simulate_ss: Simulate Silver-Standard (SS) Data

View source: R/simulate-nplcm.R

simulate_ssR Documentation

Simulate Silver-Standard (SS) Data


Simulate Silver-Standard (SS) Data


simulate_ss(set_parameter, latent_samples)



True model parameters in an npLCM specification:

  • 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 specimentestpathogen

  • pathogen_SS a vector of pathogen names measured in silver-standard (SS) data.

  • meas_nm a list of specimentest 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 ν_1, ν_2, …, ν_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 η_1, η_2, …, η_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 Θ 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


simulated latent status for all the subjects, for use in simulating SS measurements.


a data frame with first column being case-control status (case at top) and columns of silver-standard measurements

See Also

Other internal simulation functions: simulate_brs(), simulate_latent()

zhenkewu/baker documentation built on March 17, 2022, 9:54 p.m.