assign_model: Choose a model to fit
In zhenkewu/nplcm: Nested Partially-Latent Class Models (nplcm)

Description Usage Arguments Details Value

assign_model recognizes the model to fit from user input.

1	assign_model(data_nplcm, model_options, silent = TRUE)

data_nplcm

Data for model fitting. Details are

Mobs See nplcm function.
Y See nplcm function.
X See nplcm function.
Mname A list of pathogen names. Mname_BrS for BrS only pathogens, and Mname_SSonly for pathogens with only SS measures.
taxonomy A list of pathogen taxonomy. The elements include taxo_BrS and taxo_SSonly. It can be used to represent biological classifications, such as bacteria (B) versus virus (V).

model_options

See nplcm function.

silent

Default is TRUE: print assigned model descriptions on screen; otherwise, FALSE.

assign_model will also inspect the actual data supplied and check if the data conform to user's requested model. The following features of data and user inputs are checked against each other:

Available types of measurement quality, i.e., gold-, silver- or bronze-standard or any combinations;
Model for false positive rates: covariate-dependent or not;
Model for etiology: covariate-dependent or not.

A list of information for the selected model:

measurement
- quality e.g. "BrS+SS" indicates both BrS and SS measures are available
- SSonly TRUE for existence of pathogens with only SS measures; otherwise, FALSE;
- nest TRUE for conditional dependent model; FALSE for conditional independent model;
reg
- do_FPR_reg TRUE for allowing FPR to be covariate-dependent; FALSE otherwise;
- do_Eti_reg TRUE for allowing etiology to be covariate-dependent; FALSE otherwise;