Function
Hening Cui
2024-07-25
Here load all the functions and parameters needed
library and dataset needed
library(tidyverse)
library(ggplot2)
library(viridis)
library(Rcpp)
library(dampack)
library(DT)
library(lhs)
load("data/tb_mortality_model.Rdata")
load("result/simulated.RData")The distribution calculation function
betapar <- function(tgt) {
tgt <- as.numeric(tgt)
mn <- tgt[1]; cir <- (tgt[3]-tgt[2])
xopt <- function(xx,mn=mn,cir=cir) {
cir2 <- qbeta(c(1,39)/40,xx*(mn/(1-mn)),xx);
cir2 <- cir2[2]-cir2[1]
sum((cir2-cir)^2) }
zz <- optimize(xopt,c(0.2,100000),mn=mn,cir=cir)$minimum
bp <- c(zz*(mn/(1-mn)),zz)
if(sum(abs(bp-1))<0.2) { c(1,1) } else { bp }
}gammapar <- function(tgt) {
tgt <- as.numeric(tgt)
mn <- tgt[1]; cir <- (tgt[3]-tgt[2])
xopt <- function(b,mn,cir) {
cir2 <- qgamma(c(1,39)/40,mn*b,b);
cir2 <- cir2[2]-cir2[1]
(cir2-cir)^2 }
zz <- optimize(xopt,c(0.1,100000),mn=mn,cir=cir)$minimum
gp = c(zz*mn,zz) }The model function
# for each input is binary either 1 or 0 exlcude the age and sex
# test tst-0, igra-1
# notest if test-0, no test -1
# us = 1 in us, us =0 non us
generate_p2 <- function(n_age_start, gender, hiv, dia, gas, renal, immu, trans, can, bmi,kid, smoke, ltc, test, notest, prison, homeless, us, t4r, t3hp,t1hp, t6h, ttb, d_s, d_lf, d_ls, d_l0, cycle_length=1, cycle_n){
#time age dependent base mortality rate
v_r_mort_by_age <- mor%>%
filter(sex==gender) %>%
filter(age >= n_age_start & age < 100) %>%
select(monthly_rate) %>%
as.matrix()
v_r_HDage = rep(v_r_mort_by_age, each = 12)
# calculate the TB mortality
tb_r_mort_by_age <- mor%>%
filter(sex==gender) %>%
filter(age >= n_age_start & age < 100) %>%
select(tb_mortality_rate ) %>%
as.matrix()
v_tb_HDage = rep(tb_r_mort_by_age, each = 12)
reactivation_data <- tibble(
age_group = c("6-14", "15-24", "25-34", "35-44", "45-54", "55-64", "65-74", "75+"),
rate= c(sim_tb_0_14[cycle_n], sim_tb_15_24[cycle_n], sim_tb_25_34[cycle_n], sim_tb_35_44[cycle_n], sim_tb_45_54[cycle_n], sim_tb_55_64[cycle_n], sim_tb_65_74[cycle_n], sim_tb_75[cycle_n])
)
# Expand the age groups to cover ages 0-100
age_range <- 0:100
ltbi_reacti <- tibble(age = age_range)
ltbi_reacti<- ltbi_reacti %>%
mutate(
rate = case_when(
age <= 14 ~ reactivation_data$rate[reactivation_data$age_group == "6-14" ],
age <= 24 ~ reactivation_data$rate[reactivation_data$age_group == "15-24" ],
age <= 34 ~ reactivation_data$rate[reactivation_data$age_group == "25-34" ],
age <= 44 ~ reactivation_data$rate[reactivation_data$age_group == "35-44"],
age <= 54 ~ reactivation_data$rate[reactivation_data$age_group == "45-54"],
age <= 64 ~ reactivation_data$rate[reactivation_data$age_group == "55-64" ],
age <= 74 ~ reactivation_data$rate[reactivation_data$age_group == "65-74"],
age >= 75 ~ reactivation_data$rate[reactivation_data$age_group == "75+"]
)
)
#calculate the TB reactivation rate
ltbi_react_by_age <- ltbi_reacti%>%
filter(age >= n_age_start & age < 100) %>%
select(rate ) %>%
as.matrix()
v_ltbi_HDage = rep(ltbi_react_by_age, each = 12)
# the risk factor
r_SD = v_r_HDage*(1+hiv*(sim_d_HIV[cycle_n]-1)+dia*(sim_d_dia[cycle_n]-1)+gas*(sim_d_gas[cycle_n]-1)+renal*(sim_d_renal[cycle_n]-1)+immu*(sim_d_immu[cycle_n]-1)+trans*(sim_d_trans[cycle_n]-1)+can*(sim_d_can[cycle_n]-1)+bmi*(sim_d_bmi[cycle_n]-1)+kid*(sim_d_kid[cycle_n]-1)+smoke*(sim_d_smok[cycle_n]-1)+ ltc*(sim_d_ltc[cycle_n]-1)+ homeless*(sim_d_homeless[cycle_n]-1))
r_LFD = v_r_HDage*(1+hiv*(sim_d_HIV[cycle_n]-1)+dia*(sim_d_dia[cycle_n]-1)+gas*(sim_d_gas[cycle_n]-1)+renal*(sim_d_renal[cycle_n]-1)+immu*(sim_d_immu[cycle_n]-1)+trans*(sim_d_trans[cycle_n]-1)+can*(sim_d_can[cycle_n]-1)+bmi*(sim_d_bmi[cycle_n]-1)+kid*(sim_d_kid[cycle_n]-1)+smoke*(sim_d_smok[cycle_n]-1)+ ltc*(sim_d_ltc[cycle_n]-1)+ homeless*(sim_d_homeless[cycle_n]-1))
r_LFI = (v_ltbi_HDage/100/12) * (1+hiv*(sim_i_hiv[cycle_n]-1)+dia*(sim_i_dia[cycle_n]-1)+gas*(sim_i_gas[cycle_n]-1)+renal*(sim_i_renal[cycle_n]-1)+immu*(sim_i_immu[cycle_n]-1)+trans*(sim_i_trans[cycle_n]-1)+can*(sim_i_can[cycle_n]-1)+bmi*(sim_i_bmi[cycle_n]-1)+kid*(sim_i_kid[cycle_n]-1)+smoke*(sim_i_smok[cycle_n]-1))
r_LSD = v_r_HDage * (1+hiv*(sim_d_HIV[cycle_n]-1)+dia*(sim_d_dia[cycle_n]-1)+gas*(sim_d_gas[cycle_n]-1)+renal*(sim_d_renal[cycle_n]-1)+immu*(sim_d_immu[cycle_n]-1)+trans*(sim_d_trans[cycle_n]-1)+can*(sim_d_can[cycle_n]-1)+bmi*(sim_d_bmi[cycle_n]-1)+kid*(sim_d_kid[cycle_n]-1)+smoke*(sim_d_smok[cycle_n]-1)+ ltc*(sim_d_ltc[cycle_n]-1)+ homeless*(sim_d_homeless[cycle_n]-1))
# r_LSL0 = 0.03 constant monthly rate of becoming L0 when LS
r_LSI = (v_ltbi_HDage/100/12) *(1+hiv*(sim_i_hiv[cycle_n]-1)+dia*(sim_i_dia[cycle_n]-1)+gas*(sim_i_gas[cycle_n]-1)+renal*(sim_i_renal[cycle_n]-1)+immu*(sim_i_immu[cycle_n]-1)+trans*(sim_i_trans[cycle_n]-1)+can*(sim_i_can[cycle_n]-1)+bmi*(sim_i_bmi[cycle_n]-1)+kid*(sim_i_kid[cycle_n]-1)+smoke*(sim_i_smok[cycle_n]-1))
r_L0D = v_r_HDage*(1+hiv*(sim_d_HIV[cycle_n]-1)+dia*(sim_d_dia[cycle_n]-1)+gas*(sim_d_gas[cycle_n]-1)+renal*(sim_d_renal[cycle_n]-1)+immu*(sim_d_immu[cycle_n]-1)+trans*(sim_d_trans[cycle_n]-1)+can*(sim_d_can[cycle_n]-1)+bmi*(sim_d_bmi[cycle_n]-1)+kid*(sim_d_kid[cycle_n]-1)+smoke*(sim_d_smok[cycle_n]-1)+ ltc*(sim_d_ltc[cycle_n]-1)+ homeless*(sim_d_homeless[cycle_n]-1))
#need update for false treatment
r_StD = v_r_HDage* (1+hiv*(sim_d_HIV[cycle_n]-1)+dia*(sim_d_dia[cycle_n]-1)+gas*(sim_d_gas[cycle_n]-1)+renal*(sim_d_renal[cycle_n]-1)+immu*(sim_d_immu[cycle_n]-1)+trans*(sim_d_trans[cycle_n]-1)+can*(sim_d_can[cycle_n]-1)+bmi*(sim_d_bmi[cycle_n]-1)+kid*(sim_d_kid[cycle_n]-1)+smoke*(sim_d_smok[cycle_n]-1)+ ltc*(sim_d_ltc[cycle_n]-1)+ homeless*(sim_d_homeless[cycle_n]-1))
r_LFtD = v_r_HDage *(1+hiv*(sim_d_HIV[cycle_n]-1)+dia*(sim_d_dia[cycle_n]-1)+gas*(sim_d_gas[cycle_n]-1)+renal*(sim_d_renal[cycle_n]-1)+immu*(sim_d_immu[cycle_n]-1)+trans*(sim_d_trans[cycle_n]-1)+can*(sim_d_can[cycle_n]-1)+bmi*(sim_d_bmi[cycle_n]-1)+kid*(sim_d_kid[cycle_n]-1)+smoke*(sim_d_smok[cycle_n]-1)+ ltc*(sim_d_ltc[cycle_n]-1)+ homeless*(sim_d_homeless[cycle_n]-1))
r_LStD = v_r_HDage * (1+hiv*(sim_d_HIV[cycle_n]-1)+dia*(sim_d_dia[cycle_n]-1)+gas*(sim_d_gas[cycle_n]-1)+renal*(sim_d_renal[cycle_n]-1)+immu*(sim_d_immu[cycle_n]-1)+trans*(sim_d_trans[cycle_n]-1)+can*(sim_d_can[cycle_n]-1)+bmi*(sim_d_bmi[cycle_n]-1)+kid*(sim_d_kid[cycle_n]-1)+smoke*(sim_d_smok[cycle_n]-1)+ ltc*(sim_d_ltc[cycle_n]-1)+ homeless*(sim_d_homeless[cycle_n]-1))
r_L0tD = v_r_HDage * (1+hiv*(sim_d_HIV[cycle_n]-1)+dia*(sim_d_dia[cycle_n]-1)+gas*(sim_d_gas[cycle_n]-1)+renal*(sim_d_renal[cycle_n]-1)+immu*(sim_d_immu[cycle_n]-1)+trans*(sim_d_trans[cycle_n]-1)+can*(sim_d_can[cycle_n]-1)+bmi*(sim_d_bmi[cycle_n]-1)+kid*(sim_d_kid[cycle_n]-1)+smoke*(sim_d_smok[cycle_n]-1)+ ltc*(sim_d_ltc[cycle_n]-1)+ homeless*(sim_d_homeless[cycle_n]-1))
r_ID = v_tb_HDage * (1+hiv*(sim_d_HIV[cycle_n]-1)+dia*(sim_d_dia[cycle_n]-1)+gas*(sim_d_gas[cycle_n]-1)+renal*(sim_d_renal[cycle_n]-1)+immu*(sim_d_immu[cycle_n]-1)+trans*(sim_d_trans[cycle_n]-1)+can*(sim_d_can[cycle_n]-1)+bmi*(sim_d_bmi[cycle_n]-1)+kid*(sim_d_kid[cycle_n]-1)+smoke*(sim_d_smok[cycle_n]-1)+ ltc*(sim_d_ltc[cycle_n]-1)+ homeless*(sim_d_homeless[cycle_n]-1)) # need update with time dependent equation, is side effect/
r_IIt = 12/4/12
r_ItR = 12/8/12
r_ItD = v_tb_HDage* (1+ hiv*(sim_d_HIV[cycle_n]-1)+dia*(sim_d_dia[cycle_n]-1)+gas*(sim_d_gas[cycle_n]-1)+renal*(sim_d_renal[cycle_n]-1)+immu*(sim_d_immu[cycle_n]-1)+trans*(sim_d_trans[cycle_n]-1)+can*(sim_d_can[cycle_n]-1)+bmi*(sim_d_bmi[cycle_n]-1)+kid*(sim_d_kid[cycle_n]-1)+smoke*(sim_d_smok[cycle_n]-1)+ ltc*(sim_d_ltc[cycle_n]-1)+ homeless*(sim_d_homeless[cycle_n]-1))
r_RD = v_r_HDage* (1+hiv*(sim_d_HIV[cycle_n]-1)+dia*(sim_d_dia[cycle_n]-1)+gas*(sim_d_gas[cycle_n]-1)+renal*(sim_d_renal[cycle_n]-1)+immu*(sim_d_immu[cycle_n]-1)+trans*(sim_d_trans[cycle_n]-1)+can*(sim_d_can[cycle_n]-1)+bmi*(sim_d_bmi[cycle_n]-1)+kid*(sim_d_kid[cycle_n]-1)+smoke*(sim_d_smok[cycle_n]-1)+ ltc*(sim_d_ltc[cycle_n]-1)+ homeless*(sim_d_homeless[cycle_n]-1))
p_values = list(
# the initial distribution should be proportion
ini_S= (1-notest)*d_s*(1-
(1- (hiv*us)*sim_tst_spe_us_hiv[cycle_n]
-(1-hiv)*us*sim_tst_spe_us[cycle_n]
-hiv*(1-us)*sim_tst_spe_nus_hiv[cycle_n]
-(1-hiv)*(1-us)*sim_tst_spe_nus[cycle_n])*0.762*(1-test)
- (1- (hiv*us)*sim_igra_spe_us_hiv[cycle_n]
-(1-hiv)*us*sim_igra_spe_us[cycle_n]
-hiv*(1-us)*sim_igra_spe_nus_hiv[cycle_n]
-(1-hiv)*(1-us)*sim_igra_spe_nus[cycle_n])*0.762*test) + notest*d_s,
ini_LF = (1-notest) *d_lf *(1-( (hiv*us)*sim_tst_sen_us_hiv[cycle_n] +(1-hiv)*us*sim_tst_sen_us[cycle_n] +hiv*(1-us)*sim_tst_sen_nus_hiv[cycle_n] +(1-hiv)*(1-us)*sim_tst_sen_nus[cycle_n])*0.762*(1-test) - ((hiv*us)*sim_igra_sen_us_hiv[cycle_n] +(1-hiv)*us*sim_igra_sen_us[cycle_n] +hiv*(1-us)*sim_igra_sen_nus_hiv[cycle_n] + (1-hiv)*(1-us)*sim_igra_sen_nus[cycle_n])*0.762*test) + notest*d_lf,
ini_LS =(1-notest) * d_ls *(1-( (hiv*us)*sim_tst_sen_us_hiv[cycle_n] +(1-hiv)*us*sim_tst_sen_us[cycle_n] +hiv*(1-us)*sim_tst_sen_nus_hiv[cycle_n] +(1-hiv)*(1-us)*sim_tst_sen_nus[cycle_n])*0.762*(1-test) - ((hiv*us)*sim_igra_sen_us_hiv[cycle_n] +(1-hiv)*us*sim_igra_sen_us[cycle_n] +hiv*(1-us)*sim_igra_sen_nus_hiv[cycle_n] + (1-hiv)*(1-us)*sim_igra_sen_nus[cycle_n])*0.762*test)+ notest*d_ls,
ini_L0 = (1-notest) * d_l0 *(1-( (hiv*us)*sim_tst_sen_us_hiv[cycle_n] +(1-hiv)*us*sim_tst_sen_us[cycle_n] +hiv*(1-us)*sim_tst_sen_nus_hiv[cycle_n] +(1-hiv)*(1-us)*sim_tst_sen_nus[cycle_n])*0.762*(1-test) - ((hiv*us)*sim_igra_sen_us_hiv[cycle_n] +(1-hiv)*us*sim_igra_sen_us[cycle_n] +hiv*(1-us)*sim_igra_sen_nus_hiv[cycle_n] + (1-hiv)*(1-us)*sim_igra_sen_nus[cycle_n])*0.762*test)+ notest*d_l0,
# before the cycle, first go through the test and then based on test result go to treatment
# only false positive from S will go to St
# if test
ini_St =(1-notest) * d_s*((1-(hiv*us)*sim_tst_spe_us_hiv[cycle_n] -(1-hiv)*us*sim_tst_spe_us[cycle_n] -hiv*(1-us)*sim_tst_spe_nus_hiv[cycle_n] -(1-hiv)*(1-us)*sim_tst_spe_nus[cycle_n])*0.762*(1-test) + (1- (hiv*us)*sim_igra_spe_us_hiv[cycle_n] -(1-hiv)*us*sim_igra_spe_us[cycle_n] -hiv*(1-us)*sim_igra_spe_nus_hiv[cycle_n] -(1-hiv)*(1-us)*sim_igra_spe_nus[cycle_n])*0.762*test),
# only true positive from L will go to Lt
ini_LFt=(1-notest) * d_lf *(((hiv*us)*sim_tst_sen_us_hiv[cycle_n] +(1-hiv)*us*sim_tst_sen_us[cycle_n] +hiv*(1-us)*sim_tst_sen_nus_hiv[cycle_n] +(1-hiv)*(1-us)*sim_tst_sen_nus[cycle_n])*0.762*(1-test) + ((hiv*us)*sim_igra_sen_us_hiv[cycle_n] +(1-hiv)*us*sim_igra_sen_us[cycle_n] +hiv*(1-us)*sim_igra_sen_nus_hiv[cycle_n] + (1-hiv)*(1-us)*sim_igra_sen_nus[cycle_n])*0.762*test),
ini_LSt =(1-notest) * d_ls *(( (hiv*us)*sim_tst_sen_us_hiv +(1-hiv)*us*sim_tst_sen_us[cycle_n] +hiv*(1-us)*sim_tst_sen_nus_hiv[cycle_n] +(1-hiv)*(1-us)*sim_tst_sen_nus[cycle_n])*0.762*(1-test) + ((hiv*us)*sim_igra_sen_us_hiv[cycle_n] +(1-hiv)*us*sim_igra_sen_us[cycle_n] +hiv*(1-us)*sim_igra_sen_nus_hiv[cycle_n] + (1-hiv)*(1-us)*sim_igra_sen_nus[cycle_n])*0.762*test),
ini_L0t =(1-notest) * d_l0 *(( (hiv*us)*sim_tst_sen_us_hiv[cycle_n] +(1-hiv)*us*sim_tst_sen_us[cycle_n] +hiv*(1-us)*sim_tst_sen_nus_hiv[cycle_n] +(1-hiv)*(1-us)*sim_tst_sen_nus[cycle_n])*0.762*(1-test) + ((hiv*us)*sim_igra_sen_us_hiv[cycle_n] +(1-hiv)*us*sim_igra_sen_us[cycle_n] +hiv*(1-us)*sim_igra_sen_nus_hiv[cycle_n] + (1-hiv)*(1-us)*sim_igra_sen_nus[cycle_n])*0.762*test),
ini_I= 1-d_s-d_ls-d_lf-d_l0,
ini_It = 0,
ini_R=0,
ini_D=0,
p_SD = 1 - exp( - r_SD * cycle_length),
#p_SSt = 0
p_LFD = (1- exp(-(r_LFD)*cycle_length)),
#p_LFLFt = 0
p_LFI = (1- exp(-(r_LFI)*cycle_length)),
p_LSD = (1-exp(-(r_LSD)*cycle_length)),
#p_LSLSt = 0
p_LSL0 = ((0.03/12)/((0.03/12)+r_LSI))*(1-exp(-((0.03/12)+r_LSI)*cycle_length)),
p_LSI =(r_LSI/((0.03/12)+r_LSI))*(1-exp(-((0.03/12)+r_LSI)*cycle_length)),
p_L0D = 1 -exp(-r_L0D*cycle_length),
#P_L0L0t = 0
p_StD = (1 -exp(-r_StD*cycle_length)) + sim_d_4R[cycle_n]*sim_s_4R[cycle_n]*t4r +sim_d_3HP[cycle_n]*sim_s_3HP[cycle_n]*t3hp + sim_d_1HP[cycle_n]*sim_s_1HP[cycle_n]*t1hp+sim_d_6H[cycle_n]*sim_s_6H[cycle_n]*t6h ,
# p_StS = 0/1 # if we assume complete treatment rationally, then no one would go back. After treatment, all go back to S
p_LFtD = (1 -exp(-r_LFtD*cycle_length)) + sim_d_4R[cycle_n]*sim_s_4R[cycle_n]*t4r +sim_d_3HP[cycle_n]*sim_s_3HP[cycle_n]*t3hp + sim_d_1HP[cycle_n]*sim_s_1HP[cycle_n]*t1hp+sim_d_6H[cycle_n]*sim_s_6H[cycle_n]*t6h,# if complete cycle
p_LFtL0 = sim_e_4R[cycle_n]*t4r + sim_e_3HP[cycle_n]*t3hp + sim_e_1HP[cycle_n]*t1hp + sim_e_6H[cycle_n]*t6h,
p_LFtLF = 1- (sim_e_4R[cycle_n]*t4r + sim_e_3HP[cycle_n]*t3hp + sim_e_1HP[cycle_n]*t1hp + sim_e_6H[cycle_n]*t6h), # if complete cycle
p_LStD = (1 -exp(-r_LStD*cycle_length)) + sim_d_4R[cycle_n]*sim_s_4R[cycle_n]*t4r +sim_d_3HP[cycle_n]*sim_s_3HP[cycle_n]*t3hp + sim_d_1HP[cycle_n]*sim_s_1HP[cycle_n]*t1hp+sim_d_6H[cycle_n]*sim_s_6H[cycle_n]*t6h,
p_LStL0 = sim_e_4R[cycle_n]*t4r + sim_e_3HP[cycle_n]*t3hp + sim_e_1HP[cycle_n]*t1hp + sim_e_6H[cycle_n]*t6h,# if complete cycle
p_LStLS = 1- (sim_e_4R[cycle_n]*t4r + sim_e_3HP[cycle_n]*t3hp + sim_e_1HP[cycle_n]*t1hp + sim_e_6H[cycle_n]*t6h), # if complete cycle
p_L0tD = (1 -exp(-r_L0tD*cycle_length)) + sim_d_4R[cycle_n]*sim_s_4R[cycle_n]*t4r +sim_d_3HP[cycle_n]*sim_s_3HP[cycle_n]*t3hp + sim_d_1HP[cycle_n]*sim_s_1HP[cycle_n]*t1hp+sim_d_6H[cycle_n]*sim_s_6H[cycle_n]*t6h,
p_L0tL0 = 1, #if complete cycle,
p_ID = (1 -exp(-(r_ID)*cycle_length)),
p_IR = 0,# assumed, need update # after 6 cycle also assumed
p_IIt =(1 -exp(-(r_IIt)*cycle_length)),
p_ItD = (1 -exp(-(r_ItD)*cycle_length)),
p_ItR = (1 -exp(-(r_ItR)*cycle_length)),
p_ItI = 0, #Assume stick to the treatment
p_RD = 1-exp(-r_RD*cycle_length),
p_tcom=sim_p_tcom[cycle_n],
tb_r_mort_by_age= tb_r_mort_by_age,
r_ID=r_ID,
r_ItD = r_ItD,
r_ItR = r_ItR
#p_DD = 1
)
cat("The original tb mortaliry rate")
print(v_tb_HDage)
cat("The incidence state mortality risk factor")
print(r_ID)
plot(r_ID)
cat("The incidence treatment state mortality risk factor")
print(r_ItD)
plot(r_ItD)
cat("Ensure the risk factor is 1")
print(mean(r_ID/v_tb_HDage))
cat("The treatmetn completion rate(monthly)")
print(r_ItR)
cat("The treatmetn initiation rate(monthly)")
print(r_IIt)
cat("The incidence state mortality probability")
print(p_values[["p_ID"]])
plot(p_values[["p_ID"]])
cat("The incidence treatment state mortality probability")
print(p_values[["p_ItD"]])
plot(p_values[["p_ItD"]])
return (p_values)
}RCPP function
cppFunction('
List updateProbabilies_v1 (int n_age_init, int n_age_max, NumericVector p_values,
double t4r, double t3hp, double t1hp, double t6h,
double t_4R, double t_3HP, double t_1HP, double t_6H,
std::vector<double> v_p_SS, std::vector<double> v_p_SD,
std::vector<double> a_P_LFLF,
std::vector<double> a_P_LSLS,
std::vector<double> a_P_L0L0, std::vector<double> a_P_LSL0,
double a_P_com,std::vector<double> a_P_LFtL0,
std::vector<double> a_P_LFtLF, std::vector<double> a_P_LStL0,
std::vector<double> a_P_LStLS,
std::vector<double> a_P_II, std::vector<double> a_P_LFI,
std::vector<double> a_P_LSI, std::vector<double> a_P_ItI,
std::vector<double> a_P_ItIt, std::vector<double> a_P_IIt,
std::vector<double> a_P_RR,std::vector<double> a_P_IR,
std::vector<double> a_P_ItR, double a_P_DD, std::vector<double> a_P_LFD,
std::vector<double> a_P_LSD, std::vector<double> a_P_L0D,
std::vector<double> a_P_StD, std::vector<double> a_P_LFtD,
std::vector<double> a_P_LStD, std::vector<double> a_P_L0tD,
std::vector<double> a_P_ID, std::vector<double> a_P_ItD, std::vector<double> a_P_RD, double cycle_length, double n_state) {
int n_cycles = (n_age_max - n_age_init) / cycle_length * 12;
double m_M_native[n_cycles][12];
double lifein[n_cycles][3];
for (int j = 0; j < n_state; ++j) {
m_M_native[0][j] = p_values[j];
}
lifein [0][0]= 0;
lifein [0][1]= 0;
lifein [0][2]= 0;
double ltbi_tcycle = t4r*4 + t3hp*3+ t1hp*1 + t6h*6;
//Rcpp::Rcout << "ltbi_tcycle: " << ltbi_tcycle << std::endl;
if (ltbi_tcycle == 0) {
for (int cycle = 0; cycle < n_cycles-1; cycle++) {
m_M_native[cycle+1][0] = m_M_native[cycle][0] * v_p_SS[cycle]; // Update for S
m_M_native[cycle+1][1] = m_M_native[cycle][1] * a_P_LFLF[cycle]; // Update for LF
m_M_native[cycle+1][2] = m_M_native[cycle][2] * a_P_LSLS[cycle]; // Update for LS
m_M_native[cycle+1][3] = m_M_native[cycle][3] * a_P_L0L0[cycle] + m_M_native[cycle][2] * a_P_LSL0[cycle]; // Update for L0
m_M_native[cycle+1][4] = m_M_native[cycle][4] - m_M_native[cycle][4]*a_P_StD[cycle];
//LFt
m_M_native[cycle+1][5] = m_M_native[cycle][5]- m_M_native[cycle][5]*a_P_LFtD[cycle];
//LSt
m_M_native[cycle+1][6] = m_M_native[cycle][6]-m_M_native[cycle][6]*a_P_LStD[cycle];
//L0t
m_M_native[cycle+1][7] = m_M_native[cycle][7]-m_M_native[cycle][7]*a_P_L0tD[cycle];
//I
m_M_native[cycle+1][8] = m_M_native[cycle][8]* a_P_II[cycle] +m_M_native[cycle][1]*a_P_LFI[cycle]+m_M_native[cycle][2]*a_P_LSI[cycle]+m_M_native[cycle][9]*a_P_ItI[cycle];
//It
m_M_native[cycle+1][9] = m_M_native[cycle][8]*a_P_IIt[cycle] + m_M_native[cycle][9]*a_P_ItIt[cycle] ;
//R
m_M_native[cycle+1][10] = m_M_native[cycle][10]*a_P_RR[cycle] +m_M_native[cycle][8]*a_P_IR[cycle]+ m_M_native[cycle][9]*a_P_ItR[cycle];
//D
m_M_native[cycle+1][11] = m_M_native[cycle][11]*a_P_DD+ m_M_native[cycle][0]*v_p_SD[cycle]+m_M_native[cycle][1]*a_P_LFD[cycle]
+m_M_native[cycle][2]*a_P_LSD[cycle]+ m_M_native[cycle][3]*a_P_L0D[cycle] + m_M_native[cycle][4]*a_P_StD[cycle] +
m_M_native[cycle][5]*a_P_LFtD[cycle]+ m_M_native[cycle][6]*a_P_LStD[cycle]+ m_M_native[cycle][7]*a_P_L0tD[cycle]+
m_M_native[cycle][8]*a_P_ID[cycle]+ m_M_native[cycle][9]*a_P_ItD[cycle]+ m_M_native[cycle][10]*a_P_RD[cycle];
// transition proportion
//Cumulative life time incidence
lifein[cycle + 1][0] = m_M_native[cycle][1] * a_P_LFI[cycle] + m_M_native[cycle][2] * a_P_LSI[cycle];
//Cumulative mortality
lifein[cycle + 1][1] = m_M_native[cycle][8] *a_P_ID[cycle];
lifein[cycle + 1][2] = m_M_native[cycle][9] *a_P_ItD[cycle];
}
} else {
for (int cycle = 0; cycle < 1; cycle++) {
m_M_native[cycle+1][0] = m_M_native[cycle][0] * v_p_SS[cycle]; // Update for S
m_M_native[cycle+1][1] = m_M_native[cycle][1] * a_P_LFLF[cycle]; // Update for LF
m_M_native[cycle+1][2] = m_M_native[cycle][2] * a_P_LSLS[cycle]; // Update for LS
m_M_native[cycle+1][3] = m_M_native[cycle][3] * a_P_L0L0[cycle] + m_M_native[cycle][2] * a_P_LSL0[cycle]; // Update for L0
m_M_native[cycle+1][4] = m_M_native[cycle][4] - m_M_native[cycle][4]*a_P_StD[cycle];
//LFt
m_M_native[cycle+1][5] = m_M_native[cycle][5]- m_M_native[cycle][5]*a_P_LFtD[cycle];
//LSt
m_M_native[cycle+1][6] = m_M_native[cycle][6]-m_M_native[cycle][6]*a_P_LStD[cycle];
//L0t
m_M_native[cycle+1][7] = m_M_native[cycle][7]-m_M_native[cycle][7]*a_P_L0tD[cycle];
// I
m_M_native[cycle+1][8] = m_M_native[cycle][8]* a_P_II[cycle]+ m_M_native[cycle][1]*a_P_LFI[cycle]+m_M_native[cycle][2]*a_P_LSI[cycle]+m_M_native[cycle][9]*a_P_ItI[cycle];
//It
m_M_native[cycle+1][9] = m_M_native[cycle][8]*a_P_IIt[cycle]+ m_M_native[cycle][9]*a_P_ItIt[cycle] ;
//R
m_M_native[cycle+1][10] = m_M_native[cycle][10]*a_P_RR[cycle] +m_M_native[cycle][8]*a_P_IR[cycle]+ m_M_native[cycle][9]*a_P_ItR[cycle];
//D
m_M_native[cycle+1][11] = m_M_native[cycle][11]*a_P_DD+ m_M_native[cycle][0]*v_p_SD[cycle]+m_M_native[cycle][1]*a_P_LFD[cycle]
+m_M_native[cycle][2]*a_P_LSD[cycle]+ m_M_native[cycle][3]*a_P_L0D[cycle] + m_M_native[cycle][4]*a_P_StD[cycle] +
m_M_native[cycle][5]*a_P_LFtD[cycle]+ m_M_native[cycle][6]*a_P_LStD[cycle]+ m_M_native[cycle][7]*a_P_L0tD[cycle]+
m_M_native[cycle][8]*a_P_ID[cycle]+ m_M_native[cycle][9]*a_P_ItD[cycle]+ m_M_native[cycle][10]*a_P_RD[cycle];
// transition proportion
//Cumulative life time incidence
lifein[cycle + 1][0] = m_M_native[cycle][1] * a_P_LFI[cycle] + m_M_native[cycle][2] * a_P_LSI[cycle];
//Cumulative mortality
lifein[cycle + 1][1] = m_M_native[cycle][8] *a_P_ID[cycle];
lifein[cycle + 1][2] = m_M_native[cycle][9] *a_P_ItD[cycle];
}
for (int cycle = 1; cycle < 2; cycle++) {
m_M_native[cycle+1][0] = m_M_native[cycle][0] * v_p_SS[cycle]+ (m_M_native[cycle][4] - m_M_native[cycle][4]*a_P_StD[cycle])*(1-a_P_com); // Update for S
m_M_native[cycle+1][1] = m_M_native[cycle][1] * a_P_LFLF[cycle]+(m_M_native[cycle][5]- m_M_native[cycle][5]*a_P_LFtD[cycle])*(1-a_P_com); // Update for LF
m_M_native[cycle+1][2] = m_M_native[cycle][2] * a_P_LSLS[cycle] + (m_M_native[cycle][6]-m_M_native[cycle][6]*a_P_LStD[cycle])*(1-a_P_com); // Update for LS
m_M_native[cycle+1][3] = m_M_native[cycle][3] * a_P_L0L0[cycle] + m_M_native[cycle][2] * a_P_LSL0[cycle] + (m_M_native[cycle][7]-m_M_native[cycle][7]*a_P_L0tD[cycle])*(1-a_P_com); // Update for L0
m_M_native[cycle+1][4] = (m_M_native[cycle][4] - m_M_native[cycle][4]*a_P_StD[cycle])*a_P_com;
//LFt
m_M_native[cycle+1][5] = (m_M_native[cycle][5]- m_M_native[cycle][5]*a_P_LFtD[cycle])*a_P_com;
//LSt
m_M_native[cycle+1][6] = (m_M_native[cycle][6]-m_M_native[cycle][6]*a_P_LStD[cycle])*a_P_com;
//L0t
m_M_native[cycle+1][7] = (m_M_native[cycle][7]-m_M_native[cycle][7]*a_P_L0tD[cycle])*a_P_com;
// I
m_M_native[cycle+1][8] = m_M_native[cycle][8]* a_P_II[cycle]+ m_M_native[cycle][1]*a_P_LFI[cycle]+m_M_native[cycle][2]*a_P_LSI[cycle]+m_M_native[cycle][9]*a_P_ItI[cycle];
//It
m_M_native[cycle+1][9] = m_M_native[cycle][8]*a_P_IIt[cycle]+ m_M_native[cycle][9]*a_P_ItIt[cycle] ;
//R
m_M_native[cycle+1][10] = m_M_native[cycle][10]*a_P_RR[cycle] +m_M_native[cycle][8]*a_P_IR[cycle]+ m_M_native[cycle][9]*a_P_ItR[cycle];
//D
m_M_native[cycle+1][11] = m_M_native[cycle][11]*a_P_DD+ m_M_native[cycle][0]*v_p_SD[cycle]+m_M_native[cycle][1]*a_P_LFD[cycle]
+m_M_native[cycle][2]*a_P_LSD[cycle]+ m_M_native[cycle][3]*a_P_L0D[cycle] + m_M_native[cycle][4]*a_P_StD[cycle] +
m_M_native[cycle][5]*a_P_LFtD[cycle]+ m_M_native[cycle][6]*a_P_LStD[cycle]+ m_M_native[cycle][7]*a_P_L0tD[cycle]+
m_M_native[cycle][8]*a_P_ID[cycle]+ m_M_native[cycle][9]*a_P_ItD[cycle]+ m_M_native[cycle][10]*a_P_RD[cycle];
// transition proportion
//Cumulative life time incidence
lifein[cycle + 1][0] = m_M_native[cycle][1] * a_P_LFI[cycle] + m_M_native[cycle][2] * a_P_LSI[cycle];
//Cumulative mortality
lifein[cycle + 1][1] = m_M_native[cycle][8] *a_P_ID[cycle];
lifein[cycle + 1][2] = m_M_native[cycle][9] *a_P_ItD[cycle];
}
for (int cycle = 2; cycle < ltbi_tcycle; cycle++) {
m_M_native[cycle+1][0] = m_M_native[cycle][0] * v_p_SS[cycle]; // Update for S
m_M_native[cycle+1][1] = m_M_native[cycle][1] * a_P_LFLF[cycle]; // Update for LF
m_M_native[cycle+1][2] = m_M_native[cycle][2] * a_P_LSLS[cycle]; // Update for LS
m_M_native[cycle+1][3] = m_M_native[cycle][3] * a_P_L0L0[cycle] + m_M_native[cycle][2] * a_P_LSL0[cycle]; // Update for L0
m_M_native[cycle+1][4] = m_M_native[cycle][4] - m_M_native[cycle][4]*a_P_StD[cycle];
//LFt
m_M_native[cycle+1][5] = m_M_native[cycle][5]- m_M_native[cycle][5]*a_P_LFtD[cycle];
//LSt
m_M_native[cycle+1][6] = m_M_native[cycle][6]-m_M_native[cycle][6]*a_P_LStD[cycle];
//L0t
m_M_native[cycle+1][7] = m_M_native[cycle][7]-m_M_native[cycle][7]*a_P_L0tD[cycle];
// I
m_M_native[cycle+1][8] = m_M_native[cycle][8]* a_P_II[cycle]+ m_M_native[cycle][1]*a_P_LFI[cycle]+m_M_native[cycle][2]*a_P_LSI[cycle]+m_M_native[cycle][9]*a_P_ItI[cycle];
//It
m_M_native[cycle+1][9] = m_M_native[cycle][8]*a_P_IIt[cycle]+ m_M_native[cycle][9]*a_P_ItIt[cycle] ;
//R
m_M_native[cycle+1][10] = m_M_native[cycle][10]*a_P_RR[cycle] +m_M_native[cycle][8]*a_P_IR[cycle]+ m_M_native[cycle][9]*a_P_ItR[cycle];
//D
m_M_native[cycle+1][11] = m_M_native[cycle][11]*a_P_DD+ m_M_native[cycle][0]*v_p_SD[cycle]+m_M_native[cycle][1]*a_P_LFD[cycle]
+m_M_native[cycle][2]*a_P_LSD[cycle]+ m_M_native[cycle][3]*a_P_L0D[cycle] + m_M_native[cycle][4]*a_P_StD[cycle] +
m_M_native[cycle][5]*a_P_LFtD[cycle]+ m_M_native[cycle][6]*a_P_LStD[cycle]+ m_M_native[cycle][7]*a_P_L0tD[cycle]+
m_M_native[cycle][8]*a_P_ID[cycle]+ m_M_native[cycle][9]*a_P_ItD[cycle]+ m_M_native[cycle][10]*a_P_RD[cycle];
// transition proportion
//Cumulative life time incidence
lifein[cycle + 1][0] = m_M_native[cycle][1] * a_P_LFI[cycle] + m_M_native[cycle][2] * a_P_LSI[cycle];
//Cumulative mortality
lifein[cycle + 1][1] = m_M_native[cycle][8] *a_P_ID[cycle];
lifein[cycle + 1][2] = m_M_native[cycle][9] *a_P_ItD[cycle];
}
for (int cycle = ltbi_tcycle; cycle < n_cycles-1; cycle++) {
m_M_native[cycle+1][0] = m_M_native[cycle][0] * v_p_SS[cycle] +m_M_native[cycle][4] ; // Update for S
m_M_native[cycle+1][1] = m_M_native[cycle][1] * a_P_LFLF[cycle] + m_M_native[cycle][5]*a_P_LFtLF[cycle]; // Update for LF
m_M_native[cycle+1][2] = m_M_native[cycle][2] * a_P_LSLS[cycle] + m_M_native[cycle][6]*a_P_LStLS[cycle]; // Update for LS
m_M_native[cycle+1][3] = m_M_native[cycle][3] * a_P_L0L0[cycle] + m_M_native[cycle][2] * a_P_LSL0[cycle] +m_M_native[cycle][5]*a_P_LFtL0[cycle] + m_M_native[cycle][6]*a_P_LStL0[cycle] + m_M_native[cycle][7] ; // Update for L0
m_M_native[cycle+1][4] = 0;//update for St
//LFt
m_M_native[cycle+1][5] = 0;
//LSt
m_M_native[cycle+1][6] = 0;
//L0t
m_M_native[cycle+1][7] = 0;
//I
m_M_native[cycle+1][8] = m_M_native[cycle][8]* a_P_II[cycle]+ m_M_native[cycle][1]*a_P_LFI[cycle]+m_M_native[cycle][2]*a_P_LSI[cycle]+m_M_native[cycle][9]*a_P_ItI[cycle];
//It
m_M_native[cycle+1][9] = m_M_native[cycle][8]*a_P_IIt[cycle]+ m_M_native[cycle][9]*a_P_ItIt[cycle] ;
//R
m_M_native[cycle+1][10] = m_M_native[cycle][10]*a_P_RR[cycle] +m_M_native[cycle][8]*a_P_IR[cycle]+ m_M_native[cycle][9]*a_P_ItR[cycle];
//D
m_M_native[cycle+1][11] = m_M_native[cycle][11]*a_P_DD+ m_M_native[cycle][0]*v_p_SD[cycle]+m_M_native[cycle][1]*a_P_LFD[cycle]
+m_M_native[cycle][2]*a_P_LSD[cycle]+ m_M_native[cycle][3]*a_P_L0D[cycle] + m_M_native[cycle][4]*a_P_StD[cycle] +
m_M_native[cycle][5]*a_P_LFtD[cycle]+ m_M_native[cycle][6]*a_P_LStD[cycle]+ m_M_native[cycle][7]*a_P_L0tD[cycle]+
m_M_native[cycle][8]*a_P_ID[cycle]+ m_M_native[cycle][9]*a_P_ItD[cycle]+ m_M_native[cycle][10]*a_P_RD[cycle];
// transition proportion
//Cumulative life time incidence
lifein[cycle + 1][0] = m_M_native[cycle][1] * a_P_LFI[cycle] + m_M_native[cycle][2] * a_P_LSI[cycle];
//Cumulative mortality
lifein[cycle + 1][1] = m_M_native[cycle][8] *a_P_ID[cycle];
lifein[cycle + 1][2] = m_M_native[cycle][9] *a_P_ItD[cycle];
}}
NumericMatrix m_M(n_cycles,n_state);
NumericMatrix transit(n_cycles,3);
for(int i = 0; i < n_cycles-1; ++i) {
for(int j = 0; j < n_state; ++j) {
m_M(i, j) = m_M_native[i][j];
}
for(int j = 0; j < 3; ++j) {
transit(i, j) = lifein[i][j];
}
}
double case_averted = (m_M(ltbi_tcycle,5) + m_M(ltbi_tcycle,6) + m_M(ltbi_tcycle,7));
return List::create(Named("m_M") = m_M, Named("transit") = transit, Named("case_averted") = case_averted);
}')Main function
main_model = function(age_init, gender, hiv, dia, gas, renal, immu, trans, can, bmi, kid, smoke, ltc, test, prison, homeless, us, t4r, t3hp, t1hp, t6h, ttb, notest, d_s, d_lf, d_ls, d_l0, d_i, cycle_length, cycle_n){
p_values = generate_p2(n_age_start =age_init, gender=gender, hiv=hiv, dia=dia, gas=gas, renal=renal, immu=immu, trans=trans, can=can, bmi=bmi, kid=kid, smoke=smoke, ltc=ltc, test=test, prison=prison, homeless=homeless, us=us, t4r=t4r, t3hp=t3hp,t1hp=t1hp, t6h=t6h, ttb=ttb,notest=notest,d_s=d_s, d_lf=d_lf, d_ls=d_ls, d_l0=d_l0, cycle_length=1, cycle_n = cycle_n)
p_values_vector= unlist(p_values)
# from s
v_p_SS<- (1 - p_values[["p_SD"]])
v_p_SSt <- 0
v_p_SD <- p_values[["p_SD"]]
# From LS
a_P_LSLSt <- 0
a_P_LSL0 <- (1 - p_values[["p_LSD"]]) * p_values [["p_LSL0"]]
a_P_LSI <- (1 - p_values[["p_LSD"]]) * p_values [["p_LSI"]]
a_P_LSLS <- (1 - p_values[["p_LSD"]]) * (1-(p_values [["p_LSI"]] + p_values [["p_LSL0"]]))
a_P_LSD <- p_values[["p_LSD"]]
# From LF
a_P_LFLFt <- 0
a_P_LFI <- (1 - p_values[["p_LFD"]]) * p_values [["p_LFI"]]
a_P_LFLF <- (1 - p_values[["p_LFD"]]) * (1-p_values [["p_LFI"]])
a_P_LFD <- p_values[["p_LFD"]]
# From L0
a_P_L0L0t <-0
a_P_L0L0 <- (1 - p_values[["p_L0D"]])
a_P_L0D <- p_values[["p_L0D"]]
# From St
a_P_StS <- 1
a_P_StSt <- (1-p_values[["p_StD"]])*(1-p_values[["p_StS"]])
a_P_StD <- p_values[["p_StD"]]
# From LSt
a_P_LStLS <- (1 - p_values[["p_LStD"]]) * p_values [["p_LStLS"]]
a_P_LStL0 <- (1 - p_values[["p_LStD"]]) * p_values [["p_LStL0"]]
a_P_LStLSt <- 1
a_P_LStD <- p_values[["p_LStD"]]
# From LFt
a_P_LFtLF <- (1 - p_values[["p_LFtD"]]) * p_values [["p_LFtLF"]]
a_P_LFtL0 <- (1 - p_values[["p_LFtD"]]) * p_values [["p_LFtL0"]]
a_P_LFtLFt <- 1
a_P_LFtD <- p_values[["p_LFtD"]]
# From L0t
a_P_L0tL0 <- (1 - p_values[["p_L0tD"]]) * p_values [["p_L0tL0"]]
a_P_L0tL0t <- 1
a_P_L0tD <- p_values[["p_L0tD"]]
# From I
a_P_II <- (1 - p_values[["p_ID"]]) * (1-p_values [["p_IIt"]]-p_values [["p_IR"]])
a_P_IIt <- (1 - p_values[["p_ID"]]) * p_values [["p_IIt"]]
a_P_IR <- (1 - p_values[["p_ID"]]) * p_values [["p_IR"]]
a_P_ID <- p_values[["p_ID"]]
cat("The I to D transition probability")
print(a_P_ID)
# From It
a_P_ItIt <- (1 - p_values[["p_ItD"]])*(1-p_values [["p_ItI"]]-p_values [["p_ItR"]])
a_P_ItI <- (1 - p_values[["p_ItD"]]) * p_values [["p_ItI"]]
a_P_ItR <- (1 - p_values[["p_ItD"]]) * p_values [["p_ItR"]]
a_P_ItD <- p_values[["p_ItD"]]
cat("The It to D transition probability")
print(a_P_ItD)
# From R
a_P_RR <- (1-p_values[["p_RD"]])
a_P_RD <- p_values[["p_RD"]]
# From D
a_P_DD<- 1
a_P_com <- p_values[["p_tcom"]]
result <- updateProbabilies_v1 (n_age_init=age_init, 100, p_values_vector,
t4r=t4r, t3hp=t3hp, t1hp=t1hp, t6h=t6h,
t_4R, t_3HP, t_1HP, t_6H,
v_p_SS, v_p_SD,
a_P_LFLF,
a_P_LSLS,
a_P_L0L0, a_P_LSL0,
a_P_com,a_P_LFtL0,
a_P_LFtLF, a_P_LStL0,
a_P_LStLS,
a_P_II, a_P_LFI,
a_P_LSI, a_P_ItI,
a_P_ItIt,a_P_IIt,
a_P_RR, a_P_IR,
a_P_ItR, a_P_DD, a_P_LFD,
a_P_LSD, a_P_L0D,
a_P_StD,a_P_LFtD,
a_P_LStD, a_P_L0tD,
a_P_ID, a_P_ItD, a_P_RD,
cycle_length=1, n_states)
return (result)
}# treatment duration
t_4R = 4
t_3HP = 3
t_1HP = 1
t_6H = 6
# Utilities
u_S <- 1 # montly utility of being Healthy
u_LS <- 1# montly utility of being LS
u_LF <- 1 # montly untilty of being LF
u_L0 <- 1 # montly untilty of being L0
u_St <- 1
u_St_tox <- 0.75
u_LSt <- 1 # annual utility of being LSt
u_LSt_tox <- 0.75
u_LFt <- 1 # annual untilty of being LFt
u_LFt_tox <- 0.75
u_L0t <- 1 # annual untilty of being L0
u_L0t_tox <- 0.75
u_I <- 0.76 # annual utility of being TB incidence
u_It_tox <- 0.76
u_D <- 0 # annual utility of being dead
u_R <- 0.9
u_It <- 0.76
v_names_states <- c("S", "LF", "LS", "L0", "St", "LFt", "LSt", "L0t","I", "It", "R", "D")
n_states <- length(v_names_states)Test and chek
c= main_model(age_init = 60, gender=1, hiv=0, dia=0, gas=0, renal=0, immu=0, trans=0, can=0, bmi=0, kid=0, smoke=0, ltc=0, test=1, prison=0, homeless=0, us=1, t4r=1, t3hp=0,t1hp=0, t6h=0, ttb=0,notest=0,d_s=0, d_lf=1, d_ls=0, d_l0=0, d_i=0, cycle_length=1, cycle_n = 1)## The original tb mortaliry rate [1] 0.01475668 0.01475668 0.01475668 0.01475668 0.01475668 0.01475668
## [7] 0.01475668 0.01475668 0.01475668 0.01475668 0.01475668 0.01475668
## [13] 0.01592052 0.01592052 0.01592052 0.01592052 0.01592052 0.01592052
## [19] 0.01592052 0.01592052 0.01592052 0.01592052 0.01592052 0.01592052
## [25] 0.01708932 0.01708932 0.01708932 0.01708932 0.01708932 0.01708932
## [31] 0.01708932 0.01708932 0.01708932 0.01708932 0.01708932 0.01708932
## [37] 0.01824332 0.01824332 0.01824332 0.01824332 0.01824332 0.01824332
## [43] 0.01824332 0.01824332 0.01824332 0.01824332 0.01824332 0.01824332
## [49] 0.01941715 0.01941715 0.01941715 0.01941715 0.01941715 0.01941715
## [55] 0.01941715 0.01941715 0.01941715 0.01941715 0.01941715 0.01941715
## [61] 0.01373412 0.01373412 0.01373412 0.01373412 0.01373412 0.01373412
## [67] 0.01373412 0.01373412 0.01373412 0.01373412 0.01373412 0.01373412
## [73] 0.01473079 0.01473079 0.01473079 0.01473079 0.01473079 0.01473079
## [79] 0.01473079 0.01473079 0.01473079 0.01473079 0.01473079 0.01473079
## [85] 0.01576539 0.01576539 0.01576539 0.01576539 0.01576539 0.01576539
## [91] 0.01576539 0.01576539 0.01576539 0.01576539 0.01576539 0.01576539
## [97] 0.01685262 0.01685262 0.01685262 0.01685262 0.01685262 0.01685262
## [103] 0.01685262 0.01685262 0.01685262 0.01685262 0.01685262 0.01685262
## [109] 0.01799433 0.01799433 0.01799433 0.01799433 0.01799433 0.01799433
## [115] 0.01799433 0.01799433 0.01799433 0.01799433 0.01799433 0.01799433
## [121] 0.01920244 0.01920244 0.01920244 0.01920244 0.01920244 0.01920244
## [127] 0.01920244 0.01920244 0.01920244 0.01920244 0.01920244 0.01920244
## [133] 0.02061972 0.02061972 0.02061972 0.02061972 0.02061972 0.02061972
## [139] 0.02061972 0.02061972 0.02061972 0.02061972 0.02061972 0.02061972
## [145] 0.02203648 0.02203648 0.02203648 0.02203648 0.02203648 0.02203648
## [151] 0.02203648 0.02203648 0.02203648 0.02203648 0.02203648 0.02203648
## [157] 0.02440279 0.02440279 0.02440279 0.02440279 0.02440279 0.02440279
## [163] 0.02440279 0.02440279 0.02440279 0.02440279 0.02440279 0.02440279
## [169] 0.02654375 0.02654375 0.02654375 0.02654375 0.02654375 0.02654375
## [175] 0.02654375 0.02654375 0.02654375 0.02654375 0.02654375 0.02654375
## [181] 0.01403804 0.01403804 0.01403804 0.01403804 0.01403804 0.01403804
## [187] 0.01403804 0.01403804 0.01403804 0.01403804 0.01403804 0.01403804
## [193] 0.01538333 0.01538333 0.01538333 0.01538333 0.01538333 0.01538333
## [199] 0.01538333 0.01538333 0.01538333 0.01538333 0.01538333 0.01538333
## [205] 0.01711008 0.01711008 0.01711008 0.01711008 0.01711008 0.01711008
## [211] 0.01711008 0.01711008 0.01711008 0.01711008 0.01711008 0.01711008
## [217] 0.01887437 0.01887437 0.01887437 0.01887437 0.01887437 0.01887437
## [223] 0.01887437 0.01887437 0.01887437 0.01887437 0.01887437 0.01887437
## [229] 0.02086312 0.02086312 0.02086312 0.02086312 0.02086312 0.02086312
## [235] 0.02086312 0.02086312 0.02086312 0.02086312 0.02086312 0.02086312
## [241] 0.02300274 0.02300274 0.02300274 0.02300274 0.02300274 0.02300274
## [247] 0.02300274 0.02300274 0.02300274 0.02300274 0.02300274 0.02300274
## [253] 0.02549970 0.02549970 0.02549970 0.02549970 0.02549970 0.02549970
## [259] 0.02549970 0.02549970 0.02549970 0.02549970 0.02549970 0.02549970
## [265] 0.02843888 0.02843888 0.02843888 0.02843888 0.02843888 0.02843888
## [271] 0.02843888 0.02843888 0.02843888 0.02843888 0.02843888 0.02843888
## [277] 0.03171747 0.03171747 0.03171747 0.03171747 0.03171747 0.03171747
## [283] 0.03171747 0.03171747 0.03171747 0.03171747 0.03171747 0.03171747
## [289] 0.03549827 0.03549827 0.03549827 0.03549827 0.03549827 0.03549827
## [295] 0.03549827 0.03549827 0.03549827 0.03549827 0.03549827 0.03549827
## [301] 0.06605043 0.06605043 0.06605043 0.06605043 0.06605043 0.06605043
## [307] 0.06605043 0.06605043 0.06605043 0.06605043 0.06605043 0.06605043
## [313] 0.07378666 0.07378666 0.07378666 0.07378666 0.07378666 0.07378666
## [319] 0.07378666 0.07378666 0.07378666 0.07378666 0.07378666 0.07378666
## [325] 0.08312292 0.08312292 0.08312292 0.08312292 0.08312292 0.08312292
## [331] 0.08312292 0.08312292 0.08312292 0.08312292 0.08312292 0.08312292
## [337] 0.09346329 0.09346329 0.09346329 0.09346329 0.09346329 0.09346329
## [343] 0.09346329 0.09346329 0.09346329 0.09346329 0.09346329 0.09346329
## [349] 0.10487116 0.10487116 0.10487116 0.10487116 0.10487116 0.10487116
## [355] 0.10487116 0.10487116 0.10487116 0.10487116 0.10487116 0.10487116
## [361] 0.11740292 0.11740292 0.11740292 0.11740292 0.11740292 0.11740292
## [367] 0.11740292 0.11740292 0.11740292 0.11740292 0.11740292 0.11740292
## [373] 0.13110519 0.13110519 0.13110519 0.13110519 0.13110519 0.13110519
## [379] 0.13110519 0.13110519 0.13110519 0.13110519 0.13110519 0.13110519
## [385] 0.14601151 0.14601151 0.14601151 0.14601151 0.14601151 0.14601151
## [391] 0.14601151 0.14601151 0.14601151 0.14601151 0.14601151 0.14601151
## [397] 0.16213912 0.16213912 0.16213912 0.16213912 0.16213912 0.16213912
## [403] 0.16213912 0.16213912 0.16213912 0.16213912 0.16213912 0.16213912
## [409] 0.17948583 0.17948583 0.17948583 0.17948583 0.17948583 0.17948583
## [415] 0.17948583 0.17948583 0.17948583 0.17948583 0.17948583 0.17948583
## [421] 0.19802706 0.19802706 0.19802706 0.19802706 0.19802706 0.19802706
## [427] 0.19802706 0.19802706 0.19802706 0.19802706 0.19802706 0.19802706
## [433] 0.21771359 0.21771359 0.21771359 0.21771359 0.21771359 0.21771359
## [439] 0.21771359 0.21771359 0.21771359 0.21771359 0.21771359 0.21771359
## [445] 0.23846997 0.23846997 0.23846997 0.23846997 0.23846997 0.23846997
## [451] 0.23846997 0.23846997 0.23846997 0.23846997 0.23846997 0.23846997
## [457] 0.26019412 0.26019412 0.26019412 0.26019412 0.26019412 0.26019412
## [463] 0.26019412 0.26019412 0.26019412 0.26019412 0.26019412 0.26019412
## [469] 0.28275799 0.28275799 0.28275799 0.28275799 0.28275799 0.28275799
## [475] 0.28275799 0.28275799 0.28275799 0.28275799 0.28275799 0.28275799
## The incidence state mortality risk factor [1] 0.01475668 0.01475668 0.01475668 0.01475668 0.01475668 0.01475668
## [7] 0.01475668 0.01475668 0.01475668 0.01475668 0.01475668 0.01475668
## [13] 0.01592052 0.01592052 0.01592052 0.01592052 0.01592052 0.01592052
## [19] 0.01592052 0.01592052 0.01592052 0.01592052 0.01592052 0.01592052
## [25] 0.01708932 0.01708932 0.01708932 0.01708932 0.01708932 0.01708932
## [31] 0.01708932 0.01708932 0.01708932 0.01708932 0.01708932 0.01708932
## [37] 0.01824332 0.01824332 0.01824332 0.01824332 0.01824332 0.01824332
## [43] 0.01824332 0.01824332 0.01824332 0.01824332 0.01824332 0.01824332
## [49] 0.01941715 0.01941715 0.01941715 0.01941715 0.01941715 0.01941715
## [55] 0.01941715 0.01941715 0.01941715 0.01941715 0.01941715 0.01941715
## [61] 0.01373412 0.01373412 0.01373412 0.01373412 0.01373412 0.01373412
## [67] 0.01373412 0.01373412 0.01373412 0.01373412 0.01373412 0.01373412
## [73] 0.01473079 0.01473079 0.01473079 0.01473079 0.01473079 0.01473079
## [79] 0.01473079 0.01473079 0.01473079 0.01473079 0.01473079 0.01473079
## [85] 0.01576539 0.01576539 0.01576539 0.01576539 0.01576539 0.01576539
## [91] 0.01576539 0.01576539 0.01576539 0.01576539 0.01576539 0.01576539
## [97] 0.01685262 0.01685262 0.01685262 0.01685262 0.01685262 0.01685262
## [103] 0.01685262 0.01685262 0.01685262 0.01685262 0.01685262 0.01685262
## [109] 0.01799433 0.01799433 0.01799433 0.01799433 0.01799433 0.01799433
## [115] 0.01799433 0.01799433 0.01799433 0.01799433 0.01799433 0.01799433
## [121] 0.01920244 0.01920244 0.01920244 0.01920244 0.01920244 0.01920244
## [127] 0.01920244 0.01920244 0.01920244 0.01920244 0.01920244 0.01920244
## [133] 0.02061972 0.02061972 0.02061972 0.02061972 0.02061972 0.02061972
## [139] 0.02061972 0.02061972 0.02061972 0.02061972 0.02061972 0.02061972
## [145] 0.02203648 0.02203648 0.02203648 0.02203648 0.02203648 0.02203648
## [151] 0.02203648 0.02203648 0.02203648 0.02203648 0.02203648 0.02203648
## [157] 0.02440279 0.02440279 0.02440279 0.02440279 0.02440279 0.02440279
## [163] 0.02440279 0.02440279 0.02440279 0.02440279 0.02440279 0.02440279
## [169] 0.02654375 0.02654375 0.02654375 0.02654375 0.02654375 0.02654375
## [175] 0.02654375 0.02654375 0.02654375 0.02654375 0.02654375 0.02654375
## [181] 0.01403804 0.01403804 0.01403804 0.01403804 0.01403804 0.01403804
## [187] 0.01403804 0.01403804 0.01403804 0.01403804 0.01403804 0.01403804
## [193] 0.01538333 0.01538333 0.01538333 0.01538333 0.01538333 0.01538333
## [199] 0.01538333 0.01538333 0.01538333 0.01538333 0.01538333 0.01538333
## [205] 0.01711008 0.01711008 0.01711008 0.01711008 0.01711008 0.01711008
## [211] 0.01711008 0.01711008 0.01711008 0.01711008 0.01711008 0.01711008
## [217] 0.01887437 0.01887437 0.01887437 0.01887437 0.01887437 0.01887437
## [223] 0.01887437 0.01887437 0.01887437 0.01887437 0.01887437 0.01887437
## [229] 0.02086312 0.02086312 0.02086312 0.02086312 0.02086312 0.02086312
## [235] 0.02086312 0.02086312 0.02086312 0.02086312 0.02086312 0.02086312
## [241] 0.02300274 0.02300274 0.02300274 0.02300274 0.02300274 0.02300274
## [247] 0.02300274 0.02300274 0.02300274 0.02300274 0.02300274 0.02300274
## [253] 0.02549970 0.02549970 0.02549970 0.02549970 0.02549970 0.02549970
## [259] 0.02549970 0.02549970 0.02549970 0.02549970 0.02549970 0.02549970
## [265] 0.02843888 0.02843888 0.02843888 0.02843888 0.02843888 0.02843888
## [271] 0.02843888 0.02843888 0.02843888 0.02843888 0.02843888 0.02843888
## [277] 0.03171747 0.03171747 0.03171747 0.03171747 0.03171747 0.03171747
## [283] 0.03171747 0.03171747 0.03171747 0.03171747 0.03171747 0.03171747
## [289] 0.03549827 0.03549827 0.03549827 0.03549827 0.03549827 0.03549827
## [295] 0.03549827 0.03549827 0.03549827 0.03549827 0.03549827 0.03549827
## [301] 0.06605043 0.06605043 0.06605043 0.06605043 0.06605043 0.06605043
## [307] 0.06605043 0.06605043 0.06605043 0.06605043 0.06605043 0.06605043
## [313] 0.07378666 0.07378666 0.07378666 0.07378666 0.07378666 0.07378666
## [319] 0.07378666 0.07378666 0.07378666 0.07378666 0.07378666 0.07378666
## [325] 0.08312292 0.08312292 0.08312292 0.08312292 0.08312292 0.08312292
## [331] 0.08312292 0.08312292 0.08312292 0.08312292 0.08312292 0.08312292
## [337] 0.09346329 0.09346329 0.09346329 0.09346329 0.09346329 0.09346329
## [343] 0.09346329 0.09346329 0.09346329 0.09346329 0.09346329 0.09346329
## [349] 0.10487116 0.10487116 0.10487116 0.10487116 0.10487116 0.10487116
## [355] 0.10487116 0.10487116 0.10487116 0.10487116 0.10487116 0.10487116
## [361] 0.11740292 0.11740292 0.11740292 0.11740292 0.11740292 0.11740292
## [367] 0.11740292 0.11740292 0.11740292 0.11740292 0.11740292 0.11740292
## [373] 0.13110519 0.13110519 0.13110519 0.13110519 0.13110519 0.13110519
## [379] 0.13110519 0.13110519 0.13110519 0.13110519 0.13110519 0.13110519
## [385] 0.14601151 0.14601151 0.14601151 0.14601151 0.14601151 0.14601151
## [391] 0.14601151 0.14601151 0.14601151 0.14601151 0.14601151 0.14601151
## [397] 0.16213912 0.16213912 0.16213912 0.16213912 0.16213912 0.16213912
## [403] 0.16213912 0.16213912 0.16213912 0.16213912 0.16213912 0.16213912
## [409] 0.17948583 0.17948583 0.17948583 0.17948583 0.17948583 0.17948583
## [415] 0.17948583 0.17948583 0.17948583 0.17948583 0.17948583 0.17948583
## [421] 0.19802706 0.19802706 0.19802706 0.19802706 0.19802706 0.19802706
## [427] 0.19802706 0.19802706 0.19802706 0.19802706 0.19802706 0.19802706
## [433] 0.21771359 0.21771359 0.21771359 0.21771359 0.21771359 0.21771359
## [439] 0.21771359 0.21771359 0.21771359 0.21771359 0.21771359 0.21771359
## [445] 0.23846997 0.23846997 0.23846997 0.23846997 0.23846997 0.23846997
## [451] 0.23846997 0.23846997 0.23846997 0.23846997 0.23846997 0.23846997
## [457] 0.26019412 0.26019412 0.26019412 0.26019412 0.26019412 0.26019412
## [463] 0.26019412 0.26019412 0.26019412 0.26019412 0.26019412 0.26019412
## [469] 0.28275799 0.28275799 0.28275799 0.28275799 0.28275799 0.28275799
## [475] 0.28275799 0.28275799 0.28275799 0.28275799 0.28275799 0.28275799
## The incidence treatment state mortality risk factor [1] 0.01475668 0.01475668 0.01475668 0.01475668 0.01475668 0.01475668
## [7] 0.01475668 0.01475668 0.01475668 0.01475668 0.01475668 0.01475668
## [13] 0.01592052 0.01592052 0.01592052 0.01592052 0.01592052 0.01592052
## [19] 0.01592052 0.01592052 0.01592052 0.01592052 0.01592052 0.01592052
## [25] 0.01708932 0.01708932 0.01708932 0.01708932 0.01708932 0.01708932
## [31] 0.01708932 0.01708932 0.01708932 0.01708932 0.01708932 0.01708932
## [37] 0.01824332 0.01824332 0.01824332 0.01824332 0.01824332 0.01824332
## [43] 0.01824332 0.01824332 0.01824332 0.01824332 0.01824332 0.01824332
## [49] 0.01941715 0.01941715 0.01941715 0.01941715 0.01941715 0.01941715
## [55] 0.01941715 0.01941715 0.01941715 0.01941715 0.01941715 0.01941715
## [61] 0.01373412 0.01373412 0.01373412 0.01373412 0.01373412 0.01373412
## [67] 0.01373412 0.01373412 0.01373412 0.01373412 0.01373412 0.01373412
## [73] 0.01473079 0.01473079 0.01473079 0.01473079 0.01473079 0.01473079
## [79] 0.01473079 0.01473079 0.01473079 0.01473079 0.01473079 0.01473079
## [85] 0.01576539 0.01576539 0.01576539 0.01576539 0.01576539 0.01576539
## [91] 0.01576539 0.01576539 0.01576539 0.01576539 0.01576539 0.01576539
## [97] 0.01685262 0.01685262 0.01685262 0.01685262 0.01685262 0.01685262
## [103] 0.01685262 0.01685262 0.01685262 0.01685262 0.01685262 0.01685262
## [109] 0.01799433 0.01799433 0.01799433 0.01799433 0.01799433 0.01799433
## [115] 0.01799433 0.01799433 0.01799433 0.01799433 0.01799433 0.01799433
## [121] 0.01920244 0.01920244 0.01920244 0.01920244 0.01920244 0.01920244
## [127] 0.01920244 0.01920244 0.01920244 0.01920244 0.01920244 0.01920244
## [133] 0.02061972 0.02061972 0.02061972 0.02061972 0.02061972 0.02061972
## [139] 0.02061972 0.02061972 0.02061972 0.02061972 0.02061972 0.02061972
## [145] 0.02203648 0.02203648 0.02203648 0.02203648 0.02203648 0.02203648
## [151] 0.02203648 0.02203648 0.02203648 0.02203648 0.02203648 0.02203648
## [157] 0.02440279 0.02440279 0.02440279 0.02440279 0.02440279 0.02440279
## [163] 0.02440279 0.02440279 0.02440279 0.02440279 0.02440279 0.02440279
## [169] 0.02654375 0.02654375 0.02654375 0.02654375 0.02654375 0.02654375
## [175] 0.02654375 0.02654375 0.02654375 0.02654375 0.02654375 0.02654375
## [181] 0.01403804 0.01403804 0.01403804 0.01403804 0.01403804 0.01403804
## [187] 0.01403804 0.01403804 0.01403804 0.01403804 0.01403804 0.01403804
## [193] 0.01538333 0.01538333 0.01538333 0.01538333 0.01538333 0.01538333
## [199] 0.01538333 0.01538333 0.01538333 0.01538333 0.01538333 0.01538333
## [205] 0.01711008 0.01711008 0.01711008 0.01711008 0.01711008 0.01711008
## [211] 0.01711008 0.01711008 0.01711008 0.01711008 0.01711008 0.01711008
## [217] 0.01887437 0.01887437 0.01887437 0.01887437 0.01887437 0.01887437
## [223] 0.01887437 0.01887437 0.01887437 0.01887437 0.01887437 0.01887437
## [229] 0.02086312 0.02086312 0.02086312 0.02086312 0.02086312 0.02086312
## [235] 0.02086312 0.02086312 0.02086312 0.02086312 0.02086312 0.02086312
## [241] 0.02300274 0.02300274 0.02300274 0.02300274 0.02300274 0.02300274
## [247] 0.02300274 0.02300274 0.02300274 0.02300274 0.02300274 0.02300274
## [253] 0.02549970 0.02549970 0.02549970 0.02549970 0.02549970 0.02549970
## [259] 0.02549970 0.02549970 0.02549970 0.02549970 0.02549970 0.02549970
## [265] 0.02843888 0.02843888 0.02843888 0.02843888 0.02843888 0.02843888
## [271] 0.02843888 0.02843888 0.02843888 0.02843888 0.02843888 0.02843888
## [277] 0.03171747 0.03171747 0.03171747 0.03171747 0.03171747 0.03171747
## [283] 0.03171747 0.03171747 0.03171747 0.03171747 0.03171747 0.03171747
## [289] 0.03549827 0.03549827 0.03549827 0.03549827 0.03549827 0.03549827
## [295] 0.03549827 0.03549827 0.03549827 0.03549827 0.03549827 0.03549827
## [301] 0.06605043 0.06605043 0.06605043 0.06605043 0.06605043 0.06605043
## [307] 0.06605043 0.06605043 0.06605043 0.06605043 0.06605043 0.06605043
## [313] 0.07378666 0.07378666 0.07378666 0.07378666 0.07378666 0.07378666
## [319] 0.07378666 0.07378666 0.07378666 0.07378666 0.07378666 0.07378666
## [325] 0.08312292 0.08312292 0.08312292 0.08312292 0.08312292 0.08312292
## [331] 0.08312292 0.08312292 0.08312292 0.08312292 0.08312292 0.08312292
## [337] 0.09346329 0.09346329 0.09346329 0.09346329 0.09346329 0.09346329
## [343] 0.09346329 0.09346329 0.09346329 0.09346329 0.09346329 0.09346329
## [349] 0.10487116 0.10487116 0.10487116 0.10487116 0.10487116 0.10487116
## [355] 0.10487116 0.10487116 0.10487116 0.10487116 0.10487116 0.10487116
## [361] 0.11740292 0.11740292 0.11740292 0.11740292 0.11740292 0.11740292
## [367] 0.11740292 0.11740292 0.11740292 0.11740292 0.11740292 0.11740292
## [373] 0.13110519 0.13110519 0.13110519 0.13110519 0.13110519 0.13110519
## [379] 0.13110519 0.13110519 0.13110519 0.13110519 0.13110519 0.13110519
## [385] 0.14601151 0.14601151 0.14601151 0.14601151 0.14601151 0.14601151
## [391] 0.14601151 0.14601151 0.14601151 0.14601151 0.14601151 0.14601151
## [397] 0.16213912 0.16213912 0.16213912 0.16213912 0.16213912 0.16213912
## [403] 0.16213912 0.16213912 0.16213912 0.16213912 0.16213912 0.16213912
## [409] 0.17948583 0.17948583 0.17948583 0.17948583 0.17948583 0.17948583
## [415] 0.17948583 0.17948583 0.17948583 0.17948583 0.17948583 0.17948583
## [421] 0.19802706 0.19802706 0.19802706 0.19802706 0.19802706 0.19802706
## [427] 0.19802706 0.19802706 0.19802706 0.19802706 0.19802706 0.19802706
## [433] 0.21771359 0.21771359 0.21771359 0.21771359 0.21771359 0.21771359
## [439] 0.21771359 0.21771359 0.21771359 0.21771359 0.21771359 0.21771359
## [445] 0.23846997 0.23846997 0.23846997 0.23846997 0.23846997 0.23846997
## [451] 0.23846997 0.23846997 0.23846997 0.23846997 0.23846997 0.23846997
## [457] 0.26019412 0.26019412 0.26019412 0.26019412 0.26019412 0.26019412
## [463] 0.26019412 0.26019412 0.26019412 0.26019412 0.26019412 0.26019412
## [469] 0.28275799 0.28275799 0.28275799 0.28275799 0.28275799 0.28275799
## [475] 0.28275799 0.28275799 0.28275799 0.28275799 0.28275799 0.28275799
## Ensure the risk factor is 1[1] 1
## The treatmetn completion rate(monthly)[1] 0.125
## The treatmetn initiation rate(monthly)[1] 0.25
## The incidence state mortality probability [1] 0.01464834 0.01464834 0.01464834 0.01464834 0.01464834 0.01464834
## [7] 0.01464834 0.01464834 0.01464834 0.01464834 0.01464834 0.01464834
## [13] 0.01579446 0.01579446 0.01579446 0.01579446 0.01579446 0.01579446
## [19] 0.01579446 0.01579446 0.01579446 0.01579446 0.01579446 0.01579446
## [25] 0.01694412 0.01694412 0.01694412 0.01694412 0.01694412 0.01694412
## [31] 0.01694412 0.01694412 0.01694412 0.01694412 0.01694412 0.01694412
## [37] 0.01807792 0.01807792 0.01807792 0.01807792 0.01807792 0.01807792
## [43] 0.01807792 0.01807792 0.01807792 0.01807792 0.01807792 0.01807792
## [49] 0.01922985 0.01922985 0.01922985 0.01922985 0.01922985 0.01922985
## [55] 0.01922985 0.01922985 0.01922985 0.01922985 0.01922985 0.01922985
## [61] 0.01364023 0.01364023 0.01364023 0.01364023 0.01364023 0.01364023
## [67] 0.01364023 0.01364023 0.01364023 0.01364023 0.01364023 0.01364023
## [73] 0.01462282 0.01462282 0.01462282 0.01462282 0.01462282 0.01462282
## [79] 0.01462282 0.01462282 0.01462282 0.01462282 0.01462282 0.01462282
## [85] 0.01564177 0.01564177 0.01564177 0.01564177 0.01564177 0.01564177
## [91] 0.01564177 0.01564177 0.01564177 0.01564177 0.01564177 0.01564177
## [97] 0.01671141 0.01671141 0.01671141 0.01671141 0.01671141 0.01671141
## [103] 0.01671141 0.01671141 0.01671141 0.01671141 0.01671141 0.01671141
## [109] 0.01783340 0.01783340 0.01783340 0.01783340 0.01783340 0.01783340
## [115] 0.01783340 0.01783340 0.01783340 0.01783340 0.01783340 0.01783340
## [121] 0.01901925 0.01901925 0.01901925 0.01901925 0.01901925 0.01901925
## [127] 0.01901925 0.01901925 0.01901925 0.01901925 0.01901925 0.01901925
## [133] 0.02040858 0.02040858 0.02040858 0.02040858 0.02040858 0.02040858
## [139] 0.02040858 0.02040858 0.02040858 0.02040858 0.02040858 0.02040858
## [145] 0.02179545 0.02179545 0.02179545 0.02179545 0.02179545 0.02179545
## [151] 0.02179545 0.02179545 0.02179545 0.02179545 0.02179545 0.02179545
## [157] 0.02410745 0.02410745 0.02410745 0.02410745 0.02410745 0.02410745
## [163] 0.02410745 0.02410745 0.02410745 0.02410745 0.02410745 0.02410745
## [169] 0.02619457 0.02619457 0.02619457 0.02619457 0.02619457 0.02619457
## [175] 0.02619457 0.02619457 0.02619457 0.02619457 0.02619457 0.02619457
## [181] 0.01393997 0.01393997 0.01393997 0.01393997 0.01393997 0.01393997
## [187] 0.01393997 0.01393997 0.01393997 0.01393997 0.01393997 0.01393997
## [193] 0.01526561 0.01526561 0.01526561 0.01526561 0.01526561 0.01526561
## [199] 0.01526561 0.01526561 0.01526561 0.01526561 0.01526561 0.01526561
## [205] 0.01696453 0.01696453 0.01696453 0.01696453 0.01696453 0.01696453
## [211] 0.01696453 0.01696453 0.01696453 0.01696453 0.01696453 0.01696453
## [217] 0.01869737 0.01869737 0.01869737 0.01869737 0.01869737 0.01869737
## [223] 0.01869737 0.01869737 0.01869737 0.01869737 0.01869737 0.01869737
## [229] 0.02064699 0.02064699 0.02064699 0.02064699 0.02064699 0.02064699
## [235] 0.02064699 0.02064699 0.02064699 0.02064699 0.02064699 0.02064699
## [241] 0.02274019 0.02274019 0.02274019 0.02274019 0.02274019 0.02274019
## [247] 0.02274019 0.02274019 0.02274019 0.02274019 0.02274019 0.02274019
## [253] 0.02517733 0.02517733 0.02517733 0.02517733 0.02517733 0.02517733
## [259] 0.02517733 0.02517733 0.02517733 0.02517733 0.02517733 0.02517733
## [265] 0.02803830 0.02803830 0.02803830 0.02803830 0.02803830 0.02803830
## [271] 0.02803830 0.02803830 0.02803830 0.02803830 0.02803830 0.02803830
## [277] 0.03121974 0.03121974 0.03121974 0.03121974 0.03121974 0.03121974
## [283] 0.03121974 0.03121974 0.03121974 0.03121974 0.03121974 0.03121974
## [289] 0.03487560 0.03487560 0.03487560 0.03487560 0.03487560 0.03487560
## [295] 0.03487560 0.03487560 0.03487560 0.03487560 0.03487560 0.03487560
## [301] 0.06391634 0.06391634 0.06391634 0.06391634 0.06391634 0.06391634
## [307] 0.06391634 0.06391634 0.06391634 0.06391634 0.06391634 0.06391634
## [313] 0.07113016 0.07113016 0.07113016 0.07113016 0.07113016 0.07113016
## [319] 0.07113016 0.07113016 0.07113016 0.07113016 0.07113016 0.07113016
## [325] 0.07976198 0.07976198 0.07976198 0.07976198 0.07976198 0.07976198
## [331] 0.07976198 0.07976198 0.07976198 0.07976198 0.07976198 0.07976198
## [337] 0.08922855 0.08922855 0.08922855 0.08922855 0.08922855 0.08922855
## [343] 0.08922855 0.08922855 0.08922855 0.08922855 0.08922855 0.08922855
## [349] 0.09955947 0.09955947 0.09955947 0.09955947 0.09955947 0.09955947
## [355] 0.09955947 0.09955947 0.09955947 0.09955947 0.09955947 0.09955947
## [361] 0.11077317 0.11077317 0.11077317 0.11077317 0.11077317 0.11077317
## [367] 0.11077317 0.11077317 0.11077317 0.11077317 0.11077317 0.11077317
## [373] 0.12287449 0.12287449 0.12287449 0.12287449 0.12287449 0.12287449
## [379] 0.12287449 0.12287449 0.12287449 0.12287449 0.12287449 0.12287449
## [385] 0.13585224 0.13585224 0.13585224 0.13585224 0.13585224 0.13585224
## [391] 0.13585224 0.13585224 0.13585224 0.13585224 0.13585224 0.13585224
## [397] 0.14967710 0.14967710 0.14967710 0.14967710 0.14967710 0.14967710
## [403] 0.14967710 0.14967710 0.14967710 0.14967710 0.14967710 0.14967710
## [409] 0.16430021 0.16430021 0.16430021 0.16430021 0.16430021 0.16430021
## [415] 0.16430021 0.16430021 0.16430021 0.16430021 0.16430021 0.16430021
## [421] 0.17965234 0.17965234 0.17965234 0.17965234 0.17965234 0.17965234
## [427] 0.17965234 0.17965234 0.17965234 0.17965234 0.17965234 0.17965234
## [433] 0.19564422 0.19564422 0.19564422 0.19564422 0.19564422 0.19564422
## [439] 0.19564422 0.19564422 0.19564422 0.19564422 0.19564422 0.19564422
## [445] 0.21216765 0.21216765 0.21216765 0.21216765 0.21216765 0.21216765
## [451] 0.21216765 0.21216765 0.21216765 0.21216765 0.21216765 0.21216765
## [457] 0.22909808 0.22909808 0.22909808 0.22909808 0.22909808 0.22909808
## [463] 0.22909808 0.22909808 0.22909808 0.22909808 0.22909808 0.22909808
## [469] 0.24629783 0.24629783 0.24629783 0.24629783 0.24629783 0.24629783
## [475] 0.24629783 0.24629783 0.24629783 0.24629783 0.24629783 0.24629783
## The incidence treatment state mortality probability [1] 0.01464834 0.01464834 0.01464834 0.01464834 0.01464834 0.01464834
## [7] 0.01464834 0.01464834 0.01464834 0.01464834 0.01464834 0.01464834
## [13] 0.01579446 0.01579446 0.01579446 0.01579446 0.01579446 0.01579446
## [19] 0.01579446 0.01579446 0.01579446 0.01579446 0.01579446 0.01579446
## [25] 0.01694412 0.01694412 0.01694412 0.01694412 0.01694412 0.01694412
## [31] 0.01694412 0.01694412 0.01694412 0.01694412 0.01694412 0.01694412
## [37] 0.01807792 0.01807792 0.01807792 0.01807792 0.01807792 0.01807792
## [43] 0.01807792 0.01807792 0.01807792 0.01807792 0.01807792 0.01807792
## [49] 0.01922985 0.01922985 0.01922985 0.01922985 0.01922985 0.01922985
## [55] 0.01922985 0.01922985 0.01922985 0.01922985 0.01922985 0.01922985
## [61] 0.01364023 0.01364023 0.01364023 0.01364023 0.01364023 0.01364023
## [67] 0.01364023 0.01364023 0.01364023 0.01364023 0.01364023 0.01364023
## [73] 0.01462282 0.01462282 0.01462282 0.01462282 0.01462282 0.01462282
## [79] 0.01462282 0.01462282 0.01462282 0.01462282 0.01462282 0.01462282
## [85] 0.01564177 0.01564177 0.01564177 0.01564177 0.01564177 0.01564177
## [91] 0.01564177 0.01564177 0.01564177 0.01564177 0.01564177 0.01564177
## [97] 0.01671141 0.01671141 0.01671141 0.01671141 0.01671141 0.01671141
## [103] 0.01671141 0.01671141 0.01671141 0.01671141 0.01671141 0.01671141
## [109] 0.01783340 0.01783340 0.01783340 0.01783340 0.01783340 0.01783340
## [115] 0.01783340 0.01783340 0.01783340 0.01783340 0.01783340 0.01783340
## [121] 0.01901925 0.01901925 0.01901925 0.01901925 0.01901925 0.01901925
## [127] 0.01901925 0.01901925 0.01901925 0.01901925 0.01901925 0.01901925
## [133] 0.02040858 0.02040858 0.02040858 0.02040858 0.02040858 0.02040858
## [139] 0.02040858 0.02040858 0.02040858 0.02040858 0.02040858 0.02040858
## [145] 0.02179545 0.02179545 0.02179545 0.02179545 0.02179545 0.02179545
## [151] 0.02179545 0.02179545 0.02179545 0.02179545 0.02179545 0.02179545
## [157] 0.02410745 0.02410745 0.02410745 0.02410745 0.02410745 0.02410745
## [163] 0.02410745 0.02410745 0.02410745 0.02410745 0.02410745 0.02410745
## [169] 0.02619457 0.02619457 0.02619457 0.02619457 0.02619457 0.02619457
## [175] 0.02619457 0.02619457 0.02619457 0.02619457 0.02619457 0.02619457
## [181] 0.01393997 0.01393997 0.01393997 0.01393997 0.01393997 0.01393997
## [187] 0.01393997 0.01393997 0.01393997 0.01393997 0.01393997 0.01393997
## [193] 0.01526561 0.01526561 0.01526561 0.01526561 0.01526561 0.01526561
## [199] 0.01526561 0.01526561 0.01526561 0.01526561 0.01526561 0.01526561
## [205] 0.01696453 0.01696453 0.01696453 0.01696453 0.01696453 0.01696453
## [211] 0.01696453 0.01696453 0.01696453 0.01696453 0.01696453 0.01696453
## [217] 0.01869737 0.01869737 0.01869737 0.01869737 0.01869737 0.01869737
## [223] 0.01869737 0.01869737 0.01869737 0.01869737 0.01869737 0.01869737
## [229] 0.02064699 0.02064699 0.02064699 0.02064699 0.02064699 0.02064699
## [235] 0.02064699 0.02064699 0.02064699 0.02064699 0.02064699 0.02064699
## [241] 0.02274019 0.02274019 0.02274019 0.02274019 0.02274019 0.02274019
## [247] 0.02274019 0.02274019 0.02274019 0.02274019 0.02274019 0.02274019
## [253] 0.02517733 0.02517733 0.02517733 0.02517733 0.02517733 0.02517733
## [259] 0.02517733 0.02517733 0.02517733 0.02517733 0.02517733 0.02517733
## [265] 0.02803830 0.02803830 0.02803830 0.02803830 0.02803830 0.02803830
## [271] 0.02803830 0.02803830 0.02803830 0.02803830 0.02803830 0.02803830
## [277] 0.03121974 0.03121974 0.03121974 0.03121974 0.03121974 0.03121974
## [283] 0.03121974 0.03121974 0.03121974 0.03121974 0.03121974 0.03121974
## [289] 0.03487560 0.03487560 0.03487560 0.03487560 0.03487560 0.03487560
## [295] 0.03487560 0.03487560 0.03487560 0.03487560 0.03487560 0.03487560
## [301] 0.06391634 0.06391634 0.06391634 0.06391634 0.06391634 0.06391634
## [307] 0.06391634 0.06391634 0.06391634 0.06391634 0.06391634 0.06391634
## [313] 0.07113016 0.07113016 0.07113016 0.07113016 0.07113016 0.07113016
## [319] 0.07113016 0.07113016 0.07113016 0.07113016 0.07113016 0.07113016
## [325] 0.07976198 0.07976198 0.07976198 0.07976198 0.07976198 0.07976198
## [331] 0.07976198 0.07976198 0.07976198 0.07976198 0.07976198 0.07976198
## [337] 0.08922855 0.08922855 0.08922855 0.08922855 0.08922855 0.08922855
## [343] 0.08922855 0.08922855 0.08922855 0.08922855 0.08922855 0.08922855
## [349] 0.09955947 0.09955947 0.09955947 0.09955947 0.09955947 0.09955947
## [355] 0.09955947 0.09955947 0.09955947 0.09955947 0.09955947 0.09955947
## [361] 0.11077317 0.11077317 0.11077317 0.11077317 0.11077317 0.11077317
## [367] 0.11077317 0.11077317 0.11077317 0.11077317 0.11077317 0.11077317
## [373] 0.12287449 0.12287449 0.12287449 0.12287449 0.12287449 0.12287449
## [379] 0.12287449 0.12287449 0.12287449 0.12287449 0.12287449 0.12287449
## [385] 0.13585224 0.13585224 0.13585224 0.13585224 0.13585224 0.13585224
## [391] 0.13585224 0.13585224 0.13585224 0.13585224 0.13585224 0.13585224
## [397] 0.14967710 0.14967710 0.14967710 0.14967710 0.14967710 0.14967710
## [403] 0.14967710 0.14967710 0.14967710 0.14967710 0.14967710 0.14967710
## [409] 0.16430021 0.16430021 0.16430021 0.16430021 0.16430021 0.16430021
## [415] 0.16430021 0.16430021 0.16430021 0.16430021 0.16430021 0.16430021
## [421] 0.17965234 0.17965234 0.17965234 0.17965234 0.17965234 0.17965234
## [427] 0.17965234 0.17965234 0.17965234 0.17965234 0.17965234 0.17965234
## [433] 0.19564422 0.19564422 0.19564422 0.19564422 0.19564422 0.19564422
## [439] 0.19564422 0.19564422 0.19564422 0.19564422 0.19564422 0.19564422
## [445] 0.21216765 0.21216765 0.21216765 0.21216765 0.21216765 0.21216765
## [451] 0.21216765 0.21216765 0.21216765 0.21216765 0.21216765 0.21216765
## [457] 0.22909808 0.22909808 0.22909808 0.22909808 0.22909808 0.22909808
## [463] 0.22909808 0.22909808 0.22909808 0.22909808 0.22909808 0.22909808
## [469] 0.24629783 0.24629783 0.24629783 0.24629783 0.24629783 0.24629783
## [475] 0.24629783 0.24629783 0.24629783 0.24629783 0.24629783 0.24629783
## The I to D transition probability [1] 0.01464834 0.01464834 0.01464834 0.01464834 0.01464834 0.01464834
## [7] 0.01464834 0.01464834 0.01464834 0.01464834 0.01464834 0.01464834
## [13] 0.01579446 0.01579446 0.01579446 0.01579446 0.01579446 0.01579446
## [19] 0.01579446 0.01579446 0.01579446 0.01579446 0.01579446 0.01579446
## [25] 0.01694412 0.01694412 0.01694412 0.01694412 0.01694412 0.01694412
## [31] 0.01694412 0.01694412 0.01694412 0.01694412 0.01694412 0.01694412
## [37] 0.01807792 0.01807792 0.01807792 0.01807792 0.01807792 0.01807792
## [43] 0.01807792 0.01807792 0.01807792 0.01807792 0.01807792 0.01807792
## [49] 0.01922985 0.01922985 0.01922985 0.01922985 0.01922985 0.01922985
## [55] 0.01922985 0.01922985 0.01922985 0.01922985 0.01922985 0.01922985
## [61] 0.01364023 0.01364023 0.01364023 0.01364023 0.01364023 0.01364023
## [67] 0.01364023 0.01364023 0.01364023 0.01364023 0.01364023 0.01364023
## [73] 0.01462282 0.01462282 0.01462282 0.01462282 0.01462282 0.01462282
## [79] 0.01462282 0.01462282 0.01462282 0.01462282 0.01462282 0.01462282
## [85] 0.01564177 0.01564177 0.01564177 0.01564177 0.01564177 0.01564177
## [91] 0.01564177 0.01564177 0.01564177 0.01564177 0.01564177 0.01564177
## [97] 0.01671141 0.01671141 0.01671141 0.01671141 0.01671141 0.01671141
## [103] 0.01671141 0.01671141 0.01671141 0.01671141 0.01671141 0.01671141
## [109] 0.01783340 0.01783340 0.01783340 0.01783340 0.01783340 0.01783340
## [115] 0.01783340 0.01783340 0.01783340 0.01783340 0.01783340 0.01783340
## [121] 0.01901925 0.01901925 0.01901925 0.01901925 0.01901925 0.01901925
## [127] 0.01901925 0.01901925 0.01901925 0.01901925 0.01901925 0.01901925
## [133] 0.02040858 0.02040858 0.02040858 0.02040858 0.02040858 0.02040858
## [139] 0.02040858 0.02040858 0.02040858 0.02040858 0.02040858 0.02040858
## [145] 0.02179545 0.02179545 0.02179545 0.02179545 0.02179545 0.02179545
## [151] 0.02179545 0.02179545 0.02179545 0.02179545 0.02179545 0.02179545
## [157] 0.02410745 0.02410745 0.02410745 0.02410745 0.02410745 0.02410745
## [163] 0.02410745 0.02410745 0.02410745 0.02410745 0.02410745 0.02410745
## [169] 0.02619457 0.02619457 0.02619457 0.02619457 0.02619457 0.02619457
## [175] 0.02619457 0.02619457 0.02619457 0.02619457 0.02619457 0.02619457
## [181] 0.01393997 0.01393997 0.01393997 0.01393997 0.01393997 0.01393997
## [187] 0.01393997 0.01393997 0.01393997 0.01393997 0.01393997 0.01393997
## [193] 0.01526561 0.01526561 0.01526561 0.01526561 0.01526561 0.01526561
## [199] 0.01526561 0.01526561 0.01526561 0.01526561 0.01526561 0.01526561
## [205] 0.01696453 0.01696453 0.01696453 0.01696453 0.01696453 0.01696453
## [211] 0.01696453 0.01696453 0.01696453 0.01696453 0.01696453 0.01696453
## [217] 0.01869737 0.01869737 0.01869737 0.01869737 0.01869737 0.01869737
## [223] 0.01869737 0.01869737 0.01869737 0.01869737 0.01869737 0.01869737
## [229] 0.02064699 0.02064699 0.02064699 0.02064699 0.02064699 0.02064699
## [235] 0.02064699 0.02064699 0.02064699 0.02064699 0.02064699 0.02064699
## [241] 0.02274019 0.02274019 0.02274019 0.02274019 0.02274019 0.02274019
## [247] 0.02274019 0.02274019 0.02274019 0.02274019 0.02274019 0.02274019
## [253] 0.02517733 0.02517733 0.02517733 0.02517733 0.02517733 0.02517733
## [259] 0.02517733 0.02517733 0.02517733 0.02517733 0.02517733 0.02517733
## [265] 0.02803830 0.02803830 0.02803830 0.02803830 0.02803830 0.02803830
## [271] 0.02803830 0.02803830 0.02803830 0.02803830 0.02803830 0.02803830
## [277] 0.03121974 0.03121974 0.03121974 0.03121974 0.03121974 0.03121974
## [283] 0.03121974 0.03121974 0.03121974 0.03121974 0.03121974 0.03121974
## [289] 0.03487560 0.03487560 0.03487560 0.03487560 0.03487560 0.03487560
## [295] 0.03487560 0.03487560 0.03487560 0.03487560 0.03487560 0.03487560
## [301] 0.06391634 0.06391634 0.06391634 0.06391634 0.06391634 0.06391634
## [307] 0.06391634 0.06391634 0.06391634 0.06391634 0.06391634 0.06391634
## [313] 0.07113016 0.07113016 0.07113016 0.07113016 0.07113016 0.07113016
## [319] 0.07113016 0.07113016 0.07113016 0.07113016 0.07113016 0.07113016
## [325] 0.07976198 0.07976198 0.07976198 0.07976198 0.07976198 0.07976198
## [331] 0.07976198 0.07976198 0.07976198 0.07976198 0.07976198 0.07976198
## [337] 0.08922855 0.08922855 0.08922855 0.08922855 0.08922855 0.08922855
## [343] 0.08922855 0.08922855 0.08922855 0.08922855 0.08922855 0.08922855
## [349] 0.09955947 0.09955947 0.09955947 0.09955947 0.09955947 0.09955947
## [355] 0.09955947 0.09955947 0.09955947 0.09955947 0.09955947 0.09955947
## [361] 0.11077317 0.11077317 0.11077317 0.11077317 0.11077317 0.11077317
## [367] 0.11077317 0.11077317 0.11077317 0.11077317 0.11077317 0.11077317
## [373] 0.12287449 0.12287449 0.12287449 0.12287449 0.12287449 0.12287449
## [379] 0.12287449 0.12287449 0.12287449 0.12287449 0.12287449 0.12287449
## [385] 0.13585224 0.13585224 0.13585224 0.13585224 0.13585224 0.13585224
## [391] 0.13585224 0.13585224 0.13585224 0.13585224 0.13585224 0.13585224
## [397] 0.14967710 0.14967710 0.14967710 0.14967710 0.14967710 0.14967710
## [403] 0.14967710 0.14967710 0.14967710 0.14967710 0.14967710 0.14967710
## [409] 0.16430021 0.16430021 0.16430021 0.16430021 0.16430021 0.16430021
## [415] 0.16430021 0.16430021 0.16430021 0.16430021 0.16430021 0.16430021
## [421] 0.17965234 0.17965234 0.17965234 0.17965234 0.17965234 0.17965234
## [427] 0.17965234 0.17965234 0.17965234 0.17965234 0.17965234 0.17965234
## [433] 0.19564422 0.19564422 0.19564422 0.19564422 0.19564422 0.19564422
## [439] 0.19564422 0.19564422 0.19564422 0.19564422 0.19564422 0.19564422
## [445] 0.21216765 0.21216765 0.21216765 0.21216765 0.21216765 0.21216765
## [451] 0.21216765 0.21216765 0.21216765 0.21216765 0.21216765 0.21216765
## [457] 0.22909808 0.22909808 0.22909808 0.22909808 0.22909808 0.22909808
## [463] 0.22909808 0.22909808 0.22909808 0.22909808 0.22909808 0.22909808
## [469] 0.24629783 0.24629783 0.24629783 0.24629783 0.24629783 0.24629783
## [475] 0.24629783 0.24629783 0.24629783 0.24629783 0.24629783 0.24629783
## The It to D transition probability [1] 0.01464834 0.01464834 0.01464834 0.01464834 0.01464834 0.01464834
## [7] 0.01464834 0.01464834 0.01464834 0.01464834 0.01464834 0.01464834
## [13] 0.01579446 0.01579446 0.01579446 0.01579446 0.01579446 0.01579446
## [19] 0.01579446 0.01579446 0.01579446 0.01579446 0.01579446 0.01579446
## [25] 0.01694412 0.01694412 0.01694412 0.01694412 0.01694412 0.01694412
## [31] 0.01694412 0.01694412 0.01694412 0.01694412 0.01694412 0.01694412
## [37] 0.01807792 0.01807792 0.01807792 0.01807792 0.01807792 0.01807792
## [43] 0.01807792 0.01807792 0.01807792 0.01807792 0.01807792 0.01807792
## [49] 0.01922985 0.01922985 0.01922985 0.01922985 0.01922985 0.01922985
## [55] 0.01922985 0.01922985 0.01922985 0.01922985 0.01922985 0.01922985
## [61] 0.01364023 0.01364023 0.01364023 0.01364023 0.01364023 0.01364023
## [67] 0.01364023 0.01364023 0.01364023 0.01364023 0.01364023 0.01364023
## [73] 0.01462282 0.01462282 0.01462282 0.01462282 0.01462282 0.01462282
## [79] 0.01462282 0.01462282 0.01462282 0.01462282 0.01462282 0.01462282
## [85] 0.01564177 0.01564177 0.01564177 0.01564177 0.01564177 0.01564177
## [91] 0.01564177 0.01564177 0.01564177 0.01564177 0.01564177 0.01564177
## [97] 0.01671141 0.01671141 0.01671141 0.01671141 0.01671141 0.01671141
## [103] 0.01671141 0.01671141 0.01671141 0.01671141 0.01671141 0.01671141
## [109] 0.01783340 0.01783340 0.01783340 0.01783340 0.01783340 0.01783340
## [115] 0.01783340 0.01783340 0.01783340 0.01783340 0.01783340 0.01783340
## [121] 0.01901925 0.01901925 0.01901925 0.01901925 0.01901925 0.01901925
## [127] 0.01901925 0.01901925 0.01901925 0.01901925 0.01901925 0.01901925
## [133] 0.02040858 0.02040858 0.02040858 0.02040858 0.02040858 0.02040858
## [139] 0.02040858 0.02040858 0.02040858 0.02040858 0.02040858 0.02040858
## [145] 0.02179545 0.02179545 0.02179545 0.02179545 0.02179545 0.02179545
## [151] 0.02179545 0.02179545 0.02179545 0.02179545 0.02179545 0.02179545
## [157] 0.02410745 0.02410745 0.02410745 0.02410745 0.02410745 0.02410745
## [163] 0.02410745 0.02410745 0.02410745 0.02410745 0.02410745 0.02410745
## [169] 0.02619457 0.02619457 0.02619457 0.02619457 0.02619457 0.02619457
## [175] 0.02619457 0.02619457 0.02619457 0.02619457 0.02619457 0.02619457
## [181] 0.01393997 0.01393997 0.01393997 0.01393997 0.01393997 0.01393997
## [187] 0.01393997 0.01393997 0.01393997 0.01393997 0.01393997 0.01393997
## [193] 0.01526561 0.01526561 0.01526561 0.01526561 0.01526561 0.01526561
## [199] 0.01526561 0.01526561 0.01526561 0.01526561 0.01526561 0.01526561
## [205] 0.01696453 0.01696453 0.01696453 0.01696453 0.01696453 0.01696453
## [211] 0.01696453 0.01696453 0.01696453 0.01696453 0.01696453 0.01696453
## [217] 0.01869737 0.01869737 0.01869737 0.01869737 0.01869737 0.01869737
## [223] 0.01869737 0.01869737 0.01869737 0.01869737 0.01869737 0.01869737
## [229] 0.02064699 0.02064699 0.02064699 0.02064699 0.02064699 0.02064699
## [235] 0.02064699 0.02064699 0.02064699 0.02064699 0.02064699 0.02064699
## [241] 0.02274019 0.02274019 0.02274019 0.02274019 0.02274019 0.02274019
## [247] 0.02274019 0.02274019 0.02274019 0.02274019 0.02274019 0.02274019
## [253] 0.02517733 0.02517733 0.02517733 0.02517733 0.02517733 0.02517733
## [259] 0.02517733 0.02517733 0.02517733 0.02517733 0.02517733 0.02517733
## [265] 0.02803830 0.02803830 0.02803830 0.02803830 0.02803830 0.02803830
## [271] 0.02803830 0.02803830 0.02803830 0.02803830 0.02803830 0.02803830
## [277] 0.03121974 0.03121974 0.03121974 0.03121974 0.03121974 0.03121974
## [283] 0.03121974 0.03121974 0.03121974 0.03121974 0.03121974 0.03121974
## [289] 0.03487560 0.03487560 0.03487560 0.03487560 0.03487560 0.03487560
## [295] 0.03487560 0.03487560 0.03487560 0.03487560 0.03487560 0.03487560
## [301] 0.06391634 0.06391634 0.06391634 0.06391634 0.06391634 0.06391634
## [307] 0.06391634 0.06391634 0.06391634 0.06391634 0.06391634 0.06391634
## [313] 0.07113016 0.07113016 0.07113016 0.07113016 0.07113016 0.07113016
## [319] 0.07113016 0.07113016 0.07113016 0.07113016 0.07113016 0.07113016
## [325] 0.07976198 0.07976198 0.07976198 0.07976198 0.07976198 0.07976198
## [331] 0.07976198 0.07976198 0.07976198 0.07976198 0.07976198 0.07976198
## [337] 0.08922855 0.08922855 0.08922855 0.08922855 0.08922855 0.08922855
## [343] 0.08922855 0.08922855 0.08922855 0.08922855 0.08922855 0.08922855
## [349] 0.09955947 0.09955947 0.09955947 0.09955947 0.09955947 0.09955947
## [355] 0.09955947 0.09955947 0.09955947 0.09955947 0.09955947 0.09955947
## [361] 0.11077317 0.11077317 0.11077317 0.11077317 0.11077317 0.11077317
## [367] 0.11077317 0.11077317 0.11077317 0.11077317 0.11077317 0.11077317
## [373] 0.12287449 0.12287449 0.12287449 0.12287449 0.12287449 0.12287449
## [379] 0.12287449 0.12287449 0.12287449 0.12287449 0.12287449 0.12287449
## [385] 0.13585224 0.13585224 0.13585224 0.13585224 0.13585224 0.13585224
## [391] 0.13585224 0.13585224 0.13585224 0.13585224 0.13585224 0.13585224
## [397] 0.14967710 0.14967710 0.14967710 0.14967710 0.14967710 0.14967710
## [403] 0.14967710 0.14967710 0.14967710 0.14967710 0.14967710 0.14967710
## [409] 0.16430021 0.16430021 0.16430021 0.16430021 0.16430021 0.16430021
## [415] 0.16430021 0.16430021 0.16430021 0.16430021 0.16430021 0.16430021
## [421] 0.17965234 0.17965234 0.17965234 0.17965234 0.17965234 0.17965234
## [427] 0.17965234 0.17965234 0.17965234 0.17965234 0.17965234 0.17965234
## [433] 0.19564422 0.19564422 0.19564422 0.19564422 0.19564422 0.19564422
## [439] 0.19564422 0.19564422 0.19564422 0.19564422 0.19564422 0.19564422
## [445] 0.21216765 0.21216765 0.21216765 0.21216765 0.21216765 0.21216765
## [451] 0.21216765 0.21216765 0.21216765 0.21216765 0.21216765 0.21216765
## [457] 0.22909808 0.22909808 0.22909808 0.22909808 0.22909808 0.22909808
## [463] 0.22909808 0.22909808 0.22909808 0.22909808 0.22909808 0.22909808
## [469] 0.24629783 0.24629783 0.24629783 0.24629783 0.24629783 0.24629783
## [475] 0.24629783 0.24629783 0.24629783 0.24629783 0.24629783 0.24629783transitc=c$transitThe transitc has three column, column 1: incidence, column 2: the mortality in Incidence state, column 3: the mortality in Incidence treatment state.
datatable(
data = transitc,
caption = "Table 1: the outcome (column 1: incidence, column 2: I state death, column 3: It state death)",
filter = "top",
style = "bootstrap4"
)The incidence plot
plot(transitc[,1])
The CFR calculation
cat("The incidence is: ", sum(transitc[,1]), "\n")## The incidence is: 0.004564769cat("The mortality of I is: ", sum(transitc[,2]), "\n")## The mortality of I is: 0.0005400072cat("The mortality of It is: ", sum(transitc[,3]), "\n")## The mortality of It is: 0.0007433464cat("The CFR of I is: ", sum(transitc[,2])/sum(transitc[,1]), "\n")## The CFR of I is: 0.1182989cat("The CFR of It is: ", sum(transitc[,3])/sum(transitc[,1]), "\n")## The CFR of It is: 0.1628442cat("The CFR is: ", (sum(transitc[,3])+ sum(transitc[,2]))/sum(transitc[,1]), "\n")## The CFR is: 0.2811432The average age of have incidence is
age_vector <- seq(from = 60, by = 1/12, length.out = nrow(transitc))
weighted_sum_ages <- sum(transitc[,1] * age_vector)
sum_weights <- sum(transitc[,1])
average_age_incidence <- weighted_sum_ages / sum_weights
# Print the result
print(average_age_incidence)## [1] 74.64691The tb overall mortality rate at incidence age is:
print(mor[mor$age == 74&mor$sex ==1, "tb_mortality_rate"]*12)## tb_mortality_rate
## 1 0.3185251The CFR at incidence age is about 21%.