Read data and other model information from a folder that stores model results.
Source:R/nplcm-read-folder.R
nplcm_read_folder.Rd
Read data and other model information from a folder that stores model results.
Value
A list with data, options and posterior samples.
bugs.dat
model_options
clean_otions
Nd
;Nu
;Y
;Mobs
;res_nplcm
.
Examples
# \donttest{
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)
#> ==[baker] Results stored in: ==
#> /tmp/Rtmpm6B4eZ_no_reg/results
res <- nplcm_read_folder(nplcm_noreg$DIR_NPLCM)
# }