set.seed(2)
# true TPR and FPR for measurement data
PsiBS0 <- cbind(c(0.25,0.25,0.2,0.15,0.15,0.15), c(0.2,0.2,0.25,0.1,0.1,0.1))
ThetaBS0 <- cbind(c(0.95,0.9,0.9,0.9,0.9,0.9), c(0.95,0.9,0.9,0.9,0.9,0.9))
ThetaSS_withNA <- c(0.15,0.1,NA,NA,NA,NA)
PsiSS_withNA <- c(0,0,NA,NA,NA,NA)
# true subclass weights
lambda <- c(0.5,0.5)
eta <- c(0,1)
# the following paramter names are set using names in the 'baker' package:
set_parameter_noreg <- list(
cause_list = cause_list,
etiology = c(0.5,0.2,0.15,0.05,0.05,0.05),
pathogen_BrS = LETTERS[1:L.CAUSE],
pathogen_SS = LETTERS[1:L.CAUSE][!is.na(ThetaSS_withNA)],
meas_nm = list(MBS = c("MBS1"),MSS=c("MSS1")), # a single slice of Bronze Standard (BrS) data
Lambda = lambda,
Eta = t(replicate(J.BrS,eta)),
PsiBS = PsiBS0,
ThetaBS = ThetaBS0,
PsiSS = PsiSS_withNA[!is.na(PsiSS_withNA)], # FPR for SS measures; 0 for perfect specificity
ThetaSS = ThetaSS_withNA[!is.na(ThetaSS_withNA)], # TPRS for MSS1
Nd = Nd,
Nu = Nu
)
simu_out_noreg <- simulate_nplcm(set_parameter_noreg)
data_nplcm_noreg <- simu_out_noreg$data_nplcm
##save the simulated data to the R package for illustration:
#save(data_nplcm_noreg, file = "data/data_nplcm_noreg.rda", compress = "xz")
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