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

In zhenkewu/baker: "Nested Partially Latent Class Models"

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

Description

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.

Usage

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

Arguments

DIR_list	The list of directory paths, each storing a model output.
slice_vec	Default are 1s, for the first slice of BrS data.
n_pat	Number of the most common BrS measurement pattern among cases and controls. Default is 10.
dodge_val	Default is 0.8; For width of boxplots.

Value

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()

Examples

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)

plot_check_common_pattern(nplcm_noreg$DIR_NPLCM)

zhenkewu/baker documentation built on May 6, 2024, 11:19 p.m.