150
# duration of full immunity before return to partial immune status
# patient protection
if(is.null(epsPPSA)) epsPPSA = 0.1
if(is.null(epsHPSA)) epsHPSA = 0.1
if(is.null(epsHPW)) epsHPW = 0.1
if(is.null(epsPPW)) epsPPW = 0.1
if(is.null(epsVPW)) epsVPW = 0.1
# healthcare workers protection
if(is.null(epsPHSA)) epsPHSA = 0.1
#from patient in SA
if(is.null(epsPHW)) epsPHW = 0.1
#from patient in W
if(is.null(epsHHW)) epsHHW = 0.1
#from HW in W
## Test in ward
if(is.null(ttestSA)) ttestSA = 2 / 24
# test duration in screening area
if(is.null(ttestPW)) ttestPW = 2 / 24
# test duration in ward for screening patients
if(is.null(ttestHW)) ttestHW = 2 / 24
# test duration in ward for screening professionals
if(is.null(ttestsymp)) ttestsymp = 2 / 24
# test duration for symptomatic
if(is.null(tbtwtestP)) tbtwtestP = 14
# duration between two tests for patient
if(is.null(tbtwtestH)) tbtwtestH = 30
# duration between two tests for HCWS
if(is.null(tbeftestPsymp)) tbeftestPsymp = 2 / 24
# duration before test of symp patient
if(is.null(tbeftestHsymp)) tbeftestHsymp = 1
# duration before test of symp HCWS
if(is.null(psympNI)) psympNI = 0.5
# probability to be symptomatic when non immune
if(is.null(psympLI)) psympLI = 0.2
# probability to be symptomatic when partially immune
if(is.null(psympHI)) psympHI = 0.1
# probability to be symptomatic when fully immune
if(is.null(psevNI)) psevNI = 0.5
# probability to develop severe symptoms when non immune
if(is.null(psevLI)) psevLI = 0.3
# probability to develop severe symptoms when partially immune
if(is.null(psevHI)) psevHI = 0.1
# probability to develop severe symptoms when fully immune
if(is.null(pISO)) pISO = 1
# contact restriction in case of positive test
if(is.null(pSL)) pSL = 0.3
# probability to take sick leave
if(is.null(pESL)) pESL = 1
# probability to take extended sick leave
if(is.null(pSLT)) pSLT = 0.01
# probability to take EL/ESL after positive test
if(is.null(pIC)) pIC = 0.3
# probability to be transfer in intensive care
if(is.null(pdieIC)) pdieIC = 0.005
# probability to die in intensive care
###################################
if(is.null(pLI)) pLI = 0.20
# probability to be PI at the admission (proportion of PI in the population)
if(is.null(pHI)) pHI = 0.5
# probability to be FI at the admission (proportion of FI in the population)
if(is.null(hNI2LI)) hNI2LI = 1 / 30
# daily probability to become partially immune
if(is.null(hLI2HI)) hLI2HI = 1 / 60
# daily probability to become fully immune
if(is.null(rinfLI)) rinfLI = 0.7
# partial immunity efficiency
if(is.null(rinfHI)) rinfHI = 0.5
# partial immunity efficiency
if(is.null(rsymp)) rsymp = 1
# Ratio adjusting probability of symptoms for patients compared to general population (professionals)
if(is.null(rsev)) rsev = 1
# Ratio adjusting probability of severity if symptoms for patients compared to general population (professionals)
if(is.null(rEA)) rEA = 0.35
# Ratio of excretion for individuals in epidemiological stage EA (exposed - contagious pre-asymptomatic)
if(is.null(rES)) rES = 1
# Ratio of excretion for individuals in epidemiological stage ES (exposed - contagious pre-symptomatic)
if(is.null(rIA)) rIA = 0.35
# Ratio of excretion for individuals in epidemiological stage IA (infectious asymptomatic)
if(is.null(rIM)) rIM = 1
# Ratio of excretion for individuals in epidemiological stage IM (infectious with mild symptoms)
if(is.null(rIS)) rIS = 1
# Ratio of excretion for individuals in epidemiological stage IS (infectious with severe symptoms)
if(is.null(ptestPSAsymp)) ptestPSAsymp = 1
# probability to test symptomatic patients in the screening area
if(is.null(ptestPSANI)) ptestPSANI = .75
# probability to test NI patients in the screening area
if(is.null(ptestPSALI)) ptestPSALI = 0.50
# probability to test PI patients in the screening area
if(is.null(ptestPSAHI)) ptestPSAHI = 0.1
# probability to test FI patients in the screening area
if(is.null(ptestPWsymp)) ptestPWsymp = 0.95
# probability to test symptomatic patients in the ward
if(is.null(ptestPWNI)) ptestPWNI = 0.75
# probability to test NI patients in the ward
if(is.null(ptestPWLI)) ptestPWLI = 0.50
# probability to test PI patients in the ward
if(is.null(ptestPWHI)) ptestPWHI = 0.10
# probability to test FI patients in the ward
if(is.null(ptestHsymp)) ptestHsymp = 0.85
# probability to test symptomatic HCWS in the ward
if(is.null(ptestHNI)) ptestHNI = 0.75
# proportion of non immune professionals (healthcare workers) tested during screening testing
if(is.null(ptestHLI)) ptestHLI = 0.50
# probability to test PI HCWS
if(is.null(ptestHHI)) ptestHHI = 0.20
# probability to test FI HCWS
if(is.null(senSA)) senSA = 0.85
if(is.null(speSA)) speSA = 0.95
if(is.null(senW)) senW = 0.85
if(is.null(speW)) speW = 0.95
if(is.null(senH)) senH = 0.85
if(is.null(speH)) speH = 0.95
if(is.null(sensymp)) sensymp = 1
if(is.null(spesymp)) spesymp = 1
}
if(disease == "Influenza"){
##### Infection
if(is.null(n_ctcH_PSA)) n_ctcH_PSA = 2
if(is.null(t_ctcH_PSA)) t_ctcH_PSA = 10 / 60 / 24
if(is.null(n_ctcP_PSA)) n_ctcP_PSA = 0
if(is.null(t_ctcP_PSA)) t_ctcP_PSA = 5 / 60 / 24
if(is.null(n_ctcH_PW)) n_ctcH_PW = 4
if(is.null(t_ctcH_PW)) t_ctcH_PW = 15 / 60 / 24
if(is.null(n_ctcP_PW)) n_ctcP_PW = 4
if(is.null(t_ctcP_PW)) t_ctcP_PW = 30 / 60 / 24
if(is.null(n_ctcH_H)) n_ctcH_H = 5
if(is.null(t_ctcH_H)) t_ctcH_H = 3 / 60 / 24
if(is.null(t_ctcV_PW)) t_ctcV_PW = 20 / 60 / 24
if(is.null(I)) I = 185 / 100000
if(is.null(d)) d = 7
if(is.null(R0)) R0 = 1.3
if(is.null(tw)) tw = 35
# https://www.gouvernement.fr/info-coronavirus/carte-et-donnees
if(is.null(tSA)) tSA = 2 / 24
# average duration before full admission (in screening area for clinical exam administrative procedure etc)
if(is.null(tIC)) tIC = 15
# average duration of stay in intensive care
if(is.null(tSL)) tSL = 14
# average duration of sick leave
if(is.null(tESL)) tESL = 28
# average duration of extended sick leave
if(is.null(tE)) tE = 1
# duration epidemiological state E
if(is.null(tEA)) tEA = 0
# duration epidemiological state EA
if(is.null(tES)) tES = 1
# duration epidemiological state ES
if(is.null(tIA)) tIA = 0
# duration epidemiological state IA
if(is.null(tIM)) tIM = 8
# duration epidemiological state IM
if(is.null(tIS)) tIS = 5
# duration epidemiological state IS
if(is.null(tLI)) tLI = 8
# duration of partial immunity before return to non immune status
if(is.null(tHI)) tHI = 150
# duration of full immunity before return to partial immune status
# patient protection
if(is.null(epsPPSA)) epsPPSA = 0.1
if(is.null(epsHPSA)) epsHPSA = 0.1
if(is.null(epsHPW)) epsHPW = 0.1
if(is.null(epsPPW)) epsPPW = 0.1
if(is.null(epsVPW)) epsVPW = 0.1
# healthcare workers protection
if(is.null(epsPHSA)) epsPHSA = 0.1
#from patient in SA
if(is.null(epsPHW)) epsPHW = 0.1
#from patient in W
if(is.null(epsHHW)) epsHHW = 0.1
#from HW in W
## Test in ward
if(is.null(ttestSA)) ttestSA = 2 / 24
# test duration in screening area
if(is.null(ttestPW)) ttestPW = 2 / 24
# test duration in ward for screening patients
if(is.null(ttestHW)) ttestHW = 2 / 24
# test duration in ward for screening professionals
if(is.null(ttestsymp)) ttestsymp = 2 / 24
# test duration for symptomatic
if(is.null(tbtwtestP)) tbtwtestP = 14
# duration between two tests for patient
if(is.null(tbtwtestH)) tbtwtestH = 30
# duration between two tests for HCWS
if(is.null(tbeftestPsymp)) tbeftestPsymp = 2 / 24
# duration before test of symp patient
if(is.null(tbeftestHsymp)) tbeftestHsymp = 1
# duration before test of symp HCWS
if(is.null(psympNI)) psympNI = 1 # 0.9
# probability to be symptomatic when non immune
if(is.null(psympLI)) psympLI = 1 # 0.8
# probability to be symptomatic when partially immune
if(is.null(psympHI)) psympHI = 1 # 0.7
# probability to be symptomatic when fully immune
if(is.null(psevNI)) psevNI = 0.6
# probability to develop severe symptoms when non immune
if(is.null(psevLI)) psevLI = 0.5
# probability to develop severe symptoms when partially immune
if(is.null(psevHI)) psevHI = 0.4
# probability to develop severe symptoms when fully immune
if(is.null(pISO)) pISO = 1
# contact restriction in case of positive test
if(is.null(pSL)) pSL = 0.3
# probability to take sick leave
if(is.null(pESL)) pESL = 1
# probability to take extended sick leave
if(is.null(pSLT)) pSLT = 0.01
# probability to take EL/ESL after positive test
if(is.null(pIC)) pIC = 0.3
# probability to be transfer in intensive care
if(is.null(pdieIC)) pdieIC = 0.005
# probability to die in intensive care
###################################
if(is.null(pLI)) pLI = 0.20
# probability to be PI at the admission (proportion of PI in the population)
if(is.null(pHI)) pHI = 0.5
# probability to be FI at the admission (proportion of FI in the population)
if(is.null(hNI2LI)) hNI2LI = 1 / 30
# daily probability to become partially immune
if(is.null(hLI2HI)) hLI2HI = 1 / 60
# daily probability to become fully immune
if(is.null(rinfLI)) rinfLI = 0.7
# partial immunity efficiency
if(is.null(rinfHI)) rinfHI = 0.5
# partial immunity efficiency
if(is.null(rsymp)) rsymp = 1
# Ratio adjusting probability of symptoms for patients compared to general population (professionals)
if(is.null(rsev)) rsev = 1
# Ratio adjusting probability of severity if symptoms for patients compared to general population (professionals)
if(is.null(rEA)) rEA = 0.35
# Ratio of excretion for individuals in epidemiological stage EA (exposed - contagious pre-asymptomatic)
if(is.null(rES)) rES = 1
# Ratio of excretion for individuals in epidemiological stage ES (exposed - contagious pre-symptomatic)
if(is.null(rIA)) rIA = 0.35
# Ratio of excretion for individuals in epidemiological stage IA (infectious asymptomatic)
if(is.null(rIM)) rIM = 1
# Ratio of excretion for individuals in epidemiological stage IM (infectious with mild symptoms)
if(is.null(rIS)) rIS = 1
# Ratio of excretion for individuals in epidemiological stage IS (infectious with severe symptoms)
if(is.null(ptestPSAsymp)) ptestPSAsymp = 1
# probability to test symptomatic patients in the screening area
if(is.null(ptestPSANI)) ptestPSANI = .75
# probability to test NI patients in the screening area
if(is.null(ptestPSALI)) ptestPSALI = 0.50
# probability to test PI patients in the screening area
if(is.null(ptestPSAHI)) ptestPSAHI = 0.1
# probability to test FI patients in the screening area
if(is.null(ptestPWsymp)) ptestPWsymp = 0.95
# probability to test symptomatic patients in the ward
if(is.null(ptestPWNI)) ptestPWNI = 0.75
# probability to test NI patients in the ward
if(is.null(ptestPWLI)) ptestPWLI = 0.50
# probability to test PI patients in the ward
if(is.null(ptestPWHI)) ptestPWHI = 0.10
# probability to test FI patients in the ward
if(is.null(ptestHsymp)) ptestHsymp = 0.85
# probability to test symptomatic HCWS in the ward
if(is.null(ptestHNI)) ptestHNI = 0.75
# proportion of non immune professionals (healthcare workers) tested during screening testing
if(is.null(ptestHLI)) ptestHLI = 0.50
# probability to test PI HCWS
if(is.null(ptestHHI)) ptestHHI = 0.20
# probability to test FI HCWS
if(is.null(senSA)) senSA = 0.85
if(is.null(speSA)) speSA = 0.95
if(is.null(senW)) senW = 0.85
if(is.null(speW)) speW = 0.95
if(is.null(senH)) senH = 0.85
if(is.null(speH)) speH = 0.95
if(is.null(sensymp)) sensymp = 0.85
if(is.null(spesymp)) spesymp = 0.95
}
### Checks
## Duration must be positive number
## Probabilities must be between 0 and 1
# Proportion of tested in dividuals
sapply(c(
ptestPSAsymp,
ptestPSANI,
ptestPSALI,
ptestPSAHI,
ptestPWsymp,
ptestPWNI,
ptestPWLI,
ptestPWHI,
ptestHsymp,
ptestHNI,
ptestHLI,
ptestHHI
), function(x)
if (x < 0 | x > 1)
stop(
"Proportion of tested individuals must fall between 0 (nobody is tested) and 1 (all group is tested)."
))
# Epidemiological stages durations
if((psympNI + psympLI + psympHI) < 3){
sapply(c(tE, tEA, tES, tIA, tIM, tIS, tLI, tHI), function(x)
if (x <= 0)
stop(
"Epidemiological stages and immunity durations must be strictly positive numbers."
))
} else {
sapply(c(tEA, tIA), function(x)
if (x != 0)
stop(
"With probabilities to be symptomatic equal to zero, asymptomatic epidemiological stages durations must be zero."
))
sapply(c(tE, tES, tIM, tIS, tLI, tHI), function(x)
if (x <= 0)
stop(
"Epidemiological stages and immunity durations must be positive numbers."
))
}
if (d <= 0)
stop(
"Epidemiological stages and immunity durations must be positive numbers."
)
if (d > sum(tE, tEA, tES, tIA, tIM, tIS))
stop(
"Total disease duration (d) must be inferior or equal to the sum of durations of all epidemiological stages (tE, tEA, tES, tIA, tIM, tIS)."
)
sapply(c(rinfLI, rinfHI), function(x)
if (x <= 0)
stop(
"Infection-reducing ratios related to immunity levels (rinfLI, rinfHI) must fall between 0 (no infection) and 1 (same probability to be infected that non immune)."
))
if (pLI + pHI < 0 | pLI + pHI > 1)
stop(
"The sum of probabilities to carry immunity (pLI and pHI) must fall between 0 (only non immune individuals at the admission) and 1 (only immune individuals at the admission)."
)
# Screening testing of patients
if (ptestPWNI > 0 | ptestPWLI > 0 | ptestPWHI > 0) {
if (tbtwtestP <= 0)
stop(
"If one of the proportions of patients tested during screening testing is positive (ptestPWNI + ptestPWLI + ptestPWHI > 0), the average duration between two screening programs (tbtwtestP) must be positive"
)
if (ttestPW <= 0)
stop(
"If one of the proportions of patients tested during screening testing is positive (ptestPWNI + ptestPWLI + ptestPWHI > 0), the average duration from test to reaction to result (ttestPW) must be positive"
)
if (senW < 0 | senW > 1 | speW < 0 | speW > 1)
stop(
"If one of the proportions of patients tested during screening testing is positive (ptestPWNI + ptestPWLI + ptestPWHI > 0), the test sensibilities and specificities must fall between 0 and 1 (senW and speW)."
)
}
if (tbtwtestP <= 0)
tbtwtestP <- 1
if (ttestPW <= 0)
ttestPW <- 1
# Screening testing of professionals
if (ptestHNI > 0 | ptestHLI > 0 | ptestHHI > 0) {
if (tbtwtestH <= 0)
stop(
"If one of the proportions of professionals tested during screening testing is positive (ptestHNI + ptestHLI + ptestHHI > 0), the average duration between two screening programs (tbtwtestH) must be positive"
)
if (ttestHW <= 0)
stop(
"If one of the proportions of professionals tested during screening testing is positive (ptestHNI + ptestHLI + ptestHHI > 0), the average duration from test to reaction to result (ttestH) must be positive"
)
if (senH < 0 | senH > 1 | speH < 0 | speH > 1)
stop(
"If one of the proportions of professionals tested during screening testing is positive (ptestHNI + ptestHLI + ptestHHI > 0), the test sensibilities and specificities must fall between 0 and 1 (senH and speH)."
)
}
if (tbtwtestH <= 0)
tbtwtestH <- 1
if (ttestHW <= 0)
ttestHW <- 1
# Screening area at the admission
if (ptestPSANI > 0 | ptestPSALI > 0 | ptestPSAHI > 0) {
if (ttestSA <= 0)
stop(
"If one of the proportions of patients tested in the screening area is positive (ptestPSANI + ptestPSALI + ptestPSAHI > 0), the average duration from test to reaction to result (ttestSA) must be positive"
)
if (senSA < 0 | senSA > 1 | speSA < 0 | speSA > 1)
stop(
"If one of the proportions of patients tested in the screening area is positive (ptestPSANI + ptestPSALI + ptestPSAHI > 0), the test sensibilities and specificities must fall between 0 and 1 (senSA and speSA)."
)
}
if (ttestSA <= 0)
ttestSA <- 1
if (tSA <= 0)
stop("The duration of screening at the admission (tSA) must be positive (in days).")
# Diagnostic testing
if (ptestPSAsymp > 0 | ptestPWsymp > 0 | ptestHsymp > 0) {
condi <-
"If one of the proportions of individuals tested for diagnostic testing is positive (ptestPSAsymp + ptestPWsymp + ptestHsymp > 0),"
if (ttestsymp <= 0)
stop(
paste(
condi,
"the average duration from test to reaction to result (ttestsymp) must be positive."
)
)
if (tbeftestPsymp <= 0 | tbeftestHsymp <= 0)
stop(
paste(
condi,
"the average duration before suspicion (tbeftestPsymp and tbeftestHsymp) must be positive."
)
)
if (sensymp < 0 | sensymp > 1 | spesymp < 0 | spesymp > 1)
stop(
"If one of the proportions of individuals tested for diagnostic testing is positive (ptestPSAsymp + ptestPWsymp + ptestHsymp > 0), the test sensibilities and specificities must fall between 0 and 1 (sensymp and spesymp)."
)
}
if (ttestsymp <= 0)
ttestsymp <- 1
if (tbeftestPsymp <= 0)
tbeftestPsymp <- 1
if (tbeftestHsymp <= 0)
tbeftestHsymp <- 1
## Contact restriction
# if (!is.logical(pISO))
# stop(
# "pISO must be logical. TRUE: patients are isolated and contacts are restricted in case of a positive test, FALSE: contact are not restricted but test is counted."
# )
## Intensive care
if (pIC < 0 | pIC > 1 | pdieIC < 0 | pdieIC > 1)
stop(
"The probability of being transfered and die in intensive care must fall between 0 (never transfered) and 1 (always transfered)."
)
if (pIC > 0 & tIC <= 0)
stop("Duration of intensive care stay (tIC) must be positive.")
## Sick leave
if (pSL < 0 | pSL > 1 | pESL < 0 | pESL > 1 | pSLT < 0 | pSLT > 1)
stop(
"The probabilities of taking sick leave (pSL, pESL, pSLT) must fall between 0 (never) and 1 (always)."
)
if (pSL + pESL + pSLT > 0 & (tSL <= 0 | tESL <= 0))
stop("Duration of sick leave (tSL and tESL) must be positive.")
### Build gdata
# p = R0 / (dCtc * nCtc * dInf)
# where
# p is the probability of transmission per minute spent in contact,
# dCtc is the average contact duration (in minutes),
# nCtc is the average number of contacts per person per day, and
# dInf is the average duration of infectivity (in days): approximately 10 days for COVID-19 [10].
bet01 <- function(x) {
if (x < 0)
x <- 0
if (x > 1)
x <- 1
x
}
psympPNI <- psympNI * rsymp %>% bet01
psevPNI <- psevNI * rsev %>% bet01
psympPLI <- psympLI * rsymp %>% bet01
psevPLI <- psevLI * rsev %>% bet01
psympPHI <- psympHI * rsymp %>% bet01
psevPHI <- psevHI * rsev %>% bet01
gdata = c(
tSA = tSA,
# average duration before full admission (in screening area for clinical exam, administrative procedure, etc)
tIC = tIC,
# average duration of stay in intensive care
tSL = tSL,
# average duration of sick leave
tESL = tESL,
# average duration of extended sick leave
tE = tE,
# duration epidemiological state E
tEA = tEA,
# duration epidemiological state EA
tES = tES,
# duration epidemiological state ES
tIA = tIA,
# duration epidemiological state IA
tIM = tIM,
# duration epidemiological state IM
tIS = tIS,
# duration epidemiological state IS
tLI = tLI,
# duration of partial immunity before return to non immune status
tHI = tHI,
# duration of full immunity before return to partial immune status
td = d,
# disease duration
## Contacts
ctcHPSA = n_ctcH_PSA * t_ctcH_PSA,
ctcPPSA = n_ctcP_PSA * t_ctcP_PSA,
ctcHPW = n_ctcH_PW * t_ctcH_PW,
ctcPPW = n_ctcP_PW * t_ctcP_PW,
ctcHH = n_ctcH_H * t_ctcH_H,
# n_ctcV_PW => see ldata
ctcV = t_ctcV_PW,
# Epsilon
# patient protection
epsPPSA = epsPPSA,
epsHPSA = epsHPSA,
epsHPW = epsHPW,
epsPPW = epsPPW,
epsVPW = epsVPW,
# healthcare workers protection
epsPHSA = epsPHSA,
#from patient in SA
epsPHW = epsPHW,
#from patient in W
epsHHW = epsHHW,
#from HW in W
## Test in ward
ttestSA = ttestSA,
# test duration in screening area
ttestPW = ttestPW,
# test duration in ward for screening of patients
ttestHW = ttestHW,
# test duration in ward for screening of professionals
ttestsymp = ttestsymp,
# test duration for symptomatic
tbtwtestP = tbtwtestP,
# duration between two tests for patient
tbtwtestH = tbtwtestH,
# duration between two tests for HCWS
tbeftestPsymp = tbeftestPsymp,
# duration before test of symp patient
tbeftestHsymp = tbeftestHsymp,
# duration before test of symp HCWS
# daily incidence in the community
hinc = I,
# daily incidence in the community
prev = I * d,
# prevalence (probability to be infected at the admission)
pconta = R0 / (8 * (30 / 60 / 24) * d),
# https://doi.org/10.1093/cid/ciaa682
# proportion of time outside of work
ptow = 1 - tw / ((24 - 8) * 7),
# 24 hours per days minus 8 sleeping hours time 7 days
psympNI = psympNI,
# probability to be symptomatic when non immune
psympLI = psympLI,
# probability to be symptomatic when partially immune
psympHI = psympHI,
# probability to be symptomatic when fully immune
psevNI = psevNI,
# probability to develop severe symptoms when non immune
psevLI = psevLI,
# probability to develop severe symptoms when partially immune
psevHI = psevHI,
# probability to develop severe symptoms when fully immune
pISO = pISO,
pSL = pSL,
# probability to take sick leave
pESL = pESL,
# probability to take extended sick leave
pSLT = pSLT,
# probability to take EL/ESL after positive test
pIC = pIC,
# probability to be transfer in intensive care
pdieIC = pdieIC,
# probability to die in intensive care
###################################
pLI = pLI,
# probability to be PI at the admission (proportion of PI in the population)
pHI = pHI,
# probability to be FI at the admission (proportion of FI in the population)
hNI2LI = hNI2LI,
# daily probability to become partially immune
hLI2HI = hLI2HI,
# daily probability to become fully immune
rinfLI = rinfLI,
# partial immunity efficiency
rinfHI = rinfHI,
# partial immunity efficiency
rEA = rEA,
# Ratio of excretion for individuals in epidemiological stage EA (exposed - contagious pre-asymptomatic)
rES = rES,
# Ratio of excretion for individuals in epidemiological stage ES (exposed - contagious pre-symptomatic)
rIA = rIA,
# Ratio of excretion for individuals in epidemiological stage IA (infectious asymptomatic)
rIM = rIM,
# Ratio of excretion for individuals in epidemiological stage IM (infectious with mild symptoms)
rIS = rIS,
# Ratio of excretion for individuals in epidemiological stage IS (infectious with severe symptoms)
# probability of symptoms for patients compared to general population (professionals)
psympPNI = psympPNI,
psevPNI = psevPNI,
psympPLI = psympPLI,
psevPLI = psevPLI,
psympPHI = psympPHI,
psevPHI = psevPHI,
ptestPSAsymp = ptestPSAsymp,
# probability to test symptomatic patients in the screening area
ptestPSANI = ptestPSANI,
# probability to test NI patients in the screening area
ptestPSALI = ptestPSALI,
# probability to test PI patients in the screening area
ptestPSAHI = ptestPSAHI,
# probability to test FI patients in the screening area
ptestPWsymp = ptestPWsymp,
# probability to test symptomatic patients in the ward
ptestPWNI = ptestPWNI,
# probability to test NI patients in the ward
ptestPWLI = ptestPWLI,
# probability to test PI patients in the ward
ptestPWHI = ptestPWHI,
# probability to test FI patients in the ward
ptestHsymp = ptestHsymp,
# probability to test symptomatic HCWS in the ward
ptestHNI = ptestHNI,
# probability to test NI HCWS
ptestHLI = ptestHLI,
# probability to test PI HCWS
ptestHHI = ptestHHI,
# probability to test FI HCWS
senSA = senSA,
speSA = speSA,
senW = senW,
speW = speW,
senH = senH,
speH = speH,
sensymp = sensymp,
spesymp = spesymp
)
# Use psevNI >> worst case scenario
with(data.frame(gdata %>% t),
cumd <<-
(1 - psympNI) * (tE + tEA + tIA) + psympNI * ((1 - psevNI) * (tE + tES + tIM) + psevNI * (tE + tES + tIS)))
gdata <- c(gdata,
with(
data.frame(gdata %>% t),
c(
rtE = tE / cumd,
# time ratio of the epidemiological state E over the whole infectious period (probability to be E at the admission when non susceptible)
rtEA = (1 - psympNI) * (tEA / cumd),
# time ratio of the epidemiological state EA over the whole infectious period (probability to be EA at the admission when non susceptible)
rtES = psympNI * (tES / cumd),
# time ratio of the epidemiological state ES over the whole infectious period (probability to be ES at the admission when non susceptible)
rtIA = (1 - psympNI) * (tIA / cumd),
# time ratio of the epidemiological state IA over the whole infectious period (probability to be IA at the admission when non susceptible)
rtIM = psympNI * (1 - psevNI) * (tIM / cumd),
# time ratio of the epidemiological state IM over the whole infectious period (probability to be IM at the admission when non susceptible)
rtIS = psympNI * psevNI * (tIS / cumd) # time ratio of the epidemiological state IS over the whole infectious period (probability to be IS at the admission when non susceptible)
)
))
return(gdata)
}
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