plot_check_common_pattern: Posterior predictive checking for the nested partially class...

View source: R/plot-model-check.R

plot_check_common_patternR Documentation

Posterior predictive checking for the nested partially class models - frequent patterns in the BrS data. (for multiple folders)


At each MCMC iteration, we generate a new data set based on the model and parameter values at that iteration. The sample size of the new data set equals that of the actual data set, i.e. the same number of cases and controls.


  slice_vec = rep(1, length(DIR_list)),
  n_pat = 10,
  dodge_val = 0.8



The list of directory paths, each storing a model output.


Default are 1s, for the first slice of BrS data.


Number of the most common BrS measurement pattern among cases and controls. Default is 10.


Default is 0.8; For width of boxplots.


A figure of posterior predicted frequencies compared with the observed frequencies of the most common patterns for the BrS data.

See Also

Other visualization functions: plot.nplcm(), plot_BrS_panel(), plot_SS_panel(), plot_check_pairwise_SLORD(), plot_etiology_regression(), plot_etiology_strat(), plot_panels(), plot_pie_panel(), plot_subwt_regression()


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

# 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(clean_options, file.path(thedir, "data_clean_options.txt"))


nplcm_noreg <- nplcm(data_nplcm_noreg,model_options_no_reg,mcmc_options_no_reg)


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