cause_list a vector of disease class names among cases (since
the causes could be multi-agent (e.g., multiple pathogens may cause an individual case's
pneumonia), so its length could be longer than the total number of unique
causative agents)
etiology a vector of proportions that sum to 100 percent
pathogen_BrS a vector of putative causative agents' names measured in bronze-standard (BrS) data.
This function simulates only one slice defined by specimen``test``pathogen
pathogen_SS a vector of pathogen names measured in silver-standard (SS) data.
meas_nm a list of specimen``test names e.g., list(MBS = c("NPPCR"),MSS="BCX")
for nasopharyngeal (NP) specimen tested by polymerase chain reaction (PCR) - NPPCR and
blood (B) tested by culture (Cx) - BCX
Lambda controls' subclass weights \nu_1, \nu_2, \ldots, \nu_K
a vector of K probabilities that sum to 1.
Eta a matrix of dimension length(cause_list) by K;
each row represents a disease class (among cases); the values in that row
are subclass weights \eta_1, \eta_2, \ldots, \eta_K for that disease class,
so needs to sum to one. In Wu et al. 2016 (JRSS-C), the subclass weights are the same across disease
classes across rows. But when simulating data, one can specify rows with distinct
subclass weights - it is a matter whether we can recover these parameters (possible when
some cases' true disease classes are observed)
PsiBS/PsiSS False positive rates for Bronze-Standard data and
for Silver-Standard data. For example, the rows of PsiBS correspond to the dimension of the particular
slice of BrS measures, e.g., 10 for 10 causative agents measured by NPPCR; the
columns correspond to K subclasses; generically, the dimension is J by K
PsiSS is supposed to be a vector of all zeros (perfect specificity in silver-standard measures).
ThetaBS/ThetaSS True positive rates \Theta for Bronze-Standard data and
for Silver-Standard data. Dimension is J by K (can contain NA if the total number of
causative agents measured by BrS or SS exceeds the measured causative agents in SS. For example,
in PERCH study, nasopharyngeal polymerase chain reaction (NPPCR; bronze-standard) may target 30 distinct pathogens, but blood culture (BCX; silver-standard) may only target a subset of the 30,
so we have to specify NA in ThetaSSfor those pathogens not targeted by BCX).
Nu the number of control subjects
Nd the number of case subjects