# Read data and other model information from a folder that stores model results. ```r nplcm_read_folder(DIR_NPLCM) ``` ## Arguments - `DIR_NPLCM`: File path to the folder containing posterior samples ## Returns A list with data, options and posterior samples. * `bugs.dat` * `model_options` * `clean_otions` * `Nd`; `Nu`; `Y`; `Mobs`; * `res_nplcm`. ## Examples ```r data(data_nplcm_noreg) cause_list <- LETTERS[1:6] J.BrS <- 6 model_options_no_reg <- list( likelihood = list( cause_list = cause_list, k_subclass = 2, Eti_formula = ~-1, # no covariate for the etiology regression FPR_formula = list( MBS1 = ~-1) # no covariate for the subclass weight regression ), use_measurements = c("BrS"), # use bronze-standard data only for model estimation. prior= list( Eti_prior = overall_uniform(1,cause_list), # Dirichlet(1,...,1) prior for the etiology. TPR_prior = list(BrS = list( info = "informative", # informative prior for TPRs input = "match_range", # specify the informative prior for TPRs by specifying a plausible range. val = list(MBS1 = list(up = list(rep(0.99,J.BrS)), # upper ranges: matched to 97.5% quantile of a Beta prior low = list(rep(0.55,J.BrS)))) # lower ranges: matched to 2.5% quantile of a Beta prior ) ) ) ) set.seed(1) # include stratification information in file name: thedir <- paste0(tempdir(),"_no_reg") # create folders to store the model results dir.create(thedir, showWarnings = FALSE) result_folder_no_reg <- file.path(thedir,paste("results",collapse="_")) thedir <- result_folder_no_reg dir.create(thedir, showWarnings = FALSE) # options for MCMC chains: mcmc_options_no_reg <- list( debugstatus = TRUE, n.chains = 1, n.itermcmc = as.integer(200), n.burnin = as.integer(100), n.thin = 1, individual.pred = FALSE, ppd = TRUE, result.folder = thedir, bugsmodel.dir = thedir ) BrS_object_1 <- make_meas_object(patho = LETTERS[1:6], specimen = "MBS", test = "1", quality = "BrS", cause_list = cause_list) clean_options <- list(BrS_objects = make_list(BrS_object_1)) # place the nplcm data and cleaning options into the results folder dput(data_nplcm_noreg,file.path(thedir,"data_nplcm.txt")) dput(clean_options, file.path(thedir, "data_clean_options.txt")) rjags::load.module("glm") nplcm_noreg <- nplcm(data_nplcm_noreg,model_options_no_reg,mcmc_options_no_reg) res <- nplcm_read_folder(nplcm_noreg$DIR_NPLCM) ```

nplcm_read_folder function