## ----include = FALSE----------------------------------------------------------
is_cran_check <- !isTRUE(as.logical(Sys.getenv("NOT_CRAN", "false")))
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width = 7,
  fig.height = 5,
  eval = !is_cran_check
)

## ----setup--------------------------------------------------------------------
# library(mfrmr)
# 
# toy <- load_mfrmr_data("example_operational")
# 
# # The vignette uses compact quadrature so optional local execution stays fast.
# # For final manuscript reporting, refit with the package default or a higher
# # quadrature setting and record that setting in the analysis log.
# fit <- fit_mfrm(
#   toy,
#   person = "Person",
#   facets = c("Rater", "Criterion"),
#   score = "Score",
#   method = "MML",
#   model = "RSM",
#   quad_points = 7
# )
# 
# diag <- diagnose_mfrm(fit, residual_pca = "none")

## ----checklist----------------------------------------------------------------
# chk <- reporting_checklist(fit, diagnostics = diag)
# 
# head(
#   chk$checklist[, c("Section", "Item", "DraftReady", "Priority", "NextAction")],
#   10
# )

## ----precision----------------------------------------------------------------
# prec <- precision_review_report(fit, diagnostics = diag)
# 
# prec$profile
# prec$checks
# prec$fit_separation_basis

## ----apa----------------------------------------------------------------------
# apa <- build_apa_outputs(
#   fit,
#   diagnostics = diag,
#   context = list(
#     assessment = "Writing assessment",
#     setting = "Local scoring study",
#     scale_desc = "0-4 rubric scale",
#     rater_facet = "Rater"
#   )
# )
# 
# cat(apa$report_text)

## ----section-map--------------------------------------------------------------
# apa$section_map[, c("SectionId", "Heading", "Available")]

## ----publication-boundary-----------------------------------------------------
# res <- mfrm_results(fit, include = "publication")
# report <- mfrm_report(res, style = "apa")
# 
# report$first_screen
# report$claim_readiness
# report$report_gaps
# head(report$template_index[, c(
#   "Area", "Topic", "BoundaryType", "ClaimStrength", "RecommendedUse"
# )])

## ----fit-to-html-bundle, eval=FALSE-------------------------------------------
# bundle <- export_mfrm_bundle(
#   fit,
#   diagnostics = diag,
#   output_dir = "mfrmr-report-bundle",
#   prefix = "analysis01",
#   include = c(
#     "core_tables", "checklist", "dashboard", "apa",
#     "summary_tables", "manifest", "script", "html"
#   ),
#   overwrite = TRUE,
#   acknowledge_sensitive = TRUE
# )
# 
# bundle$written_files[bundle$written_files$Format == "html", ]

## ----apa-tables---------------------------------------------------------------
# tbl_summary <- apa_table(fit, which = "summary")
# tbl_reliability <- apa_table(fit, which = "reliability", diagnostics = diag)
# 
# tbl_summary$caption
# tbl_reliability$note

## ----visuals------------------------------------------------------------------
# vis <- build_visual_summaries(
#   fit,
#   diagnostics = diag,
#   threshold_profile = "standard"
# )
# 
# names(vis)
# names(vis$warning_map)

## ----bias-screen--------------------------------------------------------------
# bias_df <- load_mfrmr_data("example_bias")
# 
# fit_bias <- fit_mfrm(
#   bias_df,
#   person = "Person",
#   facets = c("Rater", "Criterion"),
#   score = "Score",
#   method = "MML",
#   model = "RSM",
#   quad_points = 7
# )
# 
# diag_bias <- diagnose_mfrm(fit_bias, residual_pca = "none")
# bias <- estimate_bias(fit_bias, diag_bias, facet_a = "Rater", facet_b = "Criterion")
# apa_bias <- build_apa_outputs(fit_bias, diagnostics = diag_bias, bias_results = bias)
# 
# apa_bias$section_map[, c("SectionId", "Available", "Heading")]

## ----model-choice-route, eval=FALSE-------------------------------------------
# cmp <- compare_mfrm(RSM = fit_rsm, PCM = fit_pcm, GPCM = fit_gpcm)
# review <- build_model_choice_review(
#   RSM = fit_rsm,
#   PCM = fit_pcm,
#   GPCM = fit_gpcm,
#   run_weighting_review = TRUE
# )
# model_choice_tables <- build_summary_table_bundle(
#   review,
#   appendix_preset = "recommended"
# )
# 
# cmp[, c("Model", "LogLik", "AIC", "BIC", "ICComparable")]
# model_choice_tables$table_index

## ----latent-regression-reporting, eval=FALSE----------------------------------
# s_pop <- summary(fit_pop)
# s_pop$population_overview
# s_pop$population_coefficients
# s_pop$population_coding
# s_pop$caveats